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Musiyiwa K, Simbanegavi TT, Marumure J, Makuvara Z, Chaukura N, Gwenzi W. The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:12666-12682. [PMID: 38253827 DOI: 10.1007/s11356-023-31788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024]
Abstract
The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.
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Affiliation(s)
- Kumbirai Musiyiwa
- Department of Crop Science and Post-Harvest Technology, School of Agricultural Science and Technology, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
| | - Tinoziva T Simbanegavi
- Department of Soil Science and Environment, Faculty of Agriculture, Environment, and Food Systems, University of Zimbabwe, Mt. Pleasant, P.O. Box MP167, Harare, Zimbabwe
| | - Jerikias Marumure
- Department of Physics, Geography and Environmental Science, School of Natural Sciences, Great Zimbabwe University, P.O. Box 1235, Masvingo, Zimbabwe
- Department of Life and Consumer Sciences, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Zakio Makuvara
- Department of Physics, Geography and Environmental Science, School of Natural Sciences, Great Zimbabwe University, P.O. Box 1235, Masvingo, Zimbabwe
- Department of Life and Consumer Sciences, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Nhamo Chaukura
- Department of Physical and Earth Sciences, Sol Plaatje University, Kimberley, 8301, South Africa
| | - Willis Gwenzi
- Grassland Science and Renewable Plant Resources, Universitat Kassel, Steinstraβe 19, 37213, Witzenhausen, Germany.
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Un Jan Contreras S, Gardner CM. Environmental fate and behaviour of antibiotic resistance genes and small interference RNAs released from genetically modified crops. J Appl Microbiol 2022; 133:2877-2892. [PMID: 35892194 DOI: 10.1111/jam.15741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/30/2022]
Abstract
Rising global populations have amplified food scarcity across the world and ushered in the development of genetically modified (GM) crops to overcome these challenges. Cultivation of major crops such as corn and soy has favoured GM crops over conventional varieties to meet crop production and resilience needs. Modern GM crops containing small interference RNA molecules and antibiotic resistance genes have become increasingly common in the United States. However, the use of these crops remains controversial due to the uncertainty regarding the unintended release of its genetic material into the environment and possible downstream effects on human and environmental health. DNA or RNA transgenes may be exuded from crop tissues during cultivation or released during plant decomposition and adsorbed by soil. This can contribute to the persistence and bioavailability in soil or water environment and possible uptake by soil microbial communities and further passing of this information to neighbouring bacteria, disrupting microbial ecosystem services such as nutrient cycling and soil fertility. In this review, transgene mechanisms of action, uses in crops, and knowledge regarding their environmental fate and impact to microbes are evaluated. This aims to encapsulate the current knowledge and promote further research regarding unintended effects transgenes may cause.
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Affiliation(s)
- Sandra Un Jan Contreras
- Department of Civil and Environmental Engineering, Washington State University, Pullman, Washington, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, Pullman, Washington, USA
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Hu J, Park JH, Kim IH. Effect of dietary supplementation with Lactobacillus plantarum on growth performance, fecal score, fecal microbial counts, gas emission and nutrient digestibility in growing pigs. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tetz VV, Tetz GV. A new biological definition of life. Biomol Concepts 2020; 11:1-6. [PMID: 31934876 DOI: 10.1515/bmc-2020-0001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 11/22/2019] [Indexed: 11/15/2022] Open
Abstract
Here we have proposed a new biological definition of life based on the function and reproduction of existing genes and creation of new ones, which is applicable to both unicellular and multicellular organisms. First, we coined a new term "genetic information metabolism" comprising functioning, reproduction, and creation of genes and their distribution among living and non-living carriers of genetic information. Encompassing this concept, life is defined as organized matter that provides genetic information metabolism. Additionally, we have articulated the general biological function of life as Tetz biological law: "General biological function of life is to provide genetic information metabolism" and formulated novel definition of life: "Life is an organized matter that provides genetic information metabolism". New definition of life and Tetz biological law allow to distinguish in a new way living and non-living objects on Earth and other planets based on providing genetic information metabolism.
