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Ali SA, Mittal D, Kaur G. In-situ monitoring of xenobiotics using genetically engineered whole-cell-based microbial biosensors: recent advances and outlook. World J Microbiol Biotechnol 2021; 37:81. [PMID: 33843020 DOI: 10.1007/s11274-021-03024-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
Industrialisation, directly or indirectly, exposes humans to various xenobiotics. The increased magnitude of chemical pesticides and toxic heavy metals in the environment, as well as their intrusion into the food chain, seriously threatens human health. Therefore, the surveillance of xenobiotics is crucial for social safety and security. Online investigation by traditional methods is not sufficient for the detection and identification of such compounds because of the high costs and their complexity. Advancement in the field of genetic engineering provides a potential opportunity to use genetically modified microorganisms. In this regard, whole-cell-based microbial biosensors (WCBMB) represent an essential tool that couples genetically engineered organisms with an operator/promoter derived from a heavy metal-resistant operon combined with a regulatory protein in the gene circuit. The plasmid controls the expression of the reporter gene, such as gfp, luc, lux and lacZ, to an inducible gene promoter and has been widely applied to assay toxicity and bioavailability. This review summarises the recent trends in the development and application of microbial biosensors and the use of mobile genes for biomedical and environmental safety concerns.
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Affiliation(s)
- Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India. .,Proteomics and Cell Biology Lab, Animal Biotechnology Center, ICAR-National Dairy Research Institute, 132001, Karnal, Haryana, India.
| | - Deepti Mittal
- Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052, Sydney, NSW, Australia
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Kayar Dogan E, Abaci Gunyar O, Topal F, Alper E, Ekinci N. Bacterial species and total bacterial load in the distal oesophagus in patients with and without clinical gastric reflux. J Appl Microbiol 2019; 126:1891-1898. [PMID: 30873693 DOI: 10.1111/jam.14250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/25/2019] [Accepted: 03/11/2019] [Indexed: 12/01/2022]
Abstract
AIMS The purpose of this study is to compare distal oesophagus of persons with and without gastric reflux in terms of bacterial load and presence of certain bacterial species. METHODS AND RESULTS Two biopsy specimens were obtained from the distal oesophagus at 5 cm above the gastroesophageal junction of each of the 50 patients (20 with normal oesophagus and 30 with reflux oesophagitis) under endoscopic examination and used for histological examination and DNA isolation. We used a real-time PCR-based assay to quantify the bacterial load and the presence of certain bacterial species from one of the biopsy samples. The biopsy specimens taken from the patients with reflux oesophagitis were consistent with gastroesophageal reflux disease (GERD). The bacterial load did not significantly differ between the groups (P < 0·005). CONCLUSION While there was no difference between the bacterial load in the two groups, variation was observed in bacterial species. Most of the bacteria identified in distal oesophagus of the patients with gastroesophageal reflux were Gram negative. SIGNIFICANCE AND IMPACT OF THE STUDY The human oesophagus was considered sterile until quite recently. Molecular techniques displayed the presence of a diverse bacterial species in the oesophagus. Although it is known that dysbiosis in the oesophagus causes GERD, and that Barrett's oesophagus can trigger the development of oesophageal adenocarcinoma, its etiopathogenesis is not clear. A limited number of published studies support the importance of the present study.
