51
|
Brown KE, Bagci H, Soza-Ried J, Fisher AG. Atypical heterochromatin organization and replication are rapidly acquired by somatic cells following fusion-mediated reprogramming by mouse ESCs. Cell Cycle 2013; 12:3253-61. [PMID: 24036550 DOI: 10.4161/cc.26223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We recently reported that mouse embryonic stem cells (ESCs) in S/G 2 are more efficient at reprogramming somatic cells than ESCs at other stages of the cell cycle. We also provided evidence that DNA replication is induced in the nuclei of somatic partners upon fusion with ESC partners, and showed that this was critical for their conversion toward a pluripotent state. (1) Here we have used counterflow centrifugal elutriation to enrich for ESCs at different cell cycle phases, so as to examine in detail the properties of S/G 2 phase cells. This revealed that the replication and organization of DAPI-intense heterochromatin in ESCs is unusual in two respects. First, replication of heterochromatin occurred earlier during S phase and was associated with precocious H3S10 phosphorylation. Second, heterochromatin protein 1 α (HP1α), which invariably marks DAPI-intense and H3K9me3-enriched pericentromeric domains in mouse somatic cells, (2) was not necessarily associated with these H3K9me3-enriched domains in undifferentiated ESCs. These data, which complement recent replication timing (3) and electron spectroscopic imaging (ESI) analyses, (4) suggest that heterochromatin is atypical in ESCs. Interestingly, as these unusual features were rapidly acquired by somatic nuclei upon ESC fusion-mediated reprogramming, our results suggest that fundamental changes in cell cycle structure and heterochromatin dynamics may be important for conferring pluripotency.
Collapse
Affiliation(s)
- Karen E Brown
- Lymphocyte Development Group; MRC Clinical Sciences Centre; Imperial College London; London, UK
| | | | | | | |
Collapse
|
52
|
Hall SRR, Jiang Y, Leary E, Yavanian G, Eminli S, O'Neill DW, Marasco WA. Identification and isolation of small CD44-negative mesenchymal stem/progenitor cells from human bone marrow using elutriation and polychromatic flow cytometry. Stem Cells Transl Med 2013; 2:567-78. [PMID: 23847000 DOI: 10.5966/sctm.2012-0155] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The method of isolation of bone marrow (BM) mesenchymal stem/stromal cells (MSCs) is a limiting factor in their study and therapeutic use. MSCs are typically expanded from BM cells selected on the basis of their adherence to plastic, which results in a heterogeneous population of cells. Prospective identification of the antigenic profile of the MSC population(s) in BM that gives rise to cells with MSC activity in vitro would allow the preparation of very pure populations of MSCs for research or clinical use. To address this issue, we used polychromatic flow cytometry and counterflow centrifugal elutriation to identify a phenotypically distinct population of mesenchymal stem/progenitor cells (MSPCs) within human BM. The MSPC activity resided within a population of rare, small CD45⁻CD73⁺CD90⁺CD105⁺ cells that lack CD44, an antigen that is highly expressed on culture-expanded MSCs. In culture, these MSPCs adhere to plastic, rapidly proliferate, and acquire CD44 expression. They form colony forming units-fibroblast and are able to differentiate into osteoblasts, chondrocytes, and adipocytes under defined in vitro conditions. Their acquired expression of CD44 can be partially downregulated by treatment with recombinant human granulocyte-colony stimulating factor, a response not found in BM-MSCs derived from conventional plastic adherence methods. These observations indicate that MSPCs within human BM are rare, small CD45⁻CD73⁺CD90⁺CD105⁺ cells that lack expression of CD44. These MSPCs give rise to MSCs that have phenotypic and functional properties that are distinct from those of BM-MSCs purified by plastic adherence.
