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Moll CJ, Versluis J, Bakker HJ. Bulk Response of Carboxylic Acid Solutions Observed with Surface Sum-Frequency Generation Spectroscopy. J Phys Chem B 2021; 126:270-277. [PMID: 34962792 PMCID: PMC8762667 DOI: 10.1021/acs.jpcb.1c09051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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We study the molecular
properties of aqueous acetic acid and formic
acid solutions with heterodyne-detected vibrational sum-frequency
generation spectroscopy (HD-VSFG). For acid concentrations up to ∼5
M, we observe a strong increase of the responses of the acid hydroxyl
and carbonyl stretch vibrations with increasing acid concentration
due to an increase of the surface coverage by the acid molecules.
At acid concentrations >5 M we observe first a saturation of these
responses and then a decrease. For pure carboxylic acids we even observe
a change of sign of the Im[χ(2)] response of the
carbonyl vibration. The decrease of the response of the hydroxyl vibration
and the decrease and sign change of the response of the carbonyl vibration
indicate the formation of cyclic dimers, which only show a quadrupolar
bulk response in the HD-VSFG spectrum because of their antiparallel
conformation. We also find evidence for the presence of a quadrupolar
response of the CH vibrations of the acid molecules.
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Affiliation(s)
- Carolyn J Moll
- Ultrafast Spectroscopy, AMOLF, Science Park 104,1098 XG Amsterdam, Netherlands
| | - Jan Versluis
- Ultrafast Spectroscopy, AMOLF, Science Park 104,1098 XG Amsterdam, Netherlands
| | - Huib J Bakker
- Ultrafast Spectroscopy, AMOLF, Science Park 104,1098 XG Amsterdam, Netherlands
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2
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Sartsanga C, Phengchat R, Fukui K, Wako T, Ohmido N. Surface structures consisting of chromatin fibers in isolated barley (Hordeum vulgare) chromosomes revealed by helium ion microscopy. Chromosome Res 2021; 29:81-94. [PMID: 33615407 DOI: 10.1007/s10577-021-09649-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 11/24/2022]
Abstract
The chromosome compaction of chromatin fibers results in the formation of the nucleosome, which consists of a DNA unit coiled around a core of histone molecules associated with linker histone. The compaction of chromatin fibers has been a topic of controversy since the discovery of chromosomes in the 19th century. Although chromatin fibers were first identified using electron microscopy, the chromatin fibers on the surface of chromosome structures in plants remain unclear due to shrinking and breaking caused by prior chromosome isolation or preparation with alcohol and acid fixation, and critical point drying occurred into dehydration and denatured chromosomal proteins. This study aimed to develop a high-quality procedure for the isolation and preparation of plant chromosomes, maintaining the native chromosome structure, to elucidate the organization of chromatin fibers on the surface of plant chromosomes by electron microscopy. A simple technique to isolate intact barley (Hordeum vulgare) chromosomes with a high yield was developed, allowing chromosomes to be observed with a high-resolution scanning ion microscopy and helium ion microscopy (HIM) imaging technology, based on a scanning helium ion beam. HIM images from the surface chromatin fibers were analyzed to determine the size and alignment of the chromatin fibers. The unit size of the chromatin fibers was 11.6 ± 3.5 nm and was closely aligned to the chromatin network model. Our findings indicate that compacting the surface structure of barley via a chromatin network and observation via HIM are powerful tools for investigating the structure of chromatin.
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Affiliation(s)
- Channarong Sartsanga
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Rinyaporn Phengchat
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshiyuki Wako
- Institute of Crop Sciences, National Agriculture and Food Research Organization, 2-1-1 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan.
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3
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Khrustaleva L, Jiang J, Havey MJ. High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:535-545. [PMID: 26704420 DOI: 10.1007/s00122-015-2646-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
Tyramide FISH was used to locate relatively small genomic amplicons from molecular markers linked to Ms locus onto onion chromosome 2 near the centromere, a region of relatively low recombination. Fluorescence in situ hybridization (FISH) has not been readily exploited for physical mapping of molecular markers in plants due to the technical challenge of visualizing small single-copy probes. Signal amplification using tyramide (tyr) FISH can increase sensitivity up to 100-fold. We used tyr-FISH to physically locate molecular markers tightly linked to the nuclear male-fertility (Ms) restoration locus of onion onto mitotic metaphase, pachytene, and super-stretched pachytene chromosomes. Relatively short genomic amplicons (846-2251 bp) and a cDNA clone (666 bp) were visualized in 9-42 % of observed cells. The markers were assigned to proximal locations close to the centromere on the long arm of chromosome 2, a region of lower recombination, revealing that tightly linked markers may be physically distant from Ms. This result explains why several labs have identified molecular markers tightly linked to the Ms locus after screening relatively few DNA clones or primers and segregating progenies. Although these markers are still useful for marker-aided selection, our results indicate that map-based cloning of Ms will likely be difficult due to reduced recombination near this gene.
