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[学术文献 ] Natural variation of an E3 ubiquitin ligase encoding gene Chalk9 regulates grain chalkiness in rice 进入全文
nature communications
Grain chalkiness is an undesirable trait affecting rice quality, concerning both consumers and breeders. However, the genetic mechanisms underlying rice chalkiness remain largely elusive. Here, we identify Chalk9 as a major gene associated with grain chalkiness in a natural population. Chalk9 encodes an E3 ubiquitin ligase that targets OsEBP89 for its ubiquitination and degradation. Low expression of Chalk9 results in excessive accumulation of OsEBP89, disrupting the homeostasis of storage components and leading to the chalkiness phenotype. A 64-bp insertion/deletion in the Chalk9 promoter contributes to its differential transcriptional levels, thus causing chalkiness variation among rice varieties. Moreover, the elite allele Chalk9-L reduces grain chalkiness, without compromising yield. Chalk9-L is strongly selected in japonica but exhibits a complex evolutionary trajectory in indica. Our findings reveal the molecular and genetic mechanisms underlying chalkiness and provide a potential strategy for breeding rice varieties with improved quality.
[学术文献 ] Targeting lignocellulolytic gene clusters in novel Trichoderma atroviride and Trichoderma harzianum strains through bacterial artificial chromosome–guided analysis 进入全文
Mycologia
Lignocellulosic biomass is a complex carbon source with recalcitrant properties whose degradation via industrial enzymatic hydrolysis is challenging, directly affecting the cost of reliable energy production. In nature, filamentous fungi, including Trichoderma species, degrade lignocellulose via an arsenal of hydrolytic and oxidative enzymes that act synergistically to process it into soluble sugar monomers. This work explored the genomic content of Trichoderma atroviride and Trichoderma harzianum strains with hydrolytic abilities by identifying regions possessing degradative enzyme–encoding genes, namely, hydrolytic clusters. We employed bacterial artificial chromosome (BAC) methodology to target specific genomic regions and explore their genetic organization, proximal gene context, and gene expression under degradative conditions. With this tool, it was possible to inspect the linear structure and expression profile of target hydrolytic-rich genomic regions. The present work offers a perspective on the organization of genome regions related to carbohydrate metabolism. This study revealed novel genes and genome regions that are positively regulated during cellulose degradation, contributing to elucidating differences in gene organization that potentially impact hydrolysis among Trichoderma species.
[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 ] Genome assembly of two allotetraploid cotton germplasms reveals mechanisms of somatic embryogenesis and enables precise genome editing 进入全文
nature genetics
Somatic embryogenesis is crucial for plant genetic engineering, yet the underlying mechanisms in cotton remain poorly understood. Here we present a telomere-to-telomere assembly of Jin668 and a high-quality assembly of YZ1, two highly regenerative allotetraploid cotton germplasms. The completion of the Jin668 genome enables characterization of ~30.1 Mb of centromeric regions invaded by centromeric retrotransposon of maize and Tekay retrotransposons, an ~8.1 Mb 5S rDNA array containing 25,190 copies and a ~75.1 Mb major 45S rDNA array with 8,131 copies. Comparative analyses of regenerative and recalcitrant genotypes reveal dynamic transcriptional patterns and chromatin accessibility during the initial regeneration process. A hierarchical gene regulatory network identifies AGL15 as a contributor to regeneration. Additionally, we demonstrate that genetic variation affects sgRNA target sites, while the Jin668 genome assembly reduces the risk of off-target effects in CRISPR-based genome editing. Together, the complete Jin668 genome reveals the complexity of genomic regions and cotton regeneration, and improves the precision of genome editing.
[前沿资讯 ] European boost for global food security: Dutch biotech Solynta gets €20 million EIB backing for highly disease resistant potato varieties 进入全文
Solynta
EIB lends €20 million to Dutch biotechnology company Solynta to develop potato seeds with strong resistance to disease and resilience to climate change. The focus of the EIB loan, which is supported under the European Commission’s InvestEU programme, is on the use of true potato seeds instead of traditional tubers for cultivation. Solynta’s technology holds promise of securing successful potato harvests and enhancing food supplies worldwide. Through proven hybrid breeding technology, Solynta has been able to create more robust potato varieties that require much fewer crop protection inputs. Solynta’s breeding method, which excludes genetically modified organisms (GMOs), can adapt potato characteristics relatively quickly to different needs including resistance to diseases such as late blight – a destructive fungal illness – and adaptation to climate change. As a result, the company’s potato varieties contribute to the United Nations sustainable-development goals (SDGs) such as ending poverty and hunger and promoting responsible consumption and production.
[学术文献 ] A generalized platform for artificial intelligence-powered autonomous enzyme engineering 进入全文
nature communications
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.