Collapse
|
53
|
Tsubouchi T, Soza-Ried J, Brown K, Piccolo FM, Cantone I, Landeira D, Bagci H, Hochegger H, Merkenschlager M, Fisher AG. DNA synthesis is required for reprogramming mediated by stem cell fusion. Cell 2013; 152:873-83. [PMID: 23415233 PMCID: PMC3605571 DOI: 10.1016/j.cell.2013.01.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 02/14/2012] [Accepted: 01/07/2013] [Indexed: 01/09/2023]
Abstract
Embryonic stem cells (ESCs) can instruct the conversion of differentiated cells toward pluripotency following cell-to-cell fusion by a mechanism that is rapid but poorly understood. Here, we used centrifugal elutriation to enrich for mouse ESCs at sequential stages of the cell cycle and showed that ESCs in S/G2 phases have an enhanced capacity to dominantly reprogram lymphocytes and fibroblasts in heterokaryon and hybrid assays. Reprogramming success was associated with an ability to induce precocious nucleotide incorporation within the somatic partner nuclei in heterokaryons. BrdU pulse-labeling experiments revealed that virtually all successfully reprogrammed somatic nuclei, identified on the basis of Oct4 re-expression, had undergone DNA synthesis within 24 hr of fusion with ESCs. This was essential for successful reprogramming because drugs that inhibited DNA polymerase activity effectively blocked pluripotent conversion. These data indicate that nucleotide incorporation is an early and critical event in the epigenetic reprogramming of somatic cells in experimental ESC-heterokaryons.
Collapse
Affiliation(s)
- Tomomi Tsubouchi
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
54
|
Rosner M, Schipany K, Hengstschläger M. Merging high-quality biochemical fractionation with a refined flow cytometry approach to monitor nucleocytoplasmic protein expression throughout the unperturbed mammalian cell cycle. Nat Protoc 2013; 8:602-26. [DOI: 10.1038/nprot.2013.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
55
|
Lozano-Núñez A, Ikeda KN, Sauer T, de Graffenried CL. An analogue-sensitive approach identifies basal body rotation and flagellum attachment zone elongation as key functions of PLK in Trypanosoma brucei. Mol Biol Cell 2013; 24:1321-33. [PMID: 23447704 PMCID: PMC3639044 DOI: 10.1091/mbc.e12-12-0846] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Polo-like kinase homologue in Trypanosoma brucei (TbPLK) regulates the assembly of a series of organelles necessary for positioning the parasite's flagellum. An analogue-sensitive strategy is used to acutely and specifically inhibit the kinase with a small molecule, making it possible to identify novel TbPLK functions. Polo-like kinases are important regulators of cell division, playing diverse roles in mitosis and cytoskeletal inheritance. In the parasite Trypanosoma brucei, the single PLK homologue TbPLK is necessary for the assembly of a series of essential organelles that position and adhere the flagellum to the cell surface. Previous work relied on RNA interference or inhibitors of undefined specificity to inhibit TbPLK, both of which have significant experimental limitations. Here we use an analogue-sensitive approach to selectively and acutely inhibit TbPLK. T. brucei cells expressing only analogue-sensitive TbPLK (TbPLKas) grow normally, but upon treatment with inhibitor develop defects in flagellar attachment and cytokinesis. TbPLK cannot migrate effectively when inhibited and remains trapped in the posterior of the cell throughout the cell cycle. Using synchronized cells, we show that active TbPLK is a direct requirement for the assembly and extension of the flagellum attachment zone, which adheres the flagellum to the cell surface, and for the rotation of the duplicated basal bodies, which positions the new flagellum so that it can extend without impinging on the old flagellum. This approach should be applicable to the many kinases found in the T. brucei genome that lack an ascribed function.
Collapse
Affiliation(s)
- Ana Lozano-Núñez
- Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, 1030 Vienna, Austria
| | | | | | | |
Collapse
|
56
|
Shaw J, Payer K, Son S, Grover WH, Manalis SR. A microfluidic "baby machine" for cell synchronization. LAB ON A CHIP 2012; 12:2656-2663. [PMID: 22627487 DOI: 10.1039/c2lc40277g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Common techniques used to synchronize eukaryotic cells in the cell cycle often impose metabolic stress on the cells or physically select for size rather than age. To address these deficiencies, a minimally perturbing method known as the "baby machine" was developed previously. In the technique, suspension cells are attached to a membrane, and as the cells divide, the newborn cells are eluted to produce a synchronous population of cells in the G1 phase of the cell cycle. However, the existing "baby machine" is only suitable for cells which can be chemically attached to a surface. Here, we present a microfluidic "baby machine" in which cells are held onto a surface by pressure differences rather than chemical attachment. As a result, our method can in principle be used to synchronize a variety of cell types, including cells which may have weak or unknown surface attachment chemistries. We validate our microfluidic "baby machine" by using it to produce a synchronous population of newborn L1210 mouse lymphocytic leukemia cells in G1 phase.
