Scholarly Literature
This is an aggregation of scholarly literature from peer-reviewed journals, bioRxiv , medRxiv and arXiv preprint servers focused on natural and engineered selfish genetic elements and genetic biocontrol. New citations are added as they appear. This content is intended for anyone interested in the scholarly literature on gene drive and genetic biocontrol.
CRISPR/Cas9 -mediated gene knockout of Anopheles gambiae FREP1 suppresses malaria parasite infection
3973Dong, YS, Maria L.; Marois, Eric; Dimopoulos, George, PLOS Pathogens, 14:e1006898. 2018-01-11 00:00:00.
The causative agent of malaria, Plasmodium, has to complete a complex infection cycle in the Anopheles gambiae mosquito vector in order to reach the salivary gland from where it can be transmitted to a human host. The parasite’s development in the mosquito relies on numerous host factors (agonists), and their inhibition or inactivation can thereby result in suppression of infection and consequently malaria transmission. The recently developed CRISPR/Cas9-based genome editing tools for Anopheles mosquitoes provide new and promising opportunities to delete (inactivate) Plasmodium agonists to better understand their function and for blocking malaria transmission. Here we have established a modified CRISPR/Cas9 genome editing technique for malaria vector A. gambiae mosquitoes. Through this approach we have inactivated the fibrinogen-related protein 1 (FREP1) gene, via CRISPR/Cas9 genome editing, and the impact of this manipulation on the mosquito’s susceptibility to Plasmodium and on mosquito fitness. FREP1 knockout mutants showed a profound suppression of infection with both human and rodent malaria parasites, while it also resulted in fitness costs: a significantly lower blood-feeding propensity, fecundity and egg hatching rate, and a retarded larval development and pupation time, and reduced longevity after a blood meal.
Genetically engineered mosquitoes, Zika and other arboviruses, community engagement, costs, and patents: Ethical issues
3993Meghani, ZB, Christophe, PLOS Neglected Tropical Diseases, 12:e0006501. 2018-01-11 00:00:00.
We discuss here key ethical questions raised by the use of GE insects, with the aim of fostering discussion between the public, researchers, policy makers, healthcare organizations, and regulatory agencies at the local, national, and international levels. We affect that goal by outlining a procedural approach to decision-making about the use of the biotechnology that goes beyond community engagement. The protocol we advocate for entails informed deliberations and decision-making at the community level. It is designed to ensure that the voices of the marginalized and vulnerable groups that would be disproportionately affected by the decision are heard during the community-wide discussions. Moreover, we make the case that the values embedded in the risk assessment should be identified so that the community can make an informed decision about the use of GE insects. In addition, we advocate for the involvement of a variety of actors whose responsibility would be to ensure that the community has the opportunity to make an informed decision based on deliberations about the use of the biotechnology.
Carrying a selfish genetic element predicts increased migration propensity in free-living wild house mice
4012Runge, J-NL, Anna K., Proceedings of the Royal Society B: Biological Sciences, 285:20181333. 2018-01-10 00:00:00.
Life is built on cooperation between genes, which makes it vulnerable to parasitism. Selfish genetic elements that exploit this cooperation can achieve large fitness gains by increasing their transmission relative to the rest of the genome. This leads to counter-adaptations that generate unique selection pressures on the selfish genetic element. This arms race is similar to host–parasite coevolution, as some multi-host parasites alter the host’s behaviour to increase the chance of transmission to the next host. Here, we ask if, similarly to these parasites, a selfish genetic element in house mice, the t haplotype, also manipulates host behaviour, specifically the host’s migration propensity. Variants of the t that manipulate migration propensity could increase in fitness in a meta-population. We show that juvenile mice carrying the t haplotype were more likely to emigrate from and were more often found as migrants within a long-term free-living house mouse population. This result may have applied relevance as the t has been proposed as a basis for artificial gene drive systems for use in population control.
CRISPR-based gene drives for pest control
3992McFarlane, GRW, C. Bruce A.; Lillico, Simon G., Trends in Biotechnology, 36:130-133. 2018-01-10 00:00:00.
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drives (GDs) could be used to spread desirable genetic elements through wild populations. With the imminent development of this technology in vertebrates, we believe that it is timely to highlight two forms of sex-ratio distorting GDs that show potential as pest management tools.
Invasion and migration of spatially self-limiting gene drives: A comparative analysis
3972Dhole, S.; Vella, M. R; Lloyd, A. L.; Gould, F., Evolutionary Applications, 11:794-808. 2018-01-10 00:00:00.
Recent advances in research on gene drives have produced genetic constructs that could theoretically spread a desired gene (payload) into all populations of a species, with a single release in one place. This attribute has advantages, but also comes with risks and ethical concerns. There has been a call for research on gene drive systems that are spatially and/or temporally self?limiting. Here, we use a population genetics model to compare the expected characteristics of three spatially self?limiting gene drive systems: one?locus underdominance, two?locus underdominance and daisy?chain drives. We find large differences between these gene drives in the minimum release size required for successfully driving a payload into a population. The daisy?chain system is the most efficient, requiring the smallest release, followed by the two?locus underdominance system, and then the one?locus underdominance system. However, when the target population exchanges migrants with a nontarget population, the gene drives requiring smaller releases suffer from higher risks of unintended spread. For payloads that incur relatively low fitness costs (up to 30%), a simple daisy?chain drive is practically incapable of remaining localized, even with migration rates as low as 0.5% per generation. The two?locus underdominance system can achieve localized spread under a broader range of migration rates and of payload fitness costs, while the one?locus underdominance system largely remains localized. We also find differences in the extent of population alteration and in the permanence of the alteration achieved by the three gene drives. The two?locus underdominance system does not always spread the payload to fixation, even after successful drive, while the daisy?chain system can, for a small set of parameter values, achieve a temporally limited spread of the payload. These differences could affect the suitability of each gene drive for specific applications.
Can CRISPR-based gene drive be confined in the Wild? A question for molecular and population biology
3991Marshall, JMA, Omar S., ACS Chemical Biology, 13:424-430. 2018-01-09 00:00:00.
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.
