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Almeida Machado Costa C, Wang XF, Ellsworth C, Deng WM. Polyploidy in development and tumor models in Drosophila. Semin Cancer Biol 2021; 81:106-118. [PMID: 34562587 DOI: 10.1016/j.semcancer.2021.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 09/03/2021] [Accepted: 09/18/2021] [Indexed: 12/26/2022]
Abstract
Polyploidy, a cell status defined as more than two sets of genomic DNA, is a conserved strategy across species that can increase cell size and biosynthetic production, but the functional aspects of polyploidy are nuanced and vary across cell types. Throughout Drosophila developmental stages (embryo, larva, pupa and adult), polyploid cells are present in numerous organs and help orchestrate development while contributing to normal growth, well-being and homeostasis of the organism. Conversely, increasing evidence has shown that polyploid cells are prevalent in Drosophila tumors and play important roles in tumor growth and invasiveness. Here, we summarize the genes and pathways involved in polyploidy during normal and tumorigenic development, the mechanisms underlying polyploidization, and the functional aspects of polyploidy in development, homeostasis and tumorigenesis in the Drosophila model.
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Affiliation(s)
- Caique Almeida Machado Costa
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, United States
| | - Xian-Feng Wang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, United States
| | - Calder Ellsworth
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, United States
| | - Wu-Min Deng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, United States.
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Loganathan R, Kim JH, Wells MB, Andrew DJ. Secrets of secretion-How studies of the Drosophila salivary gland have informed our understanding of the cellular networks underlying secretory organ form and function. Curr Top Dev Biol 2020; 143:1-36. [PMID: 33820619 DOI: 10.1016/bs.ctdb.2020.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Secretory organs are critical for organismal survival. Yet, the transcriptional regulatory mechanisms governing their development and maintenance remain unclear for most model secretory organs. The Drosophila embryonic salivary gland (SG) remedies this deficiency as one of the few organs wherein direct connections from the expression of the early patterning genes to cell specification to organ architecture and functional specialization can be made. Few other models of secretion can be accorded this distinction. Studies from the past three decades have made enormous strides in parsing out the roles of distinct transcription factors (TFs) that direct major steps in furnishing this secretory organ. In the first step of specifying the salivary gland, the activity of the Hox factors Sex combs reduced, Extradenticle, and Homothorax activate expression of fork head (fkh), sage, and CrebA, which code for the major suite of TFs that carry forward the task of organ building and maintenance. Then, in the second key step of building the SG, the program for cell fate maintenance and morphogenesis is deployed. Fkh maintains the secretory cell fate by regulating its own expression and that of sage and CrebA. Fkh and Sage maintain secretory cell viability by actively blocking apoptotic cell death. Fkh, along with two other TFs, Hkb and Rib, also coordinates organ morphogenesis, transforming two plates of precursor cells on the embryo surface into elongated internalized epithelial tubes. Acquisition of functional specialization, the third key step, is mediated by CrebA and Fkh working in concert with Sage and yet another TF, Sens. CrebA directly upregulates expression of all of the components of the secretory machinery as well as other genes (e.g., Xbp1) necessary for managing the physiological stress that inexorably accompanies high secretory load. Secretory cargo specificity is controlled by Sage and Sens in collaboration with Fkh. Investigations have also uncovered roles for various signaling pathways, e.g., Dpp signaling, EGF signaling, GPCR signaling, and cytoskeletal signaling, and their interactions within the gene regulatory networks that specify, build, and specialize the SG. Collectively, studies of the SG have expanded our knowledge of secretory dynamics, cell polarity, and cytoskeletal mechanics in the context of organ development and function. Notably, the embryonic SG has made the singular contribution as a model system that revealed the core function of CrebA in scaling up secretory capacity, thus, serving as the pioneer system in which the conserved roles of the mammalian Creb3/3L-family orthologues were first discovered.
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Affiliation(s)
- Rajprasad Loganathan
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ji Hoon Kim
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Michael B Wells
- Idaho College of Osteopathic Medicine, Meridian, ID, United States
| | - Deborah J Andrew
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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Kolesnikova TD, Antonenko OV, Makunin IV. Replication timing in Drosophila and its peculiarities in polytene chromosomes. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Drosophila melanogaster is one of the popular model organisms in DNA replication studies. Since the 1960s, DNA replication of polytene chromosomes has been extensively studied by cytological methods. In the recent two decades, the progress in our understanding of DNA replication was associated with new techniques. Use of fluorescent dyes increased the resolution of cytological methods significantly. High-throughput methods allowed analysis of DNA replication on a genome scale, as well as its correlation with chromatin structure and gene activi ty. Precise mapping of the cytological structures of polytene chromosomes to the genome assembly allowed comparison of replication between polytene chromosomes and chromosomes of diploid cells. New features of replication characteristic for D. melanogaster were described for both diploid and polytene chromosomes. Comparison of genomic replication profiles revealed a significant similarity between Drosophila and other well-studi ed eukaryotic species, such as human. Early replication is often confined to intensely transcribed gene-dense regions characterized by multiple replication initiation sites. Features of DNA replication in Drosophila might be explained by a compact genome. The organization of replication in polytene chromosomes has much in common with the organization of replication in chromosomes in diploid cells. The most important feature of replication in polytene chromosomes is its low rate and the dependence of S-phase duration on many factors: external and internal, local and global. The speed of replication forks in D. melanogaster polytene chromosomes is affected by SUUR and Rif1 proteins. It is not known yet how universal the mechanisms associated with these factors are, but their study is very promising.
