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[学术文献 ] Exploring multiobjective evolutionary algorithms for designing Ribonucleic Acid sequences: An experimental analysis 进入全文
Engineering Applications of Artificial Intelligence
"Evolutionary algorithms have proven effective in addressing the Ribonucleic Acid (RNA) inverse folding problem, a critical challenge in Biomedical Engineering. This problem, involving the discovery of a nucleotide RNA sequence that folds into a desired secondary structure, is formulated as a Multiobjective Optimization Problem. In this study, we introduce an approach incorporating three objective functions (Partition Function, Ensemble Diversity, and Nucleotides Composition) and a constraint (Similarity), utilizing a real-valued chromosome encoding. The primary focus is on analyzing and comparing the performance of four multiobjective evolutionary algorithms. We explore various crossover (Simulated Binary, Differential Evolution, One-Point, Two-Point, K-Point, and Exponential) and selection (Random and Tournament) operators, coupled with a fixed mutation operator (Polynomial). Our investigation involves 48 distinct algorithm-operator combinations, with the aim of solving a well-known benchmark set. This research makes a significant contribution to the field of Artificial Intelligence by addressing a complex problem through the lens of Multiobjective Optimization. The proposed framework not only advances our understanding of RNA inverse folding but also demonstrates the versatility of evolutionary algorithms in tackling real-world challenges in Biomedical Engineering. Our findings provide valuable insights into the behavior of different algorithmic elements and combinations, identifying optimal and suboptimal performers for future research and practical applications."
[学术文献 ] Transcriptomic profiles reveal hormonal regulation of sugar-induced stolon initiation in potato 进入全文
nature
Potato (Solanum tuberosum L.) is one of the world’s most important non-cereal food crops, with stolon development playing a crucial role in determining tuber yield. While some studies have examined the effects of sugars on potato stolon growth, their influence—particularly that of sucrose—on early stolon development remains unclear. Furthermore, the regulatory role of plant hormones in this process has yet to be established. Using a combination of in vitro culture, transcriptomics, gene expression analysis, and biochemical approaches, we investigated the contribution of sucrose (3% or 8%) on potato seedling stem nodes and stolon initials through phenotypic observation, RNA sequencing (RNA-seq), comparison of expression patterns, and hormone quantification. Firstly, compared to other types of sugars, we found that high concentrations of sucrose were the most effective in inducing stolon initial formation in potato seedlings. Furthermore, RNA-seq data showed that high sucrose levels significantly up-regulated the expression of genes involved in sugar metabolism and plant hormone metabolism. Additionally, the development of stem nodes and stolon initials under high sucrose conditions was also closely linked to hormone metabolism. Notably, high sucrose concentrations contributed to stem node and stolon initial development by modulating the IAA, CK, and GA signaling pathways. Based on the endogenous hormone measurement, and exogenous hormone application, together with heterologous overexpression of a potato Auxin response factor 9 (StARF9), we concluded that the early development of potato stolons was regulated by plant hormones, particularly auxin. In summary, this study elucidates the hormonal regulation of stolon initiation under high sucrose concentrations, offering a theoretical foundation and potential targets for in vitro culture and genetic improvement of potato.
[学术文献 ] A genomic variation map provides insights into potato evolution and key agronomic traits 进入全文
Cell
Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop, which requires a deep understanding of potato domestication and differentiation. In the present study, we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants. Using the variome map, we discovered the reshaping of tuber transcriptome during potato domestication, characterized genome-wide differentiation between landrace groups Stenotomum and Phureja. We identified a jasmonic acid biosynthetic gene possibly affecting the tuber dormancy period. Genome-wide association studies revealed a UDP-glycosyltransferase gene for the biosynthesis of anti-nutritional steroidal glycoalkaloids (SGAs), and a Dehydration Responsive Element Binding (DREB) transcription factor conferring increased average tuber weight. In addition, genome similarity and group-specific SNP analyses indicated that tetraploid potatoes originated from the diploid Solanum tuberosum group Stenotomum. These findings shed light on the evolutionary trajectory of potato domestication and improvement, providing a solid foundation for advancing hybrid potato-breeding practices.
[学术文献 ] Genome synthesis in plants 进入全文
Nature Reviews Bioengineering
Owing to advances in genome sequencing and editing, a genome can now be redesigned, synthesized and introduced into cells as desired. The field of synthetic genomics not only aims to provide deeper understanding of how the genome functions but can also be harnessed for a wide range of synthetic biology and bioengineering applications, from rapid evolution and screening for favourable strains to biotechnological and bioproduction tool development. Although genome synthesis has been carried out mainly in simple unicellular organisms, plants and animals are now also being investigated. Compared with animals, plants have unique advantages, such as fewer ethical concerns, simpler experimental operations and easier regeneration from cells to organisms. In this Review, we focus on genome synthesis in plants, discuss the current research landscape and assess possible future directions.
[学术文献 ] Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée 进入全文
Nature
Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser, providing a valuable resource for the potato research community.
[学术文献 ] Cell state-specific cytoplasmic density controls spindle architecture and scaling 进入全文
Nature Cell Biology
Mitotic spindles are dynamically intertwined with the cytoplasm they assemble in. How the physicochemical properties of the cytoplasm affect spindle architecture and size remains largely unknown. Using quantitative biochemistry in combination with adaptive feedback microscopy, we investigated mitotic cell and spindle morphology during neural differentiation of embryonic stem cells. While tubulin biochemistry and microtubule dynamics remained unchanged, spindles changed their scaling behaviour; in differentiating cells, spindles were considerably smaller than those in equally sized undifferentiated stem cells. Integrating quantitative phase imaging, biophysical perturbations and theory, we found that as cells differentiated, their cytoplasm became more dilute. The concomitant decrease in free tubulin activated CPAP (centrosomal P4.1-associated protein) to enhance the centrosomal nucleation capacity. As a consequence, in differentiating cells, microtubule mass shifted towards spindle poles at the expense of the spindle bulk, explaining the differentiation-associated switch in spindle architecture. This study shows that cell state-specific cytoplasmic density tunes mitotic spindle architecture. Thus, we reveal physical properties of the cytoplasm as a major determinant in organelle size control.
