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Palomba E, Chiaiese P, Termolino P, Paparo R, Filippone E, Mazzoleni S, Chiusano ML. Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111436. [PMID: 35684209 PMCID: PMC9183124 DOI: 10.3390/plants11111436] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.
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Affiliation(s)
- Emanuela Palomba
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, 80121 Naples, Italy;
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources, National Research Council, 80055 Portici, Italy; (P.T.); (R.P.)
| | - Rosa Paparo
- Institute of Biosciences and Bioresources, National Research Council, 80055 Portici, Italy; (P.T.); (R.P.)
| | - Edgardo Filippone
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
| | - Maria Luisa Chiusano
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, 80121 Naples, Italy;
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, 80055 Portici, Italy; (P.C.); (E.F.); (S.M.)
- Correspondence: ; Tel.: +39-81-2539492
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Kinetics of circulating cell-free DNA for biomedical applications: critical appraisal of the literature. Future Sci OA 2018; 4:FSO295. [PMID: 29682327 PMCID: PMC5905581 DOI: 10.4155/fsoa-2017-0140] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/30/2018] [Indexed: 12/15/2022] Open
Abstract
Circulating cell-free DNA is considered as one of the major breakthroughs in the field of innovative diagnosis, used as a liquid biopsy. The kinetic parameters of a biomarker are mandatory to assess its usefulness as a diagnostic tool. Obtaining precise mathematical values for the kinetic parameters (e.g., half-life) is then crucial because it could be used for therapeutic monitoring as a prognostic factor. However, little is known about the intrinsic properties of circulating cell-free DNA, more especially, its kinetic properties within the organism. We summarized the basic principles that may affect the kinetics of circulating cell-free DNA within the organism in the light of biological and clinical evidence. We also meta-analyzed the reported data in the literature and the methodologies that have been used to study the kinetic parameters of human circulating cell-free DNA in vivo. Circulating cell-free DNA as a biomarker was a major breakthrough in the field of diagnostics. Understanding the kinetic parameters of a biomarker is mandatory to assess its usefulness as a diagnostic tool, especially for therapeutic monitoring. However, at the present time little is known about its kinetic properties within the organism. This review provides an overview of the basic principles that may impact the kinetics of cell-free DNA within the organism and analyzes the reported data thus far.
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Thierry AR, El Messaoudi S, Gahan PB, Anker P, Stroun M. Origins, structures, and functions of circulating DNA in oncology. Cancer Metastasis Rev 2017; 35:347-76. [PMID: 27392603 PMCID: PMC5035665 DOI: 10.1007/s10555-016-9629-x] [Citation(s) in RCA: 539] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While various clinical applications especially in oncology are now in progress such as diagnosis, prognosis, therapy monitoring, or patient follow-up, the determination of structural characteristics of cell-free circulating DNA (cirDNA) are still being researched. Nevertheless, some specific structures have been identified and cirDNA has been shown to be composed of many “kinds.” This structural description goes hand-in-hand with the mechanisms of its origins such as apoptosis, necrosis, active release, phagocytosis, and exocytose. There are multiple structural forms of cirDNA depending upon the mechanism of release: particulate structures (exosomes, microparticles, apoptotic bodies) or macromolecular structures (nucleosomes, virtosomes/proteolipidonucleic acid complexes, DNA traps, links with serum proteins or to the cell-free membrane parts). In addition, cirDNA concerns both nuclear and/or mitochondrial DNA with both species exhibiting different structural characteristics that potentially reveal different forms of biological stability or diagnostic significance. This review focuses on the origins, structures and functional aspects that are paradoxically less well described in the literature while numerous reviews are directed to the clinical application of cirDNA. Differentiation of the various structures and better knowledge of the fate of cirDNA would considerably expand the diagnostic power of cirDNA analysis especially with regard to the patient follow-up enlarging the scope of personalized medicine. A better understanding of the subsequent fate of cirDNA would also help in deciphering its functional aspects such as their capacity for either genometastasis or their pro-inflammatory and immunological effects.
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Affiliation(s)
- A R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France.
| | - S El Messaoudi
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France
| | - P B Gahan
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France
| | - P Anker
- , 135 route des fruitières, 74160, Beaumont, France
| | - M Stroun
- , 6 Pedro-meylan, 1208, Geneva, Switzerland
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles. Cell Mol Life Sci 2016; 73:4355-4381. [PMID: 27652382 PMCID: PMC11108302 DOI: 10.1007/s00018-016-2370-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/20/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.
