Allison Wilson - Academia.edu (original) (raw)
Papers by Allison Wilson
Rethinking Food and Agriculture, 2021
Abstract The role of genetically modified (GM) crops in supporting sustainable food systems is an... more Abstract The role of genetically modified (GM) crops in supporting sustainable food systems is an ongoing controversy. Underlying this controversy, I will argue, are radically different definitions of agricultural sustainability. One is a narrow definition, based on amelioration of current unsustainable practices, such as the use of synthetic pesticides in agriculture. The other is a broad definition, based on the long-term promotion of human and ecosystem health. To assess the sustainability impacts of GM crops, this review first provides (1) a brief summary of the sustainability impacts of herbicide-tolerant and Bacillus thuringiensis pesticidal GM crops and (2) an overview of GM plant breeding, with a focus on the problem of unintended traits (UTs) in commercial GM crops. These UTs, I argue, are a major yet underappreciated contributor to their lack of sustainability. The review asks next whether new and complex GM traits such as biofortification, or the subset of new GM techniques called gene editing, can benefit sustainable agriculture. Golden Rice provides a case study of UTs in GM crops carrying complex traits. Given the failings of Golden Rice, caused in part by UTs, a key question is whether gene editing techniques are more precise and their outcomes more predictable. To address this, the review summarizes the known unintended effects of gene editing and their potential for introducing UTs. I conclude that, despite the promise of new traits and techniques, GM crops, including gene-edited crops, are unlikely to meet either the narrow agronomic or broader social and environmental requirements of sustainable agriculture. The review ends with a discussion of how plant breeders can best support and promote sustainable agriculture, and thus help create sustainable food systems.
Genetics, Dec 1, 1994
The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones aux... more The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones auxin, ethylene, and abscisic acid. In addition, axr2-1 has pleiotropic effects on plant morphology which include gravitropic defects in roots, hypocotyls and inflorescences of axr2-1 plants. Two genetic screens were conducted to isolate new mutations at the AXR2 locus. First, axr2-1 pollen was yirradiated, crossed onto wild-type plants, and the M, progeny screened for loss of the axr2-1 phenotype. Large deletions of the axr2-1 region on chromosome 3 resulted; however, none of these deletions appeared to be heritable. In the second, M, seed obtained from axr2-1 gl-1 plantswas screened for reversion of the axr2-1 phenotype. One revertant line, axr2-r3, has a distinctive phenotype caused by a second mutation at the axr2 locus. To learn more about the nature of the axr2-1 mutation, the effects of varying the ratio of wild-type to mutant copies of the AXR2 gene were examined by comparing plants of the following genotypes: +/+, +/+/+, axr2-l/axr2-1, axr2-l/+ and a x r 2-1 / + / +. Additionally, accumulation of transcripts from the auxin-inducible SA UR-AC1 gene was examined to determine the response of wild-type and mutant plants to auxin. Wild-type seedlings and mature plants accumulate transcripts with auxin treatment. In contrast, axr2-1 tissue does not accumulate SAUR-AC1 transcripts in response to auxin. Taken together, these results indicate that axr2-1 is a neomorphic or hypermorphic mutation that disrupts an early step in an auxin response pathway.
Molecular Plant Pathology, Nov 22, 2007
In plants, viral synergisms occur when one virus enhances infection by a distinct or unrelated vi... more In plants, viral synergisms occur when one virus enhances infection by a distinct or unrelated virus. Such synergisms may be unidirectional or mutualistic but, in either case, synergism implies that protein(s) from one virus can enhance infection by another. A mechanistically related phenomenon is transcomplementation, in which a viral protein, usually expressed from a transgene, enhances or supports the infection of a virus from a distinct species. To gain an insight into the characteristics and limitations of these helper functions of individual viral genes, and to assess their effects on the plant-pathogen relationship, reports of successful synergism and transcomplementation were compiled from the peer-reviewed literature and combined with data from successful viral gene exchange experiments. Results from these experiments were tabulated to highlight the phylogenetic relationship between the helper and dependent viruses and, where possible, to identify the protein responsible for the altered infection process. The analysis of more than 150 publications, each containing one or more reports of successful exchanges, transcomplementation or synergism, revealed the following: (i) diverse viral traits can be enhanced by synergism and transcomplementation; these include the expansion of host range, acquisition of mechanical transmission, enhanced specific infectivity, enhanced cell-to-cell and long-distance movement, elevated or novel vector transmission, elevated viral titre and enhanced seed transmission; (ii) transcomplementation and synergism are mediated by many viral proteins, including inhibitors of gene silencing, replicases, coat proteins and movement proteins; (iii) although more frequent between closely related viruses, transcomplementation and synergism can occur between viruses that are phylogenetically highly divergent. As indicators of the interoperability of viral genes, these results are of general interest, but they can also be applied to the risk assessment of transgenic crops expressing viral proteins. In particular, they can contribute to the identification of potential hazards, and can be used to identify data gaps and limitations in predicting the likelihood of transgene-mediated transcomplementation.
Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes.... more Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes. It is now being used for the breeding of commercial crops. A central feature of transformation is insertion of the transgene into plant chromosomal DNA. Transgene insertion is infrequently, if ever, a precise event. Mutations found at transgene insertion sites include deletions and rearrangements of host chromosomal DNA and introduction of superfluous DNA. Insertion sites introduced using Agrobacterium tumefaciens tend to have simpler structures but can be associated with extensive chromosomal rearrangements, while those of particle bombardment appear invariably to be associated with deletion and extensive scrambling of inserted and chromosomal DNA. Ancillary procedures associated with plant transformation, including tissue culture and infection with A tumefaciens, can also introduce mutations. These genome-wide mutations can number from hundreds to many thousands per diploid genome. De...
In the course of analysis to identify potential allergens in GMO crops, the European Food Safety ... more In the course of analysis to identify potential allergens in GMO crops, the European Food Safety Authority (EFSA) has belatedly discovered that the most common genetic regulatory sequence in commercial GMOs also encodes a significant fragment of a viral gene (Podevin and du Jardin 2012) [1]. This finding has serious ramifications for crop biotechnology and its regulation, but possibly even greater ones for consumers and farmers. This is because there are clear indications that this viral gene (called Gene VI) might not be safe for human consumption. It also may disturb the normal functioning of crops, including their natural pest resistance.
Molecular and Cellular Biology, 1999
In the ciliate Tetrahymena thermophila , thousands of DNA segments of variable size are eliminate... more In the ciliate Tetrahymena thermophila , thousands of DNA segments of variable size are eliminated from the developing somatic macronucleus by specific DNA rearrangements. It is unclear whether rearrangement of the many different DNA elements occurs via a single mechanism or via multiple rearrangement systems. In this study, we characterized in vivo cis -acting sequences required for the rearrangement of the 1.1-kbp R deletion element. We found that rearrangement requires specific sequences flanking each side of the deletion element. The required sequences on the left side appear to span roughly a 70-bp region that is located at least 30 bp from the rearrangement boundary. When we moved the location of the left cis -acting sequences closer to the eliminated region, we observed a rightward shift of the rearrangement boundary such that the newly formed deletion junction retained its original distance from this flanking region. Likewise, when we moved the flanking region as much as 500...
Nature Biotechnology, 2005
To the editor: In presenting their justifications for reducing the regulatory burden on transgeni... more To the editor: In presenting their justifications for reducing the regulatory burden on transgenic food crops (Nat. Biotechnol. 23, 439-444, 2005), we feel that Strauss and colleagues significantly misrepresent the implications and rationale of our report Genome Scrambling-Myth or Reality? Transformation-Induced Mutations in Transgenic Crop Plants 1. Unlike their characterization of our work, we did not specifically "argue for rejection if even a single base pair is changed." In full, our relevant recommendations were that "transgenic lines containing genomic alterations at the site of transgene insertions be rejected" and that "the insertion of superfluous DNA be considered unacceptable." Leaving aside the fact that a single base pair change may result in serious phenotypic consequences, these recommendations are best viewed in context. As documented in the report, thorough analysis reveals that all particle bombardment transgene insertion events include extensive rearrangements or loss of host DNA as well as insertion of superfluous DNA. Furthermore, a large fraction of even apparently simple Agrobacterium tumefaciens-mediated transgene insertion events also result in large-scale host DNA rearrangement or deletion and superfluous DNA insertion 2. For example, loss of 76 kbp of host DNA 3 and duplication/ translocation of up to 40 kbp of host DNA have been reported at T-DNA insertion sites 4. Widespread use of transgenic crops carrying insertion-site mutations of this magnitude will, in our opinion, lead sooner or later to harmful consequences. Nevertheless, detailed inspection has shown that mutations such as these would almost certainly pass unnoticed through both the molecular and phenotypic characterization stages of the regulatory systems of both the European Union and the United States 5-8. We do agree with Strauss and colleagues that analysis of the phenotype is the one true measure of safety. However, rigorous assessment only at the phenotypic level is time consuming, expensive and, more importantly, of unproven effectiveness 9. In this context, our recommendations for the detection and elimination of transformation-induced mutations from commercial crop plants are conceived as a straightforward and effective way to reduce the probability of unexpected deleterious phenotypes arising in transgenic crop plants and of protecting consumers and others from an unnecessary risk.
