Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza

Background: Terpenoids constitute the largest class of secondary metabolites made by plants and display vast chemical diversity among and within species. Terpene synthases (TPSs) are the pivotal enzymes for terpenoid biosynthesis that create the basic carbon skeletons of this class. Functional divergence of paralogous and orthologous TPS genes is a major mechanism for the diversification of terpenoid biosynthesis. However, little is known about the evolutionary forces that have shaped the evolution of plant TPS genes leading to terpenoid diversity. Results: The orthologs of Oryza Terpene Synthase 1 (OryzaTPS1), a rice terpene synthase gene involved in indirect defense against insects in Oryza sativa, were cloned from six additional Oryza species. In vitro biochemical analysis showed that the enzymes encoded by these OryzaTPS1 genes functioned either as (E)-β-caryophyllene synthases (ECS), or (E)-β-caryophyllene & germacrene A synthases (EGS), or germacrene D & germacrene A synthases (DAS). Because the orthologs of OryzaTPS1 in maize and sorghum function as ECS, the ECS activity was inferred to be ancestral. Molecular evolutionary detected the signature of positive Darwinian selection in five codon substitutions in the evolution from ECS to DAS. Homology-based structure modeling and the biochemical analysis of laboratory-generated protein variants validated the contribution of the five positively selected sites to functional divergence of OryzaTPS1. The changes in the in vitro product spectra of OryzaTPS1 proteins also correlated closely to the changes in in vivoblends of volatile terpenes released from insect-damaged rice plants. Conclusions: In this study, we found that positive Darwinian selection is a driving force for the functional divergence of OryzaTPS1. This finding suggests that the diverged sesquiterpene blend produced by the Oryza species containing DASmay be adaptive, likely in the attraction of the natural enemies of insect herbivores

MOELoRA: An MOE-based Parameter Efficient Fine-Tuning Method for Multi-task Medical Applications

The recent surge in the field of Large Language Models (LLMs) has gained significant attention in numerous domains. In order to tailor an LLM to a specific domain such as a web-based healthcare system, fine-tuning with domain knowledge is necessary. However, two issues arise during fine-tuning LLMs for medical applications. The first is the problem of task variety, where there are numerous distinct tasks in real-world medical scenarios. This diversity often results in suboptimal fine-tuning due to data imbalance and seesawing problems. Additionally, the high cost of fine-tuning can be prohibitive, impeding the application of LLMs. The large number of parameters in LLMs results in enormous time and computational consumption during fine-tuning, which is difficult to justify. To address these two issues simultaneously, we propose a novel parameter-efficient fine-tuning framework for multi-task medical applications called MOELoRA. The framework aims to capitalize on the benefits of both MOE for multi-task learning and LoRA for parameter-efficient fine-tuning. To unify MOE and LoRA, we devise multiple experts as the trainable parameters, where each expert consists of a pair of low-rank matrices to maintain a small number of trainable parameters. Additionally, we propose a task-motivated gate function for all MOELoRA layers that can regulate the contributions of each expert and generate distinct parameters for various tasks. To validate the effectiveness and practicality of the proposed method, we conducted comprehensive experiments on a public multi-task Chinese medical dataset. The experimental results demonstrate that MOELoRA outperforms existing parameter-efficient fine-tuning methods. The implementation is available online for convenient reproduction of our experiments

Diffusion Augmentation for Sequential Recommendation

Sequential recommendation (SRS) has become the technical foundation in many applications recently, which aims to recommend the next item based on the user's historical interactions. However, sequential recommendation often faces the problem of data sparsity, which widely exists in recommender systems. Besides, most users only interact with a few items, but existing SRS models often underperform these users. Such a problem, named the long-tail user problem, is still to be resolved. Data augmentation is a distinct way to alleviate these two problems, but they often need fabricated training strategies or are hindered by poor-quality generated interactions. To address these problems, we propose a Diffusion Augmentation for Sequential Recommendation (DiffuASR) for a higher quality generation. The augmented dataset by DiffuASR can be used to train the sequential recommendation models directly, free from complex training procedures. To make the best of the generation ability of the diffusion model, we first propose a diffusion-based pseudo sequence generation framework to fill the gap between image and sequence generation. Then, a sequential U-Net is designed to adapt the diffusion noise prediction model U-Net to the discrete sequence generation task. At last, we develop two guide strategies to assimilate the preference between generated and origin sequences. To validate the proposed DiffuASR, we conduct extensive experiments on three real-world datasets with three sequential recommendation models. The experimental results illustrate the effectiveness of DiffuASR. As far as we know, DiffuASR is one pioneer that introduce the diffusion model to the recommendation

Diversity and Functional Evolution of Terpene Synthases in Dictyostelid Social Amoebae

Dictyostelids, or social amoebae, have a unique life style in forming multicellular fruiting bodies from unicellular amoeboids upon starvation. Recently, dictyostelids were found to contain terpene synthase (TPS) genes, a gene type of secondary metabolism previously known to occur only in plants, fungi and bacteria. Here we report an evolutionary functional study of dictyostelid TPS genes. The number of TPS genes in six species of dictyostelids examined ranges from 1 to 19; and the model species Dictyostelium purpureum contains 12 genes. Using in vitro enzyme assays, the 12 TPS genes from D. purpureum were shown to encode functional enzymes with distinct product profiles. The expression of the 12 TPS genes in D. purpureum is developmentally regulated. During multicellular development, D. purpureum releases a mixture of volatile terpenes dominated by sesquiterpenes that are the in vitro products of a subset of the 12 TPS genes. The quality and quantity of the terpenes released from D. purpureum, however, bear little resemblance to those of D. discoideum, a closely related dictyostelid. Despite these variations, the conserved clade of dictyostelid TPSs, which have an evolutionary distance of more than 600 million years, has the same biochemical function, catalyzing the formation of a sesquiterpene protoillud-7-ene. Taken together, our results indicate that the dynamic evolution of dictyostelid TPS genes includes both purifying selection of an orthologous group and species-specific expansion with functional divergence. Consequently, the terpenes produced by these TPSs most likely have conserved as well as speciesadaptive biological functions as chemical languages in dictyostelids

Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha

Marchantia polymorpha is a basal terrestrial land plant, which like most liverworts accumulates structurally diverse terpenes believed to serve in deterring disease and herbivory. Previous studies have suggested that the mevalonate and methylerythritol phosphate pathways, present in evolutionarily diverged plants, are also operative in liverworts. However, the genes and enzymes responsible for the chemical diversity of terpenes have yet to be described. In this study, we resorted to a HMMER search tool to identify 17 putative terpene synthase genes from M. polymorpha transcriptomes. Functional characterization identified four diterpene synthase genes phylogenetically related to those found in diverged plants and nine rather unusual monoterpene and sesquiterpene synthase-like genes. The presence of separate monofunctional diterpene synthases for ent-copalyl diphosphate and ent-kaurene biosynthesis is similar to orthologs found in vascular plants, pushing the date of the underlying gene duplication and neofunctionalization of the ancestral diterpene synthase gene family to \u3e400 million years ago. By contrast, the mono- and sesquiterpene synthases represent a distinct class of enzymes, not related to previously described plant terpene synthases and only distantly so to microbial-type terpene synthases. The absence of a Mg2+ binding, aspartate-rich, DDXXD motif places these enzymes in a noncanonical family of terpene synthases

2D materials for conducting holes from grain boundaries in perovskite solar cells

Grain boundaries in organic-inorganic halide perovskite solar cells (PSCs) have been found to be detrimental to the photovoltaic performance of devices. Here, we develop a unique approach to overcome this problem by modifying the edges of perovskite grain boundaries with flakes of high-mobility two-dimensional (2D) materials via a convenient solution process. A synergistic effect between the 2D flakes and perovskite grain boundaries is observed for the first time, which can significantly enhance the performance of PSCs. We find that the 2D flakes can conduct holes from the grain boundaries to the hole transport layers in PSCs, thereby making hole channels in the grain boundaries of the devices. Hence, 2D flakes with high carrier mobilities and short distances to grain boundaries can induce a more pronounced performance enhancement of the devices. This work presents a cost-effective strategy for improving the performance of PSCs by using high-mobility 2D materials

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP

The water lily genome and the early evolution of flowering plants

Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1–3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.Supplementary Tables: This file contains Supplementary Tables 1-21.National Natural Science Foundation of China, the open funds of the State Key Laboratory of Crop Genetics and Germplasm Enhancement (ZW201909) and State Key Laboratory of Tree Genetics and Breeding, the Fujian provincial government in China, the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement and the Special Research Fund of Ghent University.http://www.nature.com/naturecommunicationsam2021BiochemistryGeneticsMicrobiology and Plant Patholog

Diversity and Functional Evolution of Terpene Synthases in Dictyostelid Social Amoebae

Dictyostelids, or social amoebae, have a unique life style in forming multicellular fruiting bodies from unicellular amoeboids upon starvation. Recently, dictyostelids were found to contain terpene synthase (TPS) genes, a gene type of secondary metabolism previously known to occur only in plants, fungi and bacteria. Here we report an evolutionary functional study of dictyostelid TPS genes. The number of TPS genes in six species of dictyostelids examined ranges from 1 to 19; and the model species Dictyostelium purpureum contains 12 genes. Using in vitro enzyme assays, the 12 TPS genes from D. purpureum were shown to encode functional enzymes with distinct product profiles. The expression of the 12 TPS genes in D. purpureum is developmentally regulated. During multicellular development, D. purpureum releases a mixture of volatile terpenes dominated by sesquiterpenes that are the in vitro products of a subset of the 12 TPS genes. The quality and quantity of the terpenes released from D. purpureum, however, bear little resemblance to those of D. discoideum, a closely related dictyostelid. Despite these variations, the conserved clade of dictyostelid TPSs, which have an evolutionary distance of more than 600 million years, has the same biochemical function, catalyzing the formation of a sesquiterpene protoillud-7-ene. Taken together, our results indicate that the dynamic evolution of dictyostelid TPS genes includes both purifying selection of an orthologous group and species-specific expansion with functional divergence. Consequently, the terpenes produced by these TPSs most likely have conserved as well as speciesadaptive biological functions as chemical languages in dictyostelids

Novel multi-objective topology optimization method for stiffness and stress of continuum structures

In this paper, a topology optimization method combining Bi-directional Evolutionary Structural Optimization (BESO) and Fast Non-dominated Sorting Genetic Algorithm II (NSGA-II) is proposed, which is called BESO-NSGA-II. To effectively fuse the two algorithms, a semi-random double-penalized crossover and mutation operator is developed. The proposed algorithm extends the traditional single-objective optimization to a double objective optimization problem, and investigates the influence of the stress norm parameters on the optimization results. To verify the effectiveness of the new method, several examples of 2D structural stiffness and stress optimization are given. At the same time, the optimization design of each model was repeated six times to demonstrate the ability of the new method to converge to a solution. Compared with BESO, BESO-NSGA-II can effectively realize the double objective optimization of stiffness and stress, and eliminate the stress concentration phenomenon on the premise of ensuring that the structure has greater stiffness