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Expanding the catalytic repertoire of C–C bond–forming pyridoxal 5′-phosphate-dependent enzymes for noncanonical amino acid formation 扩大C-C键形成吡哆醛5 ' -磷酸依赖酶对非规范氨基酸形成的催化范围
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-21 DOI: 10.1016/j.copbio.2026.103437
Taku Mizutani , Ikuro Abe
Noncanonical amino acids (ncAAs) are pharmaceutically important molecules with diverse biological and chemical applications. Among various production strategies, biocatalytic synthesis using pyridoxal 5′-phosphate (PLP)-dependent enzymes has attracted considerable attention owing to their high stereoselectivity and versatility in forming new C–C bonds. Recent advances in enzyme engineering have further expanded the catalytic potential of PLP-dependent enzymes, enabling the tailored synthesis of target ncAAs. In this short review, we summarize recent developments in biocatalytic ncAA synthesis achieved through engineered PLP-dependent enzymes.
非规范氨基酸(non - canonical amino acids, ncAAs)是非规范的重要分子,具有广泛的生物学和化学应用。在各种生产策略中,使用吡哆醛5 ' -磷酸(PLP)依赖性酶进行生物催化合成由于其高立体选择性和形成新的C-C键的多功能性而引起了广泛的关注。酶工程的最新进展进一步扩大了plp依赖性酶的催化潜力,使目标ncAAs的合成成为可能。在这篇简短的综述中,我们总结了通过工程plp依赖性酶实现的生物催化ncAA合成的最新进展。
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引用次数: 0
Crop models: integrating systems from the molecular to global for agricultural productivity and sustainability 作物模型:整合系统从分子到全球农业生产力和可持续性。
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-20 DOI: 10.1016/j.copbio.2026.103438
Ximin Piao , Megan L Matthews
Mathematical models that simulate crop growth in response to environmental conditions and management practices are essential tools for exploring agriculture-based strategies to address food security and environmental sustainability challenges. Early applications of crop models focused on supporting farmers in making management decisions. Applications have since expanded to estimating future impacts on local and global food production from changing climates. Emerging applications of crop models aim to leverage how these models integrate plant processes across biological scales to identify engineering or breeding strategies that account for environmentally-responsive dynamics at field scales and for exploring solutions to improve sustainability. In this review, we highlight recent studies across these four broad application areas and highlight potential future directions for the crop modeling field.
模拟作物生长对环境条件和管理实践的响应的数学模型是探索以农业为基础的战略以应对粮食安全和环境可持续性挑战的重要工具。作物模型的早期应用侧重于支持农民做出管理决策。此后,应用范围扩大到估计气候变化对当地和全球粮食生产的未来影响。作物模型的新兴应用旨在利用这些模型如何整合跨生物尺度的植物过程,以确定工程或育种策略,这些策略可以解释田间尺度上的环境响应动态,并探索提高可持续性的解决方案。在这篇综述中,我们重点介绍了这四个广泛应用领域的最新研究,并强调了作物建模领域的潜在未来方向。
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引用次数: 0
Biocatalytic surfaces in architecture 建筑中的生物催化表面。
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-19 DOI: 10.1016/j.copbio.2025.103435
Rachel Armstrong
This review explores the reconceptualisation of microbial colonisation on buildings: from a detrimental process (biofouling) to a source of beneficial, programmable biocatalysis. Strategies for embedding microbial and fungal communities into architectural materials to perform functions such as bioremediation, biomineralisation, and energy generation are explored. The analysis includes the multiscalar design of bioreceptive substrates, engineered living paints, mycelium composites, and probiotic surfaces, which transform passive structures into metabolically active interfaces. These approaches are regarded as Engineered Eco-Ornamentation, where surface design intentionally supports microbial ecology and urban metabolism. The integration of these living systems with computational modelling and digital fabrication to create adaptive building systems is considered. Key challenges include scaling biological processes for architectural application, ensuring long-term material durability, and aligning metabolic activity with practical construction constraints. Addressing these challenges positions functionally designed biocatalytic surfaces as a foundational research field for more regenerative and ecologically integrated architecture.