Molecular Plant Pathology, 2007
Biotechnology and Genetic Engineering Reviews, 2006
Genetics, 1994
The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones aux... more The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones auxin, ethylene, and abscisic acid. In addition, axr2-1 has pleiotropic effects on plant morphology which include gravitropic defects in roots, hypocotyls and inflorescences of axr2-1 plants. Two genetic screens were conducted to isolate new mutations at the AXR2 locus. First, axr2-1 pollen was gamma-irradiated, crossed onto wild-type plants, and the M1 progeny screened for loss of the axr2-1 phenotype. Large deletions of the axr2-1 region on chromosome 3 resulted; however, none of these deletions appeared to be heritable. In the second, M2 seed obtained from axr2-1 gl-1 plants was screened for reversion of the axr2-1 phenotype. One revertant line, axr2-r3, has a distinctive phenotype caused by a second mutation at the axr2 locus. To learn more about the nature of the axr2-1 mutation, the effects of varying the ratio of wild-type to mutant copies of the AXR2 gene were examined by comparing ...
Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes.... more Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes. It is now being used for the breeding of commercial crops. A central feature of transformation is insertion of the transgene into plant chromosomal DNA. Transgene insertion is infrequently, if ever, a precise event. Mutations found at transgene insertion sites include deletions and rearrangements of host chromosomal DNA and introduction of superfluous DNA. Insertion sites introduced using Agrobacterium tumefaciens tend to have simpler structures but can be associated with extensive chromosomal rearrangements, while those of particle bombardment appear invariably to be associated with deletion and extensive scrambling of inserted and chromosomal DNA. Ancillary procedures associated with plant transformation, including tissue culture and infection with A tumefaciens, can also introduce mutations. These genome-wide mutations can number from hundreds to many thousands per diploid genome. De...
Recent developments in the application of RNA interference (RNAi) to plants mean that the introdu... more Recent developments in the application of RNA interference (RNAi) to plants mean that the introduction of transgenes with defined sequences can now routinely result in the inhibition of target RNAs and therefore gene activity. Consequently, there are now greatly enhanced opportunities for the use of this technology in agriculture and speciality crops. Applications demonstrated so far include the manipulation of plant metabolism and behaviour, and resistance to pathogenic bacteria, viruses, insects, and other invertebrates. Realisation of this potential, however, will ultimately depend on the specificity with which transgene-derived RNAs act. Specificity is important within the crop plant itself but also towards exposed non-target organisms such as beneficial insects and mammals. There has been little discussion of off-target effects (OTEs) arising from plant transgenic RNAi. This review considers three classes of potential plant RNAi OTEs: (1) OTEs leading to non-specific downregula...
Plant physiology, 1990
Mutagenized populations of Arabidopsis thaliana seedlings were screened for plants capable of roo... more Mutagenized populations of Arabidopsis thaliana seedlings were screened for plants capable of root growth on inhibitory concentrations of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid. Four of the mutant lines recovered from this screen display a defect in root gravitropism as well as hormone resistance. The aerial portions of these plants are similar to wildtype in appearance. Genetic analysis of these four mutants demonstrated that hormone resistance segregated as a recessive trait and that all four mutations were alleles of the auxin-resistant mutation auxl [Maher HP, Martindale SJB (1980) Biochem Genet 18: 1041-1053]. These new mutants have been designated auxl-7, 1-12, 1-15, and 1-19. The sensitivity of wild-type and auxl-7 roots to indole-3-acetic acid, 2,4-dichlorophenoxyacetic acid, and ethylene was determined. The results of these assays show that auxl-7 plants require a 12-fold (indole-3-acetic acid) or 18-fold (2,4-dichlorophenoxyacetic acid) higher concentration of auxin than wild-type for a 50% inhibition of root growth. In addition, ethylene inhibition of root growth in auxl-7 plants is approximately 30% that of wild-type at saturating ethylene concentrations. These results indicate that auxl plants are resistant to both auxin and ethylene. We have also determined the effect of ethylene treatment on chlorophyll loss and peroxidase activity in the leaves of auxl and wild-type plants. No difference between mutant and wild-type plants was observed in these experiments, indicating that hormone resistance in auxl plants may be limited to root growth. Our studies suggest that the AUX1 gene may have a specific function in the hormonal regulation of gravitropism.