Gene drives in our future: challenges of and opportunities for using a self-sustaining technology in pest and vector management
3971Collins, JP, BMC Proceedings, 12:9. 2018-01-09 00:00:00.
Gene drives are systems of biased inheritance that enhance the likelihood a sequence of DNA passes between generations through sexual reproduction and potentially throughout a local population and ultimately all connected populations of a species. Gaps in our knowledge of gene drive systems prompted the US National Institutes of Health (NIH) and the Foundation for the NIH to ask the US National Academies of Sciences, Engineering, and Medicine (NASEM) to convene an expert panel to provide an independent, objective examination of what we know about gene drive systems. The report, “Gene drives on the horizon: Advancing science, navigating uncertainty, and aligning research with public values,” outlines our understanding of the science, ethics, public engagement, governance, and risk assessment pertaining to gene drive research.
Gene drive gets safety features limiting risk for a tool that could alter entire species
Collins, CH, Scientific American, 319:37-38. 2018-01-08 00:00:00.Research into a genetic engineering technology that can permanently change the traits of a population or even an entire species is progressing rapidly. The approach uses gene drives—genetic elements that pass from parents to unusually high numbers of their offspring, thereby spreading through populations rather quickly. Gene drives occur naturally but can also be engineered, and doing so could be a boon to humanity in many ways. The technology has the potential to stop insects from transmitting malaria and other terrible infections, enhance crop yields by altering pests that attack plants, render corals resistant to environmental stress, and keep invasive plants and animals from destroying ecosystems. Yet investigators are deeply aware that altering or even eliminating a species could have profound consequences. In response, they are developing rules to govern the transfer of gene drives from the laboratory into future field tests and wider use.
Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta
4010Ross, KGS, DeWayne, BMC Genetics, 19:101. 2018-01-08 00:00:00.
The Sb supergene in the fire ant Solenopsis invicta determines the form of colony social organization, with colonies whose inhabitants bear the element containing multiple reproductive queens and colonies lacking it containing only a single queen. Several features of this supergene — including suppressed recombination, presence of deleterious mutations, association with a large centromere, and “green-beard” behavior — suggest that it may be a selfish genetic element that engages in transmission ratio distortion (TRD), defined as significant departures in progeny allele frequencies from Mendelian inheritance ratios. We tested this possibility by surveying segregation ratios in embryo progenies of 101 queens of the “polygyne” social form (3512 embryos) using three supergene-linked markers and twelve markers outside the supergene.
Veni, vidi, vici: the success of wtf meiotic drivers in fission yeast
3990López Hernández, JFZ, Sarah E., Yeast, 35:447-453. 2018-01-08 00:00:00.
Meiotic drivers are selfish DNA loci that can bias their own transmission into gametes. Owing to their transmission advantages, meiotic drivers can spread in populations even if the drivers or linked variants decrease organismal fitness. Meiotic drive was first formally described in the 1950s and is thought to be a powerful force shaping eukaryotic genomes. Classic genetic analyses have detected the action of meiotic drivers in plants, filamentous fungi, insects and vertebrates. Several of these drive systems have limited experimental tractability and relatively little is known about the molecular mechanisms of meiotic drive. Recently, however, meiotic drivers were discovered in a yeast species. The Schizosaccharomyces pombe wtf gene family contains several active meiotic drive genes. This review summarizes what is known about the wtf family and highlights its potential as a highly tractable experimental model for molecular and evolutionary characterization of meiotic drive.
Development of a multi-locus CRISPR gene drive system in budding yeast
4029Yan, YF, Gregory C., Scientific reports, 8:17277-17277. 2018-01-07 00:00:00.
The discovery of CRISPR/Cas gene editing has allowed for major advances in many biomedical disciplines and basic research. One arrangement of this biotechnology, a nuclease-based gene drive, can rapidly deliver a genetic element through a given population and studies in fungi and metazoans have demonstrated the success of such a system. This methodology has the potential to control biological populations and contribute to eradication of insect-borne diseases, agricultural pests, and invasive species. However, there remain challenges in the design, optimization, and implementation of gene drives including concerns regarding biosafety, containment, and control/inhibition. Given the numerous gene drive arrangements possible, there is a growing need for more advanced designs. In this study, we use budding yeast to develop an artificial multi-locus gene drive system. Our minimal setup requires only a single copy of S. pyogenes Cas9 and three guide RNAs to propagate three gene drives. We demonstrate how this system could be used for targeted allele replacement of native genes and to suppress NHEJ repair systems by modifying DNA Ligase IV. A multi-locus gene drive configuration provides an expanded suite of options for complex attributes including pathway redundancy, combatting evolved resistance, and safeguards for control, inhibition, or reversal of drive action.
Population dynamics of underdominance gene drive systems in continuous space
3969Champer, JZ, Joanna; Champer, Sam; Liu, Jingxian; Messer, Philipp W., bioRxiv, 449355:1-23. 2018-01-07 00:00:00.
Underdominance gene drive systems promise a mechanism for rapidly spreading payload alleles through a local population while otherwise remaining confined, unable to spread into neighboring populations due to their frequency-dependent dynamics. Such systems could provide a new tool in the fight against vector-borne diseases by disseminating transgenic payloads through vector populations. If local confinement can indeed be achieved, the decision-making process for the release of such constructs would likely be considerably simpler compared to other gene drive mechanisms such as CRISPR homing drives. So far, the confinement ability of underdominance systems has only been demonstrated in models of panmictic populations linked by migration. How such systems would behave in realistic populations where individuals move over continuous space remains largely unknown. Here, we study several underdominance systems in continuous-space population models and show that their dynamics are drastically altered from those in panmictic populations. Specifically, we find that all underdominance systems we studied can fail to persist in such environments, even after successful local establishment. At the same time, we find that a two-locus two-toxin-antitoxin system can still successfully invade neighboring populations in many scenarios even under weak migration. This suggests that the parameter space for underdominance systems to both establish in a given region and remain confined to that region would likely be highly limited. Overall, these results indicate that spatial context must be considered when assessing strategies for the deployment of underdominance systems.
Recent advances in threshold-dependent gene drives for mosquitoes
3989Leftwich, PTE, Matthew P.; Harvey-Samuel, Tim; Carabajal Paladino, Leonela Z.; Norman, Victoria C.; Alphey, Luke, Biochemical Society Transactions, 46:1203-1212. 2018-01-07 00:00:00.
