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Schmøkel SS, Nordentoft I, Lindskrog SV, Lamy P, Knudsen M, Jensen JB, Dyrskjøt L. Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies. Nucleus 2023; 14:2186686. [PMID: 36878883 PMCID: PMC10012951 DOI: 10.1080/19491034.2023.2186686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection: sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed that a combination of IgePal lysis buffer, tissue dissection by sectioning, and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well-described clinical and histopathological information and known clinical outcomes with snRNA-seq.
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Affiliation(s)
- Sofie S Schmøkel
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sia V Lindskrog
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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Daniels RR, Taylor RS, Robledo D, Macqueen DJ. Single cell genomics as a transformative approach for aquaculture research and innovation. Rev Aquac 2023; 15:1618-1637. [PMID: 38505116 PMCID: PMC10946576 DOI: 10.1111/raq.12806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/21/2024]
Abstract
Single cell genomics encompasses a suite of rapidly maturing technologies that measure the molecular profiles of individual cells within target samples. These approaches provide a large up-step in biological information compared to long-established 'bulk' methods that profile the average molecular profiles of all cells in a sample, and have led to transformative advances in understanding of cellular biology, particularly in humans and model organisms. The application of single cell genomics is fast expanding to non-model taxa, including aquaculture species, where numerous research applications are underway with many more envisaged. In this review, we highlight the potential transformative applications of single cell genomics in aquaculture research, considering barriers and potential solutions to the broad uptake of these technologies. Focusing on single cell transcriptomics, we outline considerations for experimental design, including the essential requirement to obtain high quality cells/nuclei for sequencing in ectothermic aquatic species. We further outline data analysis and bioinformatics considerations, tailored to studies with the under-characterized genomes of aquaculture species, where our knowledge of cellular heterogeneity and cell marker genes is immature. Overall, this review offers a useful source of knowledge for researchers aiming to apply single cell genomics to address biological challenges faced by the global aquaculture sector though an improved understanding of cell biology.
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Affiliation(s)
- Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Richard S. Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
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3
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Xie P, Ke Y, Kuo L. Modified CTAB protocols for high-molecular-weight DNA extractions from ferns. Appl Plant Sci 2023; 11:e11526. [PMID: 37342164 PMCID: PMC10278929 DOI: 10.1002/aps3.11526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 06/22/2023]
Abstract
Premise Efficient protocols for extracting high-molecular-weight (HMW) DNA from ferns facilitate the long-read sequencing of their large and complex genomes. Here, we perform two cetyltrimethylammonium bromide (CTAB)-based protocols to extract HMW DNA and evaluate their applicability in diverse fern taxa for the first time. Methods and Results We describe two modified CTAB protocols, with key adjustments to minimize mechanical disruption during lysis to prevent DNA shearing. One of these protocols uses a small amount of fresh tissue but yields a considerable quantity of HMW DNA with high efficiency. The other accommodates a large amount of input tissue, adopts an initial step of nuclei isolation, and thus ensures a high yield in a short period of time. Both methods were proven to be robust and effective in obtaining HMW DNA from diverse fern lineages, including 33 species in 19 families. The DNA extractions mostly had high DNA integrity, with mean sizes larger than 50 kbp, as well as high purity (A260/A230 and A260/A280 > 1.8). Conclusions This study provides HMW DNA extraction protocols for ferns in the hope of facilitating further attempts to sequence their genomes, which will bridge our genomic understanding of land plant diversity.
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Affiliation(s)
- Pei‐Jun Xie
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Ya‐Ting Ke
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Li‐Yaung Kuo
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
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Zhang Q, Kim SW, Gorham JM, DeLaughter D, Ward T, Seidman C, Seidman J. Multiplexed Single-Nucleus RNA Sequencing Using Lipid-Oligo Barcodes. Curr Protoc 2022; 2:e579. [PMID: 36286606 PMCID: PMC9614549 DOI: 10.1002/cpz1.579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This protocol describes a robust pipeline for simultaneously analyzing multiple samples by single-nucleus (sn)RNA-seq. cDNA obtained from each single sample are labeled with the same lipid-coupled oligonucleotide barcode (10X Genomics). Nuclei from as many as 12 individual samples can be pooled together and simultaneously processed for cDNA library construction and subsequent DNA sequencing. While previous protocols using lipid-coupled oligonucleotide barcodes were optimized for analysis of samples consisting of viable cells, this protocol is optimized for analyses of quick-frozen cell samples. The protocol ensures efficient recovery of nuclei both by incorporating high sucrose buffered solutions and by including a tracking dye (trypan blue) during nuclei isolation. The protocol also describes a procedure for removing single nuclei 'artifacts' by removing cell debris prior to single nuclear fractionation. This protocol informs the use of computational tools for filtering poorly labeled nuclei and assigning sample identity using barcode unique molecular identifier (UMI) read counts percentages. The computational pipeline is applicable to either cultured or primary, fresh or frozen cells, regardless of their cell types and species. Overall, this protocol reduces batch effects and experimental costs while enhancing sample comparison. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Labeling cells with lipid oligo barcodes and generating multiplexed single-nucleus RNA-seq libraries Basic Protocol 2: Bioinformatic deconvolution of the multiplexed snRNAseq libraries.
