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Champer, J.

Publications and source records attributed to Champer, J..

At least 37 records · Page 2Linked to original sources

A simulation-based deep learning framework for spatially explicit malaria modeling of CRISPR suppression gene drive mosquitoes

Engineered CRISPR gene drives are a promising new strategy for fighting malaria and other vector-borne diseases, made possible by genome engineering with the CRISPR-Cas9 system. One useful approach to predict the outcome of a gene drive mosquito release is individual-based modeling, which can be spatially explicit and allows flexible parameters for drive efficiency, mosquito ecology, and malaria transmission. However, the computational demand of this type of model significantly increases when including a larger number of parameters, especially due to the chasing phenomenon, which can delay or prevent successful population elimination. Thus, we built a simulation-based deep-learning model to comprehensively understand the effects of different parameters on Anopheles gambiae mosquito suppression and malaria prevalence among the human population. The results suggest that reducing the embryo resistance cut rate, reducing the functional resistance forming rate and increasing the drive conversion rate plays the major role in mosquito suppression and related phenomena. We also observed that the parameter space for eliminating malaria was substantially larger than that for mosquito suppression, suggesting that even a considerably imperfect drive may still successfully accomplish its objective despite chasing or resistance allele formation. This study shows that suppression gene drives may be highly effective at locally eliminating malaria, even in challenging conditions.

genetics↗

Aedes aegypti aminopeptidase N3 is a functional binding receptor of Bacillus thuringiensis subsp. israelensis Cry4Ba toxin

Bacillus thuringiensis is widely employed for biological control. It can effectively suppress populations of various mosquito species, including Aedes aegypti. However, the precise mechanism underlying the action of cry toxin secreted by Bacillus thuringiensis on Ae. aegypti remains elusive. In this study, we investigated one of the binding receptors of cry toxin, aminopeptidase N. Through comprehensive bioinformatics analysis involving whole-genome screening, genetic mapping, structural characterization, phylogenetic analysis, and spatiotemporal expression profiling, we identified twenty-nine homologs of Ae. aegypti aminopeptidase N. Further, we successfully expressed GST-APN3 protein in E. coli and demonstrated through ligand blot and ELISA assays that APN3 exhibits high affinity binding to Cry4Ba toxin (Kd = 20.53 nM). To elucidate the functional role of APN3 as a receptor mediating Cry4Ba activity in Ae. aegypti midgut cells (some of which express this gene at high levels), CRISPR/Cas9 technology was employed to knock out APN3. Our bioassay results revealed that APN3 knockout mosquito larvae had 2.9 to 4.1-fold higher resistance against Cry4Ba, indicating its crucial involvement as an active receptor mediating Cry4Ba activity. Overall, this study provides a foundation for elucidating the specific larvicidal mechanisms of Bt against mosquito populations.

molecular biology↗

Modeling control of invasive fire ants by gene drive

Solenopsis invicta, commonly known as the fire ant, is characterized by aggressive behavior and exceptional invasive capabilities, rendering conventional control methods largely ineffective. Here, we explore the implementation of homing suppression gene drive in fire ants by developing a spatially explicit model that incorporates both monogyne and polygyne colony structures, enabling comprehensive evaluation of genetic control strategies. Ants may present unique challenges for gene drive due to their colony structure and haplodiploidy. Our results reveal that after an extended period of time, gene drive effectively eliminates polygyne colonies, but monogyne populations often persist at low level. Though standard suppression drives in haplodiploids have reduced power, new dominant-sterile resistance or two-target strategies, as well as drives that affect the colony structure, can restore high suppressive capability. Interspecific competition can also exert a positive effect on gene drive-mediated population suppression dynamics. In particular, a gene drive release during the invasion phase significantly enhances population suppression, enabling native ants to successfully recolonize their original habitats. We also identify several conserved female fertility genes in fire ants, together with gRNA targets that may support efficient, low-resistance suppression drive designs. Overall, we conclude that while gene drive in fire ants may take place over extended time scales, its long-term results, even with imperfect efficiency, are quite promising.