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Affiliation(s)
- T. D. Kolesnikova
- Institute of Molecular and Cellular Biology, SB RAS. Novosibirsk State University
| | | | - I. V. Makunin
- Institute of Molecular and Cellular Biology, SB RAS; Research Computing Centre, The University of Queensland
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Bedo DG. CYTOGENETICS AND EVOLUTION OF SIMULIUM ORNATIPES
SKUSE (DIPTERA: SIMULIIDAE). II. TEMPORAL VARIATION IN CHROMOSOMAL POLYMORPHISMS AND HOMOSEQUENTIAL SIBLING SPECIES. Evolution 2017; 33:296-308. [DOI: 10.1111/j.1558-5646.1979.tb04683.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/1977] [Revised: 06/28/1978] [Indexed: 11/30/2022]
Affiliation(s)
- D. G. Bedo
- Department of Population Biology, Research School of Biological Sciences; Australian National University; P.O. Box 475 Canberra City A.C.T. 2601 Australia
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Dyka LD, Shakina LA, Strashnyuk VY, Shckorbatov YG. Effects of 36.6 GHz and static magnetic field on degree of endoreduplication in Drosophila melanogaster polytene chromosomes. Int J Radiat Biol 2016; 92:222-7. [PMID: 26882320 DOI: 10.3109/09553002.2016.1137105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Purpose To study the effect of microwave (MW) irradiation and consistent action of microwaves and static magnetic field (MF) on the giant chromosomes endoreduplication in Drosophila melanogaster Meig. Materials and methods Experiments were carried out on inbred wild type Canton-S strain. Exposure to microwaves (frequency - 36.64 GHz, power density - 1 W/m(2), exposure time - 30 sec) and static magnetic field (intensity - 25 mT, exposure time - 5 min) applied at the egg stage after a 2-h oviposition. Giant chromosomes were investigated in squashed preparations of the salivary glands stained by acetoorcein by the cytomorphometric method. Preparations were obtained from Drosophila larvae at the 0 h prepupae stage. Results Exposure to microwaves increased the degree of polyteny in chromosomes (DPC) by 7.5%, and the statistical power of the impact was: h(2) = 35.3%. A similar effect occurred after the sequential action of microwaves and static magnetic field: The polyteny level of chromosomes increased by 7.4%, statistical power was: h(2) = 30.6%. Conclusions Exposure to microwaves on the stage of embryogenesis has a stimulating effect on endoreduplication in Drosophila development. The effect of microwaves was not modified by the action of the static magnetic field.
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Affiliation(s)
- Liliia D Dyka
- a Institute of Biology , V. N. Karazin Kharkiv National University , Kharkiv , Ukraine
| | - Lyubov A Shakina
- a Institute of Biology , V. N. Karazin Kharkiv National University , Kharkiv , Ukraine
| | | | - Yuriy G Shckorbatov
- a Institute of Biology , V. N. Karazin Kharkiv National University , Kharkiv , Ukraine
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Nevzorova YA, Tschaharganeh D, Gassler N, Geng Y, Weiskirchen R, Sicinski P, Trautwein C, Liedtke C. Aberrant cell cycle progression and endoreplication in regenerating livers of mice that lack a single E-type cyclin. Gastroenterology 2009; 137:691-703, 703.e1-6. [PMID: 19445941 PMCID: PMC2730664 DOI: 10.1053/j.gastro.2009.05.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 04/30/2009] [Accepted: 05/06/2009] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS E-cyclins control the transition of quiescent cells into the cell cycle. Two E-cyclins, CcnE1 and CcnE2, have been described, but their specific contributions to cell cycle reentry in vivo are poorly understood. Liver regeneration following partial hepatectomy is an excellent in vivo model for the study of cell cycle reentry of quiescent cells. We investigated the relevance of E-cyclins in directing resting hepatocytes into the cell cycle after partial hepatectomy using CcnE1 and CcnE2 knockout mice. METHODS Partial hepatectomy (70%) was performed in CcnE1 (E1(-/-)) and CcnE2 (E2(-/-)) knockout and wild-type mice. Liver regeneration was monitored by cell cycle markers for G(1)/S phase, S phase, and M phase as well as by determining the liver/body weight ratio after partial hepatectomy. Ploidy of hepatocytes was determined by fluorescence-activated cell sorting and fluorescent in situ hybridization. RESULTS CcnE1 deletion resulted in normal liver regeneration with a slight delay of the G(1)/S-phase transition and a defect in endoreplication of otherwise polyploid hepatocytes. Surprisingly, E2(-/-) mice displayed accelerated and sustained DNA synthesis after partial hepatectomy, excessive endoreplication in hepatocytes, and a liver mass that was 45% greater than that of wild-type mice after termination of the regeneration process. CcnE2 depletion induced overexpression of CcnE1 and prolonged cdk2 kinase activity after partial hepatectomy. CONCLUSIONS CcnE2 has an unexpected role in repressing CcnE1; the phenotype of E2(-/-) mice appears to result from CcnE1 overexpression and cdk2 hyperactivation. CcnE1 and CcnE2 therefore have nonredundant functions for S-phase entry and endoreplication during liver regeneration.
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Affiliation(s)
- Yulia A. Nevzorova
- Department of Medicine III, University Hospital Aachen, RWTH Aachen University, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Darjus Tschaharganeh
- Department of Medicine III, University Hospital Aachen, RWTH Aachen University, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Nikolaus Gassler
- Institute of Pathology, University Hospital Aachen, RWTH Aachen University, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Yan Geng
- Dana-Farber Cancer Institute, 44 Binney Street, Smith 936, Boston, MA 02115, USA
| | - Ralf Weiskirchen
- Institute of Clinical Chemistry and Pathobiochemistry, University Hospital Aachen, RWTH Aachen University, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Peter Sicinski
- Dana-Farber Cancer Institute, 44 Binney Street, Smith 936, Boston, MA 02115, USA
| | - Christian Trautwein
- Department of Medicine III, University Hospital Aachen, RWTH Aachen University, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Christian Liedtke
- Department of Medicine III, University Hospital Aachen, RWTH Aachen University, Pauwelsstrasse 30, D-52074 Aachen, Germany
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Lima-de-Faria A. The relation between chromomeres, replicons, operons, transcription units, genes, viruses and palindromes. Hereditas 2009; 81:249-84. [PMID: 765304 DOI: 10.1111/j.1601-5223.1975.tb01039.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Visualization of Chromosome Territories in Interphase Nuclei of Ovarian Nurse Cells in Calliphora erythrocephala Mg. (Diptera: Calliphoridae). RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0207-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Raju NG, Venkatachalaiah* G. Chromosomal Characteristics of an Indian Tanyponid Midge, Anatopynia spp. (Tanypodinae Chironomidae). CYTOLOGIA 2004. [DOI: 10.1508/cytologia.69.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Weng L, Zhu C, Xu J, Du W. Critical role of active repression by E2F and Rb proteins in endoreplication during Drosophila development. EMBO J 2003; 22:3865-75. [PMID: 12881421 PMCID: PMC169046 DOI: 10.1093/emboj/cdg373] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
E2F transcription factors can activate or actively repress transcription of their target genes. The role of active repression during normal development has not been analyzed in detail. dE2F1(su89) is a novel allele of dE2F1 that disrupts dE2F1's association with RBF [the Drosophila retinoblastoma protein (Rb) homolog] but retains its transcription activation function. Interestingly, the dE2F1(su89) mutant, which has E2F activation by dE2F1(su89) and active repression by dE2F2, is viable and fertile with no gross developmental defects. In contrast, complete removal of active repression in de2f2;dE2F1(su89) mutants results in severe developmental defects in tissues with extensive endocycles but not in tissues derived from mitotic cycles. We show that the endoreplication defect resulted from a failure to downregulate the level of cyclin E during the gap phase of the endocycling cells. Importantly, reducing the gene dosage of cyclin E partially suppressed all the phenotypes associated with the endoreplication defect. These observations point to an important role for E2F-Rb complexes in the downregulation of cyclin E during the gap phase of endocycling cells in Drosophila development.