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Affiliation(s)
- Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- These authors contributed equally to this work
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- These authors contributed equally to this work
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Daniel DeLaughter
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Christine Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Cardiovascular Division, Brigham and Women’s Hospital; Boston, MA USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jonathan Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
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5
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Zhao Y, Deng H, Chen Y, Li J, Chen S, Li C, Mu X, Hu Z, Li K, Wang W. Establishment and Optimization of Molecular Cytogenetic Techniques (45S rDNA-FISH, GISH, and Fiber-FISH) in Kiwifruit ( Actinidia Lindl.). Front Plant Sci 2022; 13:906168. [PMID: 35734244 PMCID: PMC9208197 DOI: 10.3389/fpls.2022.906168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The kiwifruit (Actinidia chinensis) has long been regarded as "the king of fruits" for its nutritional importance. However, the molecular cytogenetics of kiwifruit has long been hampered because of the large number of basic chromosome (x = 29), the inherent small size and highly similar morphology of metaphase chromosomes. Fluorescence in situ hybridization (FISH) is an indispensable molecular cytogenetic technique widely used in many plant species. Herein, the effects of post-hybridization washing temperature on FISH, blocking DNA concentration on genomic in situ hybridization (GISH), extraction method on nuclei isolation and the incubation time on the DNA fiber quality in kiwifruit were evaluated. The post-hybridization washing in 2 × saline sodium citrate (SSC) solution for 3 × 5 min at 37°C ensured high stringency and distinct specific FISH signals in kiwifruit somatic chromosomes. The use of 50 × blocking DNA provided an efficient and reliable means of discriminating between chromosomes derived from in the hybrids of A. chinensis var. chinensis (2n = 2x = 58) × A. eriantha (2n = 2x = 58), and inferring the participation of parental genitors. The chopping method established in the present study were found to be very suitable for preparation of leaf nuclei in kiwifruit. A high-quality linear DNA fiber was achieved by an incubation of 20 min. The physical size of 45S rDNA signals was approximately 0.35-0.40 μm revealed by the highly reproducible fiber-FISH procedures established and optimized in this study. The molecular cytogenetic techniques (45S rDNA-FISH, GISH, and high-resolution fiber-FISH) for kiwifruit was for the first time established and optimized in the present study, which is the foundation for the future genomic and evolutionary studies and provides chromosomal characterization for kiwifruit breeding programs.
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Affiliation(s)
- Yang Zhao
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Xinxiang Academy of Agricultural Sciences, Xinxiang, China
| | - Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yao Chen
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jihan Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Silei Chen
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Chunyan Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xue Mu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Horticultural Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Zhongrong Hu
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Kunming Li
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Weixing Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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6
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Nadelmann ER, Gorham JM, Reichart D, Delaughter DM, Wakimoto H, Lindberg EK, Litviňukova M, Maatz H, Curran JJ, Gutierrez DI, Hübner N, Seidman CE, Seidman JG. Isolation of Nuclei from Mammalian Cells and Tissues for Single-Nucleus Molecular Profiling. Curr Protoc 2021; 1:e132. [PMID: 34043278 PMCID: PMC8191490 DOI: 10.1002/cpz1.132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Both single-cell RNA sequencing (scRNAseq) and single-nucleus RNA sequencing (snRNAseq) can be used to characterize the transcriptional profile of individual cells, and based on these transcriptional profiles, help define cell type distribution in mixed cell populations. However, scRNAseq analyses are confounded if some of the cells are large (>50 µm) or if some of cells adhere more tightly to some adjacent cells than to others. Further, single cell isolation for scRNAseq requires fresh tissue, which may not be available for human or animal model tissues. Additionally, the current enzymatic and mechanical methods for single-cell dissociation can lead to stress-induced transcriptional artifacts. Nuclei for snRNAseq, on the other hand, can be isolated from any cell, regardless of size, and from either fresh or frozen tissues, and compared to whole cells, they are more resistant to mechanical pressures and appear not to exhibit as many cell isolation-based transcriptional artifacts. Here, we describe a time- and cost-effective procedure to isolate nuclei from mammalian cells and tissues. The protocol incorporates steps to mechanically disrupt samples to release nuclei. Compared to conventional nuclei isolation protocols, the approach described here increases overall efficiency, eliminates risk of contaminant exposure, and reduces volumes of expensive reagents. A series of RNA quality control checks are also incorporated to ensure success and reduce costs of subsequent snRNAseq experiments. Nuclei isolated by this procedure can be separated on the 10× Genomics Chromium system for either snRNAseq and/or Single-Nucleus ATAC-Seq (snATAC-Seq), and is also compatible with other single cell platforms. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Sample preparation and quality control check via RNA Isolation and Analysis Basic Protocol 2: Nuclei Isolation.