Mosquito-borne diseases, such as malaria, dengue and chikungunya, cause morbidity and mortality around the world. Recent advances in gene drives have produced control methods that could theoretically modify all populations of a disease vector, from a single release, making whole species less able to transmit pathogens. This ability has caused both excitement, at the prospect of global eradication of mosquito-borne diseases, and concern around safeguards. Drive mechanisms that require individuals to be released at high frequency before genes will spread can therefore be desirable as they are potentially localised and reversible. These include underdominance-based strategies and use of the reproductive parasite Wolbachia. Here, we review recent advances in practical applications and mathematical analyses of these threshold-dependent gene drives with a focus on implementation in Aedes aegypti, highlighting their mechanisms and the role of fitness costs on introduction frequencies. Drawing on the parallels between these systems offers useful insights into practical, controlled application of localised drives, and allows us to assess the requirements needed for gene drive reversal.CI, cytoplasmic incompatibility; UD, underdominance; UDMEL, maternal-effect lethal underdominance
Tuning CRISPR-Cas9 gene grives in Saccharomyces cerevisiae
4009Roggenkamp, EG, Rachael M.; Schrock, Madison N.; Turnquist, Emily; Halloran, Megan; Finnigan, Gregory C., G3-Genes Genomes Genetics, 8:999. 2018-01-07 00:00:00.
Control of biological populations is an ongoing challenge in many fields, including agriculture, biodiversity, ecological preservation, pest control, and the spread of disease. In some cases, such as insects that harbor human pathogens (e.g., malaria), elimination or reduction of a small number of species would have a dramatic impact across the globe. Given the recent discovery and development of the CRISPR-Cas9 gene editing technology, a unique arrangement of this system, a nuclease-based “gene drive,” allows for the super-Mendelian spread and forced propagation of a genetic element through a population. Recent studies have demonstrated the ability of a gene drive to rapidly spread within and nearly eliminate insect populations in a laboratory setting. While there are still ongoing technical challenges to design of a more optimal gene drive to be used in wild populations, there are still serious ecological and ethical concerns surrounding the nature of this powerful biological agent. Here, we use budding yeast as a safe and fully contained model system to explore mechanisms that might allow for programmed regulation of gene drive activity. We describe four conserved features of all CRISPR-based drives and demonstrate the ability of each drive component—Cas9 protein level, sgRNA identity, Cas9 nucleocytoplasmic shuttling, and novel Cas9-Cas9 tandem fusions—to modulate drive activity within a population.
Reducing resistance allele formation in CRISPR gene drive
3968Champer, JL, Jingxian; Oh, Suh Yeon; Reeves, Riona; Luthra, Anisha; Oakes, Nathan; Clark, Andrew G.; Messer, Philipp W., Proceedings of the National Academy of Sciences of the United States of America, 115:5522-5527. 2018-01-06 00:00:00.
A functioning gene drive mechanism could fundamentally change our strategies for the control of vector-borne diseases, such as malaria, dengue, and Zika. CRISPR homing gene drive promises such a mechanism, which could be used to rapidly spread genetic modifications among the mosquitoes that transmit these diseases. However, recent studies have shown that current drives would likely be unable to spread in insect populations due to the high rate at which resistance will evolve. In this study, we provide an experimental demonstration that guide RNA multiplexing can successfully reduce resistance rates but also find that such an approach would still need to be combined with additional strategies to create drives that are efficient enough for use in wild populations.CRISPR homing gene drives can convert heterozygous cells with one copy of the drive allele into homozygotes, thereby enabling super-Mendelian inheritance. Such a mechanism could be used, for example, to rapidly disseminate a genetic payload in a population, promising effective strategies for the control of vector-borne diseases. However, all CRISPR homing gene drives studied in insects thus far have produced significant quantities of resistance alleles that would limit their spread. In this study, we provide an experimental demonstration that multiplexing of guide RNAs can both significantly increase the drive conversion efficiency and reduce germline resistance rates of a CRISPR homing gene drive in Drosophila melanogaster. We further show that an autosomal drive can achieve drive conversion in the male germline, with no subsequent formation of resistance alleles in embryos through paternal carryover of Cas9. Finally, we find that the nanos promoter significantly lowers somatic Cas9 expression compared with the vasa promoter, suggesting that nanos provides a superior choice in drive strategies where gene disruption in somatic cells could have fitness costs. Comparison of drive parameters among the different constructs developed in this study and a previous study suggests that, while drive conversion and germline resistance rates are similar between different genomic targets, embryo resistance rates can vary significantly. Taken together, our results mark an important step toward developing effective gene drives capable of functioning in natural populations and provide several possible avenues for further control of resistance rates.
RPM-Drive: A robust, safe, and reversible gene drive system that remains functional after 200+ generations
4008Reed, FAA-M, Todd G.; Costantini, Maria S.; Láruson, Áki J.; Sutton, Jolene T., arXiv, 1806.05304:1-19. 2018-01-06 00:00:00.
Despite the advent of several novel, synthetic gene drive mechanisms and their potential to one-day control a number of devastating diseases, among other applications, practical use of these systems remains contentious and risky. In particular, there is little in the way of empirical evidence of the long-term robustness of these synthetic systems against mutational breakdown. Rather, most existing systems are either known or predicted to be susceptible to rapid inactivation, though methodological designs continue to be refined. Here we evaluate a currently existing synthetic, underdominance-based gene drive system 200+ generations after it was first established in a laboratory colony of Drosophila melanogaster. Not only do we find that the system is still functioning as designed, we also show evidence that disruptions to the genetic construct are highly likely to be removed by natural selection, contributing to the system's robust, long-term stability. This stability appears to be a result of a fundamental relationship between ribosomal proteins (a novel target of the system) and natural cellular defenses that protect against cancer development. As far as we are aware, this is the longest continually functioning synthetic gene drive system thus verified, making it highly appropriate for additional research into its eventual suitability for field trials. Due to inherent properties of this gene drive, it is also likely to be adaptable for use in many different species. The insect lines established and used to test this system have been deposited at a Drosophila stock center, and are available to labs for further, independent testing.