ecology↗

A self-limiting Sterile Insect Technique alternative for Ceratitis capitata

Genetic biocontrol systems have broad applications in population control of insects implicated in both disease spread and food security. In this study we establish and characterise a novel split-CRISPR/Cas9 system we term Sex Conversion Induced by CRISPR (SCIC) in Ceratitis capitata (the Mediterranean fruit fly), a major agricultural pest with a global distribution. Using the white eye gene for toolkit selection, we achieved up to 100% CRISPR/Cas9 efficiency, displaying the feasibility of C. capitata split-CRISPR/Cas9 systems using constitutive promoters. We then induce sex-conversion by targeting the transformer gene in a SCIC approach aimed for SIT-mediated releases upon radiation-based sterilisation. Knock-out of transformer induced partial to full female-to-male sex-conversion, with remaining individuals all being intersex and sterile. SCIC population modelling shows superior performance to traditional population control strategies, allowing for faster population elimination with fewer released sterile males. Our results build the foundation for further genetic pest control methods of C. capitata and related tephritid agricultural pests. Significance statementAgricultural industry faces increasing threat from a multitude of pests including the domineering tephritid fruit flies. Genetic engineering of these pests has been recently tested to develop more efficient and affordable population control strategies. Here, we develop a new approach to improve existing population control measures by testing it in one of the most famous and dangerous tephritids, the Mediterranean fruit fly. Through optimisation, we achieved desired outcomes: female fly absence achieved via semi and full female-to-male sex conversion by CRISPR-mediated genome editing through gene mutations. For the first time in this insect, we used a split, and thus inducible, approach for such genome editing. Our work holds the potential to significantly improve tephritid population control strategies.

genetics↗

Assessing target genes for homing suppression gene drive

Gene drives are engineered alleles that bias their own inheritance in offspring, enabling the spread of specific traits throughout a population. Targeting female fertility genes in a gene drive can be an efficient strategy for population suppression. In this study, we investigated nine female fertility genes in Drosophila melanogaster using CRISPR-based homing gene drives. Employing a multiplexed gRNA approach to prevent the formation of functional resistance alleles, we aimed to maintain high drive conversion efficiency with low fitness costs in female drive carriers. Drive efficiency was assessed in individual crosses and had varied performance across different target genes. Notably, drives targeting the octopamine {beta}2 receptor (oct) and stall (stl) genes exhibited the highest drive conversion rates and were further tested in cages. A drive targeting stl successfully suppressed a cage population with a high release frequency, though suppression failed in another replicate cage with a lower initial release frequency. Fitness costs in female drive carriers were observed in test cages, impacting the overall efficiency of population suppression. Further tests on the fertility of these lines using individual crosses indicated that some fitness costs were due to maternal deposition of Cas9 combined with new gRNA expression, which would only occur in progeny of drive males when testing split drives with separate Cas9 (when mimicking cages with complete drives) but not for complete drive systems. This could enable success in complete drives with higher maternal Cas9 deposition, even if cage experiments in split drives fail. Our findings underscore the potential and challenges of assessing gene drives for population control, providing valuable insights for optimizing and testing suppression gene drive designs.

genetics↗

Assessment of drive efficiency and resistance allele formation of a homing gene drive in the mosquito Aedes aegypti

Aedes aegypti, known for transmitting viruses such as dengue, zika, and yellow fever, poses a significant public health threat. Conventional insecticides give rise to a range of issues, including ecological contamination and insect resistance. Hence, there is a pressing demand for environmentally friendly, safer, and more efficacious strategies for mosquito control. With the rapid advancement of the CRISPR/Cas9 system in gene function exploration and pest population control, substantial progress has been achieved in utilizing CRISPR/Cas9-based gene drive systems across various mosquito species. Only a few studies on gene drive technology have been conducted in A. aegypti. In this study, we constructed two complete drives for A. aegypti with different Cas9 promoters, each targeting kmo. Our drive based on Pub-Cas9 had limited activity, but one with exu-Cas9 exhibited super-Mendelian inheritance rates of approximately 60%. We observed low but detectable somatic activity of the drive and no evidence of maternally deposited Cas9. Germline resistance allele formation rates were similar to drive conversion rates, but most wild-type alleles in the germline remained uncut. Injections into the exu-Cas9 drive line had 100% knockout efficiency among surviving offspring at three separate target genes. These results support the development and application of novel genetic pest control technologies aimed at combating A. aegypti.

genetics↗

A comparative assessment of self-limiting genetic control strategies for population suppression