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Affiliation(s)
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Eric K. Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Monika Litviňukova
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Justin J. Curran
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | | | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | | | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
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7
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Burns EN, Bordbari MH, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F, Gianino G, Giulotto E, Kalbfleisch TS, Katzman SA, Lassaline M, Leeb T, Mack M, Müller EJ, MacLeod JN, Ming-Whitfield B, Alanis CR, Raudsepp T, Scott E, Vig S, Zhou H, Petersen JL, Bellone RR, Finno CJ. Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. Anim Genet 2018; 49:564-570. [PMID: 30311254 DOI: 10.1111/age.12717] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2018] [Indexed: 12/13/2022]
Abstract
The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.
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Affiliation(s)
- E N Burns
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - M H Bordbari
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - M J Mienaltowski
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - V K Affolter
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - M V Barro
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - F Gianino
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - G Gianino
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - E Giulotto
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, Pavia, I-27100, Italy
| | - T S Kalbfleisch
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40292, USA
| | - S A Katzman
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - M Lassaline
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - M Mack
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - E J Müller
- Department of Biomedical Research, Molecular Dermatology and Stem Cell Research, Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, 3001, Switzerland
| | - J N MacLeod
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40546, USA
| | - B Ming-Whitfield
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - C R Alanis
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - T Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA
| | - E Scott
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - S Vig
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - H Zhou
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska - Lincoln, Lincoln, NE, 68583, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
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8
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Park K, Frost JM, Adair AJ, Kim DM, Yun H, Brooks JS, Fischer RL, Choi Y. Optimized Methods for the Isolation of Arabidopsis Female Central Cells and Their Nuclei. Mol Cells 2016; 39:768-775. [PMID: 27788573 PMCID: PMC5104886 DOI: 10.14348/molcells.2016.0209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022] Open
Abstract
The Arabidopsis female gametophyte contains seven cells with eight haploid nuclei buried within layers of sporophytic tissue. Following double fertilization, the egg and central cells of the gametophyte develop into the embryo and endosperm of the seed, respectively. The epigenetic status of the central cell has long presented an enigma due both to its inaccessibility, and the fascinating epigenome of the endosperm, thought to have been inherited from the central cell following activity of the DEMETER demethylase enzyme, prior to fertilization. Here, we present for the first time, a method to isolate pure populations of Arabidopsis central cell nuclei. Utilizing a protocol designed to isolate leaf mesophyll protoplasts, we systematically optimized each step in order to efficiently separate central cells from the female gametophyte. We use initial manual pistil dissection followed by the derivation of central cell protoplasts, during which process the central cell emerges from the micropylar pole of the embryo sac. Then, we use a modified version of the Isolation of Nuclei TAgged in specific Cell Types (INTACT) protocol to purify central cell nuclei, resulting in a purity of 75-90% and a yield sufficient to undertake downstream molecular analyses. We find that the process is highly dependent on the health of the original plant tissue used, and the efficiency of protoplasting solution infiltration into the gametophyte. By isolating pure central cell populations, we have enabled elucidation of the physiology of this rare cell type, which in the future will provide novel insights into Arabidopsis reproduction.
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Affiliation(s)
- Kyunghyuk Park
- Department of Biological Sciences, Seoul National University, Seoul 08826,
Korea
| | - Jennifer M. Frost
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720,
USA
| | - Adam James Adair
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720,
USA
| | - Dong Min Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826,
Korea
| | - Hyein Yun
- Department of Biological Sciences, Seoul National University, Seoul 08826,
Korea
| | - Janie S. Brooks
- Department of Science, Seoul Foreign School, Seoul 09723,
Korea
| | - Robert L. Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720,
USA
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826,
Korea
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9
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Nath S, Mallick SK, Jha S. An improved method of genome size estimation by flow cytometry in five mucilaginous species of Hyacinthaceae. Cytometry A 2014; 85:833-40. [PMID: 24853918 DOI: 10.1002/cyto.a.22489] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 02/11/2014] [Accepted: 05/02/2014] [Indexed: 11/07/2022]
Abstract
The family Hyacinthaceae constitutes about 900 species of bulbous geophytes usually characterized by high mucilage content. Taxonomic delimitation of Hyacinthaceae has been controversial since the time of Linnaeus due to the absence of reliable discriminating characters. Pattern of genome size variation can thus be considered as an added character to aid intergeneric and intrageneric relationship of the group. However, reports on genome size estimation by flow cytometric analysis of these plants are rare due to the presence of mucilage, which causes problem with nuclei sample preparation. To overcome this problem five reported nuclei isolation buffers were tested in Drimia indica of which Galbraith's buffer gave comparatively better results and was further modified by increasing pH, detergent concentration, and replacing sodium citrate by citric acid. The modified buffer enabled better sample preparation with increased yield, lesser debris, and improved DNA peak CV. The standardized buffer was used to estimate the 2C values of Drimia indica, Drimia nagarjunae, Drimia wightii, Drimia coromandeliana, and Ledebouria revoluta for the first time by flow cytometric analysis. This study also opens up the scope for further improvement in sample preparation for flow cytometric analysis of mucilaginous plants, which is otherwise problematic due to nuclei clumping and increased viscosity of sample.
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Affiliation(s)
- Sayantani Nath
- Department of Botany, Center of Advanced study, University of Calcutta, Kolkata, 700019, West Bengal, India
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