Collapse
Affiliation(s)
- Josephine Shaw
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | |
Collapse
|
57
|
Grosse J, Meier K, Bauer TJ, Eilles C, Grimm D. Cell separation by countercurrent centrifugal elutriation: recent developments. Prep Biochem Biotechnol 2012; 42:217-33. [PMID: 22509848 DOI: 10.1080/10826068.2011.602799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Countercurrent centrifugal elutriation (CCE) is a cell separation technique that separates particles predominantly according to their size, and to some degree according to their specific density, without a need for antibodies or ligands tagging cell surfaces. The principles of this technique have been known for half a century. Still, numerous recent publications confirmed that CCE is a valuable supplement to current cell separation technology. It is mainly applied when homogeneous populations of cells, which mirror an in vivo situation, are required for answering scientific questions or for clinical transplantation, while antibodies or ligands suitable for cell isolation are not available. Currently, new technical developments are expanding its application toward fractionation of healthy and malignant tissue cells and the preparation of dendritic cells for immunotherapy.
Collapse
Affiliation(s)
- Jirka Grosse
- Department of Nuclear Medicine, University of Regensburg, Regensburg, Germany
| | | | | | | | | |
Collapse
|
58
|
Kinetically limited differential centrifugation as an inexpensive and readily available alternative to centrifugal elutriation. Biotechniques 2012; 53:104-8. [DOI: 10.2144/0000113853] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 07/24/2012] [Indexed: 11/23/2022] Open
Abstract
When separating two species with similar densities but differing sedimentation velocities (because of differences in size), centrifugal elutriation is generally the method of choice. However, a major drawback to this approach is the requirement for specialized equipment. Here, we present a new method that achieves similar separations using standard benchtop centrifuges by loading the seperands as a layer on top of a dense buffer of a specified length, and running the benchtop centrifugation process for a calculated amount of time, thereby ensuring that all faster moving species are collected at the bottom, while all slower moving species remain in the buffer. We demonstrate the use of our procedure to isolate bacteria from blood culture broth (a mixture of bacterial growth media, blood, and bacteria).
Collapse
|
59
|
Optimization of Cell Cycle Measurement by Time-Lapse Microscopy. Methods Cell Biol 2012. [DOI: 10.1016/b978-0-12-405914-6.00007-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
60
|
Trencsenyi G, Nagy G, Bako F, Kertai P, Banfalvi G. Incomplete chromatin condensation in enlarged rat myelocytic leukemia cells. DNA Cell Biol 2011; 31:470-8. [PMID: 21942442 DOI: 10.1089/dna.2011.1374] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The distinguishable morphologic features of nuclei of acute myelogenous leukemia cells with enlarged size and finely distributed nuclear chromatin indicate incomplete chromosome condensation that can be related to elevated gene expression. To confirm this, interphase chromosome structures were studied in exponentially growing rat myelomonocytic leukemia 1 cells isolated at the University of Debrecen (My1/De cells). This cell line was established from primary rat leukemia chemically induced by 7,12-dimethylbenz[a]anthracene treatment. The enlarged nuclei of My1/De cells allowed improved fluorescent visualization of chromosomal structures. Increased resolution revealed major interphase intermediates consisting of (1) veil-like chromatin, (2) chromatin ribbon, (3) chromatin funnel, (4) chromatin bodies, (5) elongated prechromosomes, (6) seal-ring, spiral shaped, and circular chromosomal subunits, (7) elongated, bent, u- and v-shaped prechromosomes, and (8) metaphase chromosomes. Results confirmed the existence of the chromatin funnel, the first visible interphase chromosome generated by the supercoiling of the chromatin ribbon. Other intermediates not seen previously included the spiral subunits that are involved in the chromonemic folding of metaphase chromosomes. The existence of spiral subunits favors the helical coil model of chromosome condensation. Incomplete chromatin condensation in leukemia cells throughout the cell cycle is an indication of euchromatization contributing to enhanced gene expression and is regarded as a leukemic factor.