这篇综述探讨了微生物在建筑物上定植的重新概念:从有害的过程(生物污染)到有益的、可编程的生物催化的来源。探讨了将微生物和真菌群落嵌入建筑材料中以执行生物修复、生物矿化和能源生成等功能的策略。分析包括多标量设计的生物接受底物、工程活漆、菌丝体复合材料和益生菌表面,它们将被动结构转化为代谢活性界面。这些方法被认为是工程生态装饰,其中表面设计有意支持微生物生态和城市代谢。考虑将这些生活系统与计算建模和数字制造相结合,以创建自适应建筑系统。关键的挑战包括建筑应用的生物过程,确保材料的长期耐久性,以及将代谢活动与实际建筑限制相结合。为了解决这些挑战,功能性设计的生物催化表面成为了再生和生态一体化建筑的基础研究领域。
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引用次数: 0
Harnessing plant natural products for enhanced biotic stress resistance 利用植物天然产物增强生物抗逆性
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-14 DOI: 10.1016/j.copbio.2025.103432
Yoshiahu Goldstein, Guy Polturak
Plant natural products (PNPs) are specialized metabolites with diverse biological activities that are central to plant adaptation to biotic stresses. They act as chemical defenses against pathogens and pests, supporting plant survival under attack. Harnessing their potential as eco-friendly biopesticides requires a detailed understanding of their biosynthetic pathways and biological functions. This review highlights recent advances in the discovery and pathway elucidation of defensive PNPs and discusses strategies for their application through heterologous expression and enhanced in planta production.
植物天然产物(PNPs)是具有多种生物活性的特殊代谢物,是植物适应生物胁迫的核心。它们作为对抗病原体和害虫的化学防御,支持植物在受到攻击时存活。利用它们作为生态友好型生物农药的潜力,需要详细了解它们的生物合成途径和生物功能。本文综述了防御性PNPs的发现和途径阐明的最新进展,并讨论了通过外源表达和在植物生产中增强其应用的策略。
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引用次数: 0
Strategies and challenges for synthetic apomixis 合成无融合的策略和挑战。
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-13 DOI: 10.1016/j.copbio.2025.103433
Hui Ren , Venkatesan Sundaresan
Harnessing heterosis has been important to agriculture, but its full potential remains constrained by the inability to clonally propagate hybrid seeds. Synthetic apomixis, engineering asexual seed formation in sexual crops, provides a path to fix heterosis through generations. This review compiles current advances in engineering synthetic apomixis, focusing on two major components: the substitution of mitosis for meiotic divisions and maternally derived embryo development by haploid inducer or parthenogenesis. Despite rapid progress made in rice, significant challenges remain for general implementation and extension to other crops. We discuss these challenges and the possible paths forward to make synthetic apomixis feasible for widespread application in agriculture.
利用杂种优势对农业很重要,但由于无法无性繁殖杂交种子,其充分潜力仍然受到限制。合成无融合是一种在有性作物中进行无性繁殖的工程,它提供了一种通过世代固定杂种优势的途径。本文综述了工程合成无融合生殖的最新进展,重点介绍了有丝分裂替代减数分裂和单倍体诱导剂或孤雌生殖母源胚胎发育这两个主要组成部分。尽管在水稻方面取得了迅速进展,但在全面实施和推广到其他作物方面仍存在重大挑战。我们讨论了这些挑战以及使合成无融合生殖在农业上广泛应用的可能途径。
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引用次数: 0
Beyond the model: data infrastructure as the foundation for autonomous virtual laboratories 超越模型:数据基础设施作为自主虚拟实验室的基础
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-13 DOI: 10.1016/j.copbio.2025.103434
Lea M Sommer, Teddy Groves, Alberto Santos
Artificial intelligence (AI) and machine learning are reshaping biotechnology, but their impact is still constrained by inadequate data infrastructure. Although recent advances have focused on model architectures, data quality, standardization, and interoperability remain the main bottlenecks. A data-centric approach that strengthens data practices across the design-build-test-learn cycle is needed to advance AI-enabled biomanufacturing. In this review, we argue that curated repositories, consistent metadata, real-time validation, and efficient learning strategies are essential prerequisites. We highlight the manual test-to-learn ingestion step as a critical source of latency that can be mitigated through semantic standardization and structured data collection. By addressing these data-centric limitations, the field can move toward reliable, scalable, and ultimately autonomous virtual laboratories that adhere to the Findable, Accessible, Interoperable, Reusable principles.