Nature Biotechnology, 2005
Independent Science News, 2020
Synopsis: SARS-CoV-2, the virus responsible for the current pandemic, is in many ways an enigma t... more Synopsis: SARS-CoV-2, the virus responsible for the current pandemic, is in many ways an enigma to virologists. First, the virus enters human cells using a viral spike protein that is a tremendous fit for its human receptor (a protein called ACE2). This close fit allows the virus to spread very efficiently between people but such precision cannot plausibly have arisen by chance. Thus the virus appears to have evolved in the presence of that human receptor. Furthermore, the virus has a region on its spike protein called a furin site. This furin site allows the virus to access multiple cell types, making it able to infect and spread through lungs and other tissue types. The furin site is thus key to making SARS-CoV-2 a powerful pathogen. Since none of the closest known virus relatives of SARS-CoV-2 have a furin site, where did it come from? Third, any virus that recently jumped to humans from bats (or any other species) should undergo a period of rapid adapation to its new host. This is what happened when the coronaviruses SARS and MERS jumped to humans. Yet since the pandemic began, SARS-CoV-2 mutations have arisen but the virus has hardly evolved (in an adaptive sense) at all. Current zoonotic origin theories for SARS-CoV-2 have no satisfactory explanation for any of these evolutionary puzzles. Indeed, recent studies have made natural zoonotic origin hypotheses even less viable. For example, the Chinese CDC has ruled out Wuhan’s live market as the epidemic’s origin.
In our search for the origins of the pandemic we focussed on the nearest genetic relative of SARS-CoV-2, a bat coronavirus called RaTG13. This virus was obtained during 2012 and 2013 virus collecting trips to a mine where, shortly before, six miners had developed a mystery illness while shoveling bat feces. To learn more, we arranged the translation of a neglected Chinese Master’s thesis that documented the symptoms and hospital treatment of these miners. This thesis contains many surprises. Foremost, the miners were diagnosed as having coronavirus infections, and second, their symptoms are now recognisable as those of classic COVID-19. This and other information in the thesis caused us to rethink everything we thought we knew about the origins of the pandemic. In A Proposed Origin for SARS-CoV-2 and the COVID-19 Pandemic, we set out what we call the Mojiang Miners Passaging hypothesis. The theory proposes (1) that the miners acquired a coronavirus from the bats in the mine and (2) that this bat virus evolved extensively inside their bodies to become a highly human-adapted virus. This evolution occurred during a hospitalisation period that, for some of them, lasted many months. From the thesis we also know that blood and other samples were extracted from the miners and some of these were sent to the Wuhan Institute of Virology (WIV). We suggest that these samples contained highly human-adapted viruses and were used at the WIV for research. During this research the virus escaped, initiating the 2019 COVID-19 pandemic.
As we show, the theory solves the currently mysterious evolutionary and biological features of SARS-CoV-2 as well as explaining its eventual appearance in Wuhan. It also explains subsequent attempts to obscure the deaths of the miners and the Mojiang mine origin of RATG13.
Read the full story at: https://www.independentsciencenews.org/commentaries/a-proposed-origin-for-sars-cov-2-and-the-covid-19-pandemic/
Independent Science News, 2020
Synopsis: The view that COVID-19 (Sars-CoV-2) has a potential laboratory origin is being attribut... more Synopsis: The view that COVID-19 (Sars-CoV-2) has a potential laboratory origin is being attributed to President Trump. But plenty of scientists are raising this issue too. What are the chances, after all, that the epicentre of the COVID-19 outbreak should occur within literal walking distance of the leading research and collection centre in the world for SARS-like bat coronaviruses? Much additional data points in the direction of a lab escape of the kind that some researchers have long warned of. On the other hand, new information has made the zoonotic origin thesis less likely. This article explains the specific lab accident scenarios and describes how the kind of research conducted at the WIV makes a lab accident a strong possibility.