Collapse
Affiliation(s)
- Gyorgy Trencsenyi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, Debrecen, Hungary
| | | | | | | | | |
Collapse
|
61
|
Abstract
Major intermediates of chromosome condensation in erythroleukemia K562 cells are presented. Interphase chromatin structures became visible after reversal of permeabilization. Large-scale chromatin structures and the development of individual interphase chromosomes were observed by fluorescence microscopy. In the linear arrangement the following major intermediates of K562 chromatin condensation could be distinguished: (1) the most decondensed chromatin veil, (2) chromatin ribbon, (3) chromatin funnel, a new intermediate regarded as the earliest visible form of interphase chromosomes, (4) chromatin body, (5) 300 nm chromatin fiber, (6) u, v, or s forms of chromosomes, and (7) linear chromosomes. The observations made in nuclei of K562 cells conform to the model of helical coil chromosome condensation.
Collapse
Affiliation(s)
- Gaspar Banfalvi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, Debrecen, Hungary.
| | | |
Collapse
|
62
|
Lee WC, Bhagat AAS, Huang S, Van Vliet KJ, Han J, Lim CT. High-throughput cell cycle synchronization using inertial forces in spiral microchannels. LAB ON A CHIP 2011; 11:1359-67. [PMID: 21336340 DOI: 10.1039/c0lc00579g] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Efficient synchronization and selection of cells at different stages of the cell replication cycle facilitates both fundamental research and development of cell cycle-targeted therapies. Current chemical-based synchronization methods are unfavorable as these can disrupt cell physiology and metabolism. Microfluidic systems developed for physical cell separation offer a potential alternative over conventional cell synchronization approaches. Here we introduce a spiral microfluidic device for cell cycle synchronization, using the combined effects of inertial forces and Dean drag force. By exploiting the relationship between cell diameter and cell cycle (DNA content/ploidy), we have successfully fractionated several asynchronous mammalian cell lines, as well as primary cells comprising bone marrow-derived human mesenchymal stem cells (hMSCs), into enriched subpopulations of G0/G1 (>85%), S, and G2/M phases. This level of cell cycle enrichment is comparable to existing microfluidic systems, but the throughput (∼ 15 × 10(6) cells per h) and viability (∼ 95%) of cells thus synchronized are significantly greater. Further, this platform provides rapid collection of synchronized cells or of diameter-sorted cells post-separation, to enable diverse applications in the study and manipulation of cell proliferation.
Collapse
Affiliation(s)
- Wong Cheng Lee
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore
| | | | | | | | | | | |
Collapse
|
63
|
The cell cycle regulated transcriptome of Trypanosoma brucei. PLoS One 2011; 6:e18425. [PMID: 21483801 PMCID: PMC3069104 DOI: 10.1371/journal.pone.0018425] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 03/07/2011] [Indexed: 11/19/2022] Open
Abstract
Progression of the eukaryotic cell cycle requires the regulation of hundreds of genes to ensure that they are expressed at the required times. Integral to cell cycle progression in yeast and animal cells are temporally controlled, progressive waves of transcription mediated by cell cycle-regulated transcription factors. However, in the kinetoplastids, a group of early-branching eukaryotes including many important pathogens, transcriptional regulation is almost completely absent, raising questions about the extent of cell-cycle regulation in these organisms and the mechanisms whereby regulation is achieved. Here, we analyse gene expression over the Trypanosoma brucei cell cycle, measuring changes in mRNA abundance on a transcriptome-wide scale. We developed a “double-cut” elutriation procedure to select unperturbed, highly synchronous cell populations from log-phase cultures, and compared this to synchronization by starvation. Transcriptome profiling over the cell cycle revealed the regulation of at least 430 genes. While only a minority were homologous to known cell cycle regulated transcripts in yeast or human, their functions correlated with the cellular processes occurring at the time of peak expression. We searched for potential target sites of RNA-binding proteins in these transcripts, which might earmark them for selective degradation or stabilization. Over-represented sequence motifs were found in several co-regulated transcript groups and were conserved in other kinetoplastids. Furthermore, we found evidence for cell-cycle regulation of a flagellar protein regulon with a highly conserved sequence motif, bearing similarity to consensus PUF-protein binding motifs. RNA sequence motifs that are functional in cell-cycle regulation were more widespread than previously expected and conserved within kinetoplastids. These findings highlight the central importance of post-transcriptional regulation in the proliferation of parasitic kinetoplastids.
