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Table 4 An overview of studies on cell-free nucleic acid, authors, publishing journals, year of publication and PubMed citation ID

From: Water bodies are potential hub for spatio-allotment of cell-free nucleic acid and pandemic: a pentadecadal (1969–2021) critical review on particulate cell-free DNA reservoirs in water nexus

PMID Title Authors Citation First author Journal/book Publication year PMCID NIHMS ID DOI
30013526 Extra-chromosomal DNA sequencing reveals episomal prophages capable of impacting virulence factor expression in Staphylococcus aureus Deutsch DR, Utter B, Verratti KJ, Sichtig H, Tallon LJ, Fischetti VA Front Microbiol. 2018 Jul 2;9:1406. https://doi.org/10.3389/fmicb.2018.01406. eCollection 2018 Deutsch DR Front Microbiol 2018 PMC6036120 https://doi.org/10.3389/fmicb.2018.01406
30849712 The role of transposable elements and DNA damage repair mechanisms in gene duplications and gene fusions in plant genomes Krasileva KV Curr Opin Plant Biol. 2019 Apr;48:18–25. https://doi.org/10.1016/j.pbi.2019.01.004. Epub 2019 Mar 5 Krasileva KV Curr Opin Plant Biol 2019    https://doi.org/10.1016/j.pbi.2019.01.004
31889879 Isolation and characterization of two novel plasmids pCYM01 and pCYM02 of Cylindrospermum stagnale Ganesan V, Raja R, Hemaiswarya S, Carvalho IS, Anand N Saudi J Biol Sci. 2020 Jan;27(1):535–542. https://doi.org/10.1016/j.sjbs.2019.11.017. Epub 2019 Nov 23 Ganesan V Saudi J Biol Sci 2020 PMC6933252 https://doi.org/10.1016/j.sjbs.2019.11.017
27581613 Uncovering novel mobile genetic elements and their dynamics through an extra-chromosomal sequencing approach Deutsch DR, Utter B, Fischetti VA Mob Genet Elements. 2016 May 17;6(4):e1189987. https://doi.org/10.1080/2159256X.2016.1189987. eCollection 2016 Jul-Aug Deutsch DR Mob Genet Elements 2016 PMC4993567 https://doi.org/10.1080/2159256X.2016.1189987
28936238 Biodistribution, Uptake and Effects Caused by Cancer-Derived Extracellular Vesicles Sadovska L, Santos CB, Kalniņa Z, Linē A J Circ Biomark. 2015 Mar 25;4:2. https://doi.org/10.5772/60522. eCollection 2015 Jan-Dec Sadovska L J Circ Biomark 2015 PMC5572990 https://doi.org/10.5772/60522
29593241 Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum Lima DC, Nyberg LK, Westerlund F, Batistuzzo de Medeiros SR Sci Rep. 2018 Mar 28;8(1):5327. https://doi.org/10.1038/s41598-018-23708-5 Lima DC Sci Rep 2018 PMC5871888 https://doi.org/10.1038/s41598-018-23708-5
20586577 Plasmid segregation: how to survive as an extra piece of DNA Salje J Crit Rev Biochem Mol Biol. 2010 Aug;45(4):296–317. https://doi.org/10.3109/10409238.2010.494657 Salje J Crit Rev Biochem Mol Biol 2010    https://doi.org/10.3109/10409238.2010.494657
10208801 Development and evaluation of an extra chromosomal DNA-based PCR test for diagnosing bovine babesiosis Salem GH, Liu X, Johnsrude JD, Dame JB, Roman Reddy G Mol Cell Probes. 1999 Apr;13(2):107–13. https://doi.org/10.1006/mcpr.1998.0223 Salem GH Mol Cell Probes 1999    https://doi.org/10.1006/mcpr.1998.0223