To read the full article go to: https://www.independentsciencenews.org/health/the-case-is-building-that-covid-19-had-a-lab-origin/
Rethinking Food and Agriculture, 2021
Abstract The role of genetically modified (GM) crops in supporting sustainable food systems is an... more Abstract The role of genetically modified (GM) crops in supporting sustainable food systems is an ongoing controversy. Underlying this controversy, I will argue, are radically different definitions of agricultural sustainability. One is a narrow definition, based on amelioration of current unsustainable practices, such as the use of synthetic pesticides in agriculture. The other is a broad definition, based on the long-term promotion of human and ecosystem health. To assess the sustainability impacts of GM crops, this review first provides (1) a brief summary of the sustainability impacts of herbicide-tolerant and Bacillus thuringiensis pesticidal GM crops and (2) an overview of GM plant breeding, with a focus on the problem of unintended traits (UTs) in commercial GM crops. These UTs, I argue, are a major yet underappreciated contributor to their lack of sustainability. The review asks next whether new and complex GM traits such as biofortification, or the subset of new GM techniques called gene editing, can benefit sustainable agriculture. Golden Rice provides a case study of UTs in GM crops carrying complex traits. Given the failings of Golden Rice, caused in part by UTs, a key question is whether gene editing techniques are more precise and their outcomes more predictable. To address this, the review summarizes the known unintended effects of gene editing and their potential for introducing UTs. I conclude that, despite the promise of new traits and techniques, GM crops, including gene-edited crops, are unlikely to meet either the narrow agronomic or broader social and environmental requirements of sustainable agriculture. The review ends with a discussion of how plant breeders can best support and promote sustainable agriculture, and thus help create sustainable food systems.
Genetics, Dec 1, 1994
The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones aux... more The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones auxin, ethylene, and abscisic acid. In addition, axr2-1 has pleiotropic effects on plant morphology which include gravitropic defects in roots, hypocotyls and inflorescences of axr2-1 plants. Two genetic screens were conducted to isolate new mutations at the AXR2 locus. First, axr2-1 pollen was yirradiated, crossed onto wild-type plants, and the M, progeny screened for loss of the axr2-1 phenotype. Large deletions of the axr2-1 region on chromosome 3 resulted; however, none of these deletions appeared to be heritable. In the second, M, seed obtained from axr2-1 gl-1 plantswas screened for reversion of the axr2-1 phenotype. One revertant line, axr2-r3, has a distinctive phenotype caused by a second mutation at the axr2 locus. To learn more about the nature of the axr2-1 mutation, the effects of varying the ratio of wild-type to mutant copies of the AXR2 gene were examined by comparing plants of the following genotypes: +/+, +/+/+, axr2-l/axr2-1, axr2-l/+ and a x r 2-1 / + / +. Additionally, accumulation of transcripts from the auxin-inducible SA UR-AC1 gene was examined to determine the response of wild-type and mutant plants to auxin. Wild-type seedlings and mature plants accumulate transcripts with auxin treatment. In contrast, axr2-1 tissue does not accumulate SAUR-AC1 transcripts in response to auxin. Taken together, these results indicate that axr2-1 is a neomorphic or hypermorphic mutation that disrupts an early step in an auxin response pathway.
Molecular Plant Pathology, Nov 22, 2007
In plants, viral synergisms occur when one virus enhances infection by a distinct or unrelated vi... more In plants, viral synergisms occur when one virus enhances infection by a distinct or unrelated virus. Such synergisms may be unidirectional or mutualistic but, in either case, synergism implies that protein(s) from one virus can enhance infection by another. A mechanistically related phenomenon is transcomplementation, in which a viral protein, usually expressed from a transgene, enhances or supports the infection of a virus from a distinct species. To gain an insight into the characteristics and limitations of these helper functions of individual viral genes, and to assess their effects on the plant-pathogen relationship, reports of successful synergism and transcomplementation were compiled from the peer-reviewed literature and combined with data from successful viral gene exchange experiments. Results from these experiments were tabulated to highlight the phylogenetic relationship between the helper and dependent viruses and, where possible, to identify the protein responsible for the altered infection process. The analysis of more than 150 publications, each containing one or more reports of successful exchanges, transcomplementation or synergism, revealed the following: (i) diverse viral traits can be enhanced by synergism and transcomplementation; these include the expansion of host range, acquisition of mechanical transmission, enhanced specific infectivity, enhanced cell-to-cell and long-distance movement, elevated or novel vector transmission, elevated viral titre and enhanced seed transmission; (ii) transcomplementation and synergism are mediated by many viral proteins, including inhibitors of gene silencing, replicases, coat proteins and movement proteins; (iii) although more frequent between closely related viruses, transcomplementation and synergism can occur between viruses that are phylogenetically highly divergent. As indicators of the interoperability of viral genes, these results are of general interest, but they can also be applied to the risk assessment of transgenic crops expressing viral proteins. In particular, they can contribute to the identification of potential hazards, and can be used to identify data gaps and limitations in predicting the likelihood of transgene-mediated transcomplementation.
Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes.... more Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes. It is now being used for the breeding of commercial crops. A central feature of transformation is insertion of the transgene into plant chromosomal DNA. Transgene insertion is infrequently, if ever, a precise event. Mutations found at transgene insertion sites include deletions and rearrangements of host chromosomal DNA and introduction of superfluous DNA. Insertion sites introduced using Agrobacterium tumefaciens tend to have simpler structures but can be associated with extensive chromosomal rearrangements, while those of particle bombardment appear invariably to be associated with deletion and extensive scrambling of inserted and chromosomal DNA. Ancillary procedures associated with plant transformation, including tissue culture and infection with A tumefaciens, can also introduce mutations. These genome-wide mutations can number from hundreds to many thousands per diploid genome. De...
In the course of analysis to identify potential allergens in GMO crops, the European Food Safety ... more In the course of analysis to identify potential allergens in GMO crops, the European Food Safety Authority (EFSA) has belatedly discovered that the most common genetic regulatory sequence in commercial GMOs also encodes a significant fragment of a viral gene (Podevin and du Jardin 2012) [1]. This finding has serious ramifications for crop biotechnology and its regulation, but possibly even greater ones for consumers and farmers. This is because there are clear indications that this viral gene (called Gene VI) might not be safe for human consumption. It also may disturb the normal functioning of crops, including their natural pest resistance.
Molecular and Cellular Biology, 1999
In the ciliate Tetrahymena thermophila , thousands of DNA segments of variable size are eliminate... more In the ciliate Tetrahymena thermophila , thousands of DNA segments of variable size are eliminated from the developing somatic macronucleus by specific DNA rearrangements. It is unclear whether rearrangement of the many different DNA elements occurs via a single mechanism or via multiple rearrangement systems. In this study, we characterized in vivo cis -acting sequences required for the rearrangement of the 1.1-kbp R deletion element. We found that rearrangement requires specific sequences flanking each side of the deletion element. The required sequences on the left side appear to span roughly a 70-bp region that is located at least 30 bp from the rearrangement boundary. When we moved the location of the left cis -acting sequences closer to the eliminated region, we observed a rightward shift of the rearrangement boundary such that the newly formed deletion junction retained its original distance from this flanking region. Likewise, when we moved the flanking region as much as 500...
Nature Biotechnology, 2005
To the editor: In presenting their justifications for reducing the regulatory burden on transgeni... more To the editor: In presenting their justifications for reducing the regulatory burden on transgenic food crops (Nat. Biotechnol. 23, 439-444, 2005), we feel that Strauss and colleagues significantly misrepresent the implications and rationale of our report Genome Scrambling-Myth or Reality? Transformation-Induced Mutations in Transgenic Crop Plants 1. Unlike their characterization of our work, we did not specifically "argue for rejection if even a single base pair is changed." In full, our relevant recommendations were that "transgenic lines containing genomic alterations at the site of transgene insertions be rejected" and that "the insertion of superfluous DNA be considered unacceptable." Leaving aside the fact that a single base pair change may result in serious phenotypic consequences, these recommendations are best viewed in context. As documented in the report, thorough analysis reveals that all particle bombardment transgene insertion events include extensive rearrangements or loss of host DNA as well as insertion of superfluous DNA. Furthermore, a large fraction of even apparently simple Agrobacterium tumefaciens-mediated transgene insertion events also result in large-scale host DNA rearrangement or deletion and superfluous DNA insertion 2. For example, loss of 76 kbp of host DNA 3 and duplication/ translocation of up to 40 kbp of host DNA have been reported at T-DNA insertion sites 4. Widespread use of transgenic crops carrying insertion-site mutations of this magnitude will, in our opinion, lead sooner or later to harmful consequences. Nevertheless, detailed inspection has shown that mutations such as these would almost certainly pass unnoticed through both the molecular and phenotypic characterization stages of the regulatory systems of both the European Union and the United States 5-8. We do agree with Strauss and colleagues that analysis of the phenotype is the one true measure of safety. However, rigorous assessment only at the phenotypic level is time consuming, expensive and, more importantly, of unproven effectiveness 9. In this context, our recommendations for the detection and elimination of transformation-induced mutations from commercial crop plants are conceived as a straightforward and effective way to reduce the probability of unexpected deleterious phenotypes arising in transgenic crop plants and of protecting consumers and others from an unnecessary risk.
