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Liehr T, Ziegler M, Person L, Kankel S, Padutsch N, Weise A, Weimer JP, Williams H, Ferreira S, Melo JB, Carreira IM. Small supernumerary marker chromosomes derived from human chromosome 11. Front Genet 2023; 14:1293652. [PMID: 38174048 PMCID: PMC10763568 DOI: 10.3389/fgene.2023.1293652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction: With only 39 reported cases in the literature, carriers of a small supernumerary marker chromosome (sSMC) derived from chromosome 11 represent an extremely rare cytogenomic condition. Methods: Herein, we present a review of reported sSMC(11), add 18 previously unpublished cases, and closely review eight cases classified as 'centromere-near partial trisomy 11' and a further four suited cases from DECIPHER. Results and discussion: Based on these data, we deduced the borders of the pericentric regions associated with clinical symptoms into a range of 2.63 and 0.96 Mb for chromosome 11 short (p) and long (q) arms, respectively. In addition, the minimal pericentric region of chromosome 11 without triplo-sensitive genes was narrowed to positions 47.68 and 60.52 Mb (GRCh37). Furthermore, there are apparent differences in the presentation of signs and symptoms in carriers of larger sSMCs derived from chromosome 11 when the partial trisomy is derived from different chromosome arms. However, the number of informative sSMC(11) cases remains low, with overlapping presentation between p- and q-arm-imbalances. In addition, uniparental disomy (UPD) of 'normal' chromosome 11 needs to be considered in the evaluation of sSMC(11) carriers, as imprinting may be an influencing factor, although no such cases have been reported. Comprehensively, prenatal sSMC(11) cases remain a diagnostic and prognostic challenge.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Monika Ziegler
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Luisa Person
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Stefanie Kankel
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Jörg Paul Weimer
- Department of Gynecology and Obstetrics, University Hospital of Schleswig-Holstein, University Kiel, Kiel, Germany
| | | | - Susana Ferreira
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Joana B. Melo
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel M. Carreira
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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Normala J, Okomoda VT, Mohd AA, Nur AA, Abol-Munafi AB, Md Sheriff S. Genetic Variation between Triploid and Diploid Clarias gariepinus (Burchell, 1822) Using RAPD Markers. Vet Sci 2021; 8:vetsci8050075. [PMID: 34064306 PMCID: PMC8147776 DOI: 10.3390/vetsci8050075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
This study was designed to examine the use of RAPD markers in discriminating triploid and diploid African catfish Clarias gariepinus (Burchell, 1822). Following a routine technique, triploidy was induced by cold shock and confirm by erythrocyte measurement in C. gariepinus. Thereafter, 80 RAPD markers were screened; out of which, three showed the highest percentage of polymorphism (i.e., OPB 16 = 71.43%; OPC 14 = 61.9%; OPD 12 = 75%). The results obtained showed genotype differences between triploid and diploid without overlapping. However, the development of a Sequence Characterized Amplified Region (SCAR) marker was not achievable because progenies of triploid and diploid C. gariepinus could not be differentiated based on a specific fragment. Consequently, the genetic distance showed high similarities for both treatments and the UPGMA-generated dendrogram could not separate the treatments into two distinct clusters. It was concluded that RAPD makers cannot be used to separate the ploidy status of fishes.
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Affiliation(s)
- Jalil Normala
- Faculty of Food Science and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia; (J.N.); (A.A.M.); (A.A.N.)
| | - Victor Tosin Okomoda
- Department of Fisheries and Aquaculture, College of Forestry and Fisheries, University of Agriculture, Makurdi P.M.B. 2373, Nigeria
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries Research (AQUATROP), Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia
- Correspondence: (V.T.O.); (A.B.A.-M.); (S.M.S.); Tel.: +23-4803-3319-959 (V.T.O.); +60-199-851-868 (A.B.A.-M.); +60-192-867-794 (S.M.S.)
| | - Azizul Alim Mohd
- Faculty of Food Science and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia; (J.N.); (A.A.M.); (A.A.N.)
| | - Asma Ariffin Nur
- Faculty of Food Science and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia; (J.N.); (A.A.M.); (A.A.N.)
| | - Ambok Bolong Abol-Munafi
- Faculty of Food Science and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia; (J.N.); (A.A.M.); (A.A.N.)
