RESUMEN
Efficient and precise genome editing requires a fast, quantitative, and inexpensive assay to assess genotype following editing. Here, we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs, and then determines which are supported by the data via regression. The ICE algorithm is robust and reproducible, and it can be used to analyze CRISPR experiments within days after transfection. We also confirm that ICE produces accurate estimates of editing outcomes across a variety of benchmarks, and within the context of other existing Sanger analysis tools. The ICE tool is free to use and open source, and offers several improvements over current analysis tools, such as batch analysis and support for a variety of editing conditions. It is available online at ice.synthego.com, and the source code is available at github.com/synthego-open/ice.
Asunto(s)
Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Edición Génica , Sistemas CRISPR-Cas/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , ARN Guía de Kinetoplastida/genética , Programas InformáticosRESUMEN
Parents often face an investment trade-off between either producing many small or fewer large offspring. When environments vary predictably, the fittest parental solution matches available resources by varying only number of offspring and never optimal individual size. However when mismatches occur often between parental expectations and true resource levels, dynamic models like multifaceted parental investment (MFPI) and parental optimism (PO) both predict offspring size can vary significantly. MFPI is a "realist" strategy: parents assume future environments of average richness. When resources exceed expectations and it is too late to add more offspring, the best-case solution increases investment per individual. Brood size distributions therefore track the degree of mismatch from right-skewed around an optimal size (slight underestimation of resources) to left-skewed around a maximal size (gross underestimation). Conversely, PO is an "optimist" strategy: parents assume maximally good resource futures and match numbers to that situation. Normal or lean years do not affect "core" brood as costs primarily fall on excess "marginal" siblings who die or experience stunted growth (producing left-skewed distributions). Investment patterns supportive of both MFPI and PO models have been observed in nature, but studies that directly manipulate food resources to test predictions are lacking. Ant colonies produce many offspring per reproductive cycle and are amenable to experimental manipulation in ways that can differentiate between MFPI and PO investment strategies. Colonies in a natural population of a harvester ant (Pogonomyrmex salinus) were protein-supplemented over 2 years, and mature sexual offspring were collected annually prior to their nuptial flight. Several results support either MFPI or PO in terms of patterns in offspring size distributions and how protein differentially affected male and female production. Unpredicted by either model, however, is that supplementation affected distributions more strongly across years than within (e.g., small females are significantly rarer in the year after colonies receive protein). Parental investment strategies in P. salinus vary dynamically across years and conditions. Finding that past conditions can more strongly affect reproductive decisions than current ones, however, is not addressed by models of parental investment.
Asunto(s)
Hormigas/fisiología , Proteínas en la Dieta/análisis , Animales , Tamaño Corporal , California , Femenino , Masculino , Modelos Biológicos , ReproducciónRESUMEN
Eusocial insects organize themselves into behavioral castes whose regulation has been proposed to involve epigenetic processes, including histone modification. In the carpenter ant Camponotus floridanus, morphologically distinct worker castes called minors and majors exhibit pronounced differences in foraging and scouting behaviors. We found that these behaviors are regulated by histone acetylation likely catalyzed by the conserved acetyltransferase CBP. Transcriptome and chromatin analysis in brains of scouting minors fed pharmacological inhibitors of CBP and histone deacetylases (HDACs) revealed hundreds of genes linked to hyperacetylated regions targeted by CBP. Majors rarely forage, but injection of a HDAC inhibitor or small interfering RNAs against the HDAC Rpd3 into young major brains induced and sustained foraging in a CBP-dependent manner. Our results suggest that behavioral plasticity in animals may be regulated in an epigenetic manner via histone modification.
Asunto(s)
Hormigas , Conducta Animal , Epigénesis Genética , Histona Desacetilasa 2 , Conducta Social , Animales , Acetilación , Hormigas/efectos de los fármacos , Hormigas/genética , Hormigas/fisiología , Cromatina/metabolismo , Histona Desacetilasa 2/antagonistas & inhibidores , Histona Desacetilasa 2/genética , Histona Desacetilasa 2/fisiología , Inhibidores de Histona Desacetilasas/farmacología , Procesamiento Proteico-Postraduccional , TranscriptomaRESUMEN
The sophisticated organization of eusocial insect societies is largely based on the regulation of complex behaviors by hydrocarbon pheromones present on the cuticle. We used electrophysiology to investigate the detection of cuticular hydrocarbons (CHCs) by female-specific olfactory sensilla basiconica on the antenna of Camponotus floridanus ants through the utilization of one of the largest family of odorant receptors characterized so far in insects. These sensilla, each of which contains multiple olfactory receptor neurons, are differentially sensitive to CHCs and allow them to be classified into three broad groups that collectively detect every hydrocarbon tested, including queen and worker-enriched CHCs. This broad-spectrum sensitivity is conserved in a related species, Camponotus laevigatus, allowing these ants to detect CHCs from both nestmates and non-nestmates. Behavioral assays demonstrate that these ants are excellent at discriminating CHCs detected by the antenna, including enantiomers of a candidate queen pheromone that regulates the reproductive division of labor.
Asunto(s)
Antenas de Artrópodos/fisiología , Hidrocarburos/farmacología , Percepción Olfatoria , Feromonas/metabolismo , Conducta Social , Animales , Hormigas/metabolismo , Hormigas/fisiología , Antenas de Artrópodos/citología , Antenas de Artrópodos/metabolismo , Femenino , Hidrocarburos/análisis , Masculino , Neuronas Receptoras Olfatorias/efectos de los fármacos , Neuronas Receptoras Olfatorias/metabolismo , Neuronas Receptoras Olfatorias/fisiología , Feromonas/química , Feromonas/farmacología , OlfatoRESUMEN
The role of the ant colony largely consists of non-reproductive tasks, such as foraging, tending brood, and defense. However, workers are vitally linked to reproduction through their provisioning of sexual offspring, which are produced annually to mate and initiate new colonies. Gynes (future queens) have size-associated variation in colony founding strategy (claustrality), with each strategy requiring different energetic investments from their natal colony. We compared the per capita production cost required for semi-claustral, facultative, and claustral gynes across four species of Pogonomyrmex harvester ants. We found that the claustral founding strategy is markedly expensive, costing approximately 70% more energy than that of the semi-claustral strategy. Relative to males, claustral gynes also had the largest differential investment and smallest size variation. We applied these investment costs to a model by Brown and Bonhoeffer (2003) that predicts founding strategy based on investment cost and foraging survivorship. The model predicts that non-claustral foundresses must survive the foraging period with a probability of 30-36% in order for a foraging strategy to be selectively favored. These results highlight the importance of incorporating resource investment at the colony level when investigating the evolution of colony founding strategies in ants.