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Affiliation(s)
- Janine Aucamp
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
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A Historical and Evolutionary Perspective on Circulating Nucleic Acids and Extracellular Vesicles: Circulating Nucleic Acids as Homeostatic Genetic Entities. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 924:91-95. [PMID: 27753025 DOI: 10.1007/978-3-319-42044-8_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The quantitative and qualitative differences of circulating nucleic acids (cirNAs) between healthy and diseased individuals have motivated researchers to utilize these differences in the diagnosis and prognosis of various pathologies. The position maintained here is that reviewing the rather neglected early work associated with cirNAs and extracellular vesicles (EVs) is required to fully describe the nature of cirNAs. This review consists of an empirically up-to-date schematic summary of the major events that developed and integrated the concepts of heredity, genetic information and cirNAs. This reveals a clear pattern implicating cirNA as a homeostatic entity or messenger of genetic information. The schematic summary paints a picture of how cirNAs may serve as homeostatic genetic entities that promote synchrony of both adaptation and damage in tissues and organs depending on the source of the message.
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Trejo-Becerril C, Pérez-Cárdenas E, Taja-Chayeb L, Anker P, Herrera-Goepfert R, Medina-Velázquez LA, Hidalgo-Miranda A, Pérez-Montiel D, Chávez-Blanco A, Cruz-Velázquez J, Díaz-Chávez J, Gaxiola M, Dueñas-González A. Cancer progression mediated by horizontal gene transfer in an in vivo model. PLoS One 2012; 7:e52754. [PMID: 23285175 PMCID: PMC3532306 DOI: 10.1371/journal.pone.0052754] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 11/20/2012] [Indexed: 02/06/2023] Open
Abstract
It is known that cancer progresses by vertical gene transfer, but this paradigm ignores that DNA circulates in higher organisms and that it is biologically active upon its uptake by recipient cells. Here we confirm previous observations on the ability of cell-free DNA to induce in vitro cell transformation and tumorigenesis by treating NIH3T3 recipient murine cells with serum of colon cancer patients and supernatant of SW480 human cancer cells. Cell transformation and tumorigenesis of recipient cells did not occur if serum and supernatants were depleted of DNA. It is also demonstrated that horizontal cancer progression mediated by circulating DNA occurs via its uptake by recipient cells in an in vivo model where immunocompetent rats subjected to colon carcinogenesis with 1,2-dimethylhydrazine had increased rate of colonic tumors when injected in the dorsum with human SW480 colon carcinoma cells as a source of circulating oncogenic DNA, which could be offset by treating these animals with DNAse I and proteases. Though the contribution of biologically active molecules other than DNA for this phenomenon to occur cannot be ruled out, our results support the fact that cancer cells emit into the circulation biologically active DNA to foster tumor progression. Further exploration of the horizontal tumor progression phenomenon mediated by circulating DNA is clearly needed to determine whether its manipulation could have a role in cancer therapy.
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Affiliation(s)
| | | | - Lucía Taja-Chayeb
- Division of Basic Research, Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | | | - Luis A. Medina-Velázquez
- Instituto de Física, Universidad Nacional Autónoma de México/Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | - Delia Pérez-Montiel
- Department of Pathology, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Alma Chávez-Blanco
- Division of Basic Research, Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | - José Díaz-Chávez
- Division of Basic Research, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Miguel Gaxiola
- Unidad de Investigación, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Alfonso Dueñas-González
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM/Instituto Nacional de Cancerología, México City, Mexico
- * E-mail:
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Gahan PB, Stroun M. The virtosome-a novel cytosolic informative entity and intercellular messenger. Cell Biochem Funct 2011; 28:529-38. [PMID: 20941743 DOI: 10.1002/cbf.1690] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Studies on a range of prokaryote and eukaryote cells and tissues have shown that a newly synthesized DNA/RNA-lipoprotein complex is released in a regulated manner. This complex, termed a virtosome, is a novel cytosolic component of eukaryote cells. The released virtosomes can readily enter other cells where they can modify the biology of the recipient cells. Such modifications include immunological changes and transformation from normal to cancer cells. The virtosomes form a normal component of the circulating nucleic acids in plasma and serum currently used for clinical diagnostic purposes. Given the transformative powers of virtosomes released from tumour cells, the presence of such a complex in human plasma could readily offer the basis of an alternative mechanism for the initiation of metastases.
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Nagata T. Macromolecular synthesis in the livers of aging mice as revealed by electron microscopic radioautography. ACTA ACUST UNITED AC 2010; 45:1-79. [DOI: 10.1016/j.proghi.2009.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 11/26/2009] [Indexed: 11/25/2022]
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Gahan PB, Stroun M. The Biology of Circulating Nucleic Acids in Plasma and Serum (CNAPS). NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2010. [DOI: 10.1007/978-3-642-12617-8_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Abstract
The circulation of both foreign and endogenous DNA within plants and its ability to be expressed in the host plants and FI generation is described. These data, together with those from animal systems are used to support the concept that a DNA fraction can act as a messenger between cells and tissues.
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Affiliation(s)
- P B Gahan
- Anatomy and Human Sciences, King's College London, London Bridge, London SE1 1UL.