The use of driving endonuclease genes to suppress mosquito vectors of malaria in temporally variable environments
3988Lambert, BN, Ace; Burt, Austin; Godfray, H. Charles J., Malaria Journal, 17:154. 2018-01-06 00:00:00.
The use of gene drive systems to manipulate populations of malaria vectors is currently being investigated as a method of malaria control. One potential system uses driving endonuclease genes (DEGs) to spread genes that impose a genetic load. Previously, models have shown that the introduction of DEG-bearing mosquitoes could suppress or even extinguish vector populations in spatially-heterogeneous environments which were constant over time. In this study, a stochastic spatially-explicit model of mosquito ecology is combined with a rainfall model which enables the generation of a variety of daily precipitation patterns. The model is then used to investigate how releases of a DEG that cause a bias in population sex ratios towards males are affected by seasonal or random rainfall patterns. The parameters of the rainfall model are then fitted using data from Bamako, Mali, and Mbita, Kenya, to evaluate release strategies in similar climatic conditions.
A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes
3987Kyrou, KH, Andrew M.; Galizi, Roberto; Kranjc, Nace; Burt, Austin; Beaghton, Andrea K.; Nolan, Tony; Crisanti, Andrea, Nature Biotechnology, 36:1062–1066. 2018-01-05 00:00:00.
In the human malaria vector Anopheles gambiae, the gene doublesex (Agdsx) encodes two alternatively spliced transcripts, dsx-female (AgdsxF) and dsx-male (AgdsxM), that control differentiation of the two sexes. The female transcript, unlike the male, contains an exon (exon 5) whose sequence is highly conserved in all Anopheles mosquitoes so far analyzed. We found that CRISPR–Cas9-targeted disruption of the intron 4–exon 5 boundary aimed at blocking the formation of functional AgdsxF did not affect male development or fertility, whereas females homozygous for the disrupted allele showed an intersex phenotype and complete sterility. A CRISPR–Cas9 gene drive construct targeting this same sequence spread rapidly in caged mosquitoes, reaching 100% prevalence within 7–11 generations while progressively reducing egg production to the point of total population collapse. Owing to functional constraint of the target sequence, no selection of alleles resistant to the gene drive occurred in these laboratory experiments. Cas9-resistant variants arose in each generation at the target site but did not block the spread of the drive.
Catch me if you can: A spatial model for a brake-driven gene drive reversal
3967Calvez, V,,Debarre, F., Girardin, Leo, arXiv, 1812.06641:1-30. 2018-01-05 00:00:00.
We successfully prove that, whenever the drive fitness is at most 50% of the wild-type one while the brake fitness is close to the wild-type one, co-extinction of the brake and the drive occurs in the long run.
Correction to ‘Dodging silver bullets: good CRISPR gene-drive design is critical for eradicating exotic vertebrates’
4007Prowse, TAAC, Phillip; Ross, Joshua V.; Pfitzner, Chandran; Wittmann, Talia; Thomas, Paul, Proceedings of the Royal Society B: Biological Sciences, 285:1-2. 2018-01-05 00:00:00.
Proc. R. Soc. B 284, 20170799. (Published Online 9 August 2017). (doi:10.1098/rspb.2017.0799)We recently found an error in our calculation of the probability of a wild-type allele moving from s to j susceptible sites (), and acquiring the gene drive (), during gene-drive homing, under the assumption that multiplexed gRNAs are expressed simultaneously. In the R code provided (function GeneDriveSimRec, appendix S1), these probabilities are calculated recursively and the multiplier was missing (from line 11), where j is the number of cut target sites along an inter-site NHEJ-mediated deletion at which NHEJ …
Rationally-engineered reproductive barriers using CRISPR & CRISPRa: an evaluation of the synthetic species concept in Drosophila melanogaster
4027Waters, AJC, Paolo; Gaboriau, David C. A.; Papathanos, Philippos Aris; Windbichler, Nikolai, Scientific Reports, 8:13125. 2018-01-05 00:00:00.
The ability to erect rationally-engineered reproductive barriers in animal or plant species promises to enable a number of biotechnological applications such as the creation of genetic firewalls, the containment of gene drives or novel population replacement and suppression strategies for genetic control. However, to date no experimental data exist that explores this concept in a multicellular organism. Here we examine the requirements for building artificial reproductive barriers in the metazoan model Drosophila melanogaster by combining CRISPR-based genome editing and transcriptional transactivation (CRISPRa) of the same loci. We directed 13 single guide RNAs (sgRNAs) to the promoters of 7 evolutionary conserved genes and used 11 drivers to conduct a misactivation screen. We identify dominant-lethal activators of the eve locus and find that they disrupt development by strongly activating eve outside its native spatio-temporal context. We employ the same set of sgRNAs to isolate, by genome editing, protective INDELs that render these loci resistant to transactivation without interfering with target gene function. When these sets of genetic components are combined we find that complete synthetic lethality, a prerequisite for most applications, is achievable using this approach. However, our results suggest a steep trade-off between the level and scope of dCas9 expression, the degree of genetic isolation achievable and the resulting impact on fly fitness. The genetic engineering strategy we present here allows the creation of single or multiple reproductive barriers and could be applied to other multicellular organisms such as disease vectors or transgenic organisms of economic importance.
Ban on ‘gene drives’ is back on the UN’s agenda – worrying scientists
Callaway, E, Nature, 563:454-455. 2018-01-04 00:00:00.Government representatives from nearly 170 countries will this month consider whether to temporarily ban the release of organisms carrying gene drives — a controversial technology that can quickly propagate a chosen gene throughout a population. The technique has the potential to eradicate disease, control pests and alter entire ecosystems, but with unpredictable consequences — leading some groups to call for a global moratorium on its field applications.
Modelling Allee effects in a transgenic mosquito population during range expansion
4026Walker, MB, Julie C.; Brown, Vicki; Childs, Lauren M., Journal of Biological Dynamics, 13:2-22. 2018-01-04 00:00:00.
