The Experts below are selected from a list of 43992 Experts worldwide ranked by ideXlab platform
Christian Schroeder Kaas - One of the best experts on this subject based on the ideXlab platform.
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a crispr cas9 based Gene Drive platform for Genetic interaction analysis in candida albicans
Nature microbiology, 2018Co-Authors: Rebecca S Shapiro, Alejandro Chavez, Caroline B M Porter, Meagan Hamblin, Christian Schroeder KaasAbstract:Candida albicans is the leading cause of fungal infections; yet, complex Genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR–Cas9-based ‘Gene Drive array’ platform to facilitate efficient Genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish Genetic element, replaces the targeted site and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different Gene Drive disabling a Gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants. We Generate double-Gene deletion libraries to demonstrate this technology, targeting antifungal efflux and biofilm adhesion factors. We screen these libraries to identify virulence regulators and determine how Genetic networks shift under diverse conditions. This platform transforms our ability to perform Genetic interaction analysis in C. albicans and is readily extended to other fungal pathogens. A CRISPR–Cas9-based Gene Drive array platform is developed and combined with mating-competent Candida albicans haploids to Generate homozygous double-deletion mutants, transforming our ability to do Genetic interaction analyses in fungi.
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a crispr cas9 based Gene Drive platform for Genetic interaction analysis in candida albicans
Nature microbiology, 2018Co-Authors: Rebecca S Shapiro, Alejandro Chavez, Caroline B M Porter, Meagan Hamblin, Christian Schroeder KaasAbstract:Candida albicans is the leading cause of fungal infections; yet, complex Genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR-Cas9-based 'Gene Drive array' platform to facilitate efficient Genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish Genetic element, replaces the targeted site and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different Gene Drive disabling a Gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants. We Generate double-Gene deletion libraries to demonstrate this technology, targeting antifungal efflux and biofilm adhesion factors. We screen these libraries to identify virulence regulators and determine how Genetic networks shift under diverse conditions. This platform transforms our ability to perform Genetic interaction analysis in C. albicans and is readily extended to other fungal pathogens.
Philipp W Messer - One of the best experts on this subject based on the ideXlab platform.
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performance analysis of novel toxin antidote crispr Gene Drive systems
BMC Biology, 2020Co-Authors: Jackson Champer, Andrew G Clark, Isabel Kim, Samuel E Champer, Philipp W MesserAbstract:CRISPR Gene Drive systems allow the rapid spread of a Genetic construct throughout a population. Such systems promise novel strategies for the management of vector-borne diseases and invasive species by suppressing a target population or modifying it with a desired trait. However, current homing-type Drives have two potential shortcomings. First, they can be thwarted by the rapid evolution of resistance. Second, they lack any mechanism for confinement to a specific target population. In this study, we conduct a comprehensive performance assessment of several new types of CRISPR-based Gene Drive systems employing toxin-antidote (TA) principles, which should be less prone to resistance and allow for the confinement of Drives to a target population due to invasion frequency thresholds. The underlying principle of the proposed CRISPR toxin-antidote Gene Drives is to disrupt an essential target Gene while also providing rescue by a recoded version of the target as part of the Drive allele. Thus, Drive alleles tend to remain viable, while wild-type targets are disrupted and often rendered nonviable, thereby increasing the relative frequency of the Drive allele. Using individual-based simulations, we show that Toxin-Antidote Recessive Embryo (TARE) Drives targeting an haplosufficient but essential Gene (lethal when both copies are disrupted) can enable the design of robust, regionally confined population modification strategies with high flexibility in choosing promoters and targets. Toxin-Antidote Dominant Embryo (TADE) Drives require a haplolethal target Gene and a germline-restricted promoter, but they could permit faster regional population modification and even regionally confined population suppression. Toxin-Antidote Dominant Sperm (TADS) Drives can be used for population modification or suppression. These Drives are expected to spread rapidly and could employ a variety of promoters, but unlike TARE and TADE, they would not be regionally confined and also require highly specific target Genes. Overall, our results suggest that CRISPR-based TA Gene Drives provide promising candidates for flexible ecological engineering strategies in a variety of organisms.