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries Research (AQUATROP), Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia
- Correspondence: (V.T.O.); (A.B.A.-M.); (S.M.S.); Tel.: +23-4803-3319-959 (V.T.O.); +60-199-851-868 (A.B.A.-M.); +60-192-867-794 (S.M.S.)
| | - Shahreza Md Sheriff
- Faculty of Food Science and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia; (J.N.); (A.A.M.); (A.A.N.)
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries Research (AQUATROP), Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia
- Correspondence: (V.T.O.); (A.B.A.-M.); (S.M.S.); Tel.: +23-4803-3319-959 (V.T.O.); +60-199-851-868 (A.B.A.-M.); +60-192-867-794 (S.M.S.)
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3
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Yao Q, Gao J, Chen F, Li W. Development and application of an optimized drop-slide technique for metaphase chromosome spreads in maize. Biotech Histochem 2019; 95:276-284. [PMID: 31762324 DOI: 10.1080/10520295.2019.1686167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Chromosome spreads are important for complex molecular cytogenetic studies. An adequate chromosome spreading method for identification and isolation of the maize B chromosome, however, has not been reported. We used the maize inbred lines, B73 and Mo17, the hybrid YD08 line and the landrace DP76 to develop an optimized chromosome spreading method. We investigated the effects of four treatment factors on the quality of metaphase chromosome spreads using a factorial analysis of variance. Optimal conditions for metaphase spreading were identified using regression analysis based on multifactor orthogonal design of four treatment factors with five levels for each factor. We developed optimal conditions for metaphase spreading as follows: nitrous oxide treatment for 2 h, glacial acetic acid fixation for 2 h, enzyme hydrolysis for 6.0 h, and a drop height of 35 cm for cell suspension. We obtained high quality metaphase chromosome spreads with large metaphase areas, large numbers of chromosomes, few chromosome overlaps and high frequency of intact metaphases. Our optimized drop-slide procedure was markedly better than the traditional flame smear technique. We identified 487 B chromosomes in three forms from maize landraces from Southwest China. We found no relation between the C-band number and B chromosome. Single B chromosomes also were isolated directly from a metaphase chromosome drop-slide using a micromanipulator. Our optimized method provides a simple, efficient and reproducible procedure for preparing high quality plant chromosome spreads.
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Affiliation(s)
- Qilun Yao
- Department of Life Sciences, Yangtze Normal University, Fuling 408100, P. R. China.,Centre for Green Development and Collaborative Innovation in Wuling Mountain Region, Yangtze Normal University, Fuling, 408100, P. R. China
| | - Jian Gao
- Department of Life Sciences, Yangtze Normal University, Fuling 408100, P. R. China.,Centre for Green Development and Collaborative Innovation in Wuling Mountain Region, Yangtze Normal University, Fuling, 408100, P. R. China
| | - Fabo Chen
- Department of Life Sciences, Yangtze Normal University, Fuling 408100, P. R. China.,Centre for Green Development and Collaborative Innovation in Wuling Mountain Region, Yangtze Normal University, Fuling, 408100, P. R. China
| | - Wenbo Li
- Department of Life Sciences, Yangtze Normal University, Fuling 408100, P. R. China.,Centre for Green Development and Collaborative Innovation in Wuling Mountain Region, Yangtze Normal University, Fuling, 408100, P. R. China
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Liehr T. From Human Cytogenetics to Human Chromosomics. Int J Mol Sci 2019; 20:E826. [PMID: 30769866 PMCID: PMC6413437 DOI: 10.3390/ijms20040826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/30/2019] [Accepted: 02/12/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The concept of "chromosomics" was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a "chromosomic view" of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is dedicated to the memory of Prof. Uwe Claussen (30 April 1945⁻20 July 2008). RECENT FINDINGS Chromosomics is the study of chromosomes, their three-dimensional positioning in the interphase nucleus, the consequences from plasticity of chromosomal subregions and gene interactions, the influence of chromatin-modification-mediated events on cells, and even individuals, evolution, and disease. Progress achieved in recent years is summarized, including the detection of chromosome-chromosome-interactions which, if damaged, lead to malfunction and disease. However, chromosomics in the Human Genetics field is not progressing presently, as research interest has shifted from single cell to high throughput, genomic approaches. CONCLUSION Chromosomics and its impact were predicted correctly in 2005 by Prof. Claussen. Although some progress was achieved, present reconsiderations of the role of the chromosome and the single cell in Human Genetic research are urgently necessary.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, D-07747 Jena, Germany.