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Affiliation(s)
- Victor V Tetz
- Human Microbiology Institute, 101 Avenue of Americas, New York, NY 10013, United States of America
| | - George V Tetz
- Human Microbiology Institute, 101 Avenue of Americas, New York, NY 10013, United States of America
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5
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Chen C, Fu X, Peng R, Tian Y, Yao Q. Detoxifying processes during kanamycin-induced stress to Arabidopsis thaliana seedling growth. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1798811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Chen Chen
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiaoyan Fu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Rihe Peng
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yongsheng Tian
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Quanhong Yao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
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6
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Liu G, Massel K, Tabet B, Godwin ID. Biolistic DNA Delivery and Its Applications in Sorghum bicolor. Methods Mol Biol 2020; 2124:197-215. [PMID: 32277455 DOI: 10.1007/978-1-0716-0356-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Biolistic DNA delivery has been considered a universal tool for genetic manipulation to transfer exotic genes to cells or tissues due to its simplicity, versatility, and high efficiency. It has been a preferred method for investigating plant gene function in most monocot crops. The first transgenic sorghum plants were successfully regenerated through biolistic DNA delivery in 1993, with a relatively low transformation efficiency of 0.3%. Since then, tremendous progress has been made in recent years where the highest transformation efficiency was reported at 46.6%. Overall, the successful biolistic DNA delivery system is credited to three fundamental cornerstones: robust tissue culture system, effective gene expression in sorghum, and optimal parameters of DNA delivery. In this chapter, the history, application, and current development of biolistic DNA delivery in sorghum are reviewed, and the prospect of sorghum genetic engineering is discussed.
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Affiliation(s)
- Guoquan Liu
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia.
| | - Karen Massel
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Basam Tabet
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Ian D Godwin
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
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Addressing concerns over the fate of DNA derived from genetically modified food in the human body: A review. Food Chem Toxicol 2018; 124:423-430. [PMID: 30580028 DOI: 10.1016/j.fct.2018.12.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022]
Abstract
Global commercialization of GM food and feed has stimulated much debate over the fate of GM food-derived DNA in the body of the consumer and as to whether it poses any health risks. We reviewed the fate of DNA derived from GM food in the human body. During mechanical/chemical processing, integrity of DNA is compromised. Food-DNA can survive harsh processing and digestive conditions with fragments up to a few hundred bp detectable in the gastrointestinal tract. Compelling evidence supported the presence of food (also GM food) derived DNA in the blood and tissues of human/animal. There is limited evidence of food-born DNA integrating into the genome of the consumer and of horizontal transfer of GM crop DNA into gut-bacteria. We find no evidence that transgenes in GM crop-derived foods have a greater propensity for uptake and integration than the host DNA of the plant-food. We found no evidence of plant-food DNA function/expression following transfer to either the gut-bacteria or somatic cells. Strong evidence suggested that plant-food-miRNAs can survive digestion, enter the body and affect gene expression patterns. We envisage that this multi-dimensional review will address questions regarding the fate of GM food-derived DNA and gene-regulatory-RNA in the human body.
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de Santis B, Stockhofe N, Wal JM, Weesendorp E, Lallès JP, van Dijk J, Kok E, De Giacomo M, Einspanier R, Onori R, Brera C, Bikker P, van der Meulen J, Kleter G. Case studies on genetically modified organisms (GMOs): Potential risk scenarios and associated health indicators. Food Chem Toxicol 2018; 117:36-65. [DOI: 10.1016/j.fct.2017.08.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/03/2017] [Accepted: 08/22/2017] [Indexed: 01/07/2023]
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9
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Pandeya D, Campbell LM, Nunes E, Lopez-Arredondo DL, Janga MR, Herrera-Estrella L, Rathore KS. ptxD gene in combination with phosphite serves as a highly effective selection system to generate transgenic cotton (Gossypium hirsutum L.). PLANT MOLECULAR BIOLOGY 2017; 95:567-577. [PMID: 29032395 DOI: 10.1007/s11103-017-0670-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/09/2017] [Indexed: 05/22/2023]
Abstract
This report demonstrates the usefulness of ptxD/phosphite as a selection system that not only provides a highly efficient and simple means to generate transgenic cotton plants, but also helps address many of the concerns related to the use of antibiotic and herbicide resistance genes in the production of transgenic crops. Two of the most popular dominant selectable marker systems for plant transformation are based on either antibiotic or herbicide resistance genes. Due to concerns regarding their safety and in order to stack multiple traits in a single plant, there is a need for alternative selectable marker genes. The ptxD gene, derived from Pseudomonas stutzeri WM88, that confers to cells the ability to convert phosphite (Phi) into orthophosphate (Pi) offers an alternative selectable marker gene as demonstrated for tobacco and maize. Here, we show that the ptxD gene in combination with a protocol based on selection medium containing Phi, as the sole source of phosphorus (P), can serve as an effective and efficient system to select for transformed cells and generate transgenic cotton plants. Fluorescence microscopy examination of the cultures under selection and molecular analyses on the regenerated plants demonstrate the efficacy of the system in recovering cotton transformants following Agrobacterium-mediated transformation. Under the ptxD/Phi selection, an average of 3.43 transgenic events per 100 infected explants were recovered as opposed to only 0.41% recovery when bar/phosphinothricin (PPT) selection was used. The event recovery rates for nptII/kanamycin and hpt/hygromycin systems were 2.88 and 2.47%, respectively. Molecular analysis on regenerated events showed a selection efficiency of ~ 97% under the ptxD/Phi system. Thus, ptxD/Phi has proven to be a very efficient, positive selection system for the generation of transgenic cotton plants with equal or higher transformation efficiencies compared to the commonly used, negative selection systems.