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suppression Gene Drive in continuous space can result in unstable persistence of both Drive and wild type alleles
bioRxiv, 2019Co-Authors: Jackson Champer, Andrew G Clark, Isabel Kim, Samuel E Champer, Philipp W MesserAbstract:ABSTRACT Rapid evolutionary processes can produce drastically different outcomes when studied in panmictic population models versus spatial models where the rate of evolution is limited by dispersal. One such process is Gene Drive, which allows “selfish” Genetic elements to quickly spread through a population. Engineered Gene Drive systems are being considered as a means for suppressing disease vector populations or invasive species. While laboratory experiments and modeling in panmictic populations have shown that such Drives can rapidly eliminate a population, it is not yet clear how well these results translate to natural environments where individuals inhabit a continuous landscape. Using spatially explicit simulations, we show that instead of population elimination, release of a suppression Drive can result in what we term “chasing” dynamics. This describes a condition in which wild-type individuals quickly recolonize areas where the Drive has locally eliminated the population. Despite the Drive subsequently chasing the wild-type allele into these newly re-colonized areas, complete population suppression often fails or is substantially delayed. This delay increases the likelihood that the Drive becomes lost or that resistance evolves. We systematically analyze how chasing dynamics are influenced by the type of Drive, its efficiency, fitness costs, as well as ecological and demographic factors such as the maximal growth rate of the population, the migration rate, and the level of inbreeding. We find that chasing is Generally more common for lower efficiency Drives and in populations with low dispersal. However, we further find that some Drive mechanisms are substantially more prone to chasing behavior than others. Our results demonstrate that the population dynamics of suppression Gene Drives are determined by a complex interplay of Genetic and ecological factors, highlighting the need for realistic spatial modeling to predict the outcome of Drive releases in natural populations.
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resistance is futile a crispr homing Gene Drive targeting a haplolethal Gene
bioRxiv, 2019Co-Authors: Jackson Champer, Yoo Lim Lee, Emily Yang, Andrew G Clark, Jingxian Liu, Philipp W MesserAbstract:ABSTRACT Engineered Gene Drives are being explored as a potential strategy for the control of vector-borne diseases due to their ability to rapidly spread Genetic modifications through a population. While an effective CRISPR homing Gene Drive for population suppression has recently been demonstrated in mosquitoes, formation of resistance alleles that prevent Cas9 cleavage remains the major obstacle for Drive strategies aiming at population modification, rather than elimination. Here, we present a homing Drive in Drosophila melanogaster that reduces resistance allele formation below detectable levels by targeting a haplolethal Gene with two gRNAs while also providing a rescue allele. This is because any resistance alleles that form by end-joining repair will typically disrupt the haplolethal target Gene, rendering the individuals carrying them nonviable. We demonstrate that our Drive is highly efficient, with 91% of the progeny of Drive heterozygotes inheriting the Drive allele and with no resistance alleles observed in the remainder. In a large cage experiment, the Drive allele successfully spread to all individuals. These results show that a haplolethal homing Drive can be a highly effective tool for population modification.