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Affiliation(s)
- Li Weng
- Committee on Cancer Biologyand Ben May Institute for Cancer Research and Center for Molecular Oncology, The University of Chicago, 924 E 57th Street, Chicago, IL 60637, USA
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Abstract
Posttranslational modifications of the N-terminal tails of the core histones within the nucleosome particle are thought to act as signals from the chromatin to the cell for various processes. The experiments presented here show that the acetylation of histones H3 and H4 in polytene chromosomes does not change during heat shock. In contrast, the global level of phosphorylated H3 decreased dramatically during a heat shock, with an observed increase in H3 phosphorylation at the heat shock loci. Additional experiments confirm that this change in phosphorylated H3 distribution is dependent on functional heat shock transcription factor activity. These experiments suggest that H3 phosphorylation has an important role in the induction of transcription during the heat shock response.
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Affiliation(s)
- S J Nowak
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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12
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Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, Hartzell G, Harvey D, Hong L, Houston K, Hoskins R, Johnson G, Martin C, Moshrefi A, Palazzolo M, Reese MG, Spradling A, Tsang G, Wan K, Whitelaw K, Celniker S. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. Genetics 1999; 153:179-219. [PMID: 10471707 PMCID: PMC1460734 DOI: 10.1093/genetics/153.1.179] [Citation(s) in RCA: 183] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species. Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926
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Affiliation(s)
- M Ashburner
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, England.
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Zhimulev IF. Polytene chromosomes, heterochromatin, and position effect variegation. ADVANCES IN GENETICS 1997; 37:1-566. [PMID: 9352629 DOI: 10.1016/s0065-2660(08)60341-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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Lilly MA, Spradling AC. The Drosophila endocycle is controlled by Cyclin E and lacks a checkpoint ensuring S-phase completion. Genes Dev 1996; 10:2514-26. [PMID: 8843202 DOI: 10.1101/gad.10.19.2514] [Citation(s) in RCA: 233] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Early during Drosophila oogenesis the 16 interconnected cells of each germ-line cyst choose between two alternative fates. The single future oocyte enters meiosis, arrests, and becomes transcriptionally quiescent. The remaining 15 cells initiate a series of polyploid cell cycles to prepare for their role as nurse cells. Like many other polyploid and polytene cells, during nurse cell growth the major satellite DNAs become highly under-represented by a mechanism that has remained obscure. We implicate the cell-cycle regulator cyclin E in DNA under-representation by identifying a hypomorphic, female sterile cycE mutation, cycE01672, that increases the amount of satellite DNA propagated in nurse cells. In mutant but not wild-type endomitotic nurse cells, "late S" patterns of bromodeoxyuridine incorporation are observed similar to those in mitotic cells. CycE protein still cycles in cycE01672 germ-line cysts but at reduced levels, and it is found throughout a longer fraction of the cell cycle. Our experiments support the view that oscillating levels of CycE control the polyploid S phase. Moreover, they indicate that a checkpoint linking the presence of unreplicated DNA to the CycE oscillator is lacking, leading to incomplete replication of late-replicating sequences such as satellite DNAs. Unexpectedly, two to three of the 16 cells in cycE01672 cysts frequently differentiate as oocytes, implicating cell-cycle programming in oocyte determination.
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Affiliation(s)
- M A Lilly
- Howard Hughes Medical Institute Research Laboratories, Carnegie Institution of Washington, Baltimore, Maryland 21210, USA
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Mukabayire O, Besansky NJ. Distribution of T1, Q, Pegasus and mariner transposable elements on the polytene chromosomes of PEST, a standard strain of Anopheles gambiae. Chromosoma 1996; 104:585-95. [PMID: 8662251 DOI: 10.1007/bf00352298] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The chromosomal locations of four families of transposable elements, T1, Q, Pegasus and mariner, have been determined by in situ hybridization to polytene chromosomes of ovarian nurse cells of the mosquito Anopheles gambiae. As part of this effort, we have developed a vigorous pink-eyed laboratory strain of A. gambiae (PEST), rendered homozygous standard for chromosomal inversions on all autosomes. Ten different individuals of this strain were studied with each transposable element probe. The average number of hybridization sites per genome was 83.9 for T1, 63.4 for Q, 31.5 for Pegasus and 64.7 for mariner, excluding pericentric and centromeric regions. However, some degree of polymorphism was observed within each family such that, considering all ten individuals, 94 different sites were detected for T1, 82 sites for Q, 45 sites for Pegasus and 71 sites for mariner. The mean occupancy per site varied from 0.70 (Pegasus) to 0.91 (mariner), which, while significantly higher than that seen for transposable elements in natural populations of Drosophila melanogaster, is comparable to that seen in established laboratory stocks. In addition, these element families were not randomly distributed. All but Pegasus were concentrated in centromeric heterochromatin and centromere-proximal euchromatin, most showed a deficit of hybridization sites in the distal section of chromosomes, and a significant proportion of sites were coincident between families. These results provide the first detailed examination of the cytogenetic location of transposable elements in a nondrosophilid insect, and, through comparison with the behavior of transposable elements in Drosophila, may provide insight into the interaction between elements and host. The mapped elements are also expected to serve as landmarks useful in integrating the developing physical map of the PEST strain with the chromosomal banding pattern.
