Keywords: models
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Incorporating ecology into gene drive modellingJ. Kim, K. D. Harris, I. K. Kim, S. Shemesh, P. W. Messer and G. Greenbaum, Ecology Letters, 26:S62-S80. 2023.
Abstract Gene drive technology, in which fast-spreading engineered drive alleles are introduced into wild populations, represents a promising new tool in the fight against vector-borne diseases, agricultural pests and invasive species. Due to the risks involved, gene drives have ... |
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Expansions to the MGDrivE suite for simulating the efficacy of novel gene-drive constructs in the control of mosquito-borne diseasesJ. B. Bennett, S. L. Wu, P. R. Chennuri, K. M. Myles and M. L. Ndeffo-Mbah, BMC Research Notes, 16:258. 2023.
The MGDrivE (MGDrivE 1 and MGDrivE 2) modeling framework provides a flexible and expansive environment for testing the efficacy of novel gene-drive constructs for the control of mosquito-borne diseases. However, the existing model framework did not previously support several ... |
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Making waves: Comparative analysis of gene drive spread characteristics in a continuous space modelPan, Mingzuyu Champer, Jackson, Molecular Ecology, 2023.
Abstract With their ability to rapidly increase in frequency, gene drives can be used to modify or suppress target populations after an initial release of drive individuals. Recent advances have revealed many possibilities for different types of drives, and several of these have ... |
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Optimizing the delivery of self-disseminating vaccines in fluctuating wildlife populationsC. Schreiner, A. Basinski, C. Remien and S. Nuismer, PLOS Neglected Tropical Diseases, 17:e0011018. 2023.
Author summary Pathogens such as Ebola, rabies, and Lassa virus that usually infect wildlife can jump to the human population. In the worst case, this can lead to outbreaks or pandemics such as happened in 2014 with Ebola and 2019 with SARS-CoV-2. One approach to mitigate the ... |
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Leveraging eco-evolutionary models for gene drive risk assessmentM. A. Combs, A. J. Golnar, J. M. Overcash, A. L. Lloyd, K. R. Hayes, D. A. O’Brochta and K. M. Pepin, Trends in Genetics, 2023.
As development of gene drive systems accelerates and diversifies, predicting outcomes for target populations and the potential for human and environmental risks requires accounting for numerous eco-evolutionary processes.Gene drive dynamic models quantify the influence of ... |
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Leveraging eco-evolutionary models for gene drive risk assessmentM. A. Combs, A. J. Golnar, J. M. Overcash, A. L. Lloyd, K. R. Hayes, D. A. O’Brochta and K. M. Pepin, Trends in Genetics, 2023.
As development of gene drive systems accelerates and diversifies, predicting outcomes for target populations and the potential for human and environmental risks requires accounting for numerous eco-evolutionary processes.Gene drive dynamic models quantify the influence of ... |
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Mathematical modeling of the performance of wild and transgenic mosquitoes in malaria transmissionA. P. Wyse, A. J. B. dos Santos, J. D. Azevedo, A. C. de Meneses and V. M. D. Santos, Plos One, 18:23. 2023.
A mathematical model that simulates malaria transmission under the influence of transgenic mosquitoes refractory to malaria is presented in this paper. The zygosity of transgenic mosquitoes is taken into account and, consequently, the total population of mosquitoes is comprised ... |
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Modelling the effect of migration on the localisation and spread of a gene driveC. Benjamin James and F.-L. Alexandre Jules Hen, bioRxiv, 2023.04.02.535303. 2023.
Gene drives have the potential to address pressing ecological issues. Through the super-Mendelian inheritance of a gene drive, a trait can be spread through a population even in spite of a fitness cost. This ability to spread is both its greatest quality and detractor. We may not ... |
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Modelling the effect of migration on the localisation and spread of a gene driveC. Benjamin and F.-L. Alexandre, bioRxiv, 2023.
Gene drives have the potential to address pressing ecological issues. Through the super-Mendelian inheritance of a gene drive, a trait can be spread through a population even in spite of a fitness cost. This ability to spread is both its greatest quality and detractor. We may not ... |
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Hybrid incompatibilities in the anopheles gambiae species complexA. Kriezis, Imperial College London, 2023.