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performance analysis of novel toxin antidote crispr Gene Drive systems
bioRxiv, 2019Co-Authors: Jackson Champer, Andrew G Clark, Isabel Kim, Samuel E Champer, Philipp W MesserAbstract:ABSTRACT Gene Drives can potentially fixate in a population by biasing inheritance in their favor, opening up a variety of potential applications in areas such as disease-vector control and conservation. CRISPR homing Gene Drives have shown much promise for providing an effective Drive mechanism, but they typically suffer from the rapid formation of resistance alleles. Even if the problem of resistance can be overcome, the utility of such Drives would still be limited by their tendency to spread into all areas of a population. To provide additional options for Gene Drive applications that are substantially less prone to the formation of resistance alleles and could potentially remain confined to a target area, we developed several designs for CRISPR-based Gene Drives utilizing toxin-antidote (TA) principles. These Drives target and disrupt an essential Gene with the Drive providing rescue. Here, we assess the performance of several types of TA Gene Drive systems using modeling and individual-based simulations. We show that Toxin-Antidote Recessive Embryo (TARE) Drive should allow for the design of robust, regionally confined, population modification strategies with high flexibility in choosing Drive promoters and recessive lethal targets. Toxin-Antidote Dominant Embryo (TADE) Drive requires a haplolethal target Gene and a germline-restricted promoter but should enable the design of both faster regional population modification Drives and even regionally-confined population suppression Drives. Toxin-antidote dominant sperm (TADS) Drive can be used for population modification or suppression. It spreads nearly as quickly as a homing Drive and can flexibly use a variety of promoters, but unlike the other TA systems, it is not regionally confined and requires highly specific target Genes. Overall, our results suggest that CRISPR-based TA Gene Drives provide promising candidates for further development in a variety of organisms and may allow for flexible ecological engineering strategies.
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a toxin antidote crispr Gene Drive system for regional population modification
bioRxiv, 2019Co-Authors: Jackson Champer, Yoo Lim Lee, Chen Liu, Emily Yang, Andrew G Clark, Philipp W MesserAbstract:ABSTRACT Engineered Gene Drives have been suggested as a mechanism for rapidly spreading Genetic alterations through a population. One promising type of Drive is the CRISPR homing Drive, which has recently been demonstrated in several organisms. However, such Drives face a major obstacle in the form of resistance against the Drive that typically evolves rapidly. In addition, homing-type Drives are Generally self-sustaining, meaning that a Drive would likely spread to all individuals of a species even when introduced at low frequency in a single location. Here, we develop a new form of CRISPR Gene Drive, the Toxin-Antidote Recessive Embryo (TARE) Drive, which successfully limits resistance by targeting a recessive lethal Gene while providing a recoded sequence to rescue only Drive-carrying individuals. Our computational modeling shows that such a Drive will have threshold-dependent dynamics, spreading only when introduced above a frequency threshold that depends on the fitness cost of the Drive. We demonstrate such a Drive in Drosophila with 88-95% transmission to the progeny of female Drive heterozygotes. This Drive was able to spread through a large cage population in just six Generations following introduction at 24% frequency without any apparent evolution of resistance. Our results suggest that TARE Drives constitute promising candidates for the development of effective, regionally confined population modification Drives.
Omar S Akbari - One of the best experts on this subject based on the ideXlab platform.
