Forward genetic screens of mutated variants are a versatile strategy for protein engineering and investigation, which has been successfully applied to various studies like directed evolution (DE) and deep mutational scanning (DMS). While next-generation sequencing can track millions of variants during the screening rounds, the vast and noisy nature of the sequencing data impedes the estimation of the performance of individual variants. Here, we propose ACIDES that combines statistical inference and in-silico simulations to improve performance estimation in the library selection process by attributing accurate statistical scores to individual variants. We tested ACIDES first on a random-peptide-insertion experiment and then on multiple public datasets from DE and DMS studies. ACIDES allows experimentalists to reliably estimate variant performance on the fly and can aid protein engineering and research pipelines in a range of applications, including gene therapy.
High-Throughput Nucleotide Sequencing , Protein Engineering , Mutation , Computer Simulation
One of the great advantages of the retina as a target tissue for gene delivery is the wide array of genetic tools that have been developed in the past decade. This includes a variety of vectors for therapeutic gene delivery to most types of retinal neurons and glia, as well as cell type-specific promoters for restricted gene expression in distinct neuronal subtypes. Within the scope of neuroscience applications and for gene therapy, it is now routine to express reporter genes, replacement genes, neuronal activity indicators, and microbial opsins in specific neuronal types in the mouse retina. However, there are considerable anatomical, physiological, immunological, and behavioral differences between the mouse and the human that limit the usefulness of these tools in humans and nonhuman primates. Several advances are now being made toward the goal of applying viral targeting tools to understand the primate retina. Here, we describe these advances, consider their potential to advance our understanding of the primate retina, and describe what will be needed to move forward.
Gene Transfer Techniques , Genetic Therapy/methods , Genetic Vectors , Retinal Diseases/therapy , Adenoviridae/genetics , Adenoviridae/physiology , Animals , Humans , Lentivirus/genetics , Lentivirus/physiology , Nanoparticles , Optogenetics/methods , Primates , Promoter Regions, Genetic