Malaria is an infectious disease caused by parasites of the genus Plasmodium which is responsible for approximately 400,000 deaths annually, primarily in sub-Saharan Africa. Malaria is transmitted by mosquitoes belonging to the Anopheles gambiae species complex. While progress ... |
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Simulations Reveal High Efficiency and Confinement of a Population Suppression CRISPR Toxin-Antidote Gene DriveY. Zhu and J. Champer, ACS Synthetic Biolog, 2023.
Though engineered gene drives hold great promise for spreading through and suppressing populations of disease vectors or invasive species, complications such as resistance alleles and spatial population structure can prevent their success. Additionally, most forms of suppression ... |
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Rescue by gene swamping as a gene drive deployment strategyK. D. Harris and G. Greenbaum, bioRxiv, 2022.03.08.483503. 2022.
Gene drives are genetic constructs that can spread deleterious alleles with potential application to population suppression of harmful species. Given that a gene drive can potentially spill over to other populations or even other species, control measures and fail-safes ... |
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Modeling-informed Engineered Genetic Incompatibility strategies to overcome resistance in the invasive Drosophila suzukiiA. Sychla, N. R. Feltman, W. D. Hutchison and M. J. Smanski, Frontiers in Insect Science, 2. 2022.
Engineered Genetic Incompatibility (EGI) is an engineered extreme underdominance genetic system wherein hybrid animals are not viable, functioning as a synthetic speciation event. There are several strategies in which EGI could be leveraged for genetic biocontrol of pest ... |
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Estimating the effect of the wMel release programme on the incidence of dengue and chikungunya in Rio de Janeiro, Brazil: a spatiotemporal modelling studyG. Ribeiro dos Santos, B. Durovni, V. Saraceni, T. I. Souza Riback, S. B. Pinto, K. L. Anders, et al., The Lancet Infectious Diseases, 2022.
Summary Background Introgression of genetic material from species of the insect bacteria Wolbachia into populations of Aedes aegypti mosquitoes has been shown in randomised and non-randomised trials to reduce the incidence of dengue; however, evidence for the real-world ... |
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Daisy-chain gene drives: The role of low cut-rate, resistance mutations, and maternal depositionS. A. N. Verkuijl, M. A. E. Anderson, L. Alphey and M. B. Bonsall, PLOS Genetics, 18:e1010370. 2022.
Author summary Reducing the harm of pest species by the introgression of traits into a wild population is often limited by the difficulties of mass rearing and release of modified individuals. Gene drives present an opportunity to substantially reduce the release frequencies ... |
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Environmentally appropriate vector control is facilitated by standard metrics for simulation-based evaluationV. N. Vásquez, M. R. Reddy and J. M. Marshall, Frontiers in Tropical Diseases, 3. 2022.
As anthropogenic factors contribute to the introduction and expansion of new and established vector species, the geographic incidence of mosquito-borne disease is shifting. Computer simulations, informed by field data where possible, facilitate the cost-effective evaluation of ... |
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Wolbachia Dynamics in Mosquitoes with Incomplete CI and Imperfect Maternal Transmission by a DDE SystemY. Su, B. Zheng and X. Zou, Bulletin of Mathematical Biology, 84:95. 2022.
In this paper, we propose a delay differential equation model to describe the Wolbachia infection dynamics in mosquitoes in which the key factor of cytoplasmic incompactibility (CI) is incorporated in a more natural way than those in the literature. By analyzing the dynamics of ... |
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Scalability of genetic biocontrols for eradicating invasive alien mammalsA. Birand, P. Cassey, J. V. Ross, P. Q. Thomas and T. A. A. Prowse, NeoBiota, 74:93-103. 2022.
CRISPR-based gene drives offer novel solutions for controlling invasive alien species, which could ultimately extend eradication efforts to continental scales. Gene drives for suppressing invasive alien vertebrates are now under development. Using a landscape-scale ... |
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Slow and steady wins the race: spatial and stochastic processes and the failure of suppression gene drivesJ. F. Paril and B. L. Phillips, Molecular Ecology, 2022.
Gene drives that skew sex ratios offer a new management tool to suppress or eradicate pest populations. Early models and empirical work suggest that these suppression drives can completely eradicate well-mixed populations, but models that incorporate stochasticity and space ... |
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Perplexing dynamics of Wolbachia proteins for cytoplasmic incompatibilityT. Harumoto and T. Fukatsu, PLOS Biology, 20:e3001644. 2022.