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opinion standardizing the definition of Gene Drive
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: Luke Alphey, Andrea Crisanti, Filippo Fil Randazzo, Omar S AkbariAbstract:Gene Drive has become a hot topic in the popular press and the scientific literature, yet little consensus vocabulary on the subject exists. As members of the Gene Drive community, we have developed a core set of definitions to help stakeholders discuss the topic and communicate using a common understanding of terms. A standard consensus definition of Gene Drive and a glossary of terms, noted here, will be of great practical use to a field that has implications for both researchers and the General public. If we don’t clarify these terms, we risk hampering the field, confusing the public, and possibly losing a technology that may help solve some of the world’s most intractable problems in public health, conservation, and food security. We need to clarify Gene Drive terms, or we risk hampering the field, confusing the public, and losing a technology that may help solve otherwise intractable problems in public health, conservation, and food security. Image credit: Stephanie Gamez (University of California San Diego, La Jolla, CA). Loosely, Gene Drive refers to a phenomenon whereby a particular heritable element biases inheritance in its favor, resulting in the Gene becoming more prevalent in the population over successive Generations. Thus, the Gene is being “Driven” to progressively increase its frequency in the population. Biasing inheritance may involve, for example, more than the familiar Mendelian 50:50 inheritance chance or reducing the fitness of alternative genotypes without directly distorting Mendelian inheritance. Highly efficient Gene Drives can bias inheritance so heavily in their favor that the heritable element can rapidly reach high frequency, close to doubling its frequency from one Generation to the next. The speed of this process is inversely correlated with Generation time of the organism (for example, mosquitos have a Generation time of 2–4 weeks and rats have a Generation time … [↵][1]1To whom correspondence may be addressed. Email: oakbari{at}ucsd.edu. [1]: #xref-corresp-1-1
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synthetically engineered medea Gene Drive system in the worldwide crop pest drosophila suzukii
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: John M Marshall, Anna Buchman, Dennis Ostrovski, Ting Yang, Omar S AkbariAbstract:Synthetic Gene Drive systems possess enormous potential to replace, alter, or suppress wild populations of significant disease vectors and crop pests; however, their utility in diverse populations remains to be demonstrated. Here, we report the creation of a synthetic Medea Gene Drive system in a major worldwide crop pest, Drosophila suzukii . We demonstrate that this Drive system, based on an engineered maternal “toxin” coupled with a linked embryonic “antidote,” is capable of biasing Mendelian inheritance rates with up to 100% efficiency. However, we find that Drive resistance, resulting from naturally occurring Genetic variation and associated fitness costs, can be selected for and hinder the spread of such a Drive. Despite this, our results suggest that this Gene Drive could maintain itself at high frequencies in a wild population and spread to fixation if either its fitness costs or toxin resistance were reduced, providing a clear path forward for developing future such systems in this pest.
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can crispr based Gene Drive be confined in the wild a question for molecular and population biology
ACS Chemical Biology, 2018Co-Authors: John M Marshall, Omar S AkbariAbstract:The recent discovery of CRISPR and its application as a Gene editing tool has enabled a range of Gene Drive systems to be engineered with greater ease. In order for the benefits of this technology to be realized, in some circumstances Drive systems should be developed that are capable of both spreading into populations to achieve their desired impact and being recalled in the event of unwanted consequences or public disfavor. We review the performance of three broad categories of Drive systems at achieving these goals: threshold-dependent Drives, homing-based Drive and remediation systems, and temporally self-limiting systems such as daisy-chain Drives.
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can crispr based Gene Drive be confined in the wild a question for molecular and population biology
bioRxiv, 2017Co-Authors: John M Marshall, Omar S AkbariAbstract:The recent discovery of CRISPR and its application as a Gene editing tool has enabled a range of Gene Drive systems to be engineered with much greater ease. In order for the benefits of this technology to be realized, Drive systems must be developed that are capable of both spreading into populations to achieve their desired impact, and being recalled in the event of unwanted consequences or public disfavor. We review the performance of three broad categories of Drive systems at achieving these goals — threshold-dependent Drives, homing-based Drive and remediation systems, and temporally self-limiting systems such as daisy-chain Drives.
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rules of the road for insect Gene Drive research and testing
Nature Biotechnology, 2017Co-Authors: Zach N Adelman, Omar S Akbari, Ethan Bier, John Bauer, Cinnamon S Bloss, Sarah R Carter, Craig Callender, Adriana Costerosaint Denis, Peter F Cowhey, Brinda DassAbstract:Approximately two years ago, two of us (E.B. and V.G.) demonstrated the first experimental application of CRISPR–Cas9 to 'Drive' a desired trait throughout a population of fruit flies. In November 2015, this same team at the University of California, San Diego, joined with A.A.J. and others at the University of California, Irvine, to develop a CRISPR-based Gene Drive for population modification of the malaria vector mosquito Anopheles stephensi. A month later, a group in the United Kingdom applied a CRISPR-based Gene Drive to another malaria vector, Anopheles gambiae.