Genetic control strategies are promising solutions for control of pest populations and invasive species. Methods utilizing repeated releases of males such as Sterile Insect Technique (SIT), Release of Insects carrying a Dominant Lethal (RIDL), self-limiting gene drives, and gene disruptors are highly controllable methods, ensuring biosafety. Although models of these strategies have been built, detailed comparisons are lacking, particularly for some of the newer strategies. Here, we conducted a thorough comparative assessment of self-limiting genetic control strategies by individual-based simulation models. Specifically, we find that repeated releases greatly enhance suppression power of weak and self-limiting gene drives, enabling population elimination with even low efficiency and high fitness costs. Moreover, dominant female sterility further strengthens self-limiting systems that can either use gene drive or disruptors that target genes without a mechanism to bias their own inheritance. Some of these strategies are highly persistent, resulting in relatively low release ratios even when released males suffer high fitness costs. To quantitively evaluate different strategies independent from ecological impact, we proposed constant-population genetic load, which achieves over 95% accuracy in predicting simulation outcomes for most strategies, though it is not as precise in a few frequency-dependent systems. Our results suggest that many new self-limiting strategies are safe, flexible, and more cost-effective than traditional SIT and RIDL, and thus have great potential for population suppression of insects and other pests.

genetics↗

Population dynamics in spatial suppression gene drive models and the effect of resistance, density dependence, and life history

Due to their super-Mendelian inheritance, gene drive systems have the potential to provide revolutionary solutions to critical public health and environmental problems. For suppression drives, however, spatial structure can cause "chasing" population dynamics that may postpone target population elimination or even cause the drive to fail. In chasing, wild-type individuals elude the drive and recolonize previously suppressed areas. The drive can re-enter these recolonized areas, but often is not able to catch up to wild-type and finally eliminate it. Previous methods for chasing detection are only suitable to limited parameter ranges. In this study with expanded parameter ranges, we found that the shift from chasing dynamics to static equilibrium outcomes is continuous as drive performance is reduced. To quantify this, we defined a Weighted Average Nearest Neighbor statistic to assess the clustering degree during chasing, while also characterizing chasing by the per-generation chance of population elimination and drive loss. To detect chasing dynamics in local areas and to detect the start of chasing, we implemented Density-Based Spatial Clustering of Applications with Noise. Using these techniques, we determined the effect of arena size, resistance allele formation rate in both the germline and in the early embryo from maternally deposited Cas9, life history and reproduction strategies, and density-dependent growth curve shape on chasing outcomes. We found that larger real-world areas will be much more vulnerable to chasing and that species with overlapping generations, fecundity-based density dependence, and concave density-dependent growth curves have smaller and more clustered local chasing with a greater chance of eventual population elimination. We also found that embryo resistance and germline resistance hinder drive performance in different ways. These considerations will be important for determining the necessary drive performance parameters needed for success in different species, and whether future drives could potentially be considered as release candidates.

ecology↗

First-male sperm precedence in polyandrous Spodoptera frugiperda allows sterile males induce population suppression

Males respond to intense sperm competition by adapting reproductive strategies to promote fertilization success, which is critical for population reproduction. Thus, investigating the patterns and mechanisms of sperm competition is crucial for the development and application of pest population management techniques. In this study, we analyzed the sperm precedence pattern of a major pest, the fall armyworm, and used this pattern to manage the pest population. First, we found that females had a post-mating response and did not gain direct benefit through multiple mating. Next, in a double mating experiment, we used a molecular marker created by CRISPR/Cas9 to determine that most females use only the sperm of the first male to produce offspring. To further explore the role of fertilizing sperm in sperm competition, we constructed a sterile male line with eupyrene sperm defect by knocking out the B2t gene. Interestingly, two round mating assays showed that first mating with B2t-null males inhibited sperm fertilization from a second wild-type male. In other words, prior mating with B2t-null males significantly reduced the fertility and fecundity of females. Based on this finding, we continued to explore whether sperm-deficient sterile males could be used in the management of FAW populations. Cage experiments and mathematical modeling analyses showed that the release of excess B2t-null males induced population suppression. Our study expands our knowledge of sperm competition patterns in lepidopteran. In addition, our study provides a paradigm to develop and apply genetic control methods based on sperm competition outcome in polyandrous pests. SignificanceSperm competition is essential for maintaining population reproduction. Understanding patterns and mechanisms of sperm competition facilitates the development of appropriate pest genetic control methods. Here, we describe that a globally major pest, the fall armyworm displays the first-male sperm precedence pattern. Interestingly, first mating with B2t-null males, which produces non-functional eupyrene sperm, significantly reduces the fertility and fecundity of females. That means that the ejaculate of the first male, even if its eupyrene sperm are defective, can inhibit sperm fertilization from a second wild-type male. Based on this, the release of excess B2t-null males significantly suppresses FAW populations. These results suggest that future development of genetic control techniques based on targeting nucleated sperm can effectively control FAW populations.