The mechanism of symbiont-induced cytoplasmic incompatibility has been a long-lasting mystery. This Primer explores a new study on Wolbachia’s Cif proteins in PLOS Biology that provides supportive evidence for the “Host-Modification Model,” although the alternative ... |
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Propagation of seminal toxins through binary expression gene drives could suppress populationsJ. Hurtado, S. Revale and L. M. Matzkin, Scientific Reports, 12:6332. 2022.
Gene drives can be highly effective in controlling a target population by disrupting a female fertility gene. To spread across a population, these drives require that disrupted alleles be largely recessive so as not to impose too high of a fitness penalty. We argue that this ... |
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Modelling homing suppression gene drive in haplodiploid organismsY. Liu and J. Champer, Proceedings of the Royal Society B: Biological Sciences, 289:20220320. 2022.
Gene drives have shown great promise for suppression of pest populations.These engineered alleles can function by a variety of mechanisms, but themost common is the CRISPR homing drive, which converts wild-type allelesto drive alleles in the germline of heterozygotes. Some ... |
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Modelling homing suppression gene drive in haplodiploid organismsY. Liu and J. Champer, bioRxiv, 2021.10.12.464047. 2022.
Gene drives have shown great promise for suppression of pest populations. These engineered alleles can function by a variety of mechanisms, but the most common is the CRISPR homing drive, which converts wild-type alleles to drive alleles in the germline of heterozygotes. Some ... |
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Selfish migrants: How a meiotic driver is selected to increase dispersalJ. N. Runge, H. Kokko and A. K. Lindholm, J Evol Biol, 2022.
Meiotic drivers are selfish genetic elements that manipulate meiosis to increase their transmission to the next generation to the detriment of the rest of the genome. One example is the t haplotype in house mice, which is a naturally occurring meiotic driver with deleterious ... |
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Demographic feedbacks can hamper the spatial spread of a gene driveF. Debarre and L. Girardin, bioRxiv, 2021.12.01.470771. 2021.
This paper is concerned with a reactiond diffusion system modeling the fixation and the invasion in a population of a gene drive (an allele biasing inheritance, increasing its own transmission to offspring). In our model, the gene drive has a negative effect on the fitness of ... |
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Propagation of seminal toxins through binary expression gene drives can suppress polyandrous populationsJ. Hurtado, S. Revale and L. M. Matzkin, bioRxiv, 2021.11.23.469777. 2021.
Gene drives can be highly effective in controlling a target population by disrupting a female fertility gene. To spread across a population, these drives require that disrupted alleles be largely recessive so as not to impose too high of a fitness penalty. We argue that this ... |
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Malaria modeling and optimal control using sterile insect technique and insecticide-treated netL. Cai, L. Bao, L. Rose, J. Summers and W. Ding, Applicable Analysis, 2021.
We investigate a malaria transmission model with SEIR (susceptible-exposed-infected-recovered) classes for the human population, SEI (susceptible-exposed-infected) classes for the wild mosquitoes and an additional class for the sterile mosquitoes. The basic reproduction number ... |
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Population replacement gene drive characteristics for malaria elimination in a range of seasonal transmission settings: a modeling studyS. Leung, N. Windbichler, E. Wenger, C. Bever and P. Selvaraj, bioRxiv, 2021.11.01.466856. 2021.
Genetically engineering mosquitoes is a promising new vector control strategy to reinvigorate the fight against malaria in Sub-Saharan Africa. Using an agent-based model of malaria transmission with vector genetics, we examine the impacts of releasing population-replacement gene ... |
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Modeling homing suppression gene drive in haplodiploid organismsY. Liu and J. Champer, bioRxiv, 2021.10.12.464047. 2021.
Gene drives have shown great promise for suppression of pest populations. These engineered alleles can function by a variety of mechanisms, but the most common is the CRISPR homing drive, which converts wild-type alleles to drive alleles in the germline of heterozygotes. Some ... |
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Predicting the spread and persistence of genetically modified dominant sterile male mosquitoesA. Ickowicz, S. D. Foster, G. R. Hosack and K. R. Hayes, Parasites and Vectors, 14:480. 2021.