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Affiliation(s)
- E Kayar Dogan
- Basic and Industrial Microbiology Section, Biology Department, Science Faculty, Ege University, İzmir, Turkey
| | - O Abaci Gunyar
- Basic and Industrial Microbiology Section, Biology Department, Science Faculty, Ege University, İzmir, Turkey
| | - F Topal
- Department of Gastroenterology, Atatürk Research and Teaching Hospital, İzmir Katip Çelebi University, İzmir, Turkey
| | - E Alper
- Department of Gastroenterology, İstanbul Koç University Hospital, İzmir, Turkey
| | - N Ekinci
- Department of Pathology, Atatürk Research and Teaching Hospital, İzmir Katip Çelebi University, İzmir, Turkey
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Saltepe B, Kehribar EŞ, Su Yirmibeşoğlu SS, Şafak Şeker UÖ. Cellular Biosensors with Engineered Genetic Circuits. ACS Sens 2018; 3:13-26. [PMID: 29168381 DOI: 10.1021/acssensors.7b00728] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An increasing interest in building novel biological devices with designed cellular functionalities has triggered the search of innovative tools for biocomputation. Utilizing the tools of synthetic biology, numerous genetic circuits have been implemented such as engineered logic operation in analog and digital circuits. Whole cell biosensors are widely used biological devices that employ several biocomputation tools to program cells for desired functions. Up to the present date, a wide range of whole-cell biosensors have been designed and implemented for disease theranostics, biomedical applications, and environmental monitoring. In this review, we investigated the recent developments in biocomputation tools such as analog, digital, and mix circuits, logic gates, switches, and state machines. Additionally, we stated the novel applications of biological devices with computing functionalities for diagnosis and therapy of various diseases such as infections, cancer, or metabolic diseases, as well as the detection of environmental pollutants such as heavy metals or organic toxic compounds. Current whole-cell biosensors are innovative alternatives to classical biosensors; however, there is still a need to advance decision making capabilities by developing novel biocomputing devices.
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Affiliation(s)
- Behide Saltepe
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Ebru Şahin Kehribar
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | | | - Urartu Özgür Şafak Şeker
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
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Nielsen KM, Bøhn T, Townsend JP. Detecting rare gene transfer events in bacterial populations. Front Microbiol 2014; 4:415. [PMID: 24432015 PMCID: PMC3882822 DOI: 10.3389/fmicb.2013.00415] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/16/2013] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.
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Affiliation(s)
- Kaare M Nielsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø Tromsø, Norway ; GenØk-Centre for Biosafety, The Science Park Tromsø, Norway
| | - Thomas Bøhn
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø Tromsø, Norway ; GenØk-Centre for Biosafety, The Science Park Tromsø, Norway
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University New Haven, CT, USA ; Program in Computational Biology and Bioinformatics, Yale University New Haven, CT, USA ; Program in Microbiology, Yale University New Haven, CT, USA
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Wright O, Stan GB, Ellis T. Building-in biosafety for synthetic biology. Microbiology (Reading) 2013; 159:1221-1235. [DOI: 10.1099/mic.0.066308-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Oliver Wright
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
| | - Guy-Bart Stan
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
| | - Tom Ellis
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
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Nordgård L, Brusetti L, Raddadi N, Traavik T, Averhoff B, Nielsen KM. An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats. BMC Res Notes 2012; 5:170. [PMID: 22463741 PMCID: PMC3364145 DOI: 10.1186/1756-0500-5-170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 04/01/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes. RESULTS Plasmid DNA with two resistance genes (nptI and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, were constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. No transformants were identified among 441 tested isolates. CONCLUSIONS The analyses showed that extensive ingestion of DNA (100 μg plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit < 1 transformant per 1,1 × 10(8) cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed. This study is consistent with other studies suggesting natural transformation is not detectable in the GIT of mammals.
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Affiliation(s)
- Lise Nordgård
- GenØk, Centre for Biosafety, Science Park, 9294 Tromsø, Norway
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Townsend JP, Bøhn T, Nielsen KM. Assessing the probability of detection of horizontal gene transfer events in bacterial populations. Front Microbiol 2012; 3:27. [PMID: 22363321 PMCID: PMC3282476 DOI: 10.3389/fmicb.2012.00027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 01/16/2012] [Indexed: 11/23/2022] Open
Abstract
Experimental approaches to identify horizontal gene transfer (HGT) events of non-mobile DNA in bacteria have typically relied on detection of the initial transformants or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to be detected in a short time frame. Population genetic modeling of the growth dynamics of bacterial genotypes is therefore necessary to account for natural selection and genetic drift during the time lag and to predict realistic time frames for detection with a given sampling design. Here we draw on statistical approaches to population genetic theory to construct a cohesive probabilistic framework for investigation of HGT of exogenous DNA into bacteria. In particular, the stochastic timing of rare HGT events is accounted for. Integrating over all possible event timings, we provide an equation for the probability of detection, given that HGT actually occurred. Furthermore, we identify the key variables determining the probability of detecting HGT events in four different case scenarios that are representative of bacterial populations in various environments. Our theoretical analysis provides insight into the temporal aspects of dissemination of genetic material, such as antibiotic resistance genes or transgenes present in genetically modified organisms. Due to the long time scales involved and the exponential growth of bacteria with differing fitness, quantitative analyses incorporating bacterial generation time, and levels of selection, such as the one presented here, will be a necessary component of any future experimental design and analysis of HGT as it occurs in natural settings.