人工智能(AI)和机器学习正在重塑生物技术,但它们的影响仍然受到数据基础设施不足的限制。尽管最近的进展集中在模型体系结构上,但数据质量、标准化和互操作性仍然是主要的瓶颈。推进人工智能生物制造需要以数据为中心的方法,加强整个设计-构建-测试-学习周期的数据实践。在这篇综述中,我们认为管理存储库、一致的元数据、实时验证和有效的学习策略是必不可少的先决条件。我们强调手动测试-学习摄取步骤是延迟的关键来源,可以通过语义标准化和结构化数据收集来减轻延迟。通过解决这些以数据为中心的限制,该领域可以朝着可靠、可扩展和最终自治的虚拟实验室发展,这些实验室遵循可查找、可访问、可互操作、可重用的原则。
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引用次数: 0
Unlocking therapeutic impacts of the gut microbiota with computational tools 利用计算工具解锁肠道微生物群的治疗影响。
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-10 DOI: 10.1016/j.copbio.2025.103431
Anjali Kharb , Xuejun Zhu
The human gut microbiota, particularly the intestinal microbiota, shapes host physiology, disease risk, and therapeutic outcomes through complex metabolic and enzymatic activities. Recent advances in molecular omics, metabolomics, enzyme bioinformatics, and artificial intelligence (AI) have created unprecedented opportunities to elucidate its therapeutic roles to further enable precision microbiome medicine for personalized prevention, diagnosis, and treatment. In this review, we highlight emerging applications that leverage molecular omics and metabolomics technologies to dissect gut microbial functions, along with developments in enzyme bioinformatics and AI tools that reveal gut microbial species, enzymes, and metabolic pathways impacting human health. Finally, we discuss perspectives on data standardization, functional annotation, and interpretability, and how emerging tools are accelerating translational microbiome research.
人类肠道微生物群,特别是肠道微生物群,通过复杂的代谢和酶活性影响宿主生理、疾病风险和治疗结果。分子组学、代谢组学、酶生物信息学和人工智能(AI)的最新进展为阐明其治疗作用创造了前所未有的机会,从而进一步实现精准微生物组医学,实现个性化预防、诊断和治疗。在这篇综述中,我们重点介绍了利用分子组学和代谢组学技术来解剖肠道微生物功能的新兴应用,以及酶生物信息学和人工智能工具的发展,这些工具揭示了影响人类健康的肠道微生物物种、酶和代谢途径。最后,我们讨论了数据标准化、功能注释和可解释性的观点,以及新兴工具如何加速转化微生物组研究。
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引用次数: 0
PRRs and NLRs sans frontières: advances and challenges in transfer of immune receptors between plant species PRRs和NLRs无国界:植物物种间免疫受体转移的进展和挑战。
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-10 DOI: 10.1016/j.copbio.2025.103429
Hailong Guo , Jonathan D.G. Jones
Plants employ cell-surface and intracellular immune receptors to perceive pathogens and activate defense responses. Recent advances in mechanistic understanding of how cell-surface and intracellular immune receptors convert recognition of molecular patterns or effectors into defense activation, combined with the knowledge of receptor repertoire variation both within and between species, allow transfer of immune receptors between species to increase the spectrum of recognition specificities. Here, we summarize recent progress in the functional transfer of immune receptors within and between plant families. We also discuss challenges that limit the transferability of intracellular immune receptors, including the requirement of additional host factors or downstream components and their incompatibility between donor and recipient species. Finally, we provide an overview of future perspectives for bioengineering disease-resistant crops through immune receptor transfer.