25843804 Extra-chromosomal DNA maintenance in Bacillus subtilis, dependence on flagellation factor FliF and moonlighting mediator EdmS Hakumai Y, Shimomoto K, Ashiuchi M Biochem Biophys Res Commun. 2015 May 15;460(4):1059–62. https://doi.org/10.1016/j.bbrc.2015.03.152. Epub 2015 Apr 3 Hakumai Y Biochem Biophys Res Commun 2015    https://doi.org/10.1016/j.bbrc.2015.03.152
12212946 The food safety perspective of antibiotic resistance McDermott PF, Zhao S, Wagner DD, Simjee S, Walker RD, White DG Anim Biotechnol. 2002 May;13(1):71–84. https://doi.org/10.1081/ABIO-120005771 McDermott PF Anim Biotechnol 2002    https://doi.org/10.1081/ABIO-120005771
28837318 Rapid Isolation of Centromeres from Scheffersomyces stipitis Cao M, Seetharam AS, Severin AJ, Shao Z ACS Synth Biol. 2017 Nov 17;6(11):2028–2034. https://doi.org/10.1021/acssynbio.7b00166. Epub 2017 Sep 5 Cao M ACS Synth Biol 2017    https://doi.org/10.1021/acssynbio.7b00166
28391682 Centromeric DNA facilitates nonconventional yeast genetic engineering Cao M, Gao M, Lopez-Garcia CL, Wu Y, Seetharam AS, Severin AJ, Shao Z ACS Synth Biol. 2017 Aug 18;6(8):1545–1553. https://doi.org/10.1021/acssynbio.7b00046. Epub 2017 Apr 25 Cao M ACS Synth Biol 2017    https://doi.org/10.1021/acssynbio.7b00046
24963913 Beyond the chromosome: the prevalence of unique extra-chromosomal bacteriophages with integrated virulence genes in pathogenic Staphylococcus aureus Utter B, Deutsch DR, Schuch R, Winer BY, Verratti K, Bishop-Lilly K, Sozhamannan S, Fischetti VA PLoS One. 2014 Jun 25;9(6):e100502. https://doi.org/10.1371/journal.pone.0100502. eCollection 2014 Utter B PLoS One 2014 PMC4070920 10.1371/journal.pone.0100502
29602465 The presence of tumour extra-chromosomal circular DNA (ecDNA) as a component of liquid biopsy in blood Khatami F, Larijani B, Tavangar SM Med Hypotheses. 2018 May;114:5–7. https://doi.org/10.1016/j.mehy.2018.02.018. Epub 2018 Feb 26 Khatami F Med Hypotheses 2018    https://doi.org/10.1016/j.mehy.2018.02.018
10382074 The degradation profile of extra-chromosomal circular DNA during cisplatin-induced apoptosis is consistent with preferential cleavage at matrix attachment regions Schoenlein PV, Barrett JT, Welter D Chromosoma. 1999 May;108(2):121–31. https://doi.org/10.1007/s004120050359 Schoenlein PV Chromosoma 1999    https://doi.org/10.1007/s004120050359
19424419 Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution Pace JK 2nd, Sen SK, Batzer MA, Feschotte C PLoS Genet. 2009 May;5(5):e1000469. https://doi.org/10.1371/journal.pgen.1000469. Epub 2009 May 8 Pace JK 2nd PLoS Genet 2009 PMC2671141 https://doi.org/10.1371/journal.pgen.1000469
1335022 Extra-chromosomal human immunodeficiency virus type 1 DNA forms in fresh peripheral blood lymphocytes and in two interleukin-2-independent T cell lines derived from peripheral blood lymphocytes of an asymptomatic seropositive subject Titti F, Borsetti A, Federico M, Testa U, Meccia E, Samoggia P, Peschle C, Verani P, Rossi GB J Gen Virol. 1992 Dec;73 ( Pt 12):3087–97. https://doi.org/10.1099/0022-1317-73-12-3087 Titti F J Gen Virol 1992    https://doi.org/10.1099/0022-1317-73-12-3087