Reproductive containment provides an opportunity to implement a staged-release strategy for genetic control of malaria vectors, in particular allowing predictions about the spread and persistence of (self-limiting) sterile and male-biased strains to be compared to outcomes before ... |
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MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamicsS. L. Wu, J. B. Bennett, C. H. Sánchez, A. J. Dolgert, T. M. León and J. M. Marshall, PLoS Comput Biol, 17:e1009030. 2021.
We present MGDrivE 2 (Mosquito Gene Drive Explorer 2): a significant development from the MGDrivE 1 simulation framework that investigates the population dynamics of a variety of gene drive architectures and their spread through spatially-explicit mosquito populations. Key ... |
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A gene drive does not spread easily in populations of the honey bee parasite Varroa destructorN. R. Faber, A. B. Meiborg, G. R. McFarlane, G. Gorjanc and B. A. Harpur, bioRxiv, 2021.04.30.442149. 2021.
Varroa mites (Varroa destructor) are the most significant threat to beekeeping worldwide. They are directly or indirectly responsible for millions of colony losses each year. Beekeepers are somewhat able to control Varroa populations through the use of physical and chemical ... |
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Invasion and maintenance of meiotic drivers in populations of ascomycete fungiI. Martinossi-Allibert, C. Veller, S. L. Ament-Velasquez, A. A. Vogan, C. Rueffler and H. Johannesson, Evolution, 20. 2021.
Meiotic drivers (MDs) are selfish genetic elements that are able to become overrepresented among the products of meiosis. This transmission advantage makes it possible for them to spread in a population even when they impose fitness costs on their host organisms. Whether an MD ... |
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Quantifying the risk of vector-borne disease transmission attributable to genetically modified vectorsG. R. Hosack, A. Ickowicz and K. R. Hayes, Royal Society Open Science, 8:201525. 2021.
The relative risk of disease transmission caused by the potential release of transgenic vectors, such as through sterile insect technique or gene drive systems, is assessed with comparison with wild-type vectors. The probabilistic risk framework is demonstrated with an assessment ... |
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Designing gene drives to limit spillover to non-target populationsG. Greenbaum, M. W. Feldman, N. A. Rosenberg and J. Kim, PLOS Genetics, 17:e1009278. 2021.
We develop mathematical models of gene-drive dynamics that incorporate migration between a target and non-target populations to investigate the possibility of effectively applying a gene drive in the target population while limiting its spillovers to the non-target population ... |
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Demographic feedbacks can hamper the spatial spread of a gene driveL. Girardin and F. Débarre, arXiv, 2021.
Our results indicate that taking into account the interplay between population dynamics and population genetics might actually be crucial, as it can effectively reverse the direction of the invasion and lead to failure. Our findings can be extended to other bistable systems, such ... |
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Suppression gene drive in continuous space can result in unstable persistence of both drive and wild-type allelesJ. Champer, I. K. Kim, S. E. Champer, A. G. Clark and P. W. Messer, Mol Ecol, 2021.
Using spatially explicit simulations, we show that the release of a suppression drive can result in what we term "chasing" dynamics, in which wild-type individuals recolonize areas where the drive locally eliminated the population. Despite the drive subsequently reconquering ... |
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Making gene drive biodegradableJ. Zapletal, N. Najmitabrizi, M. Erraguntla, M. A. Lawley, K. M. Myles and Z. N. Adelman, Philosophical Transactions of the Royal Society B: Biological Sciences, 376:20190804. 2020.
Here, we consider the inclusion of self-elimination mechanisms into the design of homing-based gene drive transgenes. This approach not only caused the excision of the gene drive transgene, but also generates a transgene-free allele resistant to further action by the gene drive. ... |
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Evading resistance to gene drivesR. Gomulkiewicz, M. L. Thies and J. J. Bull, bioRxiv, 2020.08.27.270611. 2020.
Our analyses suggest that among gene drives that cause moderate suppression, toxin-antidote systems are less apt to select for resistance than homing drives. Single drives of moderate effect might cause only moderate population suppression, but multiple drives (perhaps delivered ... |
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Split drive killer-rescue provides a novel threshold-dependent gene driveM. P. Edgington, T. Harvey-Samuel and L. Alphey, Scientific Reports, 10. 2020.