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Affiliation(s)
- Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA
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Brusetti L, Glad T, Borin S, Myren P, Rizzi A, Johnsen PJ, Carter P, Daffonchio D, Nielsen KM. Low prevalence ofblaTEMgenes in Arctic environments and agricultural soil and rhizosphere. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2009. [DOI: 10.1080/08910600701838244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Lorenzo Brusetti
- Department of Food Science, Technology and Microbiology (DISTAM), University of Milan, Milan, Italy
| | - Trine Glad
- Department of Pharmacy, Faculty of Medicine, University of Tromsø, Tromsø, Norway
| | - Sara Borin
- Department of Food Science, Technology and Microbiology (DISTAM), University of Milan, Milan, Italy
| | - Petter Myren
- Department of Pharmacy, Faculty of Medicine, University of Tromsø, Tromsø, Norway
- ESR Kenepuru Science Centre, Porirua, New Zealand
| | - Aurora Rizzi
- Department of Food Science, Technology and Microbiology (DISTAM), University of Milan, Milan, Italy
| | - Pål J. Johnsen
- Department of Pharmacy, Faculty of Medicine, University of Tromsø, Tromsø, Norway
| | - Phil Carter
- ESR Kenepuru Science Centre, Porirua, New Zealand
| | - Daniele Daffonchio
- Department of Food Science, Technology and Microbiology (DISTAM), University of Milan, Milan, Italy
| | - Kaare M. Nielsen
- Department of Pharmacy, Faculty of Medicine, University of Tromsø, Tromsø, Norway
- Norwegian Institute of Gene Ecology, Science Park, Tromsø, Norway
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Detection of feed-derived maize DNA in goat milk and evaluation of the potential of horizontal transfer to bacteria. Eur Food Res Technol 2008. [DOI: 10.1007/s00217-008-0896-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Maruyama F, Tani K, Kenzaka T, Yamaguchi N, Nasu M. Application of Real-Time Long and Short Polymerase Chain Reaction for Sensitive Monitoring of the Fate of Extracellular Plasmid DNA Introduced into River Waters. Microbes Environ 2008; 23:229-36. [DOI: 10.1264/jsme2.23.229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Fumito Maruyama
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University
| | - Katsuji Tani
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University
| | - Takehiko Kenzaka
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University
| | - Nobuyasu Yamaguchi
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University
| | - Masao Nasu
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University
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Nordgård L, Nguyen T, Midtvedt T, Benno Y, Traavik T, Nielsen KM. Lack of detectable DNA uptake by bacterial gut isolates grown in vitro and by Acinetobacter baylyi colonizing rodents in vivo. ACTA ACUST UNITED AC 2007; 6:149-60. [PMID: 17961488 DOI: 10.1051/ebr:2007029] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Biological risk assessment of food containing recombinant DNA has exposed knowledge gaps related to the general fate of DNA in the gastrointestinal tract (GIT). Here, a series of experiments is presented that were designed to determine if genetic transformation of the naturally competent bacterium Acinetobacter baylyi BD413 occurs in the GIT of mice and rats, with feed-introduced bacterial DNA containing a kanamycin resistance gene (nptII). Strain BD413 was found in various gut locations in germ-free mice at 10(3)-10(5) CFU per gram GIT content 24-48 h after administration. However, subsequent DNA exposure of the colonized mice did not result in detectable bacterial transformants, with a detection limit of 1 transformant per 10(3)-10(5) bacteria. Further attempts to increase the likelihood of detection by introducing weak positive selection with kanamycin of putative transformants arising in vivo during a 4-week-long feeding experiment (where the mice received DNA and the recipient cells regularly) did not yield transformants either. Moreover, the in vitro exposure of actively growing A. baylyi cells to gut contents from the stomach, small intestine, cecum or colon contents of rats (with a normal microbiota) fed either purified DNA (50 microg) or bacterial cell lysates did not produce bacterial transformants. The presence of gut content of germfree mice was also highly inhibitory to transformation of A. baylyi, indicating that microbially-produced nucleases are not responsible for the sharp 500- to 1,000,000-fold reduction of transformation frequencies seen. Finally, a range of isolates from the genera Enterococcus, Streptococcus and Bifidobacterium spp. was examined for competence expression in vitro, without yielding any transformants. In conclusion, model choice and methodological constraints severely limit the sample size and, hence, transfer frequencies that can be measured experimentally in the GIT. Our observations suggest the contents of the GIT shield or adsorb DNA, preventing detectable exposure of feed-derived DNA fragments to competent bacteria.