Molecular Plant Pathology, 2007
Biotechnology and Genetic Engineering Reviews, 2006
Genetics, 1994
The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones aux... more The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones auxin, ethylene, and abscisic acid. In addition, axr2-1 has pleiotropic effects on plant morphology which include gravitropic defects in roots, hypocotyls and inflorescences of axr2-1 plants. Two genetic screens were conducted to isolate new mutations at the AXR2 locus. First, axr2-1 pollen was gamma-irradiated, crossed onto wild-type plants, and the M1 progeny screened for loss of the axr2-1 phenotype. Large deletions of the axr2-1 region on chromosome 3 resulted; however, none of these deletions appeared to be heritable. In the second, M2 seed obtained from axr2-1 gl-1 plants was screened for reversion of the axr2-1 phenotype. One revertant line, axr2-r3, has a distinctive phenotype caused by a second mutation at the axr2 locus. To learn more about the nature of the axr2-1 mutation, the effects of varying the ratio of wild-type to mutant copies of the AXR2 gene were examined by comparing ...
Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes.... more Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes. It is now being used for the breeding of commercial crops. A central feature of transformation is insertion of the transgene into plant chromosomal DNA. Transgene insertion is infrequently, if ever, a precise event. Mutations found at transgene insertion sites include deletions and rearrangements of host chromosomal DNA and introduction of superfluous DNA. Insertion sites introduced using Agrobacterium tumefaciens tend to have simpler structures but can be associated with extensive chromosomal rearrangements, while those of particle bombardment appear invariably to be associated with deletion and extensive scrambling of inserted and chromosomal DNA. Ancillary procedures associated with plant transformation, including tissue culture and infection with A tumefaciens, can also introduce mutations. These genome-wide mutations can number from hundreds to many thousands per diploid genome. De...
Recent developments in the application of RNA interference (RNAi) to plants mean that the introdu... more Recent developments in the application of RNA interference (RNAi) to plants mean that the introduction of transgenes with defined sequences can now routinely result in the inhibition of target RNAs and therefore gene activity. Consequently, there are now greatly enhanced opportunities for the use of this technology in agriculture and speciality crops. Applications demonstrated so far include the manipulation of plant metabolism and behaviour, and resistance to pathogenic bacteria, viruses, insects, and other invertebrates. Realisation of this potential, however, will ultimately depend on the specificity with which transgene-derived RNAs act. Specificity is important within the crop plant itself but also towards exposed non-target organisms such as beneficial insects and mammals. There has been little discussion of off-target effects (OTEs) arising from plant transgenic RNAi. This review considers three classes of potential plant RNAi OTEs: (1) OTEs leading to non-specific downregula...
Plant physiology, 1990
Mutagenized populations of Arabidopsis thaliana seedlings were screened for plants capable of roo... more Mutagenized populations of Arabidopsis thaliana seedlings were screened for plants capable of root growth on inhibitory concentrations of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid. Four of the mutant lines recovered from this screen display a defect in root gravitropism as well as hormone resistance. The aerial portions of these plants are similar to wildtype in appearance. Genetic analysis of these four mutants demonstrated that hormone resistance segregated as a recessive trait and that all four mutations were alleles of the auxin-resistant mutation auxl [Maher HP, Martindale SJB (1980) Biochem Genet 18: 1041-1053]. These new mutants have been designated auxl-7, 1-12, 1-15, and 1-19. The sensitivity of wild-type and auxl-7 roots to indole-3-acetic acid, 2,4-dichlorophenoxyacetic acid, and ethylene was determined. The results of these assays show that auxl-7 plants require a 12-fold (indole-3-acetic acid) or 18-fold (2,4-dichlorophenoxyacetic acid) higher concentration of auxin than wild-type for a 50% inhibition of root growth. In addition, ethylene inhibition of root growth in auxl-7 plants is approximately 30% that of wild-type at saturating ethylene concentrations. These results indicate that auxl plants are resistant to both auxin and ethylene. We have also determined the effect of ethylene treatment on chlorophyll loss and peroxidase activity in the leaves of auxl and wild-type plants. No difference between mutant and wild-type plants was observed in these experiments, indicating that hormone resistance in auxl plants may be limited to root growth. Our studies suggest that the AUX1 gene may have a specific function in the hormonal regulation of gravitropism.