zoology↗

Deployment of tethered gene drive for confined suppression in continuous space requires avoiding drive wave interference

Gene drives have great potential for suppression of pest populations and removal of exotic invasive species. CRISPR homing suppression drive is a powerful but unconfined drive, posing risks of uncontrolled spread. Thus, developing methods for confining a gene drive is of great significance. Tethered drive combines a confined system such as Toxin-Antidote Recessive Embryo (TARE) drive with a strong drive such as a homing suppression drive. It can prevent the homing drive from spreading beyond the confined drive and can be constructed readily, giving it good prospects for future development. However, we have found that care must be taken when deploying tethered drive systems in some scenarios. Simulations of tethered drive in a panmictic population model reveal that successful deployment requires a proper release ratio between the two components, tailored to prevent the suppression drive from eliminating the confined system before it has the chance to spread. Spatial models where the population moves over a one-dimensional landscape display a more serious phenomenon of drive wave interference between the two tethered drive components. If the faster suppression drive wave catches up to the confined drive wave, success is still possible, but it is dependent on drive performance and ecological parameters. Two-dimensional simulations further restrict the parameter range for drive success. Thus, careful consideration must be given to drive performance and ecological conditions, as well as specific release proposals for potential application of tethered drive systems.

genetics↗

Gene drive-based population suppression in the malaria vector Anopheles stephensi

Gene drives are alleles that can bias the inheritance of specific traits in target populations for the purpose of modification or suppression. Here, we constructed a homing suppression drive in the major urban malaria vector Anopheles stephensi targeting the female-specific exon of doublesex, incorporating two gRNAs and a nanos-Cas9 promoter to reduce functional resistance and improve female heterozygote fitness. Our result showed that the drive was recessive sterile in both females and males, with various intersex phenotypes in drive homozygotes. Both male and female drive heterozygotes showed only moderate drive conversion, indicating that the nos promoter has lower activity in A. stephensi than in Anopheles gambiae. By amplicon sequencing, we detected a very low level of resistance allele formation. Combination of the homing suppression and a vasa-Cas9 line demonstrated a boost in the drive conversion rate of the homing drive to 100%, suggesting the use of similar systems for population suppression in a continuous release strategy with a lower release rate than SIT or fRIDL techniques. This study contributes valuable insights to the development of more efficient and environmentally friendly pest control tools aimed at disrupting disease transmission.

genetics↗

Resource-explicit interactions in spatial population models

Continuous-space population models can yield significantly different results from their panmictic counterparts when assessing evolutionary, ecological, or population-genetic processes. However, the computational burden of spatial models is typically much greater than that of panmictic models due to the overhead of determining which individuals interact with one another and how strongly they interact. Though these calculations are necessary to model local competition that regulates the population density, they can lead to prohibitively long runtimes. Here, we present a novel modeling method in which the resources available to a population are abstractly represented as an additional layer of the simulation. Instead of interacting directly with one another, individuals interact indirectly via this resource layer. We find that this method closely matches other spatial models, yet can dramatically increase the speed of the model, allowing the simulation of much larger populations. Additionally, models structured in this manner exhibit other desirable characteristics, including more realistic spatial dynamics near the edge of the simulated area, and an efficient route for modeling more complex heterogeneous landscapes.

ecology↗

Improving the suppressive power of homing gene drive by co-targeting a distant-site female fertility gene