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Affiliation(s)
- Ludmila Khrustaleva
- Center of Molecular Biotechnology, Department of Genetics and Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, 49, Timiryazevskaya Str., 127550, Moscow, Russia.
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
| | - Michael J Havey
- USDA-ARS and Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
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4
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Tantivit K, Isobe S, Nathewet P, Okuda N, Yanagi T. The Development of a Primed In Situ Hybridization Technique for Chromosome Labeling in Cultivated Strawberry ( Fragaria× ananassa). CYTOLOGIA 2016. [DOI: 10.1508/cytologia.81.439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kirov IV, Van Laere K, Khrustaleva LI. High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa. BMC Genet 2015; 16:74. [PMID: 26134672 PMCID: PMC4488978 DOI: 10.1186/s12863-015-0233-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-based cloning, comparative genomics and evolutionary studies, no studies using high resolution physical mapping have been performed in this family. Previously we proved that physical mapping of single-copy genes as small as 1.1 kb is possible on mitotic metaphase chromosomes of Rosa wichurana using Tyramide-FISH. In this study we aimed to further improve the physical map of Rosa wichurana by applying high resolution FISH to pachytene chromosomes. RESULTS Using high resolution Tyramide-FISH and multicolor Tyramide-FISH, 7 genes (1.7-3 kb) were successfully mapped on pachytene chromosomes 4 and 7 of Rosa wichurana. Additionally, by using multicolor Tyramide-FISH three closely located genes were simultaneously visualized on chromosome 7. A detailed map of heterochromatine/euchromatine patterns of chromosome 4 and 7 was developed with indication of the physical position of these 7 genes. Comparison of the gene order between Rosa wichurana and Fragaria vesca revealed a poor collinearity for chromosome 7, but a perfect collinearity for chromosome 4. CONCLUSIONS High resolution physical mapping of short probes on pachytene chromosomes of Rosa wichurana was successfully performed for the first time. Application of Tyramide-FISH on pachytene chromosomes allowed the mapping resolution to be increased up to 20 times compared to mitotic metaphase chromosomes. High resolution Tyramide-FISH and multicolor Tyramide-FISH might become useful tools for further physical mapping of single-copy genes and for the integration of physical and genetic maps of Rosa wichurana and other members of the Rosaceae.
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Affiliation(s)
- Ilya V Kirov
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str.49, 127550, Moscow, Russia. .,Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Listvennichnaya Alleya 5, 127550, Moscow, Russia. .,Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090, Melle, Belgium.
| | - Katrijn Van Laere
- Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090, Melle, Belgium.
| | - Ludmila I Khrustaleva
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str.49, 127550, Moscow, Russia. .,Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Listvennichnaya Alleya 5, 127550, Moscow, Russia.
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Comparative analysis of clastogen-induced chromosome aberrations observed with light microscopy and by means of atomic force microscopy. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 753:29-35. [DOI: 10.1016/j.mrgentox.2012.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 10/12/2012] [Accepted: 12/15/2012] [Indexed: 11/22/2022]
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Sugiyama S, Yoshino T, Hirose T, Ohtani T. Karyotyping of barley chromosomes by a new fluorescence banding technique combined with scanning probe microscopy. SCANNING 2012; 34:186-190. [PMID: 22058025 DOI: 10.1002/sca.20287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 08/14/2011] [Indexed: 05/31/2023]
Abstract
Fluorescence banding has been used to classify chromosomes, except those of barley. Four of the seven barley chromosomes are indistinguishable by length or arm ratio. C-banding has been used for classification; however, it requires a long aging period. Here, we describe a new fluorescence banding method for barley. The chromosomes are treated with warm acetate followed by staining with a fluorescent dye, YOYO-1. Using this method, all seven barley chromosomes can be clearly distinguished. Atomic force microscopy and scanning near-field microscopy analyses revealed that the surfaces of the banded chromosomes were flat, indicating that the fluorescence intensity reflected the internal DNA density or condensation of chromatin.