Population genetics mathematical models are developed here to demonstrate the threshold-dependent nature of the proposed system and its robustness to imperfect homing, incomplete penetrance of toxins and transgene fitness costs, each of which are of practical significance given ... |
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Modeling CRISPR gene drives for suppression of invasive rodentsS. E. Champer, N. Oakes, R. Sharma, P. García-Díaz, J. Champer and P. W. Messer, bioRxiv, 2020.11.05.369942. 2020.
Here, we develop a high-fidelity model of an island population of invasive rodents that includes three types of suppression gene drive systems. The individual-based model is spatially explicit and allows for overlapping generations and a fluctuating population size. Our model ... |
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MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamicsS. L. Wu, J. B. Bennett, H. M. Sanchez C, A. J. Dolgert, T. M. Leon and J. M. Marshall, bioRxiv, 2020.10.16.343376. 2020.
We present MGDrivE 2 (Mosquito Gene Drive Explorer 2): an extension of and development from the MGDrivE 1 simulation framework that investigates the population dynamics of a variety of gene drive architectures and their spread through spatially-explicit mosquito populations. |
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Dynamics of Wild and Sterile Mosquito Population Models with Delayed ReleasingL. M. Cai, International Journal of Bifurcation and Chaos, 30:15. 2020.
We extend the previous ODE models to the delayed releasing models in two different ways of releasing sterile mosquitos, where both constant and exponentially distributed delays are considered, respectively. By applying the theory and methods of delay differential equations, the ... |
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Vector genetics, insecticide resistance and gene drives: An agent-based modeling approach to evaluate malaria transmission and eliminationP. Selvaraj, E. A. Wenger, D. Bridenbecker, N. Windbichler, J. R. Russell, J. Gerardin, C. A. Bever and M. Nikolov, PloS Computational Biology, 16:21. 2020.
Here, we investigate the reduced efficacy of current vector control measures in the presence of insecticide resistance and evaluate the likelihood of achieving local malaria elimination using gene drive mosquitoes released into a high transmission setting alongside other vector ... |
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Modelling the suppression of a malaria vector using a CRISPR-Cas9 gene drive to reduce female fertilityA. R. North, A. Burt and H. C. J. Godfray, BMC Biology, 18:98. 2020.
Gene drives based on CRISPR-Cas9 technology are increasingly being considered as tools for reducing the capacity of mosquito populations to transmit malaria, and one of the most promising options is driving endonuclease genes that reduce the fertility of female mosquitoes. Here, ... |
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Modeling the suppression dynamics of Aedes mosquitoes with mating inhomogeneityM. Huang and L. Hu, Journal of Biological Dynamics, 14:656-678. 2020.
In this work, we introduce a delay differential equation model with mating inhomogeneity to discuss mosquito population suppression based on Wolbachia. Our analyses show that the wild mosquitoes could be eliminated if either the adult mortality rate exceeds the threshold δ∗A ... |
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A One-Sided Competition Mathematical Model for the Sterile Insect TechniqueA. Ben Dhahbi, Y. Chargui, S. M. Boulaaras and S. Ben Khalifa, Complexity, 2020:12. 2020.
We study a simple mathematical model describing the dynamics of a wild-type pest insects population experiencing competition from sterile insects (one-sided competition). |
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On Nonlinear Pest/Vector Control via the Sterile Insect Technique: Impact of Residual FertilityM. S. Aronna and Y. Dumont, Bulletin of Mathematical Biology, 82:29. 2020.
We consider a minimalist model for the Sterile Insect Technique (SIT), assuming that residual fertility can occur in the sterile male population. |
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Field performance of sterile male mosquitoes released from an uncrewed aerial vehicleJ. Bouyer, N. J. Culbert, A. H. Dicko, M. G. Pacheco, J. Virginio, M. C. Pedrosa, L. Garziera, A. T. M. Pinto, A. Klaptocz, J. Germann, T. Wallner, G. Salvador-Herranz, R. A. Herrero, H. Yamada, F. Balestrino and M. J. B. Vreysen, Science Robotics, 5:10. 2020.