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Affiliation(s)
- Devendra Pandeya
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, 77843-2123, USA
| | - LeAnne M Campbell
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, 77843-2123, USA
| | - Eugenia Nunes
- Faculty of Science, The University of Porto, Porto, Portugal
| | - Damar L Lopez-Arredondo
- StelaGenomics Mexico, S de RL de CV, Av. Camino Real de Guanajuato s/n, Irapuato, 36821, Guanajuato, Mexico
| | - Madhusudhana R Janga
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, 77843-2123, USA
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Keerti S Rathore
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX, 77843-2123, USA.
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
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10
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Matuszyńska A, Angeleri M, Riseley A, Ramos-Martinez EM, Guerra T, Moejes FW. A Young Algaeneers' perspective: Communication and networking are key to successful multidisciplinary research. ALGAL RES 2017. [DOI: 10.1016/j.algal.2016.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Metabolic Engineering of Probiotic Saccharomyces boulardii. Appl Environ Microbiol 2016; 82:2280-2287. [PMID: 26850302 DOI: 10.1128/aem.00057-16] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 01/30/2016] [Indexed: 01/23/2023] Open
Abstract
Saccharomyces boulardiiis a probiotic yeast that has been used for promoting gut health as well as preventing diarrheal diseases. This yeast not only exhibits beneficial phenotypes for gut health but also can stay longer in the gut than Saccharomyces cerevisiae Therefore, S. boulardiiis an attractive host for metabolic engineering to produce biomolecules of interest in the gut. However, the lack of auxotrophic strains with defined genetic backgrounds has hampered the use of this strain for metabolic engineering. Here, we report the development of well-defined auxotrophic mutants (leu2,ura3,his3, and trp1) through clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9-based genome editing. The resulting auxotrophic mutants can be used as a host for introducing various genetic perturbations, such as overexpression or deletion of a target gene, using existing genetic tools forS. cerevisiae We demonstrated the overexpression of a heterologous gene (lacZ), the correct localization of a target protein (red fluorescent protein) into mitochondria by using a protein localization signal, and the introduction of a heterologous metabolic pathway (xylose-assimilating pathway) in the genome ofS. boulardii We further demonstrated that human lysozyme, which is beneficial for human gut health, could be secreted by S. boulardii Our results suggest that more sophisticated genetic perturbations to improveS. boulardii can be performed without using a drug resistance marker, which is a prerequisite for in vivo applications using engineeredS. boulardii.
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Woegerbauer M, Zeinzinger J, Gottsberger RA, Pascher K, Hufnagl P, Indra A, Fuchs R, Hofrichter J, Kopacka I, Korschineck I, Schleicher C, Schwarz M, Steinwider J, Springer B, Allerberger F, Nielsen KM, Fuchs K. Antibiotic resistance marker genes as environmental pollutants in GMO-pristine agricultural soils in Austria. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 206:342-351. [PMID: 26232739 DOI: 10.1016/j.envpol.2015.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 07/15/2015] [Accepted: 07/18/2015] [Indexed: 06/04/2023]
Abstract
Antibiotic resistance genes may be considered as environmental pollutants if anthropogenic emission and manipulations increase their prevalence above usually occurring background levels. The prevalence of aph(3')-IIa/nptII and aph(3')-IIIa/nptIII - frequent marker genes in plant biotechnology conferring resistance to certain aminoglycosides - was determined in Austrian soils from 100 maize and potato fields not yet exposed to but eligible for GMO crop cultivation. Total soil DNA extracts were analysed by nptII/nptIII-specific TaqMan real time PCR. Of all fields 6% were positive for nptII (median: 150 copies/g soil; range: 31-856) and 85% for nptIII (1190 copies/g soil; 13-61600). The copy-number deduced prevalence of nptIII carriers was 14-fold higher compared to nptII. Of the cultivable kanamycin-resistant soil bacteria 1.8% (95% confidence interval: 0-3.3%) were positive for nptIII, none for nptII (0-0.8%). The nptII-load of the studied soils was low rendering nptII a typical candidate as environmental pollutant upon anthropogenic release into these ecosystems.