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Affiliation(s)
- Shigeru Sugiyama
- Nanobiotechnology Laboratory, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
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8
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Abstract
As rapid divisions without growth generate progressively smaller cells within an embryo, mitotic chromosomes must also decrease in size to permit their proper segregation, but this scaling phenomenon is poorly understood. We demonstrated previously that nuclear and spindle size scale between egg extracts of the related frog species Xenopus tropicalis and Xenopus laevis, but show here that dimensions of isolated mitotic sperm chromosomes do not differ. This is consistent with the hypothesis that chromosome scaling does not occur in early embryonic development when cell and spindles sizes are large and anaphase B segregates chromosomes long distances. To recapitulate chromosome scaling during development, we combined nuclei isolated from different stage Xenopus laevis embryos with metaphase-arrested egg extracts. Mitotic chromosomes derived from nuclei of cleaving embryos through the blastula stage were similar in size to replicated sperm chromosomes, but decreased in area approximately 50% by the neurula stage, reproducing the trend in size changes observed in fixed embryos. Allowing G2 nuclei to swell in interphase prior to mitotic condensation did not increase mitotic chromosome size, but progression through a full cell cycle in egg extract did, suggesting that epigenetic mechanisms determining chromosome size can be altered during DNA replication. Comparison of different sized mitotic chromosomes assembled in vitro provides a tractable system to elucidate underlying molecular mechanisms.
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Affiliation(s)
- Esther K Kieserman
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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Di Bucchianico S, Venora G, Lucretti S, Limongi T, Palladino L, Poma A. Saponaria officinalis karyology and karyotype by means of image analyzer and atomic force microscopy. Microsc Res Tech 2008; 71:730-6. [PMID: 18618603 DOI: 10.1002/jemt.20613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The aim of this work was to offer a contribution to the characterization of taxonomic entity of Saponaria officinalis (2n = 28; an herbaceous perennial species; saporin, a type 1 Ribosome Inactivating Protein, is present in leaves and seeds) by a cytogenetic and karyomorphological approach. We investigated the karyotype's morphometry correlated with Stebbin's symmetric index; the same information has been used for computing the indices resemblance between chromosomes (REC), symmetric indices (SYI), and total form (TF%) which allow the comparison between species and evaluation of karyological evolution. Fluorescence intensities of the stained nuclei were measured by a flow cytometer and, for the first time, values for nuclear DNA content were estimated by comparing nuclei fluorescence intensities of the test population with those of appropriate internal DNA standards. Our study is also aimed to introduce chromosomal volumes, which were determined by atomic force microscopy (AFM), as novel karyomorphological parameter which could allow for chromosome discrimination especially when tiny ones are present.
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Affiliation(s)
- S Di Bucchianico
- Department of Basic and Applied Biology, University of L'Aquila, L'Aquila, Italy
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Danilova TV, Birchler JA. Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development. Chromosoma 2008; 117:345-56. [PMID: 18317793 DOI: 10.1007/s00412-008-0151-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2007] [Revised: 02/04/2008] [Accepted: 02/05/2008] [Indexed: 11/28/2022]
Abstract
To study the correlation of the sequence positions on the physical DNA finger print contig (FPC) map and cytogenetic maps of pachytene and somatic maize chromosomes, sequences located along the chromosome 9 FPC map approximately every 10 Mb were selected to place on maize chromosomes using fluorescent in situ hybridization (FISH). The probes were produced as pooled polymerase chain reaction products based on sequences of genetic markers or repeat-free portions of mapped bacterial artificial chromosome (BAC) clones. Fifteen probes were visualized on chromosome 9. The cytological positions of most sequences correspond on the pachytene, somatic, and FPC maps except some probes at the pericentromeric regions. Because of unequal condensation of mitotic metaphase chromosomes, being lower at pericentromeric regions and higher in the arms, probe positions are displaced to the distal ends of both arms. The axial resolution of FISH on somatic chromosome 9 varied from 3.3 to 8.2 Mb, which is 12-30 times lower than on pachytene chromosomes. The probe collection can be used as chromosomal landmarks or as a "banding paint" for the physical mapping of sequences including transgenes and BAC clones and for studying chromosomal rearrangements.