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Affiliation(s)
- Lise Nordgård
- Norwegian Institute of Gene Ecology, Science Park, 9294, Tromsø, Norway
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Ray JL, Andersen HK, Young S, Nielsen KM, O'Callaghan M. An assessment of the potential of herbivorous insect gut bacteria to develop competence for natural transformation. ACTA ACUST UNITED AC 2007; 6:135-47. [PMID: 17961487 DOI: 10.1051/ebr:2007032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Whereas the capability of DNA uptake has been well established for numerous species and strains of bacteria grown in vitro, the broader distribution of natural transformability within bacterial communities remains largely unexplored. Here, we investigate the ability of bacterial isolates from the gut of grass grub larvae (Costelytra zealandica (White); Coleoptera: Scarabaeidae) to develop natural genetic competence in vitro. A total of 37 mostly species-divergent strains isolated from the gut of grass grub larvae were selected for spontaneous rifampicin-resistance. Genomic DNA was subsequently isolated from the resistant strains and exposed to sensitive strains grown individually using established filter transformation protocols. DNA isolated from wild-type strains was used as a control. None of the 37 isolates tested exhibited a frequency of conversion to rifampicin-resistance in the presence of DNA at rates that were significantly higher than the rate of spontaneous mutation to rifampicin-resistance in the presence of wild-type DNA (the limit of detection was approximately < 1 culturable transformant per 10(9) exposed bacteria). To further examine if conditions were conducive to bacterial DNA uptake in the grass grubs gut, we employed the competent bacterium Acinetobacter baylyi strain BD413 as a recipient species for in vivo studies. However, no transformants could be detected above the detection limit of 1 transformant per 10(3) cells, possibly due to low population density and limited growth of A. baylyi cells in grass grub guts. PCR analysis indicated that chromosomal Acinetobacter DNA remains detectable by PCR for up to 3 days after direct inoculation into the alimentary tract of grass grub larvae. Nevertheless, neither transforming activity of the DNA recovered from the alimentary tract of grass grubs larvae nor competence of bacterial cells recovered from inoculated larvae could be shown.
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Affiliation(s)
- Jessica L Ray
- Department of Pharmacy, University of Tromsø, 9037, Tromsø, Norway
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Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D. Release and persistence of extracellular DNA in the environment. ACTA ACUST UNITED AC 2007; 6:37-53. [DOI: 10.1051/ebr:2007031] [Citation(s) in RCA: 366] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Foss GS, Rogne S. When gene medication is also genetic modification--regulating DNA treatment. Vaccine 2007; 25:5613-8. [PMID: 17544178 DOI: 10.1016/j.vaccine.2007.04.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 04/13/2007] [Accepted: 04/23/2007] [Indexed: 11/29/2022]
Abstract
The molecular methods used in DNA vaccination and gene therapy resemble in many ways the methods applied in genetic modification of organisms. In some regulatory regimes, this creates an overlap between 'gene medication' and genetic modification. In Norway, an animal injected with plasmid DNA, in the form of DNA vaccine or gene therapy, currently is viewed as being genetically modified for as long as the added DNA is present in the animal. However, regulating a DNA-vaccinated animal as genetically modified creates both regulatory and practical challenges. It is also counter-intuitive to many biologists. Since immune responses can be elicited also to alter traits, the borderline between vaccination and the modification of properties is no longer distinct. In this paper, we discuss the background for the Norwegian interpretation and ways in which the regulatory challenge can be handled.
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Affiliation(s)
- Grethe S Foss
- The Norwegian Biotechnology Advisory Board, P.O. Box 522 Sentrum, NO-0105 Oslo, Norway.
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