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Affiliation(s)
- Markus Woegerbauer
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria.
| | - Josef Zeinzinger
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Richard Alexander Gottsberger
- Division for Food Security, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Kathrin Pascher
- Department of Integrative Biology and Biodiversity Research (DIB), Institute of Zoology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Hufnagl
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Alexander Indra
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Reinhard Fuchs
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Johannes Hofrichter
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Ian Kopacka
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | | | - Corina Schleicher
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Michael Schwarz
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Johann Steinwider
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Burkhard Springer
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Franz Allerberger
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Kaare M Nielsen
- GenØk - Centre for Biosafety and Department of Pharmacy, University of Tromsø, Norway
| | - Klemens Fuchs
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
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Zhang GC, Kong II, Kim H, Liu JJ, Cate JHD, Jin YS. Construction of a quadruple auxotrophic mutant of an industrial polyploid saccharomyces cerevisiae strain by using RNA-guided Cas9 nuclease. Appl Environ Microbiol 2014; 80:7694-701. [PMID: 25281382 PMCID: PMC4249234 DOI: 10.1128/aem.02310-14] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/29/2014] [Indexed: 11/20/2022] Open
Abstract
Industrial polyploid yeast strains harbor numerous beneficial traits but suffer from a lack of available auxotrophic markers for genetic manipulation. Here we demonstrated a quick and efficient strategy to generate auxotrophic markers in industrial polyploid yeast strains with the RNA-guided Cas9 nuclease. We successfully constructed a quadruple auxotrophic mutant of a popular industrial polyploid yeast strain, Saccharomyces cerevisiae ATCC 4124, with ura3, trp1, leu2, and his3 auxotrophies through RNA-guided Cas9 nuclease. Even though multiple alleles of auxotrophic marker genes had to be disrupted simultaneously, we observed knockouts in up to 60% of the positive colonies after targeted gene disruption. In addition, growth-based spotting assays and fermentation experiments showed that the auxotrophic mutants inherited the beneficial traits of the parental strain, such as tolerance of major fermentation inhibitors and high temperature. Moreover, the auxotrophic mutants could be transformed with plasmids containing selection marker genes. These results indicate that precise gene disruptions based on the RNA-guided Cas9 nuclease now enable metabolic engineering of polyploid S. cerevisiae strains that have been widely used in the wine, beer, and fermentation industries.
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Affiliation(s)
- Guo-Chang Zhang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - In Iok Kong
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jing-Jing Liu
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jamie H D Cate
- Department of Chemistry, University of California, Berkeley, California, USA Department of Molecular and Cell Biology, University of California, Berkeley, California, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yong-Su Jin
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Lin B, Tan Z, Xiao G, Zeng J, Tang S, Han X, Wang M, Liu S. Qualitative observation on persistence and microbial transformation of recombinant DNA from transgenic rice biomass incubated in in vitrorumen system. JOURNAL OF APPLIED ANIMAL RESEARCH 2013. [DOI: 10.1080/09712119.2012.739086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Capita R, Alonso-Calleja C. Antibiotic-resistant bacteria: a challenge for the food industry. Crit Rev Food Sci Nutr 2013; 53:11-48. [PMID: 23035919 DOI: 10.1080/10408398.2010.519837] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Antibiotic-resistant bacteria were first described in the 1940s, but whereas new antibiotics were being discovered at a steady rate, the consequences of this phenomenon were slow to be appreciated. At present, the paucity of new antimicrobials coming into the market has led to the problem of antibiotic resistance fast escalating into a global health crisis. Although the selective pressure exerted by the use of antibiotics (particularly overuse or misuse) has been deemed the major factor in the emergence of bacterial resistance to these antimicrobials, concerns about the role of the food industry have been growing in recent years and have been raised at both national and international levels. The selective pressure exerted by the use of antibiotics (primary production) and biocides (e.g., disinfectants, food and feed preservatives, or decontaminants) is the main driving force behind the selection and spread of antimicrobial resistance throughout the food chain. Genetically modified (GM) crops with antibiotic resistance marker genes, microorganisms added intentionally to the food chain (probiotic or technological) with potentially transferable antimicrobial resistance genes, and food processing technologies used at sub-lethal doses (e.g., alternative non-thermal treatments) are also issues for concern. This paper presents the main trends in antibiotic resistance and antibiotic development in recent decades, as well as their economic and health consequences, current knowledge concerning the generation, dissemination, and mechanisms of antibacterial resistance, progress to date on the possible routes for emergence of resistance throughout the food chain and the role of foods as a vehicle for antibiotic-resistant bacteria. The main approaches to prevention and control of the development, selection, and spread of antibacterial resistance in the food industry are also addressed.