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Rodríguez-Domínguez JM, Ríos-Lara LL, Tapia-Campos E, Barba-Gonzalez R. An improved technique for obtaining well-spread metaphases from plants with numerous large chromosomes. Biotech Histochem 2017; 92:159-166. [PMID: 28418749 DOI: 10.1080/10520295.2017.1288927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Preparations that contain well-spread metaphase chromosomes are critical for plant cytogenetic analyses including chromosome counts, banding procedures, in situ hybridization, karyotyping and construction of ideograms. Chromosome spreading is difficult for plants with large and numerous chromosomes. We report here a technique for obtaining cytoplasm-free, well-spread metaphases from two Amaryllidaceae species: Sprekelia formosissima (2n = 120) and Hymenocallis howardii (2n = 96). The technique has three main steps: 1) pretreatment to cause chromosome condensation, 2) dripping onto tilted slides coated with a thin layer of pure acetic acid and 3) application of steam and acetic acid to produce cytoplasmic hydrolysis, which spreads the chromosomes.
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Affiliation(s)
- J M Rodríguez-Domínguez
- a Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco , A.C. Unidad de Biotecnología Vegetal , Guadalajara , Jalisco , México
| | - L L Ríos-Lara
- a Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco , A.C. Unidad de Biotecnología Vegetal , Guadalajara , Jalisco , México
| | - E Tapia-Campos
- a Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco , A.C. Unidad de Biotecnología Vegetal , Guadalajara , Jalisco , México
| | - R Barba-Gonzalez
- a Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco , A.C. Unidad de Biotecnología Vegetal , Guadalajara , Jalisco , México
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Weise A, Liehr T. Pre- and Postnatal Diagnostics and Research on Peripheral Blood, Bone Marrow, Chorion, Amniocytes, and Fibroblasts. SPRINGER PROTOCOLS HANDBOOKS 2017. [DOI: 10.1007/978-3-662-52959-1_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Weise A, Bhatt S, Piaszinski K, Kosyakova N, Fan X, Altendorf-Hofmann A, Tanomtong A, Chaveerach A, de Cioffi MB, de Oliveira E, Walther JU, Liehr T, Chaudhuri JP. Chromosomes in a genome-wise order: evidence for metaphase architecture. Mol Cytogenet 2016; 9:36. [PMID: 27123045 PMCID: PMC4847357 DOI: 10.1186/s13039-016-0243-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/12/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND One fundamental finding of the last decade is that, besides the primary DNA sequence information there are several epigenetic "information-layers" like DNA-and histone modifications, chromatin packaging and, last but not least, the position of genes in the nucleus. RESULTS We postulate that the functional genomic architecture is not restricted to the interphase of the cell cycle but can also be observed in the metaphase stage, when chromosomes are most condensed and microscopically visible. If so, it offers the unique opportunity to directly analyze the functional aspects of genomic architecture in different cells, species and diseases. Another aspect not directly accessible by molecular techniques is the genome merged from two different haploid parental genomes represented by the homologous chromosome sets. Our results show that there is not only a well-known and defined nuclear architecture in interphase but also in metaphase leading to a bilateral organization of the two haploid sets of chromosomes. Moreover, evidence is provided for the parental origin of the haploid grouping. CONCLUSIONS From our findings we postulate an additional epigenetic information layer within the genome including the organization of homologous chromosomes and their parental origin which may now substantially change the landscape of genetics.