Gene drive technology has the potential to address major biological challenges, including the management of disease vectors, invasive species, and agricultural pests. After releasing individuals carrying the gene drive in the target population, suppression gene drives are designed to spread at a rapid rate and carry a recessive fitness cost, thus bringing about a decline in population size or even complete suppression. Well-studied homing suppression drives have been shown to be highly efficient in Anopheles mosquitoes and were successful in eliminating large cage populations. However, for other organisms, including Aedes mosquitoes, homing gene drives are so far too inefficient to achieve complete population suppression, mainly due to lower rates of drive conversion, which is the rate at which wild type alleles are converted into drive alleles. Low drive conversion is also a major issue in vertebrates, as indicated by experiments in mice. To tackle this issue, we propose a novel gene drive design that has two targets: a homing site where the drive is located and drive conversion takes place (with rescue for an essential gene), and a distant site for providing the fitness cost for population suppression (preferably a female fertility gene, for which no rescue is provided). We modeled this design and found that the two-target system allows suppression to occur over a much wider range of drive conversion efficiency. Specifically, in the new design, the suppressive power depends mostly on total gRNA cutting efficiency instead of just drive conversion efficiency, which is advantageous because cut rates are often substantially higher than drive conversion rates. We constructed a proof of concept in Drosophila melanogaster and show that both components of the gene drive function successfully. However, embryo drive activity from maternally deposited Cas9 as well as fitness costs for female drive heterozygotes both remain significant challenges for two-target and standard suppression drives. Overall, our improved gene drive design eases the development of strong homing suppression gene drives for many species where drive conversion is less efficient.

genetics↗

Population suppression with dominant female-lethal alleles is boosted by homing gene drive

Methods to suppress pest insect populations using genetic constructs and repeated releases of male homozygotes have recently been shown to be an attractive alternative to older sterile insect technique based on radiation. Female-specific lethal alleles have substantially increased power, but still require large, sustained transgenic insect releases. Gene drive alleles bias their own inheritance to spread throughout populations, potentially allowing population suppression with a single, small-size release. However, suppression drives often suffer from efficiency issues, and the most well-studied type, homing drives, tend to spread without limit. In this study, we show that coupling female-specific lethal alleles with homing gene drive allowed substantial improvement in efficiency while still retaining the self-limiting nature (and thus confinement) of a lethal allele strategy. Using a mosquito model, we show the required releases sizes for population elimination in a variety of scenarios, including different density growth curves, with comparisons to other systems. Resistance alleles reduced the power of this method, but these could be overcome by targeting an essential gene with the drive while also providing rescue. A proof-of-principle demonstration of this system in Drosophila melanogaster was effective in both basing its inheritance and achieving high lethality among females that inherit the construct in the absence of antibiotic. Overall, our study shows that substantial improvements can be achieved in female-specific lethal systems for population suppression by combining them with a gene drive.

synthetic biology↗

A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance

CRISPR homing gene drive is a potent technology with considerable potential for managing populations of medically and agriculturally significant insects. It induces a bias in the inheritance of the drive allele in progeny, rapidly spreading desired genes throughout the population. Homing drives operate by Cas9 cleavage followed by homology-directed repair, copying the drive allele to the wild-type chromosome. However, resistance alleles formed by end-joining repair pose a significant obstacle to the spread of the drive. To address this challenge, we created a homing drive targeting the essential but haplosufficient hairy gene. Our strategy involves spreading the drive construct through the homing process, eliminating nonfunctional resistance, which are recessive lethal, while rescuing drive-carrying individuals with a recoded version of hairy. This strategy eliminates resistance more slowly than a previous strategy targeting haplolethal genes, but it may be easier to construct in non-model organisms. Our drive inheritance rate was moderate, and multigenerational cage studies showed quick drive spread to 96-97% of the population. However, the drive failed to reach the whole population due to the formation of functional resistance alleles, despite use of four gRNAs, a strategy that previously was successful at preventing functional resistance. Sequencing showed that these alleles had a large deletion and must have utilized an alternate start codon. The resistance allele had a modest fitness advantage over the drive in a cage study, which could prevent long-term persistence of the drive, especially if cargo genes had an additional fitness cost. Thus, revised design strategies targeting more essential regions of a target gene may often be necessary to avoid such functional resistance, even when using multiplexed gRNAs.

synthetic biology↗

Overriding Mendelian inheritance in Arabidopsis with a CRISPR toxin-antidote gene drive that impairs pollen germination