Mosquitoes are vectors for many diseases that cause significant mortality and morbidity. As mosquito populations expand their range, they may undergo mate-finding Allee effects such that their ability to successfully reproduce becomes difficult at low population density. With new technology, creating target specific gene modification may be a viable method for mosquito population control. We develop a mathematical model to investigate the effects of releasing transgenic mosquitoes into newly established, low-density mosquito populations. Our model consists of two life stages (aquatic and adults), which are divided into three genetically distinct groups: heterogeneous and homogeneous transgenic that cause female infertility and a homogeneous wild type. We perform analytical and numerical analyses on the equilibria to determine the level of saturation needed to eliminate mosquitoes in a given area. This model demonstrates the potential for a gene drive system to reduce the spread of invading mosquito populations.
Redkmer: An assembly-free pipeline for the identification of abundant and specific X-chromosome target sequences for X-shredding by CRISPR endonucleases
4006Papathanos, PAW, Nikolai, CRISPR Journal, 1:88-98. 2018-01-04 00:00:00.
CRISPR-based synthetic sex ratio distorters, which operate by shredding the X-chromosome during male meiosis, are promising tools for the area-wide control of harmful insect pest or disease vector species. X-shredders have been proposed as tools to suppress insect populations by biasing the sex ratio of the wild population toward males, thus reducing its natural reproductive potential. However, to build synthetic X-shredders based on CRISPR, the selection of gRNA targets, in the form of high-copy sequence repeats on the X chromosome of a given species, is difficult, since such repeats are not accurately resolved in genome assemblies and cannot be assigned to chromosomes with confidence. We have therefore developed the redkmer computational pipeline, designed to identify short and highly abundant sequence elements occurring uniquely on the X chromosome. Redkmer was designed to use as input minimally processed whole genome sequence data from males and females. We tested redkmer with short- and long-read whole genome sequence data of Anopheles gambiae, the major vector of human malaria, in which the X-shredding paradigm was originally developed. Redkmer established long reads as chromosomal proxies with excellent correlation to the genome assembly and used them to rank X-candidate kmers for their level of X-specificity and abundance. Among these, a high-confidence set of 25-mers was identified, many belonging to previously known X-chromosome repeats of Anopheles gambiae,including the ribosomal gene array and the selfish elements harbored within it. Data from a control strain, in which these repeats are shared with the Y chromosome, confirmed the elimination of these kmers during filtering. Finally, we show that redkmer output can be linked directly to gRNA selection and off-target prediction. In addition, the output of redkmer, including the prediction of chromosomal origin of single-molecule long reads and chromosome specific kmers, could also be used for the characterization of other biologically relevant sex chromosome sequences, a task that is frequently hampered by the repetitiveness of sex chromosome sequence content.
Production of YY Supermale and XY Physiological Female Common Carp for Potential Eradication of this Invasive Species
11508M. Y. Jiang, X. X. Wu, K. X. Chen, H. R. Luo, W. Yu, S. T. Jia, Y. M. Li, Y. F. Wang, P. H. Yang, Z. Y. Zhu and W. Hu, Journal of the World Aquaculture Society, 49:315-327. 2018-01-03 15:22:53.
The common carp, Cyprinus carpio, is the third most cultivated freshwater species worldwide, but is also considered an invasive species. The Trojan Y chromosome strategy is one of the most promising methods to eradicate this invasive species. However, obtaining fertile YY supermale (MYY) and YY physiological female (FYY) common carp was thought to be very difficult. The present study focused on the production of androgenetic MYY and XY physiological female (FXY) common carp. We first optimized the conditions for artificially induced androgenesis. The results indicated that the optimum ultraviolet (UV) exposure time was 4min at an irradiation distance of 26cm and the optimum initiation time with heat shock (40 +/- 0.5C for 2min) was 30min after fertilization. Then, we produced androgenetic MYY Yellow River carp with only paternal inheritance, which were viable and identified by paternity testing and test crossing. Finally, we successfully produced FXY Yellow River carp by feeding 60-d-old MXY with commercially available feed mixed with 17-estradiol (200mg/kg) and Flutamide (200mg/kg) for 3mo. In conclusion, by combining artificially induced androgenesis with an artificially induced sex reversal technique, we could cost-effectively produce MYY and FXY common carp.
B Chromosomes in populations of mammals revisited
4025Vujoševi?, MR, Marija; Blagojevi?, Jelena, Genes, 9:487. 2018-01-03 00:00:00.
The study of B chromosomes (Bs) started more than a century ago, while their presence in mammals dates since 1965. As the past two decades have seen huge progress in application of molecular techniques, we decided to throw a glance on new data on Bs in mammals and to review them. We listed 85 mammals with Bs that make 1.94% of karyotypically studied species. Contrary to general view, a typical B chromosome in mammals appears both as sub- or metacentric that is the same size as small chromosomes of standard complement. Both karyotypically stable and unstable species possess Bs. The presence of Bs in certain species influences the cell division, the degree of recombination, the development, a number of quantitative characteristics, the host-parasite interactions and their behaviour. There is at least some data on molecular structure of Bs recorded in nearly a quarter of species. Nevertheless, a more detailed molecular composition of Bs presently known for six mammalian species, confirms the presence of protein coding genes, and the transcriptional activity for some of them. Therefore, the idea that Bs are inert is outdated, but the role of Bs is yet to be determined. The maintenance of Bs is obviously not the same for all species, so the current models must be adapted while bearing in mind that Bs are not inactive as it was once thought.
Behavior of homing endonuclease gene drives targeting genes required for viability or female fertility with multiplexed guide RNAs
4005Oberhofer, GI, Tobin; Hay, Bruce A., Proceedings of the National Academy of Sciences of the United States of America, 115:e9343. 2018-01-03 00:00:00.