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Affiliation(s)
- Anja Weise
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Samarth Bhatt
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Katja Piaszinski
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Nadezda Kosyakova
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Xiaobo Fan
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Annelore Altendorf-Hofmann
- />Department of General, Visceral und Vascular Surgery, Jena University Hospital, Kochstr. 2, Jena, 07743 Germany
| | - Alongklod Tanomtong
- />Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd, Khon Kaen, Muang District 40002 Thailand
| | - Arunrat Chaveerach
- />Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd, Khon Kaen, Muang District 40002 Thailand
| | - Marcelo Bello de Cioffi
- />Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Edivaldo de Oliveira
- />Instituto Evandro Chagas, Seção de Meio Ambiente, Laboratório de Cultura de Tecidos e Citogenética, Ananindeua, PA Brazil
| | - Joachim-U. Walther
- />Instituto Evandro Chagas, Seção de Meio Ambiente, Laboratório de Cultura de Tecidos e Citogenética, Ananindeua, PA Brazil
| | - Thomas Liehr
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Jyoti P. Chaudhuri
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
- />Kinderklinik, Ludwig Maximillians Universität, 80337 Munich, Germany
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Taga M, Tanaka K, Kato S, Kubo Y. Cytological analyses of the karyotypes and chromosomes of three Colletotrichum species, C. orbiculare, C. graminicola and C. higginsianum. Fungal Genet Biol 2015; 82:238-50. [DOI: 10.1016/j.fgb.2015.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/28/2015] [Accepted: 07/31/2015] [Indexed: 01/03/2023]
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Experimental characterization of methanol-acetic acid fixative sessile drop dynamics in dry and humid air by video imaging and interference analysis. Colloids Surf A Physicochem Eng Asp 2014. [DOI: 10.1016/j.colsurfa.2014.02.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kirov I, Divashuk M, Van Laere K, Soloviev A, Khrustaleva L. An easy "SteamDrop" method for high quality plant chromosome preparation. Mol Cytogenet 2014; 7:21. [PMID: 24602284 PMCID: PMC3995958 DOI: 10.1186/1755-8166-7-21] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 02/26/2014] [Indexed: 12/01/2022] Open
Abstract
Background The chromosome preparation is a crucial step for obtaining satisfactory results in molecular cytogenetic researches. The preparation of plant chromosomes for molecular cytogenetic purposes remains a challenge for some species. In contrast to human chromosome preparation, the processes occurring during plant chromosome preparation and causing chromosome spreading are still poorly understood. Results We studied the dynamics of plant chromosome spreading after dropping cell suspension on slides. We showed that steam stimulates cytoplasm hydrolysis and rapid chromosome spreading and that chromosomes stretch during this chromosome spreading. Based on these observations, we developed a novel method, named “SteamDrop”, for the preparation of well-spread mitotic and pachytene chromosomes and successfully used it for 28 plant species with large and small chromosomes. We applied cell suspensions in ethanol instead of the commonly used ethanol/acetic acid fixative. Mitotic and meiotic chromosomes prepared via “SteamDrop” were used in fluorescent in situ hybridization (FISH) experiments with repetitive and unique DNA probes. Long storage of cell suspensions in ethanol did not impair the quality of chromosome preparations. Conclusion The SteamDrop procedure provides a robust and routine method for high quality plant chromosome preparations. The method can be applied for metaphase as well as pachytene chromosome preparation in wide range of species. The chromosomes prepared by SteamDrop are well suitable for repetitive and unique DNA visualization.
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Affiliation(s)
| | | | | | | | - Ludmila Khrustaleva
- Department of Genetics and Biotechnology, Russian State Agrarian University-MTAA, Timiryazevskay str, 49, 127550 Moscow, Russia.
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Ami D, Di Segni M, Forcella M, Meraviglia V, Baccarin M, Doglia SM, Terzoli G. Role of water in chromosome spreading and swelling induced by acetic acid treatment: a FTIR spectroscopy study. Eur J Histochem 2014; 58:2330. [PMID: 24705001 PMCID: PMC3980214 DOI: 10.4081/ejh.2014.2330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/11/2013] [Accepted: 12/30/2013] [Indexed: 11/23/2022] Open
Abstract
The so called chromosome preparation is a procedure consisting of three strictly connected stages that enables to obtain chromosomes of quality suitable for cytogenetic analysis. Interestingly, experimental evidence strongly suggested that chromosome spreading and swelling (key processes that allow their counting and detailed structural analysis) are induced in the last fixative-evaporation stage by the interaction, mediated by acetic acid, between water from the environmental humidity, and the cytoplasmic matrix and the chromatin. However, since a considerable variation in the quality of chromosome preparations is observed, strongly depending on the environmental conditions in which the procedure takes place, a better comprehension of the mechanisms underlying chromosome preparation is required. To this aim, here we analysed intact lymphocytes before and at each stage of the chromosome preparation protocol by Fourier transform infrared (FTIR) spectroscopy, a technique widely used for the study not only of isolated biomolecules, but also of complex biological systems, such as whole cells. Interestingly, we found that the chromosome preparation protocol induces significant structural changes of cell proteins and DNA, in particular due to the interaction with acetic acid. Moreover, noteworthy, through the monitoring of changes in the water combination band between 2300 and 1800 cm–1, we provided evidence at molecular level of the crucial role of the bound water to the cytoplasmic matrix and to the chromatin in determining the chromosome spreading and swelling. Our FTIR results, therefore, underline the need to perform the last fixative-evaporation stage in standardized and optimized temperature and relative humidity conditions, thus providing chromosomes of high quality for the cytogenetic analysis that would lead in this way to more reliable results.