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Affiliation(s)
- O Mukabayire
- Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Shadan FF, Villarreal LP. The evolution of small DNA viruses of eukaryotes: past and present considerations. Virus Genes 1995; 11:239-57. [PMID: 8828150 DOI: 10.1007/bf01728663] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Historically, viral evolution has often been considered from the perspective of the ability of the virus to maintain viral pathogenic fitness by causing disease. A predator-prey model has been successfully applied to explain genetically variable quasi-species of viruses, such as influenza virus and human immunodeficiency virus (HIV), which evolve much faster rates than the host. In contrast, small DNA viruses (polyomaviruses, papillomaviruses, and parvoviruses) are species specific but are stable genetically, and appear to have co-evolved with their host species. Genetic stability is attributable primarily to the ability to establish and maintain a benign persistent state in vivo and not to the host DNA proofreading mechanisms. The persistent state often involves a cell cycle-regulated episomal state and a tight linkage of DNA amplification mechanisms to cellular differentiation. This linkage requires conserved features among viral regulatory proteins, with characteristic host-interactive domains needed to recruit and utilize host machinery, thus imposing mechanistic constrains on possible evolutionary options. Sequence similarities within these domains are seen amongst all small mammalian DNA viruses and most of the parvo-like viruses, including those that span the entire spectrum of evolution of organisms from E. coli to humans that replicate via a rolling circle-like mechanism among the entire spectrum of organisms throughout evolution from E. coli to humans. To achieve benign inapparent viral persistence, small DNA viruses are proposed to circumvent the host acute phase reaction (characterized by minimal inflammation) by mechanisms that are evolutionarily adapted to the immune system and the related cytokine communication networks. A striking example of this is the relationship of hymenoptera to polydnaviruses, in which the crucial to the recognition of self, development, and maintenance of genetic identity of both the host and virus. These observations in aggregate suggest that viral replicons are not recent "escapies" of host replication, but rather provide relentless pressure in driving the evolution of the host through cospeciation.
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Affiliation(s)
- F F Shadan
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717, USA
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DePolo NJ, Villarreal LP. Aphidicolin-resistant polyomavirus and subgenomic cellular DNA synthesis occur early in the differentiation of cultured myoblasts to myotubes. J Virol 1993; 67:4169-81. [PMID: 8389922 PMCID: PMC237786 DOI: 10.1128/jvi.67.7.4169-4181.1993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Small DNA viruses have been historically used as probes of cellular control mechanisms of DNA replication, gene expression, and differentiation. Polyomavirus (Py) DNA replication is known to be linked to differentiation of may cells, including myoblasts. In this report, we use this linkage in myoblasts to simultaneously examine (i) cellular differentiation control of Py DNA replication and (ii) an unusual type of cellular and Py DNA synthesis during differentiation. Early proposals that DNA synthesis was involved in the induced differentiation of myoblasts to myotubes were apparently disproved by reliance on inhibitors of DNA synthesis (cytosine arabinoside and aphidicolin), which indicated that mitosis and DNA replication are not necessary for differentiation. Theoretical problems with the accessibility of inactive chromatin to trans-acting factors led us to reexamine possible involvement of DNA replication in myoblast differentiation. We show here that Py undergoes novel aphidicolin-resistant net DNA synthesis under specific conditions early in induced differentiation of myoblasts (following delayed aphidicolin addition). Under similar conditions, we also examined uninfected myoblast DNA synthesis, and we show that soon after differentiation induction, a period of aphidicolin-resistant cellular DNA synthesis can also be observed. This drug-resistant DNA synthesis appears to be subgenomic, not contributing to mitosis, and more representative of polyadenylated than of nonpolyadenylated RNA. These results renew the possibility that DNA synthesis plays a role in myoblast differentiation and suggest that the linkage of Py DNA synthesis to differentiation may involve a qualitative cellular alteration in Py DNA replication.
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Affiliation(s)
- N J DePolo
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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A transcriptional switch between the Pig-1 and Sgs-4 genes of Drosophila melanogaster. Mol Cell Biol 1993. [PMID: 8417325 DOI: 10.1128/mcb.13.1.184] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pig-1 and Sgs-4 are a pair of closely linked and divergently transcribed Drosophila melanogaster genes, which are both expressed in larval salivary glands but at different times during development. While Sgs-4 is expressed at high levels only at the end of the third instar, Pig-1 exhibits a major peak of expression during late second and early third instar. Thus, Pig-1 expression declines as Sgs-4 expression is induced. In this paper, we show that three adjacent elements located within the short region between these genes can account for the switch from Pig-1 to Sgs-4 expression. A 170-bp segment acts as an enhancer to direct Sgs-4 expression in late-third-instar salivary glands. A 64-bp sequence located just upstream from the enhancer can modify its temporal specificity so that it works throughout the third instar. Expression induced at mid-third instar by a combination of these two elements can be repressed by a negative regulatory sequence located still further upstream. We present evidence suggesting that the changing interactions between these regulatory elements and the Sgs-4 and Pig-1 promoters lead to the correct pattern of expression of the two genes.
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19
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Mougneau E, von Seggern D, Fowler T, Rosenblatt J, Jongens T, Rogers B, Gietzen D, Beckendorf SK. A transcriptional switch between the Pig-1 and Sgs-4 genes of Drosophila melanogaster. Mol Cell Biol 1993; 13:184-95. [PMID: 8417325 PMCID: PMC358898 DOI: 10.1128/mcb.13.1.184-195.1993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Pig-1 and Sgs-4 are a pair of closely linked and divergently transcribed Drosophila melanogaster genes, which are both expressed in larval salivary glands but at different times during development. While Sgs-4 is expressed at high levels only at the end of the third instar, Pig-1 exhibits a major peak of expression during late second and early third instar. Thus, Pig-1 expression declines as Sgs-4 expression is induced. In this paper, we show that three adjacent elements located within the short region between these genes can account for the switch from Pig-1 to Sgs-4 expression. A 170-bp segment acts as an enhancer to direct Sgs-4 expression in late-third-instar salivary glands. A 64-bp sequence located just upstream from the enhancer can modify its temporal specificity so that it works throughout the third instar. Expression induced at mid-third instar by a combination of these two elements can be repressed by a negative regulatory sequence located still further upstream. We present evidence suggesting that the changing interactions between these regulatory elements and the Sgs-4 and Pig-1 promoters lead to the correct pattern of expression of the two genes.