Collapse
|
64
|
Abstract
Understanding cell growth and cell division involves the study of regulatory events that occur in a cell cycle phase-dependent manner. Studies analyzing cell cycle regulatory mechanisms and cell cycle progression invariably require synchronization of cell populations at specific cell cycle stages. Several methods have been established to synchronize cells, including serum deprivation, contact inhibition, centrifugal elutriation, and drug-dependent synchronization. Despite potential adverse cellular consequences of synchronizing cells by pharmacological agents, drug-dependent methods can be advantageous when studying later cell cycle events to ensure specific enrichment at selected mitotic stages. This chapter describes protocols used in our laboratory for isolating mitotic mammalian cells in a large-scale manner. In particular, we discuss the technical aspects of adherent or suspension cell isolation, the methods necessary to enrich cells at different mitotic stages and the optimized culture conditions.
Collapse
Affiliation(s)
- Kalyan Dulla
- Department of Molecular Diagnostics, Philips Research, Eindhoven, The Netherlands.
| | | |
Collapse
|
65
|
Darzynkiewicz Z, Halicka HD, Zhao H, Podhorecka M. Cell synchronization by inhibitors of DNA replication induces replication stress and DNA damage response: analysis by flow cytometry. Methods Mol Biol 2011; 761:85-96. [PMID: 21755443 PMCID: PMC3137244 DOI: 10.1007/978-1-61779-182-6_6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Cell synchronization is often achieved by inhibition of DNA replication. The cells cultured in the presence of such inhibitors as hydroxyurea, aphidicolin, or thymidine become arrested at the entrance to S phase and upon release from the block they synchronously progress through S, G(2), and M. We recently reported that exposure of cells to these inhibitors at concentrations commonly used to synchronize cell populations led to phosphorylation of histone H2AX on Ser139 (induction of γH2AX) through activation of ataxia telangiectasia mutated and Rad3-related protein kinase (ATR). These findings imply that the induction of DNA replication stress by these inhibitors activates the DNA damage response signaling pathways and caution about interpreting data obtained with use of cells synchronized such way as representing unperturbed cells. The protocol presented in this chapter describes the methodology of assessment of phosphorylation of histone H2AX-Ser139, ATM/ATR substrate on Ser/Thr at SQ/TQ cluster domains as well as ataxia telangiectasia mutated (ATM) protein kinase in cells treated with inhibitors of DNA replication. Phosphorylation of these proteins is detected in individual cell immunocytochemically with phospho-specific antibody (Ab) and measured by flow cytometry. Concurrent measurement of cellular DNA content and phosphorylated proteins followed by multiparameter cytometric analysis allows one to correlate extent of their phosphorylation with cell cycle phase.
Collapse
Affiliation(s)
- Zbigniew Darzynkiewicz
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, 10595, Valhalla, NY, USA.
| | | | | | | |
Collapse
|
66
|
Abstract
HeLa is one of the oldest and most commonly used cell lines in biomedical research. Owing to the ease of which they can be effectively synchronized by various methods, HeLa cells have been used extensively for studies of the cell cycle. Here we describe several protocols for synchronization of HeLa cells from different phases of the cell cycle. Synchronization in G(1) phase can be achieved with the HMG-CoA reductase inhibitor lovastatin, S phase with a double thymidine block procedure, and G(2) phase with the CDK inhibitor RO3306. Cells can also be enriched in mitosis by treating with nocodazole and mechanical shake-off. Release of the cells from these blocks enables researchers to follow gene expression and other events through the cell cycle. We also describe several protocols, including flow cytometry, BrdU labeling, immunoblotting, and time-lapse microscopy, for validating the synchrony of the cells and monitoring the progression of the cell cycle after release.
