![]() ![]() Both knockout of mdm-miR171i and overexpression of MsSCL26.1 improved drought stress tolerance in the cultivated apple line 'GL-3' (M. We established that one miRNA, mdm-miR171i, specifically targeted and degraded SCARECROW-LIKE PROTEINS 26.1 (MsSCL26.1) transcripts. ![]() We experimentally verified the expression patterns of five selected miRNAs and their targets. Forty known microRNAs (miRNAs) and eight new snRNAs were differentially expressed in response to 2 or 4 h of drought stress treatment. Here, we identified various snRNAs and their targets from the wild apple species Malus sieversii via high-throughput sequencing and degradome analysis. Small non-coding RNAs (snRNAs) play critical roles in plant growth, development, and stress responses by regulating target gene expression, but their roles in drought stress tolerance in apple (Malus domestica) are poorly understood. Our results should be of interest to those in the biomolecular design community and should serve as a baseline for future experiments involving machine learning in molecule design.ĭrought stress severely restricts crop yield and quality. We find that our DQN algorithm performs by far the best in this setting, contrasting with, in which PPO performs the best among all tested algorithms. We show results of the ablation analysis that we do for these algorithms, as well as graphs indicating the algorithm's performance across batches and its ability to search the possible space of RNA sequences. In addition to experimenting with the vanilla implementations of each reinforcement learning algorithm from standard libraries, we analyze variants of each algorithm in which we modify the algorithm's reward function and tune the model's hyperparameters. In this paper, we propose a new benchmark of applying reinforcement learning to RNA sequence design, in which the objective function is defined to be the free energy in the sequence's secondary structure. Currently, the most widely used approach in biomolecular design is directed evolution, which is a greedy hill-climbing algorithm that simulates biological evolution. Rising costs in recent years of developing new drugs and treatments have led to extensive research in optimization techniques in biomolecular design. It thus may provide new breeding targets to achieve both high yield and enhanced resistance in crops. Our work also revealed unidentified new functions of the very conserved SCYL2. Collectively, we characterized a novel component of CMVT pathway in the regulation of plant immunity. We further showed that OsSCYL2-OsSPL28 interaction is mediated by OsCHC1. OsSCYL2 interacted with OsSPL28, subunit of a clathrin-associated adaptor protein that is known to regulate HR-like cell death in rice. Subcellular localization showed that OsSCYL2 localized at Golgi, trans-Golgi network (TGN) and prevacuolar compartment (PVC). Although mutants of OsSCYL2 showed additional defects in photosynthetic system, they exhibited enhanced resistance to bacterial pathogens. Here, we show that mutation of OsSCYL2 in rice gave rise to a novel phenotype - hypersensitive response-like (HR) cell death in a light dependent manner. Loss-of-function of SCYL2 in Arabidopsis led to severe growth defects. ![]() SCY1-LIKE2 (SCYL2) is evolutionally conserved among Eukaryote species. However, the molecular link between CMVT and plant immunity is largely unknown. Recently, it has been suggested that CMVT also plays important roles in the regulation of plant immunity. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for CRISPR-Cas system based chromosome imaging system.Ĭlathrin-mediated vesicle trafficking (CMVT) is a fundamental process in all eukaryotic species, and indispensable to organism's growth and development. The program has a user-friendly interface, and can analyze the BLAST results by using multiple parameters and score for each candidate spacers, generate the primers when using a certain plasmid. We here presented CRISPR Primer Designer for researchers to design primers for CRISPR applications. In addition, with the development of CRISPR derived-systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. Previous designing tools either were mostly built-in websites or ran as command-line program, and none of them ran locally and acquired a user-friendly interface. However, there are concerns rose about the specificity of the system, especially the usages of knocking out a gene. Clustered regularly interspaced short palindromic repeats – CRISPR associated system enables biologists to edit genome precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers and genome architecture. ![]()
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