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Affiliation(s)
- E Mougneau
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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20
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Villarreal LP. Relationship of eukaryotic DNA replication to committed gene expression: general theory for gene control. Microbiol Rev 1991; 55:512-42. [PMID: 1943999 PMCID: PMC372832 DOI: 10.1128/mr.55.3.512-542.1991] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The historic arguments for the participation of eukaryotic DNA replication in the control of gene expression are reconsidered along with more recent evidence. An earlier view in which gene commitment was achieved with stable chromatin structures which required DNA replication to reset expression potential (D. D. Brown, Cell 37:359-365, 1984) is further considered. The participation of nonspecific stable repressor of gene activity (histones and other chromatin proteins), as previously proposed, is reexamined. The possible function of positive trans-acting factors is now further developed by considering evidence from DNA virus models. It is proposed that these positive factors act to control the initiation of replicon-specific DNA synthesis in the S phase (early or late replication timing). Stable chromatin assembles during replication into potentially active (early S) or inactive (late S) states with prevailing trans-acting factors (early) or repressing factors (late) and may asymmetrically commit daughter templates. This suggests logical schemes for programming differentiation based on replicons and trans-acting initiators. This proposal requires that DNA replication precede major changes in gene commitment. Prior evidence against a role for DNA replication during terminal differentiation is reexamined along with other results from terminal differentiation of lower eukaryotes. This leads to a proposal that DNA replication may yet underlie terminal gene commitment, but that for it to do so there must exist two distinct modes of replication control. In one mode (mitotic replication) replicon initiation is tightly linked to the cell cycle, whereas the other mode (terminal replication) initiation is not cell cycle restricted, is replicon specific, and can lead to a terminally differentiated state. Aberrant control of mitotic and terminal modes of DNA replication may underlie the transformed state. Implications of a replicon basis for chromatin structure-function and the evolution of metazoan organisms are considered.
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Affiliation(s)
- L P Villarreal
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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21
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Baird SE, Klobutcher LA. Differential DNA amplification and copy number control in the hypotrichous ciliate Euplotes crassus. THE JOURNAL OF PROTOZOOLOGY 1991; 38:136-40. [PMID: 1902260 DOI: 10.1111/j.1550-7408.1991.tb06033.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During macronuclear development in hypotrichous ciliated protozoans, several thousand macronuclear DNA molecules are amplified several-hundred fold. We investigated the regulation of this amplification by determining the copy numbers of three different macronuclear DNA molecules in the hypotrichous ciliate Euplotes crassus. Two of the macronuclear DNA molecules were present in approximately 1,000 copies per cell, while the third was present in approximately 6,500 copies per cell. These reiteration levels were achieved either during macronuclear development, or shortly thereafter, and were maintained during vegetative growth. The most abundant macronuclear DNA molecule is present as a single-copy sequence in the micronuclear genome. Thus, its high copy number results from differential amplification. These results indicate that DNA amplification during macronuclear development is regulated individually for each macronuclear DNA molecule.
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Affiliation(s)
- S E Baird
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
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22
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Wilson C, Pearson RK, Bellen HJ, O'Kane CJ, Grossniklaus U, Gehring WJ. P-element-mediated enhancer detection: an efficient method for isolating and characterizing developmentally regulated genes in Drosophila. Genes Dev 1989; 3:1301-13. [PMID: 2558051 DOI: 10.1101/gad.3.9.1301] [Citation(s) in RCA: 297] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe a new approach for identifying and studying genes involved in Drosophila development. Single copies of an enhancer detector transposon, P[1ArB], have been introduced into flies at many different genomic locations. The beta-galactosidase reporter gene in this construct is influenced by a wide range of genomic transcriptional regulatory elements in its vicinity. Our results suggest that a significant proportion of these regulatory sequences are control elements of nearby Drosophila genes. These genes need not be disrupted for their regulatory elements to be identified by P[1ArB]. The P[1ArB] transposon has been designed to facilitate both rapid cloning and deletion analysis of genomic sequences into which it inserts. Therefore, the enhancer detection system is an efficient method of screening for genes primarily on the basis of their expression pattern and then rapidly analyzing those of particular interest at the molecular and genetic levels.
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Affiliation(s)
- C Wilson
- Department of Cell Biology, Biozentrum, University of Basel, Switzerland
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23
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Isolation and characterization of the dopa decarboxylase gene of Drosophila melanogaster. Mol Cell Biol 1988. [PMID: 6086012 DOI: 10.1128/mcb.1.6.475] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have isolated chromosomal deoxyribonucleic acid clones containing the Drosophila dopa decarboxylase gene. We describe an isolation procedure which can be applied to other nonabundantly expressed Drosophila genes. The dopa decarboxylase gene lies within or very near polytene chromosome band 37C1-2. The gene is interrupted by at least one intron, and the primary mode of regulation is pretranslational. At least two additional sequences hybridized by in vivo ribonucleic acid-derived probes are found within a 35-kilobase region surrounding the gene. The developmental profile of ribonucleic acid transcribed from one of these regions differs from that of the dopa decarboxylase transcript.
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24
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Hochstrasser M, Sedat JW. Three-dimensional organization of Drosophila melanogaster interphase nuclei. I. Tissue-specific aspects of polytene nuclear architecture. J Cell Biol 1987; 104:1455-70. [PMID: 3108264 PMCID: PMC2114489 DOI: 10.1083/jcb.104.6.1455] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Interphase chromosome organization in four different Drosophila melanogaster tissues, covering three to four levels of polyteny, has been analyzed. The results are based primarily on three-dimensional reconstructions from unfixed tissues using a computer-based data collection and modeling system. A characteristic organization of chromosomes in each cell type is observed, independent of polyteny, with some packing motifs common to several or all tissues and others tissue-specific. All chromosomes display a right-handed coiling chirality, despite large differences in size and degree of coiling. Conversely, in each cell type, the heterochromatic centromeric regions have a unique structure, tendency to associate, and intranuclear location. The organization of condensed nucleolar chromatin is also tissue-specific. The tightly coiled prothoracic gland chromosomes are arrayed in a similar fashion to the much larger salivary gland chromosomes described previously, having polarized orientations, nonintertwined spatial domains, and close packing of the arms of each autosome, whereas hindgut and especially the unusually straight midgut chromosomes display striking departures from these regularities. Surprisingly, gut chromosomes often appear to be broken in the centric heterochromatin. Severe deformations of midgut nuclei observed during gut contractions in living larvae may account for their unusual properties. Finally, morphometric measurements of chromosome and nuclear dimensions provide insights into chromosome growth and substructure and also suggest an unexpected parallel with diploid chromatin organization.
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25
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26
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Wright TR. The genetic and molecular organization of the dense cluster of functionally related, vital genes in the DOPA decarboxylase region of the Drosophila melanogaster genome. Results Probl Cell Differ 1987; 14:95-120. [PMID: 3112881 DOI: 10.1007/978-3-540-47783-9_7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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27
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Mathog D, Hochstrasser M, Sedat JW. Light microscope based analysis of three-dimensional structure: applications to the study of Drosophila salivary gland nuclei. I. Data collection and analysis. J Microsc 1985; 137:241-52. [PMID: 3999131 DOI: 10.1111/j.1365-2818.1985.tb02582.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Many biological structures of interest are large enough that they may be viewed by light microscope methods, yet they are sufficiently complicated that interpretation of what is seen is quite difficult. The salivary gland nuclei from Dipterans are an example of this. Previous attempts at determining the path of the giant chromosomes in these nuclei have depended on the laborious construction of models by hand. A unified Computer Aided Modelling and Analysis system (CAMA) has been implemented, allowing data collection and analysis of structures visible by light microscopy. This system is extendible to the analysis of electron micrographs of serial sections or of other data consisting of images present in a stack.