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Affiliation(s)
- D Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy.
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12
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Rubtsov NB. Organization of eukaryotic chromosomes: From Kol’tsov’s studies up to present day. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413010109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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FISHprep: A Novel Integrated Device for Metaphase FISH Sample Preparation. MICROMACHINES 2011. [DOI: 10.3390/mi2020116] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Metaphase FISH on a chip: miniaturized microfluidic device for fluorescence in situ hybridization. SENSORS 2010; 10:9831-46. [PMID: 22163442 PMCID: PMC3231008 DOI: 10.3390/s101109831] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/23/2010] [Accepted: 10/15/2010] [Indexed: 12/29/2022]
Abstract
Fluorescence in situ Hybridization (FISH) is a major cytogenetic technique for clinical genetic diagnosis of both inherited and acquired chromosomal abnormalities. Although FISH techniques have evolved and are often used together with other cytogenetic methods like CGH, PRINS and PNA-FISH, the process continues to be a manual, labour intensive, expensive and time consuming technique, often taking over 3 5 days, even in dedicated labs. We have developed a novel microFISH device to perform metaphase FISH on a chip which overcomes many shortcomings of the current laboratory protocols. This work also introduces a novel splashing device for preparing metaphase spreads on a microscope glass slide, followed by a rapid adhesive tape-based bonding protocol leading to rapid fabrication of the microFISH device. The microFISH device allows for an optimized metaphase FISH protocol on a chip with over a 20-fold reduction in the reagent volume. This is the first demonstration of metaphase FISH on a microfluidic device and offers a possibility of automation and significant cost reduction of many routine diagnostic tests of genetic anomalies.
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Bangs CD, Donlon TA. Metaphase chromosome preparation from cultured peripheral blood cells. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.1. [PMID: 18428376 DOI: 10.1002/0471142905.hg0401s45] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromosome preparations currently provide the only direct view of the genome as a whole. Although molecular methods allow a more detailed analysis of specific regions of the genome, the study of genetics is not complete without an appreciation of the metaphase cell. The stimulated T cell system described in this unit is the most widely used means of obtaining large numbers of mitotic cells for genetic analyses. Synchronization of the cell cycle in culture is described, combined with direct inhibition of chromosome condensation, to yield longer high-resolution prophase or prometaphase preparations. Such preparations are used for detailed analysis of microdeletions or subtle rearrangements, fine breakpoint analysis, and refined mapping. Microscope slide preparation of mitotic chromosomes from harvested cell culture suspensions is also explained in the support protocol.
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Petibone D, Morris S, Hotchkiss C, Mattison D, Tucker J. Technique for culturing Macaca mulatta peripheral blood lymphocytes for fluorescence in situ hybridization of whole chromosome paints. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2008; 653:76-81. [DOI: 10.1016/j.mrgentox.2008.03.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2008] [Revised: 03/25/2008] [Accepted: 03/26/2008] [Indexed: 11/28/2022]
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17
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Belonogova NM, Karamysheva TV, Biltueva LS, Perepelov EA, Minina JM, Polyakov AV, Zhdanova NS, Rubtsov NB, Searle JB, Borodin PM. Identification of all pachytene bivalents in the common shrew using DAPI-staining of synaptonemal complex spreads. Chromosome Res 2006; 14:673-9. [PMID: 16964574 DOI: 10.1007/s10577-006-1079-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 06/21/2006] [Accepted: 06/21/2006] [Indexed: 10/24/2022]
Abstract
A major problem in studies of synaptonemal complexes (SC) is the difficulty in distinguishing individual chromosomes. This problem can be solved combining SC immunostaining with FISH of chromosome-specific sequences. However, this procedure is expensive, time-consuming and applicable only to a very limited number of species. In this paper we show how a combination of SC immunostaining and DAPI staining can allow identification of all chromosome arms in surface-spreads of the SC of the common shrew (Sorex araneus L.). Enhancement of brightness and contrast of the images with photo editing software allowed us to reveal clear DAPI-positive and negative bands with relative sizes and positions similar to DAPI landmarks on mitotic metaphase chromosomes. Using FISH with DNA probes prepared from chromosome arms m and n we demonstrated correct recognition of the chromosomes mp and hn on the basis of their DAPI pattern. We show that the approach we describe here may be applied to other species and can provide an important tool for identification of individual bivalents in pachytene surface-spreads.