Homing endonuclease gene (HEG)-based gene drive can bring about population suppression when genes required for viability or fertility are targeted. However, these strategies are vulnerable to failure through mechanisms that create alleles resistant to cleavage but that retain wild-type gene function. We show that resistance allele creation can be prevented through the use of guide RNAs designed to cleave a gene at four target sites. However, homing rates were modest, and the HEGs were unstable during homing. In addition, use of a promoter active in the female germline resulted in levels of HEG carryover that compromised the viability or fertility of HEG-bearing heterozygotes, thereby preventing drive. We propose strategies that can help to overcome these problems in next-generation HEG systems.A gene drive method of particular interest for population suppression utilizes homing endonuclease genes (HEGs), wherein a site-specific, nuclease-encoding cassette is copied, in the germline, into a target gene whose loss of function results in loss of viability or fertility in homozygous, but not heterozygous, progeny. Earlier work in Drosophila and mosquitoes utilized HEGs consisting of Cas9 and a single guide RNA (gRNA) that together target a specific gene for cleavage. Homing was observed, but resistant alleles immune to cleavage, while retaining wild-type gene function, were also created through nonhomologous end joining. Such alleles prevent drive and population suppression. Targeting a gene for cleavage at multiple positions has been suggested as a strategy to prevent the appearance of resistant alleles. To test this hypothesis, we generated two suppression HEGs in Drosophila melanogaster targeting genes required for embryonic viability or fertility, using a HEG consisting of CRISPR/Cas9 and gRNAs designed to cleave each gene at four positions. Rates of target locus cleavage were very high, and multiplexing of gRNAs prevented resistant allele formation. However, germline homing rates were modest, and the HEG cassette was unstable during homing events, resulting in frequent partial copying of HEGs that lacked gRNAs, a dominant marker gene, or Cas9. Finally, in drive experiments, the HEGs failed to spread due to the high fitness load induced in offspring as a result of maternal carryover of Cas9/gRNA complex activity. Alternative design principles are proposed that may mitigate these problems in future gene drive engineering.
Consequences of resistance evolution in a Cas9-based sex conversion-suppression gene drive for insect pest management
3985Carrami, Eli M., ME, Kolja N.; Ahmed, Hassan M. M.; Sánchez C., Héctor M.; Dippel, Stefan; Marshall, John M.; Wimmer, Ernst A., Proceedings of the National Academy of Sciences of the United States of America, 115:6189-6194. 2018-01-03 00:00:00.
Resistance evolution caused by CRISPR/Cas9 gene-drive systems has a major impact on both the future scientific design of such gene-drive systems and on the politics of regulating experimentation and use of such systems. In our study, we show that in-frame drive-resistant alleles can be produced readily and inherently in a suppression gene-drive system. The rate at which such alleles emerge will determine the maximum size of the population that could be targeted for collapse and elimination. Here, we provide a potential target site and the modeling framework for implementation and optimization of a suppression gene-drive strategy to control Mediterranean fruit fly populations.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.
Self-limiting population genetic control with sex-linked genome editors
3965Burt, AD, Anne, Proceedings of the Royal Society B: Biological Sciences, 285:20180776. 2018-01-03 00:00:00.
In male heterogametic species the Y chromosome is transmitted solely from fathers to sons, and is selected for based only on its impacts on male fitness. This fact can be exploited to develop efficient pest control strategies that use Y-linked editors to disrupt the fitness of female descendants. With simple population genetic and dynamic models we show that Y-linked editors can be substantially more efficient than other self-limiting strategies and, while not as efficient as gene drive approaches, are expected to have less impact on non-target populations with which there is some gene flow. Efficiency can be further augmented by simultaneously releasing an autosomal X-shredder construct, in either the same or different males. Y-linked editors may be an attractive option to consider when efficient control of a species is desired in some locales but not others.
Advancing a new toolkit for conservation: From science to policy
4004Novak, BJM, T.; Phelan, R., CRISPR Journal, 1:11-15. 2018-01-02 00:00:00.
Climate change and non-native wildlife diseases are exacerbating persistent challenges to biodiversity such as habitat destruction, invasive species and over-harvesting. With these increasing threats there is a pressing need to expand the conservationists' toolbox. CRISPR-Cas9 genome editing (GE) offers a precise and potentially transformative tool to confront these challenges. Researchers, regulators, conservationists and the public are all needed to engage proactively in the thoughtful and responsible development and application of these new tools.
Gene drive: Evolved and synthetic
3964Burt, AC, Andrea, ACS Chemical Biology, 13:343-346. 2018-01-02 00:00:00.
Drive is a process of accelerated inheritance from one generation to the next that allows some genes to spread rapidly through populations even if they do not contribute to—or indeed even if they detract from—organismal survival and reproduction. Genetic elements that can spread by drive include gametic and zygotic killers, meiotic drivers, homing endonuclease genes, B chromosomes, and transposable elements. The fact that gene drive can lead to the spread of fitness-reducing traits (including lethality and sterility) makes it an attractive process to consider exploiting to control disease vectors and other pests. There are a number of efforts to develop synthetic gene drive systems, particularly focused on the mosquito-borne diseases that continue to plague us.
Strong hybrid male incompatibilities impede the spread of a selfish chromosome between populations of a fly
4024Verspoor Rudi, LSJ, M. L.; Mannion Natasha, L. M.; Hurst Gregory, D. D.; Price Tom, A. R., Evolution Letters, 2:169-179. 2018-01-02 00:00:00.
Meiotically driving sex chromosomes manipulate gametogenesis to increase their transmission at a cost to the rest of the genome. The intragenomic conflicts they produce have major impacts on the ecology and evolution of their host species. However, their ecological dynamics remain poorly understood. Simple population genetic models predict meiotic drivers will rapidly reach fixation in populations and spread across landscapes. In contrast, natural populations commonly show spatial variation in the frequency of drivers, with drive present in clines or mosaics across species ranges. For example, Drosophila subobscura harbors a sex ratio distorting drive chromosome (SRs) at 15?25% frequency in North Africa, present at less than 2% frequency in adjacent southern Spain, and absent in other European populations. Here, we investigate the forces preventing the spread of the driver northward. We show that SRs has remained at a constant frequency in North Africa, and failed to spread in Spain. We find strong evidence that spread is impeded by genetic incompatibility between SRs and Spanish autosomal backgrounds. When we cross SRs from North Africa onto Spanish genetic backgrounds we observe strong incompatibilities specific to hybrids bearing SRs. The incompatibilities increase in severity in F2 male hybrids, leading to almost complete infertility. We find no evidence supporting an alternative hypothesis, that there is resistance to drive in Spanish populations. We conclude that the source of the stepped frequency variation is genetic incompatibility between the SRs chromosome and the genetic backgrounds of the adjacent population, preventing SRs spreading northward. The low frequency of SRs in South Spain is consistent with recurrent gene flow across the Strait of Gibraltar combined with selection against the SRs element through genetic incompatibility. This demonstrates that incompatibilities between drive chromosomes and naïve populations can prevent the spread of drive between populations, at a continental scale.