Collapse
Affiliation(s)
- Hoi Tang Ma
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.
| | | |
Collapse
|
67
|
Abstract
Synchronized populations of large numbers of cells can be obtained by centrifugal elutriation on the basis of sedimentation properties of small round particles, with minimal perturbation of cellular functions. The physical characteristics of cell size and sedimentation velocity are operative in the technique of centrifugal elutriation also known as counterstreaming centrifugation. The elutriator is an advanced device for increasing the sedimentation rate to yield enhanced resolution of cell separation. A random population of cells is introduced into the elutriation chamber of an elutriator rotor running in a specially designed centrifuge. By increasing step by step the flow rate of the elutriation fluid, successive populations of relatively homogeneous cell size can be removed from the elutriation chamber and used as synchronized subpopulations. For cell synchronization by centrifugal elutriation early log S phase cell populations are most suitable where most of the cells are in G1 and S phase (>80%). Protocols for the synchronization of nuclei of murine pre-B cells and high-resolution centrifugal elutriation of CHO cells are given. The verification of purity and cell cycle positions of cells in elutriated fractions includes the measurement of DNA synthesis by [(3)H]-thymidine incorporation and DNA content by propidium iodide flow cytometry.
Collapse
Affiliation(s)
- Gaspar Banfalvi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, Debrecen, 4010, Hungary.
| |
Collapse
|
68
|
Abstract
Widespread interest in cell synchronization is maintained by the studies of control mechanisms involved in cell cycle regulation. During the synchronization distinct subpopulations of cells are obtained representing different stages of the cell cycle. These subpopulations are then used to study regulatory mechanisms of the cycle at the level of macromolecular biosynthesis (DNA synthesis, gene expression, protein synthesis), protein phosphorylation, development of new drugs, etc. Although several synchronization methods have been described, it is of general interest that scientists get a compilation and an updated view of these synchronization techniques. This introductory chapter summarizes: (1) the basic concepts and principal criteria of cell cycle synchronizations, (2) the most frequently used synchronization methods, such as physical fractionation (flow cytometry, dielectrophoresis, cytofluorometric purification), chemical blockade, (3) synchronization of embryonic cells, (4) synchronization at low temperature, (5) comparison of cell synchrony techniques, (6) synchronization of unicellular organisms, and (7) the effect of synchronization on transfection.
Collapse
Affiliation(s)
- Gaspar Banfalvi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, 4010, Debrecen, Hungary.
| |
Collapse
|
69
|
Nagy G, Pinter G, Kohut G, Adam AL, Trencsenyi G, Hornok L, Banfalvi G. Time-lapse analysis of cell death in mammalian and fungal cells. DNA Cell Biol 2010; 29:249-59. [PMID: 20218896 DOI: 10.1089/dna.2009.0980] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Time-lapse video microscopy was designed to follow the movement of single cells for an unlimited period of time under physiological conditions. The system is based on two inverted microscopes located in a CO(2) incubator and equipped with charge-coupled device cameras connected to the computer. Frames were recorded every minute and the subsequent video sequence was converted to database form. The system was applied to describe the movements of normal HaCaT cells and Pb-treated cells causing the so-called apoptotic dance during cell death. The apoptotic movement was also followed in high-osmolarity glycerol-type mitogen-activated protein kinase (MAPK) null mutant of Fusarium proliferatum, a filamentous fungus, during osmotic stress. The shortest (20 min) and most vigorous death movements were observed in apoptotic fungal cells subjected to salt stress. The necrotic process at higher Pb concentration (50 microM) took 2-3 h, whereas the apoptotic process at lower Pb concentrations lasted from minutes to days.