Nature Biotechnology, 2005
Independent Science News, 2020
Synopsis: SARS-CoV-2, the virus responsible for the current pandemic, is in many ways an enigma t... more Synopsis: SARS-CoV-2, the virus responsible for the current pandemic, is in many ways an enigma to virologists. First, the virus enters human cells using a viral spike protein that is a tremendous fit for its human receptor (a protein called ACE2). This close fit allows the virus to spread very efficiently between people but such precision cannot plausibly have arisen by chance. Thus the virus appears to have evolved in the presence of that human receptor. Furthermore, the virus has a region on its spike protein called a furin site. This furin site allows the virus to access multiple cell types, making it able to infect and spread through lungs and other tissue types. The furin site is thus key to making SARS-CoV-2 a powerful pathogen. Since none of the closest known virus relatives of SARS-CoV-2 have a furin site, where did it come from? Third, any virus that recently jumped to humans from bats (or any other species) should undergo a period of rapid adapation to its new host. This is what happened when the coronaviruses SARS and MERS jumped to humans. Yet since the pandemic began, SARS-CoV-2 mutations have arisen but the virus has hardly evolved (in an adaptive sense) at all. Current zoonotic origin theories for SARS-CoV-2 have no satisfactory explanation for any of these evolutionary puzzles. Indeed, recent studies have made natural zoonotic origin hypotheses even less viable. For example, the Chinese CDC has ruled out Wuhan’s live market as the epidemic’s origin.
In our search for the origins of the pandemic we focussed on the nearest genetic relative of SARS-CoV-2, a bat coronavirus called RaTG13. This virus was obtained during 2012 and 2013 virus collecting trips to a mine where, shortly before, six miners had developed a mystery illness while shoveling bat feces. To learn more, we arranged the translation of a neglected Chinese Master’s thesis that documented the symptoms and hospital treatment of these miners. This thesis contains many surprises. Foremost, the miners were diagnosed as having coronavirus infections, and second, their symptoms are now recognisable as those of classic COVID-19. This and other information in the thesis caused us to rethink everything we thought we knew about the origins of the pandemic. In A Proposed Origin for SARS-CoV-2 and the COVID-19 Pandemic, we set out what we call the Mojiang Miners Passaging hypothesis. The theory proposes (1) that the miners acquired a coronavirus from the bats in the mine and (2) that this bat virus evolved extensively inside their bodies to become a highly human-adapted virus. This evolution occurred during a hospitalisation period that, for some of them, lasted many months. From the thesis we also know that blood and other samples were extracted from the miners and some of these were sent to the Wuhan Institute of Virology (WIV). We suggest that these samples contained highly human-adapted viruses and were used at the WIV for research. During this research the virus escaped, initiating the 2019 COVID-19 pandemic.
As we show, the theory solves the currently mysterious evolutionary and biological features of SARS-CoV-2 as well as explaining its eventual appearance in Wuhan. It also explains subsequent attempts to obscure the deaths of the miners and the Mojiang mine origin of RATG13.
Read the full story at: https://www.independentsciencenews.org/commentaries/a-proposed-origin-for-sars-cov-2-and-the-covid-19-pandemic/
Independent Science News, 2020
Synopsis: The view that COVID-19 (Sars-CoV-2) has a potential laboratory origin is being attribut... more Synopsis: The view that COVID-19 (Sars-CoV-2) has a potential laboratory origin is being attributed to President Trump. But plenty of scientists are raising this issue too. What are the chances, after all, that the epicentre of the COVID-19 outbreak should occur within literal walking distance of the leading research and collection centre in the world for SARS-like bat coronaviruses? Much additional data points in the direction of a lab escape of the kind that some researchers have long warned of. On the other hand, new information has made the zoonotic origin thesis less likely. This article explains the specific lab accident scenarios and describes how the kind of research conducted at the WIV makes a lab accident a strong possibility.
To read the full article go to: https://www.independentsciencenews.org/health/the-case-is-building-that-covid-19-had-a-lab-origin/