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28
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Tiwari PK, Lakhotia SC. Replication in Drosophila chromosomes XIII. Comparison of late replicating sites in two polytene cell types in D. hydei. Genetica 1984. [DOI: 10.1007/bf00122909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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de Cicco DV, Spradling AC. Localization of a cis-acting element responsible for the developmentally regulated amplification of Drosophila chorion genes. Cell 1984; 38:45-54. [PMID: 6088075 DOI: 10.1016/0092-8674(84)90525-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Late in oogenesis two clusters of Drosophila chorion genes and flanking DNA sequences undergo specific amplification in ovarian follicle cells. Lines were constructed using P-element-mediated transformation in which DNA segments derived from the chorion gene cluster at 66D on chromosome III had been inserted at new chromosomal locations. Only transposons that contained a specific 3.8 kb genomic segment derived from the cluster underwent amplification during oogenesis, which occurred with apparently normal tissue and temporal specificity. Adjacent nonchorion sequences also underwent amplification. However, the ability of a transposon to replicate differentially was subject to position effect. These studies provide evidence for the existence of a specific, cis-acting element controlling chorion gene amplification, which includes an origin for disproportionate DNA replication. Attempts to induce amplification with subfragments of the 3.8 kb segment were unsuccessful, suggesting that much of this fragment may be required for amplification.
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30
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31
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Dennhöfer L. Underreplication during polytenization? : Recent cytophotometric DNA determinations and related biochemical results concerning polytene salivary gland nuclei of Drosophila melanogaster. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1982; 63:193-199. [PMID: 24270816 DOI: 10.1007/bf00303991] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/1982] [Accepted: 07/17/1982] [Indexed: 06/02/2023]
Abstract
Recent cytophotometric DNA determinations and results of labeling experiments are compared with results of biochemical experiments concerning larval polytene salivary gland nuclei of Drosophila melanogaster. Recent publications (Dennhöfer 1981; 1982 a, b) demonstrate that methodological errors both in hydrolysis of the DNA before Feulgen reaction and in interpretation of the cytophotometric values give raise to the hypothesis of heterochromatic underreplication during polytenization. It is concluded also that methodological difficulties cause the absence of polytene SAT-DNA in biochemical centrifugation experiments since, because of different solubilities of eu- and heterochromatic DNA, the latter is not resolved in DNA isolation procedures from polytene nuclei.
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Affiliation(s)
- L Dennhöfer
- Institut für Entwicklungsphysiologie der Universität Köln, Köln, Federal Republic of Germany
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32
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Steinemann M. Multiple sex chromosomes in Drosophila miranda: a system to study the degeneration of a chromosome. Chromosoma 1982; 86:59-76. [PMID: 7172863 DOI: 10.1007/bf00330730] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Drosophila miranda possesses an intriguing sex chromosome constitution. While female metaphase plates have 10 chromosomes (diploid set), in males only 9 chromosomes can be identified. The missing homologue has been translocated to the Y, forming a neo-Y chromosome which is polytenized in the salivary gland cells. This report presents a detailed characterization of DNA, isolated from D. miranda flies. In situ hybridizations, using cRNA transcribed from unfractionated D. miranda DNA, reveal hybridization to the neo-Y with label distributed over the entire chromosome. The original partner of the translocated chromosome, X2, is essentially unlabelled. These results suggest that repetitive DNA sequences "invade" the translocated chromosome. This result is discussed with reference to the hypothesis of "degeneration" of the Y chromosome, formulated by Muller (1918, 1932a).
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33
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Mishra A, Lakhotia SC. Replication in Drosophila chromosomes. VII. Influence of prolonged larval life on patterns of replication in polytene chromosomes of Drosophila melanogaster. Chromosoma 1982; 85:221-36. [PMID: 6811222 DOI: 10.1007/bf00294967] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Prolongation of larval life in Drosophila melanogaster, by growing wild type larvae at lower temperature, or in animals carrying the X-linked mutation giant is known to result in a greater proportion of nuclei in salivary glands showing the highest level of polyteny. We have examined by autoradiography the patterns of 3H-thymidine incorporation during 10 min or 1 min pulses in salivary gland polytene chromosomes of older giant larvae and of wild type late third instar larvae of D. melanogaster grown since hatching either at 24 degrees C or at 10 degrees C. The various patterns of labelling and their relative frequencies are generally similar in glands from the warm- (24 degrees C) or cold (10 degrees C)-reared wild type larvae, except the interband (IB) labelling patterns which are very frequent in the later group but rare in the former. The IB type labelled nuclei in cold-reared wild type larvae show labelling ranging from only a few puffs/interbands labelled to nearly all puffs/interbands labelled. In warm-reared wild type larvae, very low labelled IB patterns are not seen. In older giant larvae, the 3H-thymidine labelling patterns are in most respects similar to those seen in cold-reared wild type larvae. In 1 min pulsed preparations from all larvae, the IB patterns are relatively more frequent than in corresponding 10 min pulsed preparations. No nuclei with the continuous (2C or 3C) type of labelling pattern, with all bands and interbands/puffs labelled, were seen in 1 min pulsed preparations from cold-reared wild type or in giant larvae, and only a few nuclei in 1 min pulsed preparations from warm-reared wild type larvae exhibited the 2C labelling pattern. Analysis of silver grain density on specific late replicating sites in late discontinuous (ID) type labelled nuclei suggests that the rate of DNA synthesis per chromosomal site is not different at the two developmental temperatures. It is suggested that correlated with the prolongation of larval life under cold-rearing conditions or in giant larvae, the polytene replication cycles are also prolonged. It is further suggested that the polytene S-period in these larvae is longer de to a considerable asynchrony in the initiation and termination of replication of different sites during a replication cycle.