Collapse
Affiliation(s)
- Gabor Nagy
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, Debrecen, Hungary
| | | | | | | | | | | | | |
Collapse
|
70
|
Thévoz P, Adams JD, Shea H, Bruus H, Soh HT. Acoustophoretic synchronization of mammalian cells in microchannels. Anal Chem 2010; 82:3094-8. [PMID: 20199060 PMCID: PMC2848285 DOI: 10.1021/ac100357u] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the first use of ultrasonic standing waves to achieve cell cycle phase synchronization in mammalian cells in a high-throughput and reagent-free manner. The acoustophoretic cell synchronization (ACS) device utilizes volume-dependent acoustic radiation force within a microchannel to selectively purify target cells of desired phase from an asynchronous mixture based on cell cycle-dependent fluctuations in size. We show that ultrasonic separation allows for gentle, scalable, and label-free synchronization with high G(1) phase synchrony (approximately 84%) and throughput (3 x 10(6) cells/h per microchannel).
Collapse
Affiliation(s)
- Patrick Thévoz
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, USA
| | | | | | | | | |
Collapse
|
71
|
Siegal-Gaskins D, Ash JN, Crosson S. Model-based deconvolution of cell cycle time-series data reveals gene expression details at high resolution. PLoS Comput Biol 2009; 5:e1000460. [PMID: 19680537 PMCID: PMC2718844 DOI: 10.1371/journal.pcbi.1000460] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 07/08/2009] [Indexed: 11/23/2022] Open
Abstract
In both prokaryotic and eukaryotic cells, gene expression is regulated across the cell cycle to ensure “just-in-time” assembly of select cellular structures and molecular machines. However, present in all time-series gene expression measurements is variability that arises from both systematic error in the cell synchrony process and variance in the timing of cell division at the level of the single cell. Thus, gene or protein expression data collected from a population of synchronized cells is an inaccurate measure of what occurs in the average single-cell across a cell cycle. Here, we present a general computational method to extract “single-cell”-like information from population-level time-series expression data. This method removes the effects of 1) variance in growth rate and 2) variance in the physiological and developmental state of the cell. Moreover, this method represents an advance in the deconvolution of molecular expression data in its flexibility, minimal assumptions, and the use of a cross-validation analysis to determine the appropriate level of regularization. Applying our deconvolution algorithm to cell cycle gene expression data from the dimorphic bacterium Caulobacter crescentus, we recovered critical features of cell cycle regulation in essential genes, including ctrA and ftsZ, that were obscured in population-based measurements. In doing so, we highlight the problem with using population data alone to decipher cellular regulatory mechanisms and demonstrate how our deconvolution algorithm can be applied to produce a more realistic picture of temporal regulation in a cell. Time-series analyses of cellular regulatory processes have successfully drawn attention to the importance of temporal regulation in biological systems. A number of model systems can be synchronized such that data collected on cell populations better reflect the dynamic properties of the individual cell. However, experimental synchronization is never perfect, and the degree of synchrony that does exist at the outset of an experiment is quickly lost over time as cells grow at different rates and enter different developmental or physiological states on cell division. Thus, data collected from a population of synchronized cells can lead to incorrect models of temporal regulation. Here we demonstrate that the problem of relating population data to the individual cell can be resolved with a computational method that effectively removes the effects of both imperfect synchrony and time-dependent loss of synchrony. Application of this deconvolution algorithm to a cell cycle time-series data set from the model bacterium Caulobacter crescentus uncovers critical temporal details in the expression of essential genes that are not evident in the raw population-based data. The deconvolution routine presented here is a robust and general tool for extracting biochemical parameters of the average single cell from population time-series data.
Collapse
Affiliation(s)
- Dan Siegal-Gaskins
- Mathematical Biosciences Institute, Ohio State University, Columbus, OH, USA.
| | | | | |
Collapse
|
72
|
Choi S, Song S, Choi C, Park JK. Microfluidic Self-Sorting of Mammalian Cells to Achieve Cell Cycle Synchrony by Hydrophoresis. Anal Chem 2009; 81:1964-8. [PMID: 19245266 DOI: 10.1021/ac8024575] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sungyoung Choi
- Department of Bio and Brain Engineering, College of Life Science and Bioengineering, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Seungjeong Song
- Department of Bio and Brain Engineering, College of Life Science and Bioengineering, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Chulhee Choi
- Department of Bio and Brain Engineering, College of Life Science and Bioengineering, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, College of Life Science and Bioengineering, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
| |
Collapse
|