Synthetic gene drives, inspired by natural selfish genetic elements, present transformative potential for disseminating traits that benefit humans throughout wild populations, irrespective of potential fitness costs. Here, we constructed a gene drive system called CRISPR-Assisted Inheritance utilizing NPG1 (CAIN), which employs a toxin-antidote mechanism in the male germline to override Mendelian inheritance in plants. Specifically, a gRNA-Cas9 cassette targets the essential No Pollen Germination 1 (NPG1) gene, serving as the toxin to block pollen germination. A recoded, CRISPR-resistant copy of NPG1 serves as the antidote, providing rescue only in pollen cells that carry the drive. To limit potential consequences of inadvertent release, we used self-pollinating Arabidopsis thaliana as a model. The drive demonstrated a robust 88-99% transmission rate over two successive generations, producing minimal resistance alleles that are unlikely to inhibit drive spread. Our study provides a strong basis for rapid genetic modification or suppression of outcrossing plant populations.

evolutionary biology↗

Population suppression by release of insects carrying a dominant sterile homing gene drive targeting doublesex in Drosophila

Gene drive alleles, which bias their own inheritance and increase in frequency, show great promise for blocking disease transmission or directly suppressing pest populations. The most common engineered drive system is the CRISPR homing drive, which converts wild-type alleles to drive alleles in the germline of drive heterozygotes by homology-directed repair after CRISPR cleavage. One successful homing drive example targets a female-specific exon in doublesex in Anopheles mosquitos, suppressing the population by inducing recessive sterility in female drive homozygotes. We found that in Drosophila melanogaster, a 3-gRNA drive disrupting the doublesex female exon resulted in a masculine phenotype and dominant female sterility. Resistance alleles formed by end-joining repair were also dominant sterile. This was likely caused by expression of male-specific transcripts in females with drive and resistance alleles, disrupting sex development. Based on this construct, we proposed a new pest suppression system called "Release of Insects carrying a Dominant-sterile Drive" (RIDD). This entails continuously releasing drive heterozygous males, with drive and resistance alleles causing sterility in females. The drive remains at high frequency longer than currently used dominant female-lethal alleles (RIDL) due to drive conversion in males, and drive alleles also cause sterility based on resistance, both substantial advantages. With weekly releases of drive males into a cage population with overlapping generations, our RIDD system targeting dsx reached 100% prevalence within 27 weeks, progressively reducing egg production and eventually causing total population collapse. RIDD combines the merits of homing gene drive and RIDL. It is powerful but self-limiting, unlike unconfined standard homing drives, allowing for targeted population suppression.

genetics↗

New germline Cas9 promoters show improved performance for homing gene drive

Gene drive systems could be a viable strategy to prevent pathogen transmission or suppress vector populations by propagating drive alleles with super-Mendelian inheritance. CRISPR-based homing gene drives, perhaps the most powerful gene drive strategy, convert wild type alleles into drive alleles in heterozygotes with the help of Cas9 and gRNA. However, achieving successful outcomes with these drives often requires high performance. Specifically, it is desirable to identify Cas9 promoters that yield high drive conversion rates, minimize the formation rate of resistance alleles in both the germline and the early embryo, and limit somatic Cas9 expression. Thus far, high-performance promoters have only been discovered in Anopheles species. In Drosophila, the nanos promoter avoids leaky somatic expression, but at the cost of high embryo resistance from maternally deposited Cas9. To improve drive efficiency, we tested eleven Drosophila melanogaster germline promoters in several configurations. Some of the new promoters achieved higher drive conversion efficiency with minimal embryo resistance, but none could completely avoid somatic expression like nanos. However, such somatic expression often did not carry detectable fitness costs when the promoter-Cas9 elements supported a rescue homing drive targeting a haplolethal gene, suggesting somatic drive conversion. Based on our findings, we selected two Cas9 promoter lines for cage experiments with a 4-gRNA suppression drive. While one promoter exhibited substantial somatic effects, leading to a low drive equilibrium frequency, the other outperformed nanos, resulting in the successful suppression of the cage population. Overall, these novel Cas9 promoters hold potential advantages for homing drives in Drosophila species and may also possess valuable homologs in other organisms.

genetics↗