21170331 Relationships linking amplification level to gene over-expression in gliomas Vogt N, Gibaud A, Almeida A, Ourliac-Garnier I, Debatisse M, Malfoy B PLoS One. 2010 Dec 8;5(12):e14249. https://doi.org/10.1371/journal.pone.0014249 Vogt N PLoS One 2010 PMC2999539 https://doi.org/10.1371/journal.pone.0014249
5009519 The timing of meiosis and DNA synthesis during early oogenesis in the toad, Xenopus laevis Coggins LW, Gall JG J Cell Biol. 1972 Mar;52(3):569–76. https://doi.org/10.1083/jcb.52.3.569 Coggins LW J Cell Biol 1972 PMC2108647 https://doi.org/10.1083/jcb.52.3.569
20365401 Plasmid copy number noise in monoclonal populations of bacteria Wong Ng J, Chatenay D, Robert J, Poirier MG Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jan;81(1 Pt 1):011909. https://doi.org/10.1103/PhysRevE.81.011909. Epub 2010 Jan 14 Wong Ng J Phys Rev E Stat Nonlin Soft Matter Phys 2010    https://doi.org/10.1103/PhysRevE.81.011909
23568537 Inverse metabolic engineering to improve Escherichia coli as an N-glycosylation host Pandhal J, Woodruff LB, Jaffe S, Desai P, Ow SY, Noirel J, Gill RT, Wright PC Biotechnol Bioeng. 2013 Sep;110(9):2482–93. https://doi.org/10.1002/bit.24920. Epub 2013 May 17 Pandhal J Biotechnol Bioeng 2013    https://doi.org/10.1002/bit.24920
2927424 Effect of DNA damage on stable transformation of mammalian cells with integrative and episomal plasmids Vos JM, Hanawalt PC Mutat Res. 1989 Mar-May;220(2–3):205–20. https://doi.org/10.1016/0165-1110(89)90025-0 Vos JM Mutat Res 1989    https://doi.org/10.1016/0165-1110(89)90025-0
20039170 Co-existence of multidrug-resistant and multidrug-susceptible strains of Pseudomonas aeruginosa from a single clinical isolate Mahida K, Kwon DH Curr Microbiol. 2010 Jul;61(1):19–24. https://doi.org/10.1007/s00284-009-9570-0. Epub 2009 Dec 29 Mahida K Curr Microbiol 2010    https://doi.org/10.1007/s00284-009-9570-0
11515790 Glioblastoma-related gene mutations and over-expression of functional epidermal growth factor receptors in SKMG-3 glioma cells Thomas C, Ely G, James CD, Jenkins R, Kastan M, Jedlicka A, Burger P, Wharen R Acta Neuropathol. 2001 Jun;101(6):605–15. https://doi.org/10.1007/s004010000332 Thomas C Acta Neuropathol 2001    https://doi.org/10.1007/s004010000332
19763421 Cloning and molecular characterization of a novel rolling-circle replicating plasmid, pK1S-1, from Bacillus thuringiensis subsp. kurstaki K1 Li MS, Roh JY, Tao X, Yu ZN, Liu ZD, Liu Q, Xu HG, Shim HJ, Kim YS, Wang Y, Choi JY, Je YH J Microbiol. 2009 Aug;47(4):466–72. https://doi.org/10.1007/s12275-009-0020-2. Epub 2009 Sep 9 Li MS J Microbiol 2009    https://doi.org/10.1007/s12275-009-0020-2
9844068 A novel method of extracting plasmid DNA from Helicobacter species De Ungria MC, Tillett D, Neilan BA, Cox PT, Lee A Helicobacter. 1998 Dec;3(4):269–77. https://doi.org/10.1111/j.1523-5378.1997.06085.pp.x-i1 De Ungria MC Helicobacter 1998    https://doi.org/10.1111/j.1523-5378.1997.06085.pp.x-i1
23514143 Topological similarity between the 2 μm plasmid partitioning locus and the budding yeast centromere: evidence for a common evolutionary origin? Jayaram M, Chang KM, Ma CH, Huang CC, Liu YT, Sau S Biochem Soc Trans. 2013 Apr;41(2):501–7. https://doi.org/10.1042/BST20120224 Jayaram M Biochem Soc Trans 2013    https://doi.org/10.1042/BST20120224