植物利用细胞表面和细胞内的免疫受体来感知病原体并激活防御反应。细胞表面和细胞内免疫受体如何将分子模式或效应器的识别转化为防御激活的机制理解的最新进展,结合物种内和物种间受体库变化的知识,允许免疫受体在物种之间转移以增加识别特异性的频谱。本文综述了近年来植物科内和科间免疫受体功能转移的研究进展。我们还讨论了限制细胞内免疫受体可转移性的挑战,包括对额外宿主因子或下游成分的要求以及它们在供体和受体物种之间的不相容性。最后,我们对通过免疫受体转移进行抗病作物生物工程的未来前景进行了概述。
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引用次数: 0
Reprogramming immunity: TAL effector-informed genome editing in rice and other crops 免疫重编程:水稻和其他作物的TAL效应基因编辑。
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-10 DOI: 10.1016/j.copbio.2025.103430
Ajay Gupta , Priti Sharma , Bing Yang
Bacterial type III effector proteins, particularly transcription activator-like effectors (TALEs) secreted by Xanthomonas spp., play critical roles in pathogen–host dynamics. While TALEs facilitate bacterial infections, they also possess vulnerabilities that plants and scientists can exploit to develop mechanisms of resistance. This review encompasses the characteristics and functions of TALEs, examining both their virulence and avirulence roles, and the host plants’ counter-strategies. We highlight advancements in genome editing technologies aimed at combating TALE-dependent plant diseases, with a focus on bacterial blight and leaf streak of rice, but also including bacterial blights of cotton and cassava, and citrus canker. Additionally, we share perspectives on various strategies and approaches for applying genome editing tools to improve disease resistance traits in crop breeding.
细菌III型效应蛋白,特别是由黄单胞菌分泌的转录激活因子样效应蛋白(transcription activator-like effector, TALEs),在病原体-宿主动力学中起着关键作用。虽然细菌容易感染,但它们也有弱点,植物和科学家可以利用它们来开发抗性机制。本文综述了褐皮菌的特点和功能,研究了它们的毒力和无毒作用,以及寄主植物的对抗策略。我们重点介绍了基因组编辑技术的进展,这些技术旨在对抗依赖tale的植物疾病,重点是水稻的细菌性枯萎病和叶条病,但也包括棉花和木薯的细菌性枯萎病以及柑橘溃疡病。此外,我们还分享了应用基因组编辑工具提高作物育种抗病性状的各种策略和方法的观点。
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引用次数: 0
The systems biology of sleep: toward integrative understanding of molecular and circuit-based mechanisms of sleep 睡眠的系统生物学:迈向对睡眠的分子和电路机制的综合理解。
IF 7 2区 工程技术 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2026-01-10 DOI: 10.1016/j.copbio.2025.103427
Hiroyuki J Kanaya , Koji L Ode , Hiroki R Ueda
Sleep, a universal biological phenomenon, is regulated by multiscale processes, from molecular mechanisms to cellular networks. While the underlying mechanisms, particularly those governing sleep homeostasis, were poorly understood, recent technological breakthroughs have facilitated the identification of molecular and circuit-based mechanisms. Advances in mouse genetics, including next-generation genetics that bypass the need for crossing and postnatal gene knockout methods, enable the comprehensive identification of molecular components for sleep regulation by combining them with noninvasive, large-scale sleep measurements. Elucidated mechanisms include Ca2+-related and protein kinase/phosphatase-mediated signaling, supporting the phosphorylation hypothesis of sleep. The molecular signaling forms ‘cellular sleepiness’ in sleep regulatory neurons to modulate neuronal activity. These integrated understandings of multiscale mechanisms will lead to a system-level understanding of sleep regulation.
睡眠是一种普遍的生物现象,受到从分子机制到细胞网络等多尺度过程的调节。虽然潜在的机制,特别是那些控制睡眠稳态的机制,知之甚少,但最近的技术突破促进了分子和基于电路的机制的识别。小鼠遗传学的进步,包括下一代遗传学,绕过了交叉和产后基因敲除方法的需要,通过将它们与无创的大规模睡眠测量相结合,能够全面识别睡眠调节的分子成分。阐明的机制包括Ca2+相关和蛋白激酶/磷酸酶介导的信号传导,支持睡眠的磷酸化假说。分子信号在睡眠调节神经元中形成“细胞嗜睡”,以调节神经元活动。这些对多尺度机制的综合理解将导致对睡眠调节的系统级理解。
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引用次数: 0
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Current opinion in biotechnology
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