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Abstract
Extracellular nucleic acids are found in different biological fluids in the organism and in the environment: DNA is a ubiquitous component of the organic matter pool in the soil and in all marine and freshwater habitats. Data from recent studies strongly suggest that extracellular DNA and RNA play important biological roles in microbial communities and in higher organisms. DNA is an important component of bacterial biofilms and is involved in horizontal gene transfer. In recent years, the circulating extracellular nucleic acids were shown to be associated with some diseases. Attempts are being made to develop noninvasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA. Recent observations demonstrated the possibility of nucleic acids exchange between eukaryotic cells and extracellular space suggesting their participation in so far unidentified biological processes.
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Affiliation(s)
- Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
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Nagata T, Ma H. Electron microscopic radioautographic study of RNA synthesis in hepatocyte mitochondria of aging mouse. Microsc Res Tech 2005; 67:55-64. [PMID: 16037977 DOI: 10.1002/jemt.20183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In order to study the aging changes of intramitochondrial RNA synthesis in mouse hepatocytes, 10 groups of aging mice, each consisting of three individuals (total 30) from fetal day 19 to postnatal month 24 were injected with 3H-uridine, an RNA precursor, sacrificed 1 hour later, and the liver tissues processed for electron microscopic radioautography. On EM radioautograms obtained from each animal the number of mitochondria, the number of labeled mitochondria, and the mitochondrial labeling index labeled with 3H-uridine showing RNA synthesis in each hepatocytes, both mononucleate and binucleate cells, were counted and the averages in respective aging groups were compared. From the results it was demonstrated that the numbers of mitochondria, the numbers of labeled mitochondria, and the labeling indices of intramitochondrial RNA syntheses in both mononucleate and binucleate hepatocytes of mice at various ages increased and decreased according to the age of the animals.
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Affiliation(s)
- Tetsuji Nagata
- Department of Anatomy and Cell Biology, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan.
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Henderson B. Out of one eye: a life integrating cellular biochemistry and function. Cell Biochem Funct 2003; 21:201-6. [PMID: 12910470 DOI: 10.1002/cbf.1073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Brian Henderson
- Division of Infection and Immunity, Eastman Dental Institute, University College London, UK.
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Abstract
Evidence is presented that, as in animal and human cells, plant cells can release a newly-synthesized DNA which can freely circulate in the plants. This DNA enters cells and their nuclei where it may be integrated and be expressed so acting, apparently, as a messenger-DNA.
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Affiliation(s)
- Peter B Gahan
- School of Biomedical Sciences, Kings College London, London, UK
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Fisher DB, Jensen WA. Nuclear and cytoplasmic DNA synthesis in cotton embryos: a correlated light and electron microscope autoradiographic study. HISTOCHEMIE. HISTOCHEMISTRY. HISTOCHIMIE 1972; 32:1-22. [PMID: 5079512 DOI: 10.1007/bf00277467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Stockem W. [DNA- and RNA-content of mitochondria of Physarum polycephalum]. HISTOCHEMIE. HISTOCHEMISTRY. HISTOCHIMIE 1968; 15:160-83. [PMID: 5754557 DOI: 10.1007/bf00306366] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Shires TK. Tests for nucleic acid selectivity of Einarson's gallocyanin-chrome alum stain on monolayers of strain L-929 mouse fibroblasts. STAIN TECHNOLOGY 1967; 42:67-74. [PMID: 4167067 DOI: 10.3109/10520296709114984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Serra JA, Koshman RW. Nuclear changes of treptional nature in the differentiation of sperm nurse cells in snails. CANADIAN JOURNAL OF GENETICS AND CYTOLOGY. JOURNAL CANADIEN DE GENETIQUE ET DE CYTOLOGIE 1967; 9:23-30. [PMID: 5616735 DOI: 10.1139/g67-003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Nagata T, Shibata O, Nawa T. Incorporation of tritiated thymidine into mitochondrial DNA of the liver and kidney cells of chickens and mice in tissue culture. HISTOCHEMIE. HISTOCHEMISTRY. HISTOCHIMIE 1967; 10:305-8. [PMID: 5589633 DOI: 10.1007/bf00304312] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Battigelli MC, Hatch TF, Hengstenberg F, Mannella RJ. Tritiated thymidine labeling in the study of acute injury from air pollutants. ARCHIVES OF ENVIRONMENTAL HEALTH 1966; 12:747-50. [PMID: 5938576 DOI: 10.1080/00039896.1966.10664475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Eberhard A, Mazia D. Conditions for extraction of cytoplasmic DNA from embryos of a sea urchin. Biochem Biophys Res Commun 1965; 21:460-5. [PMID: 5880523 DOI: 10.1016/0006-291x(65)90405-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Gahan PB. The possible presence of aldehydes and carbohydrates in chromosomes and interphase nuclei. Histochem Cell Biol 1965. [DOI: 10.1007/bf00285794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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