Rebecca S Shapiro - One of the best experts on this subject based on the ideXlab platform.
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a crispr cas9 based Gene Drive platform for Genetic interaction analysis in candida albicans
Nature microbiology, 2018Co-Authors: Rebecca S Shapiro, Alejandro Chavez, Caroline B M Porter, Meagan Hamblin, Christian Schroeder KaasAbstract:Candida albicans is the leading cause of fungal infections; yet, complex Genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR–Cas9-based ‘Gene Drive array’ platform to facilitate efficient Genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish Genetic element, replaces the targeted site and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different Gene Drive disabling a Gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants. We Generate double-Gene deletion libraries to demonstrate this technology, targeting antifungal efflux and biofilm adhesion factors. We screen these libraries to identify virulence regulators and determine how Genetic networks shift under diverse conditions. This platform transforms our ability to perform Genetic interaction analysis in C. albicans and is readily extended to other fungal pathogens. A CRISPR–Cas9-based Gene Drive array platform is developed and combined with mating-competent Candida albicans haploids to Generate homozygous double-deletion mutants, transforming our ability to do Genetic interaction analyses in fungi.
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a crispr cas9 based Gene Drive platform for Genetic interaction analysis in candida albicans
Nature microbiology, 2018Co-Authors: Rebecca S Shapiro, Alejandro Chavez, Caroline B M Porter, Meagan Hamblin, Christian Schroeder KaasAbstract:Candida albicans is the leading cause of fungal infections; yet, complex Genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR-Cas9-based 'Gene Drive array' platform to facilitate efficient Genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish Genetic element, replaces the targeted site and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different Gene Drive disabling a Gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants. We Generate double-Gene deletion libraries to demonstrate this technology, targeting antifungal efflux and biofilm adhesion factors. We screen these libraries to identify virulence regulators and determine how Genetic networks shift under diverse conditions. This platform transforms our ability to perform Genetic interaction analysis in C. albicans and is readily extended to other fungal pathogens.
John M Marshall - One of the best experts on this subject based on the ideXlab platform.
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toward the definition of efficacy and safety criteria for advancing Gene Drive modified mosquitoes to field testing
Vector-borne and Zoonotic Diseases, 2020Co-Authors: Stephanie L James, John M Marshall, George K Christophides, Fredros O Okumu, Tony NolanAbstract:Mosquitoes containing Gene Drive systems are being developed as complementary tools to prevent transmission of malaria and other mosquito-borne diseases. As with any new tool, decision makers and other stakeholders will need to balance risks (safety) and benefits (efficacy) when considering the rationale for testing and deploying Gene Drive-modified mosquito products. Developers will benefit from standards for judging whether an investigational Gene Drive product meets acceptability criteria for advancing to field trials. Such standards may be formalized as preferred product characteristics and target product profiles, which describe the desired attributes of the product category and of a particular product, respectively. This report summarizes discussions from two scientific workshops aimed at identifying efficacy and safety characteristics that must be minimally met for an investigational Gene Drive-modified mosquito product to be deemed viable to move from contained testing to field release and the data that will be needed to support an application for first field release.
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a transcomplementing Gene Drive provides a flexible platform for laboratory investigation and potential field deployment
Nature Communications, 2020Co-Authors: Alena L Bishop, John M Marshall, Hector Sanchez M C, Jared B Bennett, Xuechun Feng, Ethan Bier, Valentino M GantzAbstract:CRISPR-based Gene Drives can spread through wild populations by biasing their own transmission above the 50% value predicted by Mendelian inheritance. These technologies offer population-engineering solutions for combating vector-borne diseases, managing crop pests, and supporting ecosystem conservation efforts. Current technologies raise safety concerns for unintended Gene propagation. Herein, we address such concerns by splitting the Drive components, Cas9 and gRNAs, into separate alleles to form a trans-complementing split–Gene-Drive (tGD) and demonstrate its ability to promote super-Mendelian inheritance of the separate transGenes. This dual-component configuration allows for combinatorial transGene optimization and increases safety by restricting escape concerns to experimentation windows. We employ the tGD and a small–molecule-controlled version to investigate the biology of component inheritance and resistant allele formation, and to study the effects of maternal inheritance and impaired homology on efficiency. Lastly, mathematical modeling of tGD spread within populations reveals potential advantages for improving current Gene-Drive technologies for field population modification. Gene Drives raise safety concerns around unintended propagation. Here the authors present a trans-complementing split-Gene Drive that requires inheritance of separate transGenes to assemble a fully functional Drive.