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Affiliation(s)
- Rosa Capita
- Department of Food Hygiene and Food Technology, Veterinary Faculty, University of León, Spain.
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Suo C, Yin Y, Wang X, Lou X, Song D, Wang X, Gu Q. Effects of lactobacillus plantarum ZJ316 on pig growth and pork quality. BMC Vet Res 2012; 8:89. [PMID: 22731747 PMCID: PMC3482153 DOI: 10.1186/1746-6148-8-89] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 06/14/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Lactobacillus plantarum is a plant-associated bacterial species but it has also been found in human, mouse and porcine gastrointestinal tracts. It can ferment a broad spectrum of plant carbohydrates; it is tolerant of bile salts and low pH, and it has antagonistic potential against intestinal pathogens. However, experiments reporting the use of L. plantarum as a probiotic are limited. In this study, the effects of L. plantarum ZJ316 isolated from infant fecal samples on pig growth and pork quality were investigated. RESULTS One hundred and fifty newly weaned pigs were selected randomly and divided into five groups. Group 1 was fed a diet supplemented with the antibiotic mequindox; Groups 2, 3 and 4 were fed a diet supplemented with L. plantarum and no antibiotic; and Group 5 was fed a mixture of mequindox and L. plantarum. After a 60 days initial treatment, samples were collected for evaluation. The results showed that, the L. plantarum ZJ316 has probiotic effects on pig growth and that these effects are dose dependent. The effects of a dose of 1 × 109 CFU/d were more pronounced than those of a dose of 5 × 109 CFU/d or 1 × 1010 CFU/d. In Group 2 (1 × 109 CFU/d), the diarrhea (p = 0.000) and mortality rates (p = 0.448) were lower than in antibiotic-treated pigs (Group 1), and the daily weight gain (p = 0.001) and food conversion ratios were better (p = 0.005). Improved pork quality was associated with Lactobacillus treatment. pH (45 min, p = 0.020), hardness (p = 0.000), stickiness (p = 0.044), chewiness (p = 0.000), gumminess (p = 0.000) and restoring force (p = 0.004) were all significantly improved in Lactobacillus-treated pigs (Group 2). Although we found that L. plantarum exerted probiotic effects on pig growth and pork quality, the mechanisms underlying its action require further study. Polymerase chain reaction-denaturing gradient gel electrophoresis results showed that the gut bacterial communities in Lactobacillus- and antibiotic-treated pigs were very similar and the quantity of L. plantarum ZJ316 was below the detection limits of DGGE-band sequencing. The concentration of short-chain fatty acids in Lactobacillus- and antibiotic-treated fecal samples were not significantly different (p = 0.086). However, the villus height of ilea (p = 0.003), jejuna (p = 0.000) and duodena (p = 0.036) were found to be significantly improved by Lactobacillus treatment. CONCLUSION L. plantarum ZJ316 was found to have probiotic effects, improving pig growth and pork quality. The probiotic mechanism might not involve L. plantarum colonization and alteration of the gut bacterial community. Rather, it might be related to the inhibition of the growth of opportunistic pathogens and promotion of increased villus height.