Transmission and drive involving parasitic B chromosomes
3984Jones, RN, Genes, 9:e388. 2018-01-02 00:00:00.
B chromosomes (Bs) are enigmatic additional elements in the genomes of thousands of species of plants, animals, and fungi. How do these non-essential, harmful, and parasitic chromosomes maintain their presence in their hosts, making demands on all the essential functions of their host genomes? The answer seems to be that they have mechanisms of drive which enable them to enhance their transmission rates by various processes of non-mendelian inheritance. It is also becoming increasingly clear that the host genomes are developing their own mechanisms to resist the impact of the harmful effects of the Bs.
Community engagement and field trials of genetically modified insects and animals
5913Neuhaus, C. P., Hastings Center Report, 48:25-36. 2018-01-01 16:29:11.
New techniques for the genetic modification of organisms are creating new strategies for addressing persistent public health challenges. For example, the company Oxitec has conducted field trials internationally?and has attempted to conduct field trials in the United States?of a genetically modified mosquito that can be used to control dengue, Zika, and some other mosquito-borne diseases. In 2016, a report commissioned by the National Academies of Sciences, Engineering, and Medicine discussed the potential benefits and risks of another strategy, using gene drives. Driving a desired genotype through a population of wild animals or insects could lead to irreversible genetic modification of an entire species. The NASEM report recommends community, stakeholder, and public engagement about potential uses of the technology, and it argues that the engagement should occur as research advances, well before gene drives are deployed. Yet what ?engagement? means in practice is unclear. This article seeks clarity on this problem by offering a justification for community engagement and drawing out implications of this argument for the implementation and desired outcomes of community engagement. Community engagement is essential when it comes to research that would release genetically modified insects or animals into the environment. By contrast, obtaining informed consent from people who live near such a proposed field trial is neither necessary nor sufficient. Drawing on the epistemic and moral arguments for deliberative democracy, I propose two discrete mechanisms of community engagement: community advisory boards and deliberative forums, neither of which has been systematically incorporated into research governance. The proposed mechanisms would engender respect for persons who live near field trials, even when the results of deliberation override some individuals? preferences. Community engagement foregrounds the community in our thinking about humans? relationship to nature, and it implies that deciding to release genetically modified insects or animals into the wild ought to be a collective decision, not one made by product developers, policy-makers, private companies, research funders, or scientists alone.
Making policies about emerging technologies
5909Kaebnick, G. E. and M. K. Gusmano, Hastings Center Report, 48:S2-S11. 2018-01-01 16:23:19.
Can we make wise policy decisions about still-emerging technologies?decisions that are grounded in facts yet anticipate unknowns and promote the public's preferences and values? There is a widespread feeling that we should try. There also seems to be widespread agreement that the central element in wise decisions is the assessment of benefits and costs, understood as a process that consists, at least in part, in measuring, tallying, and comparing how different outcomes would affect the public interest. But how benefits and costs are best weighed when making decisions about whether to move forward with an emerging technology is not clear. Many commentators feel that the weighing is often inadequate or inappropriate. Those who argue for a ?precautionary? approach to the weighing do so precisely because they feel the need for a restraint on the dominant decision-making tools and processes for assessing outcomes. This Hastings Center special report examines those tools and processes, taking the method known as cost-benefit analysis as a starting point. In U.S. governance, CBA, sometimes informed by risk assessment, is the most widely used and extensively studied method, and authoritative reports on genetic and reproductive technologies often use language suggestive of cost-benefit analysis. There is also a long-running debate about the role of values in CBA and other formal impact assessment mechanisms?and about how those mechanisms compare to the precautionary principle. The guiding idea in the report is to engage in a close examination of the strengths and limits of CBA for ensuring that emerging technologies are used in ways that square with the public's values, drawing on applications of synthetic biology to illustrate and sharpen the analysis and then considering corrections to CBA and some alternative methodologies that handle values differently.
Informed consent in field trials of gene-drive mosquitoes
15682P. A. Kolopack and J. V. Lavery, Gates Open Research, 2017-12-11 14:46:00.
We argue that informed consent from individual research participants in gene drive trials may be required: (1) when blood and other forms of clinical data are collected from them, as will likely be the case in some studies involving epidemiological endpoints, such as the incidence of new infections with dengue and malaria; (2) when they participate in social science and/or behavioral research involving the completion of surveys and questionnaires; or (3) when their home or property is accessed and the location recorded as a spatial variable for the release or collection of mosquitoes because the precise location of the household is important for entomological reasons and these data constitute identifiable private information at the household level. Importantly, most regulations and guidelines allow these requirements to be waived or modified, to various degrees, according to the judgment of Institutional Review Boards.
Conservation demands safe gene drive
13629K. M. Esvelt and N. J. Gemmell, PLOS Biology, 15:e2003850. 2017-11-16 14:03:39.
Here, we explore the risk of accidental spread posed by self-propagating gene drive technologies, highlight new gene drive designs that might achieve better outcomes, and explain why we need open and international discussions concerning a technology that could have global ramifications.
Spindle asymmetry drives non-Mendelian chromosome segregation
13518T. Akera, L. Chmátal, E. Trimm, K. Yang, C. Aonbangkhen, D. M. Chenoweth, C. Janke, R. M. Schultz and M. A. Lampson, Science, 358:668. 2017-11-03 14:19:19.
Genetic elements compete for transmission through meiosis, when haploid gametes are created from a diploid parent. Selfish elements can enhance their transmission through a process known as meiotic drive. In female meiosis, selfish elements drive by preferentially attaching to the egg side of the spindle. This implies some asymmetry between the two sides of the spindle, but the molecular mechanisms underlying spindle asymmetry are unknown. Here we found that CDC42 signaling from the cell cortex regulated microtubule tyrosination to induce spindle asymmetry and that non-Mendelian segregation depended on this asymmetry. Cortical CDC42 depends on polarization directed by chromosomes, which are positioned near the cortex to allow the asymmetric cell division. Thus, selfish meiotic drivers exploit the asymmetry inherent in female meiosis to bias their transmission.