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consequences of resistance evolution in a cas9 based sex conversion suppression Gene Drive for insect pest management
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Mohammad Karaminejadranjbar, Kolja N Eckermann, Hassan M M Ahmed, M Hector C Sanchez, Stefan Dippel, John M Marshall, Ernst A WimmerAbstract:The use of a site-specific homing-based Gene Drive for insect pest control has long been discussed, but the easy design of such systems has become possible only with the recent establishment of CRISPR/Cas9 technology. In this respect, novel targets for insect pest management are provided by new discoveries regarding sex determination. Here, we present a model for a suppression Gene Drive designed to cause an all-male population collapse in an agricultural pest insect. To evaluate the molecular details of such a sex conversion-based suppression Gene Drive experimentally, we implemented this strategy in Drosophila melanogaster to serve as a safe model organism. We Generated a Cas9-based homing Gene-Drive element targeting the transformer Gene and showed its high efficiency for sex conversion from females to males. However, nonhomologous end joining increased the rate of mutaGenesis at the target site, which resulted in the emergence of Drive-resistant alleles and therefore curbed the Gene Drive. This confirms previous studies that simple homing CRISPR/Cas9 Gene-Drive designs will be ineffective. Nevertheless, by performing population dynamics simulations using the parameters we obtained in D. melanogaster and by adjusting the model for the agricultural pest Ceratitis capitata, we were able to identify adequate modifications that could be successfully applied for the management of wild Mediterranean fruit fly populations using our proposed sex conversion-based suppression Gene-Drive strategy.
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synthetically engineered medea Gene Drive system in the worldwide crop pest drosophila suzukii
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: John M Marshall, Anna Buchman, Dennis Ostrovski, Ting Yang, Omar S AkbariAbstract:Synthetic Gene Drive systems possess enormous potential to replace, alter, or suppress wild populations of significant disease vectors and crop pests; however, their utility in diverse populations remains to be demonstrated. Here, we report the creation of a synthetic Medea Gene Drive system in a major worldwide crop pest, Drosophila suzukii . We demonstrate that this Drive system, based on an engineered maternal “toxin” coupled with a linked embryonic “antidote,” is capable of biasing Mendelian inheritance rates with up to 100% efficiency. However, we find that Drive resistance, resulting from naturally occurring Genetic variation and associated fitness costs, can be selected for and hinder the spread of such a Drive. Despite this, our results suggest that this Gene Drive could maintain itself at high frequencies in a wild population and spread to fixation if either its fitness costs or toxin resistance were reduced, providing a clear path forward for developing future such systems in this pest.
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can crispr based Gene Drive be confined in the wild a question for molecular and population biology
ACS Chemical Biology, 2018Co-Authors: John M Marshall, Omar S AkbariAbstract:The recent discovery of CRISPR and its application as a Gene editing tool has enabled a range of Gene Drive systems to be engineered with greater ease. In order for the benefits of this technology to be realized, in some circumstances Drive systems should be developed that are capable of both spreading into populations to achieve their desired impact and being recalled in the event of unwanted consequences or public disfavor. We review the performance of three broad categories of Drive systems at achieving these goals: threshold-dependent Drives, homing-based Drive and remediation systems, and temporally self-limiting systems such as daisy-chain Drives.