16093317 High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene Shaked H, Melamed-Bessudo C, Levy AA Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12,265–9. https://doi.org/10.1073/pnas.0502601102. Epub 2005 Aug 10 Shaked H Proc Natl Acad Sci U S A 2005 PMC1189313 https://doi.org/10.1073/pnas.0502601102
11997466 Genome-wide screening for trait conferring genes using DNA microarrays Gill RT, Wildt S, Yang YT, Ziesman S, Stephanopoulos G Proc Natl Acad Sci U S A. 2002 May 14;99(10):7033–8. https://doi.org/10.1073/pnas.102154799. Epub 2002 May 7 Gill RT Proc Natl Acad Sci U S A 2002 PMC124523 https://doi.org/10.1073/pnas.102154799
17109398 Targeted gene delivery to differentiated skeletal muscle: a tool to study dedifferentiation Morrison JI, Lööf S, He P, Aleström P, Collas P, Simon A Dev Dyn. 2007 Feb;236(2):481–8. https://doi.org/10.1002/dvdy.21019 Morrison JI Dev Dyn 2007    https://doi.org/10.1002/dvdy.21019
17148179 The evolution of a conjugative plasmid and its ability to increase bacterial fitness Dionisio F, Conceição IC, Marques AC, Fernandes L, Gordo I Biol Lett. 2005 Jun 22;1(2):250–2. https://doi.org/10.1098/rsbl.2004.0275 Dionisio F Biol Lett 2005 PMC1626229 https://doi.org/10.1098/rsbl.2004.0275
816990 Extra-chromosomal DNA in chloramphenicol resistant myxococcus strains Brown NL, Parish JH J Gen Microbiol. 1976 Mar;93(1):63–8. https://doi.org/10.1099/00221287-93-1-63 Brown NL J Gen Microbiol 1976    10.1099/00221287–93-1–63
12386375 Development of a Nuclear Export Signal Trapping Method for Isolating Genes with HIV Rev Activity Zhang MJ, Dayton AI J Biomed Sci. 1997 Nov-Dec;4(6):289–294. https://doi.org/10.1007/BF02258352 Zhang MJ J Biomed Sci 1997    https://doi.org/10.1007/BF02258352
3796319 Plasmid-like properties of the four virulence-associated factors of Yersinia pestis Tsukano H, Wake A, Sakakibara Y Microbiol Immunol. 1986;30(9):837–48. https://doi.org/10.1111/j.1348-0421.1986.tb03011.x Tsukano H Microbiol Immunol 1986    https://doi.org/10.1111/j.1348-0421.1986.tb03011.x
12850476 Localization of HTLV-I tax proviral DNA in mononuclear cells Zucker-Franklin D, Pancake BA, Najfeld V Blood Cells Mol Dis. 2003 Jul-Aug;31(1):1–6. https://doi.org/10.1016/s1079-9796(03)00124-4 Zucker-Franklin D Blood Cells Mol Dis 2003    https://doi.org/10.1016/s1079-9796(03)00124-4
2550376 Replication of latent Epstein-Barr virus genomes in normal and malignant lymphoid cells Adams A, Pozos TC, Purvey HV Int J Cancer. 1989 Sep 15;44(3):560–4. https://doi.org/10.1002/ijc.2910440331 Adams A Int J Cancer 1989    https://doi.org/10.1002/ijc.2910440331
12604348 Double-stranded RNA can mediate the suppression of uracil phosphoribosyltransferase expression in Toxoplasma gondii Al-Anouti F, Quach T, Ananvoranich S Biochem Biophys Res Commun. 2003 Mar 7;302(2):316–23. https://doi.org/10.1016/s0006-291x(03)00172-4 Al-Anouti F Biochem Biophys Res Commun 2003    https://doi.org/10.1016/s0006-291x(03)00172-4
5804897 Extra-chromosomal DNA in early stages of oogenesis in Acheta domesticus Cave MD, Allen ER J Cell Sci. 1969 May;4(3):593–609 Cave MD J Cell Sci 1969