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Affiliation(s)
- Tatiana V Danilova
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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11
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Narukawa J, Yamamoto K, Ohtani T, Sugiyama S. Imaging of silkworm meiotic chromosome by atomic force microscopy. SCANNING 2007; 29:123-7. [PMID: 17455263 DOI: 10.1002/sca.20032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Although structural information of mitotic chromosomes has been accumulated, little information is available for meiotic chromosome structures. Here, we applied atomic force microscopy (AFM) to investigate the ultrastructures of the silkworm, Bombyx mori, meiotic pachytene chromosome in its native state with nanometer scale resolution. Two levels of DNA folding were observed on the meiotic chromosome surface, 50-70 nm granules, which were considered to be 30 nm chromatin fibers, and spherical protrusions of 400-600 nm, which were considered to be chromomeres and arranged on the surface of the chromosome parallel to the chromosome longitudinal axis. These observations suggested that AFM study is an excellent approach for obtaining information concerning the silkworm pachytene chromosome higher order structure.
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Affiliation(s)
- J Narukawa
- Insect Genome Research Unit, Division of Insect Sciences, National Institute of Agrobiological Science, Tsukuba, Ibaraki, Japan
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Hizume K, Yoshimura SH, Kumeta M, Takeyasu K. Structural organization of dynamic chromatin. Subcell Biochem 2007; 41:3-28. [PMID: 17484121 DOI: 10.1007/1-4020-5466-1_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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Wu Y, Cai J, Cheng L, Wang C, Chen Y. Chromosome imaging by atomic force microscopy: influencing factors and comparative evaluation. J Genet 2006; 85:141-5. [PMID: 17072083 DOI: 10.1007/bf02729020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yangzhe Wu
- Chemistry Department, Jinan University, Guangzhou 510632, People's Republic of China
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Wu Y, Cai J, Cheng L, Yun K, Wang C, Chen Y. Atomic Force Microscopic Examination of Chromosomes Treated with Trypsin or Ethidium Bromide. Chem Pharm Bull (Tokyo) 2006; 54:501-5. [PMID: 16595953 DOI: 10.1248/cpb.54.501] [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: 11/22/2022]
Abstract
Trypsin treatment is frequently used during chromosome preparation for removal of cellular contaminants, and ethidium bromide (EB) staining of bands is often used to facilitate high-resolution observations by optical microscopy. However, conventional optical microscopy is unable to visualize potential aberrations of chromosome structures caused by these physicochemical treatments. In this article, we use atomic force microscopy (AFM) in the tapping mode to obtain and analyze high-resolution images of chromosome surface structure damage associated with trypsinization and EB treatment. According to our results, the trypsin-based digestion effects became more severe as incubations increased across a range from 10 to 40 s; a digestion time of 10 to 20 s appeared to be most suitable for observation by AFM. In terms of chromosomal damage induced by EB treatment, addition of EB into the media of cultured human blood cells induced chromosomal breakage in a dose-dependent fashion, and the results indicate centromeric region damnifyed severer than arms. Together, these results indicate that EB staining and the standard chromosomal preparative techniques of trypsinization can induce chromosomal damage that may affect the observed results.
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Affiliation(s)
- Yangzhe Wu
- College of Life Science and Technology, Jinan University, Guangzhou, China
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Fukushi D, Ushiki T. The structure of C-banded human metaphase chromosomes as observed by atomic force microscopy. ACTA ACUST UNITED AC 2005; 68:81-7. [PMID: 15827381 DOI: 10.1679/aohc.68.81] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ultrastructure of C-banded human metaphase chromosomes was studied by the combined use of light microscopy and atomic force microscopy (AFM). Light microscopy of the C-banded chromosomes showed that the centromeric regions of all chromosomes except the Y chromosome were positively stained. AFM further revealed that the C-positive region was higher than the C-negative region. The area of the C-positive region was specific depending on each chromosome; it ranged from the centromere to the proximal end of the long arm in chromosome 1, while it was restricted to the centromere in chromosomes 2 and 3. At higher magnification, chromatin fibers about 50 nm thick were clearly shown in the entire length of the chromosomes. In the C-positive region, these chromatin fibers were densely packed, while chromatin fibers were loosely packed with gentle twisting in the C-negative region. These AFM findings suggest that certain factors related to the chromatin fiber compaction remain in the C-positive region even after successive C-banging treatment.
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Affiliation(s)
- Daisuke Fukushi
- Division of Microscopic Anatomy and Bio-imaging, Department of Cellular Function, Niigata University Graduate School of Medical and Dental Sciences, Niigata 981-8510, USA
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