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Affiliation(s)
- N M Belonogova
- Institute of Cytology and Genetics, Siberian Department of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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Sikkema-Raddatz B, Suijkerbuijk R, Bouman K, de Jong B, Buys CHCM, te Meerman GJ. Quality aspects of prenatal cytogenetic diagnosis: determining the effect of various factors involved in handling amniotic fluid and chorionic villus material for cytogenetic diagnosis. Prenat Diagn 2006; 26:791-800. [PMID: 16821245 DOI: 10.1002/pd.1505] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVES To investigate the effect of factors involved in cell culturing and slide preparation of amniotic fluid (AF) and chorionic villus biopsies (CVB) for prenatal cytogenetic diagnosis. METHODS The effect on the outcome of our standard AF cell culture procedure of volume and appearance of the submitted AF specimen, gynaecologist performing the amniocentesis, week of gestation in which the specimen was taken and culture medium was retrospectively investigated. In a prospective study controlled experimental variation was introduced in composition of fixative, relative humidity, temperature and airflow during slide preparation from primary CVB and AF in situ cultures. For evaluation, analysis of regression or variance was used. RESULTS Provided that at least 0.8 mL AF per culture dish was admitted, none of the investigated factors appeared as critical resulting in unacceptable variation in outcome. Variation in appearance of the AF had a relatively major impact: bloody or brown AF resulted in a 3 days longer culture time. To a limited degree, metaphase quality of AF and CVB cells was affected by composition of fixative, relative humidity, ambient temperature and airflow during slide preparation. CONCLUSION Current prenatal cytogenetic practice as described here appears in general to be robust and reliable. The investigated conditions are not critical within the investigated range. Expensive measures for fine control of these conditions are, therefore, not required.
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Affiliation(s)
- Birgit Sikkema-Raddatz
- Department of Medical Genetics, University Medical Center Groningen, Postbus 300001, 9700 RB Groningen, The Netherlands.
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19
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Jiao Y, Schäffer TE. Accurate height and volume measurements on soft samples with the atomic force microscope. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:10038-10045. [PMID: 15518491 DOI: 10.1021/la048650u] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The suitability of three common atomic force microscope (AFM) imaging modes for quantitative height and volume measurements on soft samples was investigated. The height and volume of rehydrated human metaphase chromosomes in liquid were measured using the contact mode, the tapping mode, and the force mapping mode. In both the contact and tapping modes, the measured height and volume strongly depended on the imaging setpoint that sets the imaging force. Measurement deviations up to 50% were observed. The force mapping mode, on the other hand, yielded reproducible height and volume measurements independent of the imaging force. It is therefore suggested that the force mapping mode should be used whenever the height or volume of soft samples need to be accurately determined.
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Affiliation(s)
- Yuekan Jiao
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
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20
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Abstract
We review micromechanical experiments studying mechanoelastic properties of mitotic chromosomes. We discuss the history of this field, starting from the classic in vivo experiments of Nicklas (1983). We then focus on experiments where chromosomes were extracted from prometaphase cells and then studied by micromanipulation and microfluidic biochemical techniques. These experiments reveal that chromosomes have a well-behaved elastic response over a fivefold range of stretching, with an elastic modulus similar to that of a loosely tethered polymer network. Perturbation by microfluidic "spraying" of various ions reveals that the mitotic chromosome can be rapidly and reversibly decondensed or overcondensed, i.e., that the native state is not maximally compacted. We compare our results for chromosomes from cells to results of experiments by Houchmandzadeh and Dimitrov (1999) on chromatids reconstituted using Xenopus egg extracts. Remarkably, while the stretching elastic response of reconstituted chromosomes is similar to that observed for chromosomes from cells, reconstituted chromosomes are far more easily bent. This result suggests that reconstituted chromatids have a large-scale structure that is quite different from chromosomes in somatic cells. Finally, we discuss microspraying experiments of DNA-cutting enzymes, which reveal that the element that gives mitotic chromosomes their mechanical integrity is DNA itself. These experiments indicate that chromatin-condensing proteins are not organized into a mechanically contiguous "scaffold," but instead that the mitotic chromosome is best thought of as a cross-linked network of chromatin. Preliminary results from restriction enzyme digestion experiments indicate a spacing between chromatin "cross-links" of roughly 15 kb, a size similar to that inferred from classical chromatin loop isolation studies. These results suggest a general strategy for the use of micromanipulation methods for the study of chromosome structure.