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Affiliation(s)
- Cheng Suo
- Department of Biotechnology, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
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17
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Statement on a request from the European Commission for the assessment of the scientific elements supporting the prohibition for the placing on the market of GM potato EH92‐527‐1 for cultivation purposes in Austria. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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18
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Adegoke AA, Mvuyo T, Okoh AI. UbiquitousAcinetobacterspecies as beneficial commensals but gradually being emboldened with antibiotic resistance genes. J Basic Microbiol 2012; 52:620-7. [DOI: 10.1002/jobm.201100323] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 08/08/2011] [Indexed: 11/08/2022]
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Rizzi A, Raddadi N, Sorlini C, Nordgrd L, Nielsen KM, Daffonchio D. The Stability and Degradation of Dietary DNA in the Gastrointestinal Tract of Mammals: Implications for Horizontal Gene Transfer and the Biosafety of GMOs. Crit Rev Food Sci Nutr 2012; 52:142-61. [DOI: 10.1080/10408398.2010.499480] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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20
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Burris K, Mentewab A, Ripp S, Stewart CN. An Arabidopsis thaliana ABC transporter that confers kanamycin resistance in transgenic plants does not endow resistance to Escherichia coli. Microb Biotechnol 2011; 1:191-5. [PMID: 21261836 PMCID: PMC3864452 DOI: 10.1111/j.1751-7915.2007.00010.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Concerns have been raised about potential horizontal gene transfer (HGT) of antibiotic resistance markers (ARMs) from transgenic plants to bacteria of medical and environmental importance. All ARMs used in transgenic plants have been bacterial in origin, but it has been recently shown that an Arabidopsis thaliana ABC transporter, Atwbc19, confers kanamycin resistance when overexpressed in transgenic plants. Atwbc19 was evaluated for its ability to transfer kanamycin resistance to Escherichia coli, a kanamycin‐sensitive model bacterium, under simulated HGT, staged by subcloning Atwbc19 under the control of a bacterial promoter, genetically transforming to kanamycin‐sensitive bacteria, and assessing if resistance was conferred as compared with bacteria harbouring nptII, the standard kanamycin resistance gene used to produce transgenic plants. NptII provided much greater resistance than Atwbc19 and was significantly different from the no‐plasmid control at low concentrations. Atwbc19 was not significantly different from the no‐plasmid control at higher concentrations. Even though HGT risks are considered low with nptII, Atwbc19 should have even lower risks, as its encoded protein is possibly mistargeted in bacteria.
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Affiliation(s)
- Kellie Burris
- Department of Plant Sciences, The University of Tennessee, Knoxville, 252 Ellington Plant Sciences, 2431 Joe Johnson Drive, Knoxville, TN 37996-4561, USA
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21
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Can –omics inform a food safety assessment? Regul Toxicol Pharmacol 2010; 58:S62-70. [DOI: 10.1016/j.yrtph.2010.05.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 05/20/2010] [Indexed: 02/06/2023]
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22
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23
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Application of food and feed safety assessment principles to evaluate transgenic approaches to gene modulation in crops. Food Chem Toxicol 2010; 48:1773-90. [DOI: 10.1016/j.fct.2010.04.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 04/03/2010] [Accepted: 04/12/2010] [Indexed: 11/15/2022]
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24
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Rickard C. Response to "Health risks of genetically modified foods". Crit Rev Food Sci Nutr 2010; 50:85-91; author reply 92-5. [PMID: 20047140 DOI: 10.1080/10408390903467787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Stefani FOP, Moncalvo JM, Séguin A, Bérubé JA, Hamelin RC. Impact of an 8-year-old transgenic poplar plantation on the ectomycorrhizal fungal community. Appl Environ Microbiol 2009; 75:7527-36. [PMID: 19801471 PMCID: PMC2786396 DOI: 10.1128/aem.01120-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 09/26/2009] [Indexed: 11/20/2022] Open
Abstract
The long-term impact of field-deployed genetically modified trees on soil mutualistic organisms is not well known. This study aimed at evaluating the impact of poplars transformed with a binary vector containing the selectable nptII marker and beta-glucuronidase reporter genes on ectomycorrhizal (EM) fungi 8 years after field deployment. We generated 2,229 fungal internal transcribed spacer (ITS) PCR products from 1,150 EM root tips and 1,079 fungal soil clones obtained from the organic and mineral soil horizons within the rhizosphere of three control and three transformed poplars. Fifty EM fungal operational taxonomic units were identified from the 1,706 EM fungal ITS amplicons retrieved. Rarefaction curves from both the root tips and soil clones were close to saturation, indicating that most of the EM species present were recovered. Based on qualitative and/or quantitative alpha- and beta-diversity measurements, statistical analyses did not reveal significant differences between EM fungal communities associated with transformed poplars and the untransformed controls. However, EM communities recovered from the root tips and soil cloning analyses differed significantly from each other. We found no evidence of difference in the EM fungal community structure linked to the long-term presence of the transgenic poplars studied, and we showed that coupling root tip analysis with a soil DNA cloning strategy is a complementary approach to better document EM fungal diversity.