Genetic control methods of mosquito vectors of malaria, dengue, yellow fever, and Zika are becoming increasingly popular due to the limitations of other techniques such as the use of insecticides. The sterile insect technique is an effective genetic control method to manage ... |
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A spatially discrete, integral projection model and its application to invasive carpR. A. Erickson, E. A. Eager, P. M. Kocovsky, D. C. Glover, J. L. Kallis and K. R. Long, Ecological Modelling, 387:163-171. 2018.
Natural resource managers and ecologists often desire an understanding of spatial dynamics such as migration, dispersion, and meta-population dynamics. Network-node models can capture these salient features. Additionally, the state-variable used with many species may be ... |
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Pest demography critically determines the viability of synthetic gene drives for population controlK. E. Wilkins, T. A. A. Prowse, P. Cassey, P. Q. Thomas and J. V. Ross, Mathematical Biosciences, 305:160-169. 2018.
Synthetic gene drives offer a novel solution for the control of invasive alien species. CRISPR-based gene drives can positively bias their own inheritance, and comprise a DNA sequence that is replicated by homologous recombination. Since gene drives can be positioned to silence ... |
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Genetics-based methods for agricultural insect pest managementN. Alphey and M. B. Bonsall, Agricultural and Forest Entomology, 20:131-140. 2018.
Abstract The sterile insect technique is an area-wide pest control method that reduces agricultural pest populations by releasing mass-reared sterile insects, which then compete for mates with wild insects. Contemporary genetics-based technologies use insects that are homozygous ... |
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Daisyfield gene drive systems harness repeated genomic elements as a generational clock to limit spreadJ. Min, C. Noble, D. Najjar and K. M. Esvelt, bioRxiv, 104877. 2017.
Here we describe a novel form of gene drive based on the introduction of multiple copies of an engineered ‘daisy’ sequence into repeated elements of the genome. Each introduced copy encodes guide RNAs that target one or more engineered loci carrying the CRISPR nuclease gene ... |
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Lethal Gene Drive Selects InbreedingJ. J. Bull, bioRxiv, 046847. 2016.
ere, population genetic models are used to consider the evolution of inbreeding (specifically selfing) as a possible response to a recessively lethal HEG with complete segregation distortion. Numerical analyses indicate a rich set of outcomes, but selfing often evolves in ... |
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Global existence and asymptotic behavior of a model for biological control of invasive species via supermale introductionR. D. Parshad, S. Kouachi and J. B. Gutierrez, Communications in Mathematical Sciences, 11:971-992. 2013.
The purpose of this manuscript is to propose a model for the biological control of invasive species, via introduction of phenotypically modified organisms into a target population. We are inspired by the earlier Trojan Y Chromosome model [J.B. Gutierrez, J.L. Teem, J. Theo. Bio., ... |
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Demographic effects on the use of genetic options for the control of mosquitofish, Gambusia holbrookiR. E. Thresher, M. Canning and N. J. Bax, Ecological Applications, 23:801-814. 2013.
This study tests the sensitivity of genetically based pest control options based on sex ratio distortion to intra-and intersexual aggressive interactions that affect male and female survival and fitness. Data on these interactions and their impacts were gathered for the ... |
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Existence of global attractor for the Trojan Y Chromosome modelX. P. Zhao, B. Liu and N. Duan, Electronic Journal of Qualitative Theory of Differential Equations, 2011.
This paper is concerned with the long time behavior of solution for the equation derived by the Trojan Y Chromosome (TYC) model with spatial spread. Based on the regularity estimates for the semigroups and the classical existence theorem of global attractors, we prove that this ... |
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Analysis of the Trojan Y chromosome model for eradication of invasive species in a dendritic riverine systemJ. B. Gutierrez, M. K. Hurdal, R. D. Parshad and J. L. Teem, Journal of Mathematical Biology, 64:319-340. 2011.
The use of Trojan Y chromosomes has been proposed as a genetic strategy for the eradication of invasive species. The strategy is particularly relevant to invasive fish species that have XY sex determination system and are amenable to sex-reversal. In this paper we study the ... |
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Can transposable elements be used to drive disease refractoriness genes into vector populations?M. G. Kidwell and J. M. C. Ribeiro, Parasitology Today, 8:325-329. 1992.
A number of biological procedures are currently being considered as alternatives to insecticide-based methods for the control of insect vectors of disease. Among these are the adaptation of various genetic mechanisms to drive genes of interest, such as refractoriness to malaria ... |