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Affiliation(s)
- M G Poirier
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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21
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Deng W, Tsao SW, Lucas JN, Leung CS, Cheung ALM. A new method for improving metaphase chromosome spreading. Cytometry A 2003; 51:46-51. [PMID: 12500304 DOI: 10.1002/cyto.a.10004] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND The success of complex molecular cytogenetic studies depends on having properly spread chromosomes. However, inconsistency of optimum chromosome spreading remains a major problem in cytogenetic studies. METHODS The metaphase spreading process was carefully timed to identify the most critical phase of chromosome spreading. The effects of dropping height of cell suspension, slide condition, drying time, fixative ratio, and relative humidity on the quality of metaphase spreads were studied by quantitative examination of metaphase chromosome spreads. Normal and immortalized human epithelial ovarian cells, neuroblastoma cells, and normal lymphocytes were tested. RESULTS Humidity over the slide was the most important variable affecting the quality of chromosome spreads. Consistent improvement in chromosome spreading (larger metaphase area, less chromosome overlaps, or lower frequencies of broken metaphases) was obtained for all cell types if dynamic cell rehydration, occurring as fixative absorbs moisture from air, was made to coincide with the prompt fixation of spread chromosomes to the slide. This was achieved by dropping cells on dry glass slides placed in a shallow metal tray and then quickly lowering the tray into a covered 50 degrees C water bath for slide drying. CONCLUSIONS A new and simple method for improving metaphase chromosome spreading was developed based on our study on the characteristics of chromosome spreading.
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Affiliation(s)
- Wen Deng
- Department of Anatomy, The University of Hong Kong, Hong Kong, SAR, China
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22
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Lemke J, Claussen J, Michel S, Chudoba I, Mühlig P, Westermann M, Sperling K, Rubtsov N, Grummt UW, Ullmann P, Kromeyer-Hauschild K, Liehr T, Claussen U. The DNA-based structure of human chromosome 5 in interphase. Am J Hum Genet 2002; 71:1051-9. [PMID: 12370837 PMCID: PMC385084 DOI: 10.1086/344286] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2002] [Accepted: 08/01/2002] [Indexed: 11/03/2022] Open
Abstract
In contrast to those of metaphase chromosomes, the shape, length, and architecture of human interphase chromosomes are not well understood. This is mainly due to technical problems in the visualization of interphase chromosomes in total and of their substructures. We analyzed the structure of chromosomes in interphase nuclei through use of high-resolution multicolor banding (MCB), which paints the total shape of chromosomes and creates a DNA-mediated, chromosome-region-specific, pseudocolored banding pattern at high resolution. A microdissection-derived human chromosome 5-specific MCB probe mixture was hybridized to human lymphocyte interphase nuclei harvested for routine chromosome analysis, as well as to interphase nuclei from HeLa cells arrested at different phases of the cell cycle. The length of the axis of interphase chromosome 5 was determined, and the shape and MCB pattern were compared with those of metaphase chromosomes. We show that, in lymphocytes, the length of the axis of interphase chromosome 5 is comparable to that of a metaphase chromosome at 600-band resolution. Consequently, the concept of chromosome condensation during mitosis has to be reassessed. In addition, chromosome 5 in interphase is not as straight as metaphase chromosomes, being bent and/or folded. The shape and banding pattern of interphase chromosome 5 of lymphocytes and HeLa cells are similar to those of the corresponding metaphase chromosomes at all stages of the cell cycle. The MCB pattern also allows the detection and characterization of chromosome aberrations. This may be of fundamental importance in establishing chromosome analyses in nondividing cells.