Trojan Females and Judas Goats: Evolutionary Traps as Tools in Wildlife Management
13743B. A. Robertson, R. S. Ostfeld and F. Keesing, Bioscience, 67:982-993. 2017-11-01 19:42:43.
Here, we bring together science from the pest-control, eco-evolutionary, and conservation communities to outline how evolutionary traps can be repurposed to eliminate or control pest species. We highlight case studies and devise strategies for the selection of appropriate cues to manipulate, traits to target, and mechanisms to use in setting evolutionary traps that will most rapidly reduce animal abundance while preventing evolutionary escape. We find that evolutionary traps are demonstrably effective and unique tools with high target-species specificity that are deployable in concert with more traditional approaches.
The potential for the use of gene drives for pest control in New Zealand: a perspective
14253P. K. Dearden, N. J. Gemmell, O. R. Mercier, P. J. Lester, M. J. Scott, R. D. Newcomb, T. R. Buckley, J. M. E. Jacobs, S. G. Goldson and D. R. Penman, Journal of the Royal Society of New Zealand, 48:225-244. 2017-10-25 14:20:45.
Here we describe the current state of gene drive technologies and present a series of examples to examine the potential benefits and problems arising from gene drive approaches for pest control in New Zealand.
The sterile male release approach as a method to control invasive amphibian populations: a preliminary study on Lithobates catesbeianus
13727S. Descamps and A. De Vocht, Management of Biological Invasions, 8:361-370. 2017-09-14 18:55:55.
Widespread populations of the invasive species Lithobates catesbeianus (American bullfrog) are present in different parts of the world and are difficult to control. This study investigated the possibility to sterilize male individuals of this species in order to use the sterile male release technique in controlling these invasive populations.
Using CRISPR-based gene drive for agriculture pest control
13621V. Courtier-Orgogozo, B. Morizot and C. Boëte, EMBO Reports, 18:1481. 2017-09-01 13:15:07.
The authors respond to comments to their publication 10.15252/embr.201744205
The optimal implementation of the Trojan Y chromosome eradication strategy of invasive species
11510M. R. Kelly and X. Y. Wang, Journal of Biological Systems, 25:399-418. 2017-08-02 15:25:17.
Invasive aquatic species continue to be a persistent problem around the world. The Trojan Y Chromosome (TYC) eradication strategy has recently been developed to help fight the problem in aquatic systems by targeting only the invasive species, sparing native marine stock. It involves rearing genetically modified samples of the invasive species and introducing them into the environment to alter the sex ratio of the invasive population. The paper is devoted to finding the optimal implementation of the TYC eradication strategy of an invasive species as well as a modified, potentially more cost-effective strategy. The modified TYC strategy (MTYC) eliminates one round of exposure to sex hormones compared to the TYC strategy. After introducing both strategies, the optimal control problems for each are formulated. The two strategies are compared through numerical simulations. Our results illustrate that the MTYC strategy, with lower implementation costs, is a better strategy option when trying to minimize the overall effective cost in most scenarios.
Illinois study advances possibility of genetic control for major agricultural weeds
11589L. Quinn, ACES News, 2017-07-17 15:35:43.
Waterhemp and Palmer amaranth, two aggressive weeds that threaten the food supply in North America, are increasingly hard to kill with commercially available herbicides. A novel approach known as genetic control could one day reduce the need for these chemicals. Now, scientists are one step closer.
Current vector control challenges in the fight against malaria
16269G. Benelli and J. C. Beier, Acta Tropica, 174:91-96. 2017-07-07 16:47:31.
The majority of National Malaria Control Programs in Africa still rely on indoor residual spraying (IRS) and long-lasting insecticidal nets (LLINs). These methods reduce malaria incidence but generally have little impact on malaria prevalence. In addition to outdoor transmission, growing levels of insecticide resistance in targeted vectors threaten the efficacy of LLINs and IRS.
The IAEA and Food – Tsetse Fly Eradication – Senegal
25659International Atomic Energy Agency, IAEA/FAO, 2017-06-21 14:02:20.
Senegal has successfully integrated the Sterile Insect Technique into its tsetse fly control project in the Niayes region. This nuclear technique suppresses or even eradicates insect pest by using radiation to sterilize primarily males. The disease that tsetse flies transmit can kill livestock or make them sick.
Trends in the development of mammalian pest control technology in New Zealand
13735C. T. Eason, L. Shapiro, S. Ogilvie, C. King and M. Clout, New Zealand Journal of Zoology, 44:267-304. 2017-06-19 19:31:49.
The use of new toxins with advantages in specific settings should be complemented by improvements in resetting trap technology, barrier approaches, and novel biocontrol and genetic concepts. Sodium fluoroacetate (1080) and other important tools have been retained; we have the ingredients for transformational change, and new tools are emerging from a research and development pipeline. However, there has been limited practical experience with emerging technologies compared with traditional or 1080 baits.
A maternal-effect selfish genetic element in Caenorhabditis elegans
14450E. Ben-David, A. Burga and L. Kruglyak, Science, 356:1051. 2017-06-09 17:13:17.
We discovered a selfish element causing embryonic lethality in crosses between wild strains of the nematode Caenorhabditis elegans.
Poisons, antidotes, and selfish genes
14448N. Phadnis, Science, 356:1013. 2017-06-09 16:55:51.
On page1051 of this issue, BenDavid et al . (3) chase down a serendipitous observation of an anomaly in genetic crosses to unmask a toxin-antidote type of selfish system in worms.
Agricultural pest control with CRISPR-based gene drive: time for public debate
13636V. Courtier-Orgogozo, B. Morizot and C. Boëte, EMBO Reports, 18:878-880. 2017-06-01 14:19:16.
Gene drive technology to control disease vectors or pests has great potential for addressing humanitarian and public health problems. Its application for pest control in agriculture, however, raises important environmental, social and ethical issues.