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Affiliation(s)
- Franck O P Stefani
- Universite Laval, Faculte de Foresterie et de Geomatique, Quebec, QC G1K 7P4, Canada.
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Han L, Zhou C, Shi J, Zhi D, Xia G. Ginsenoside Rb1 in asymmetric somatic hybrid calli of Daucus carota with Panax quinquefolius. PLANT CELL REPORTS 2009; 28:627-38. [PMID: 19199101 DOI: 10.1007/s00299-009-0674-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 12/31/2008] [Accepted: 01/11/2009] [Indexed: 05/11/2023]
Abstract
American ginseng (Panax quinquefolius L.) is one of the most valuable herbs in the world. Its major active components are ginsenosides. In order to produce ginsenoside heterogeneously, somatic hybridization, a novel approach for genetic introgression, was employed in this study. Protoplasts derived from respective calli of carrot (Daucus carota var. sativus Hoffm.) and American ginseng (P. quinquefolius L.) were used as the fusion partners. Hybrid calli derived from single cell lines containing chromatin of American ginseng were confirmed by the analyses of isozyme, Random amplified polymorphic DNA (RAPD) and genomic in situ hybridization (GISH). High performance liquid chromatography (HPLC) results showed that the ginseng monomer Rb(1) was synthesized in seven of the hybrid calli identified as well as in the parent American ginseng calli but not in the parent carrot calli. Results indicated that hybrid introgression lines could produce ginsenoside Rb(1) and the ginsenoside Rb(1) biosynthesis pathway has been introgressed into carrot cells via somatic hybridization. From the point of biosafety view concerning the consumer acceptance, the potential predominance to produce ginsenosides with somatic hybridization other than with genetic transformation is discussed.
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Affiliation(s)
- Lu Han
- School of Life Sciences, Shandong University, Jinan, People's Republic of China
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27
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Foodborne antimicrobial resistance as a biological hazard - Scientific Opinion of the Panel on Biological Hazards. EFSA J 2008. [DOI: 10.2903/j.efsa.2008.765] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Kelly BG, Vespermann A, Bolton DJ. Gene transfer events and their occurrence in selected environments. Food Chem Toxicol 2008; 47:978-83. [PMID: 18639605 DOI: 10.1016/j.fct.2008.06.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 06/19/2008] [Accepted: 06/20/2008] [Indexed: 11/30/2022]
Abstract
Genes encoding virulence determinants are transferred between species in many different environments. In this review we describe gene transfer events to and from different species of bacteria, from bacteria to plants, and from plants to bacteria. Examples of the setting for these transfer events include: the GI tract, the rumen, the oral cavity, and in food matrixes. As a case study, the flux of virulence factors from E.coli O157:H7 is described as an example of gene flow in the environment.
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Affiliation(s)
- B G Kelly
- Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland.
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Abstract
Genetically modified (or GM) plants have attracted a large amount of media attention in recent years and continue to do so. Despite this, the general public remains largely unaware of what a GM plant actually is or what advantages and disadvantages the technology has to offer, particularly with regard to the range of applications for which they can be used. From the first generation of GM crops, two main areas of concern have emerged, namely risk to the environment and risk to human health. As GM plants are gradually being introduced into the European Union there is likely to be increasing public concern regarding potential health issues. Although it is now commonplace for the press to adopt 'health campaigns', the information they publish is often unreliable and unrepresentative of the available scientific evidence. We consider it important that the medical profession should be aware of the state of the art, and, as they are often the first port of call for a concerned patient, be in a position to provide an informed opinion. This review will examine how GM plants may impact on human health both directly - through applications targeted at nutrition and enhancement of recombinant medicine production - but also indirectly, through potential effects on the environment. Finally, it will examine the most important opposition currently facing the worldwide adoption of this technology: public opinion.