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34
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Lönn U. DNA replication in polytene chromosomes. Trends Biochem Sci 1982. [DOI: 10.1016/0968-0004(82)90059-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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35
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Lis JT, Ish-Horowicz D, Pinchin SM. Genomic organization and transcription of the alpha beta heat shock DNA in Drosophila melanogaster. Nucleic Acids Res 1981; 9:5297-310. [PMID: 6170940 PMCID: PMC327521 DOI: 10.1093/nar/9.20.5297] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Previous studies have shown that (i) several RNAs induced by heat shock of Drosophila melanogaster cells are homologous to tandemly repeated alpha beta units found in cloned segments of D. melanogaster DNA, and (ii) the alpha beta sequences are present both at a major heat shock locus, 87Cl, and the chromocenter of polytene chromosomes (Lis, J.T., Prestidge, L. and Hogness, D.S. [1978] Cell 14, 901-919). We have used deficiencies that delete DNA from the 87C region to examine the arrangement of alpha beta sequences at this locus and in the centromeric heterochromatin that comprises the chromocenter, and also to determine the chromosomal location of the induced transcription. The tandemly repeated alpha beta units are restricted to the 87C locus. In contrast, the chromocentral alpha beta sequences do not form intact alpha beta units, and are dispersed at heterochromatic sites in some other form. Although only half of the alpha beta DNA is at the 87C locus, essentially all alpha beta transcripts (greater than 99.5%) are derived from this locus.
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36
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Biezunski N. Structure and distribution of inverted repeats (Palindromes). I. Analysis of DNA of Drosophila melanogaster. Chromosoma 1981; 84:87-109. [PMID: 6794998 DOI: 10.1007/bf00293365] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The size and distribution of renatured inverted repeats (palindromes) in D. melanogaster DNA were studied by electron microscopy (EM). The results of these studies differ from the previously published observations regarding the number, distribution and the size of inverted repeats (ir) present in DNA. -1. In contrast to the previous published observation almost all (96%) of the ir were found in crowded clusters. The DNA strands with clustered palindromes contained 2-21 palindromes (4-42 ir), with an average of 7.25 palindromes (14.5 ir) per strand. No correlation could be found between the length of the DNA strands and the number of ir per strand. -2, Also contrary to some previously published results, most (80%) of the ir formed on renaturation unlooped palindromes and these were always clustered. Looped palindromes (hairpins, formed by renaturation of ir separated by a non-homologous sequence long enough to be seen in EM as single-stranded loop) were found 1-2 per DNA strand, as part of clusters or as solitary palindromes in a DNA strand. The average spacing length (inside clusters) between centers of all palindromes was 2.349 kb, and between centers of looped palindromes 7.6 kb. - 3. The length of the ir was found to be smaller than documented in most of the previously published results. The majority, 80-90%, of the ir found in the unlooped and looped palindromes, respectively, belonged to one main-size class with a range of 30-210 bp and an average length of 100 bp, but longer ir were also observed. The average length of the ir in unlooped palindromes was 124 bp, in looped 244 bp, and the total average was 148 bp - 4. It was calculated that there are about 30,000 palindromes (60,000 ir) in the D, melanogaster genome, of which about 24,000 are unlooped and 6,000 looped, with the spacing between centers of all palindromes averaging about 4.4 kb in length.
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37
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Hirsh J, Davidson N. Isolation and characterization of the dopa decarboxylase gene of Drosophila melanogaster. Mol Cell Biol 1981; 1:475-85. [PMID: 6086012 PMCID: PMC369691 DOI: 10.1128/mcb.1.6.475-485.1981] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We have isolated chromosomal deoxyribonucleic acid clones containing the Drosophila dopa decarboxylase gene. We describe an isolation procedure which can be applied to other nonabundantly expressed Drosophila genes. The dopa decarboxylase gene lies within or very near polytene chromosome band 37C1-2. The gene is interrupted by at least one intron, and the primary mode of regulation is pretranslational. At least two additional sequences hybridized by in vivo ribonucleic acid-derived probes are found within a 35-kilobase region surrounding the gene. The developmental profile of ribonucleic acid transcribed from one of these regions differs from that of the dopa decarboxylase transcript.
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Affiliation(s)
- J Hirsh
- Department of Biological Chemistry, Harvard Medical School, Boston, Massachusetts 02115
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38
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Pierce DA, Lucchesi JC. Analysis of a dispersed repetitive DNA sequence in isogenic lines of Drosophila. Chromosoma 1981; 82:471-92. [PMID: 6266778 DOI: 10.1007/bf00295007] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The location of sequences homologous to a cloned D. melanogaster DNA segment, Dm 25, has been examined in polytene chromosomes by hybridization in situ. Dm 25 localizes to multiple sites and shows variation in patterns between different strains and among individuals within wild-type laboratory strains. Analysis of numerous geographically distinct isogenic lines suggests that Dm 25 patterns are determined by germ-line factors and are not the product of strictly somatic events. In general there is wide variation in Dm 25 patterns among different lines, but a significant number of sites are common to two or more distinct lines. Hybridization to restriction digests of genomic DNA suggests that Dm 25 is a moderately repetitive, conserved sequence whose copies are dispersed throughout the genome. Analysis of species other than melanogaster indicates a significant divergence in structure of sequences homologous to Dm 25 as well as a drastic reduction in amount of homology to the melanogaster sequence.
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39
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Achary PM, Majumdar K, Duttagupta A, Mukherjee AS. Replication of DNA in larval salivary glands of Drosophila after in vivo synchronization. Chromosoma 1981; 82:505-14. [PMID: 6455259 DOI: 10.1007/bf00295009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The replication of DNA in the giant chromosomes in different cells of Drosophila larval salivary glands is asynchronous. A method of in vivo synchronization of the nuclei has been successfully devised by a 5'-fluorodeoxyuridine (FdU) block-release-thymidine chase technique, and the patterns of replication sequences have been examined by 3H-thymidine autoradiography. When the larvae of Drosophila melanogaster are fed on FdU for 48 h, and the block is released thereafter, most cells are found in mid-replication phase (termed 3C). When the larvae are subjected to a chase in normal Drosophila medium (or sucrose), a series of cells arrive at 3C phase about every 8 h. When they are chased in sucrose containing thymidine, the number of cells in 3C phase rises to 70%, and then drops rapidly to 1-2% of all labelled cells. The terminal phases (3D, 2D and 1D) reach a peak between 4-8 h. At 12-14 h of chase the 3D-1D peaks decline and a third peak consisting mostly of the initial phases (DD-1C) is found at 14--16 h. The replication of DNA in polytene chromosomes of Drosophila thus seems to proceed in a regular sequence of DD-3C-1D.