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Affiliation(s)
- Johannes Lemke
- Institute of Human Genetics and Anthropology, Friedrich Schiller University, Jena, Germany
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Velilla E, Escudero T, Munné S. Blastomere fixation techniques and risk of misdiagnosis for preimplantation genetic diagnosis of aneuploidy. Reprod Biomed Online 2002; 4:210-7. [PMID: 12709269 DOI: 10.1016/s1472-6483(10)61808-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
One of the most critical steps in preimplantation genetic diagnosis (PGD) studies is the fixation required to obtain good fluorescence in-situ hybridization (FISH) nuclear quality without losing any of the cells analysed. Different fixation techniques have been described. The aim of this study was to compare three fixation methods (1, acetic acid/methanol; 2, Tween 20; 3, Tween 20 and acetic acid/methanol) based on number of cells lost after fixation, average rate of informative cells, rate of signal overlaps and FISH errors. A total of 100, 106 and 114 blastomeres were fixed using techniques 1, 2 and 3 respectively. Technique 2 gave the poorest nuclear quality with higher cytoplasm, number of overlaps and FISH errors. Although technique 1 showed better nuclear quality in terms of greater nuclear diameter, fewer overlaps and FISH errors, it is difficult to perform correctly. However, technique 3 shows reasonably good nuclear quality and is both easier to learn and use for PGD studies than the others.
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Affiliation(s)
- Esther Velilla
- Institute for Reproductive Medicine and Science of Saint Barnabas Medical Centre, 101 Old Short Hills Road, Suite 501, West Orange, NJ-07052, USA
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Henegariu O, Heerema NA, Lowe Wright L, Bray-Ward P, Ward DC, Vance GH. Improvements in cytogenetic slide preparation: Controlled chromosome spreading, chemical aging and gradual denaturing. ACTA ACUST UNITED AC 2001. [DOI: 10.1002/1097-0320(20010201)43:2<101::aid-cyto1024>3.0.co;2-8] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kerndrup GB, Kjeldsen E. Acute leukemia cytogenetics: an evaluation of combining G-band karyotyping with multi-color spectral karyotyping. CANCER GENETICS AND CYTOGENETICS 2001; 124:7-11. [PMID: 11165315 DOI: 10.1016/s0165-4608(99)00223-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have, during a 12-month period, evaluated the adjuvant effect of combining G-band karyotyping and multi-color spectral karyotyping (SKY) in acute leukemia patients. Forty-four cases were evaluated; fewer cases than those routinely analyzed by G-band cytogenetics had mitoses left for SKY analysis. Of the 44 patients, 35 were acute myeloid leukemia (AML) and 9 acute lymphatic leukemia (ALL) cases. Twenty-seven of 35 AML and 7 of 9 ALL patients had an abnormal G-band karyotype. Thirteen of these 34 abnormal cases had a simple clonal chromosome aberration, and the remaining 21 cases had a complex karyotype. The SKY confirmed the simple karyotype in 11 and in 7 with a complex karyotype. In 13 of the cases with a complex karyotype, ambiguous structural aberrations were classified, in 6 of these, SKY disclosed cryptic translocations. Thus, SKY either extended or confirmed G-band karyotypes in 31 of 34 analyzed abnormal cases. Cases where SKY did not reveal the abnormal clone showed only few abnormal mitoses by G-banding (2/23, 2/25, and 4/27). Additional or confirmatory information was therefore obtained in 91% of analyzed cases, and SKY proved to be a valuable additional tool for hematologic cytogenetics.
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Affiliation(s)
- G B Kerndrup
- Department of Pathology, Chromosome Laboratory, Odense University Hospital, Odense, Denmark.
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Maraldi NM, Capitani S, Cinti C, Neri LM, Santi S, Squarzoni S, Stuppia L, Manzoli FA. Chromosome spread for confocal microscopy. Methods Enzymol 1999; 307:190-207. [PMID: 10506975 DOI: 10.1016/s0076-6879(99)07014-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- N M Maraldi
- Institute of Citomorfologia Normale e Patologica, C.N.R., Bologna, Italy
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Wen GY, Jenkins EC, Goldberg EM, Genovese M, Brown WT, Wisniewski HM. First transmission electron micrograph of continuous mitotic spindle fibers between polar area and chromosome ends. AMERICAN JOURNAL OF MEDICAL GENETICS 1999; 83:334-7. [PMID: 10208175 DOI: 10.1002/(sici)1096-8628(19990402)83:4<334::aid-ajmg22>3.0.co;2-i] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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