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Affiliation(s)
- Suzie Key
- Molecular Immunology Unit, Centre for Infection, Department of Cellular and Molecular Medicine, St George's University of London Cranmer Terrace, London SW17 0RE, UK
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Ferrini AM, Mannoni V, Pontieri E, Pourshaban M. Longer resistance of some DNA traits from BT176 maize to gastric juice from gastrointestinal affected patients. Int J Immunopathol Pharmacol 2007; 20:111-8. [PMID: 17346434 DOI: 10.1177/039463200702000113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The presence of antibiotic resistance marker genes in genetically engineered plants is one of the most controversial issues related to Genetically Modified Organism (GMO)-containing food, raising concern about the possibility that these markers could increase the pool of antibiotic resistance genes. This study investigates the in vitro survival of genes bla and cryIA(b) of maize Bt176 in human gastric juice samples. Five samples of gastric juice were collected from patients affected by gastro-esophageal reflux or celiac disease and three additional samples were obtained by pH modification with NaHCO3. DNA was extracted from maize Bt176 and incubated with samples of gastric juices at different times. The survival of the target traits (bla gene, whole 1914 bp gene cry1A(b), and its 211 bp fragment) was determined using PCR. The stability of the target genes was an inverse function of their lengths in all the samples. Survival in samples from untreated subjects was below the normal physiological time of gastric digestion. On the contrary, survival time in samples from patients under anti-acid drug treatment or in samples whose pH was modified, resulted strongly increased. Our data indicate the possibility that in particular cases the survival time could be so delayed that, as a consequence, some traits of DNA could reach the intestine. In general, this aspect must be considered for vulnerable consumers (people suffering from gastrointestinal diseases related to altered digestive functionality, physiological problems or drug side-effects) in the risk analysis usually referred to healthy subjects.
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Affiliation(s)
- A M Ferrini
- Istituto Superiore di Sanità, National Centre for Food Quality and Risk Assessment, Rome, Italy.
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Ramessar K, Peremarti A, Gómez-Galera S, Naqvi S, Moralejo M, Muñoz P, Capell T, Christou P. Biosafety and risk assessment framework for selectable marker genes in transgenic crop plants: a case of the science not supporting the politics. Transgenic Res 2007; 16:261-80. [PMID: 17436060 DOI: 10.1007/s11248-007-9083-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 02/05/2007] [Indexed: 11/25/2022]
Abstract
Selectable marker gene systems are vital for the development of transgenic crops. Since the creation of the first transgenic plants in the early 1980s and their subsequent commercialization worldwide over almost an entire decade, antibiotic and herbicide resistance selectable marker gene systems have been an integral feature of plant genetic modification. Without them, creating transgenic crops is not feasible on purely economic and practical terms. These systems allow the relatively straightforward identification and selection of plants that have stably incorporated not only the marker genes but also genes of interest, for example herbicide tolerance and pest resistance. Bacterial antibiotic resistance genes are also crucial in molecular biology manipulations in the laboratory. An unprecedented debate has accompanied the development and commercialization of transgenic crops. Divergent policies and their implementation in the European Union on one hand and the rest of the world on the other (industrialized and developing countries alike), have resulted in disputes with serious consequences on agricultural policy, world trade and food security. A lot of research effort has been directed towards the development of marker-free transformation or systems to remove selectable markers. Such research has been in a large part motivated by perceived problems with antibiotic resistance selectable markers; however, it is not justified from a safety point of view. The aim of this review is to discuss in some detail the currently available scientific evidence that overwhelmingly argues for the safety of these marker gene systems. Our conclusion, supported by numerous studies, most of which are commissioned by some of the very parties that have taken a position against the use of antibiotic selectable marker gene systems, is that there is no scientific basis to argue against the use and presence of selectable marker genes as a class in transgenic plants.
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Affiliation(s)
- Koreen Ramessar
- Departament de Produccio Vegetal i Ciencia Forestal, Universitat de Lleida, Av. Alcalde Rovira Roure, 191, Lleida 25198, Spain
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Statement on the safe use of the nptII antibiotic resistance marker gene in genetically modified plants by the Scientific Panel on genetically modified organisms (GMO). EFSA J 2007. [DOI: 10.2903/j.efsa.2007.742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Alexander TW, Reuter T, Aulrich K, Sharma R, Okine EK, Dixon WT, McAllister TA. A review of the detection and fate of novel plant molecules derived from biotechnology in livestock production. Anim Feed Sci Technol 2007. [DOI: 10.1016/j.anifeedsci.2006.08.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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