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40
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Lakhotia SC. Replication in drosophila chromosomes III. Disproportionate replication of hetero- and eu-chromatin in wing imaginal disk cells of D. nasuta larvae. Genetica 1981. [DOI: 10.1007/bf00135042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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�ber eine heterochromatin-mutation aus einer wildpopulation von chironomus nuditarsis II. Zum replikationsverhalten des ver�nderten genomabschnittes. Genetica 1980. [DOI: 10.1007/bf00122412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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42
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Mukherjee AS, Duttagupta AK, Chatterjee SN, Chatterjee RN, Majumdar D, Chatterjee C, Ghosh M, Achary PM, Dey A, Banerjee I. Regulation of DNA replication in Drosophila. BASIC LIFE SCIENCES 1980; 16:57-83. [PMID: 6779808 DOI: 10.1007/978-1-4684-7968-3_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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43
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Chromosomal proteins of Drosophila melanogaster and an approach for their localisation on polytene chromosomes. Chromosoma 1977. [DOI: 10.1007/bf00292942] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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44
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Zuckerkandl E. Gene control in eukaryotes and the c-value paradox "excess" DNA as an impediment to transcription of coding sequences. J Mol Evol 1976; 9:73-104. [PMID: 798041 DOI: 10.1007/bf01796124] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ways in which control of gene activity may lead to the observed high DNA content per haploid eukaryote genome are examined. It is proposed that deoxyribonucleoprotein (DNP) acts as a barrier to transcription at two distinct structural levels. At the lower level, melting of the nucleosome supercoil (quaternary structure) and of the nucleosomes (tertiary structure) might be brought about by the process of transcription itself. After unwinding the barrier section, the polymerase would eventually reach the structural gene. The transcripts of noncoding sequences, at least as far as their "unique" sequence components are concerned, may thus have filled their main function through the very process of transcription. The possibility of an inverse relationship between the length of the DNP barrier and the rates of transcription of the coding sequences is to some extent supported by available data. Different modes of coordination between the transcription of mRNA and of hnRNA from a single functional unit of gene action (funga) are considered. An analysis of gene control at high structural levels of DNP is made on the basis of other data, in relation to the concepts of eurygenic and stenogenic control. The concept of a euryon is introduced, namely of a set of linked fugas under common eurygenic control. Structure of order higher than quaternary can be inferred to exist in larger chromomeres of polytene chromosomes and in corresponding sections of ordinary chromosomes. Only moderate amounts of highest order interphase euchromatic structure are likely to be able to be accomodated in average chromomeres and none in very thin chromomeres. Puffs are interpreted as the melting of highest order interphase structure, and the absence of puffs during transcription as the absence of this highest order structure in the resting state of the chromomeres. Genes that are constantly active in all tissues may dispense with highest order interphase structure and with the corresponding control mechanism, and the fugas involved thus may not puff. Puffs, large chromomeres and highest order interphase euchromatic DNP structure seem to be correlated with genes that need to be transcribed only under certain developmental conditions. It is proposed that the function of high order structure is to sequester genetic material, namely mainly controller sequences. Since such high order structure, in most cases, would be built up to house the controller dependencies of just one structural gene, the amount of DNA per structural gene needed for gene control would be considerable, and the concept, if correct, would go a long way towards explaining the c-value paradox ("excess" DNA in eukaryotes). In eurygenic determination, the high order structure is thought to be conditioned for melting or to actually melt to an intermediate level of structure. From there, stenogenic control, leading to transcription, is considered to carry the melting process further to yet lower structural levels...
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Schalet AP, Sankaranarayanan K. Evaluation and re-evaluation of genetic radiation hazards in man. I. Interspecific comparison of estimates of mutation rates. Mutat Res 1976; 35:341-70. [PMID: 132611 DOI: 10.1016/0027-5107(76)90200-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A detailed presentation is made of the experimental data from the various systems used by Abrahamson et al. [2] to conclude that the per locus per rad (low LET) radiation-induced forward mutation rates in organisms, whose DNA content varies by a factor of about 1000, is proportional to genome size. Additional information pertinent in this context is also reviewed. It is emphasized that the mutation rates cited by Abrahamson et al. [2], although considered as pertaining to mutations at specific loci, actually derive from a broad variety of genetic end-points. It is argued that an initial (if not sufficient) condition for sound inter-specific mutation rate comparisions, covering a wide range of organisms and detecting systems of various sensitivities, requires a reasonalbly consistent biological definition of a specific locus mutation, namely, a transmissible intra-locus change. Granting the differences between systems in their resolving power to detect intragenic change, the data cited in this paper do not support the existence of a simple proportionality between radiotion-induced intra-locus mutation rate and genome size for the different species reviewed here. Furthermore, in Drosophila melanogaster, where individual salivary gland chromosome bands (that can differ greatly in DNA content) are usually associated with individual loci or at least distinct complementation groups, radiation-induced intra-locus mutation rates are not correlated with apparent differences in the DNA content of bands. This result is incompatible with the notion that most of the DNA in a band represents a radiation-mutable target capable of eliciting the kind of mutation observed in mutation rate experiments. All these considerations argue against the validity of the hypothesis of Abrahamson et al. [2] and their generalization that, for the evaluation of genetic radiation hazards in man, we can now "extrapolate from mutation rates obtained in lower organisms to man with greater confidence" on the basis of DNA content (italics are ours).
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Blumenthal AB. The Replication of Drosophila DNA: The Periodic Distribution of Replication Origins. Radiat Res 1975. [DOI: 10.1016/b978-0-12-523350-7.50064-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Lakhotia SC. EM autoradiographic studies on polytene nuclei of Drosophila melanogaster. 3. Localisation of non-replicating chromatin in the chromocentre heterochromatin. Chromosoma 1974; 46:145-59. [PMID: 4212008 DOI: 10.1007/bf00332513] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Zhimulev IF, Belyaeva ES. Proposals to the problem of structural and functional organization of polytene chromosomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1974; 45:335-340. [PMID: 24419544 DOI: 10.1007/bf00277673] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/1974] [Indexed: 06/03/2023]
Abstract
The concept of the structural and functional organization of polytene chromosomes is formulated. It is based on the following:Interbands are transcriptional active chromosome regions; they seem to be responsible for the base metabolism of the cell. The stability of these metabolic processes in the cells of different organs results in constancy of chromosome banding pattern. Thus, each functional state of the cell possesses its own banding pattern which may vary depending on activity level and degree of condensation of interbands.The band is considered not as a structural or functional unit, but as a region of the chromosome not involved in transcription at a certain point of time; a band may contain one or several genes.
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Novosibirsk, U.S.S.R
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