Cell systems · 2017
Stephen Bridgett、James Campbell、Christopher J Lord 等
Genes whose function is selectively essential in the presence of cancer-associated genetic aberrations represent promising targets for the development of precision therapeutics. Here, we present CancerGD, a resource that integrates genotypic profiling with large-scale loss-of-function genetic screens in tumor cell lines to identify such genetic dependencies. CancerGD provides tools for searching, visualizing, and interpreting these genetic dependencies through the integration of functional interaction networks. CancerGD includes different screen types (siRNA, shRNA, CRISPR), and we describe a simple format for submitting new datasets.
Current opinion in biotechnology · 2023
Shalni Kumar、Jeff Hasty
As engineered microbes are used in increasingly diverse applications across human health and bioproduction, the field of synthetic biology will need to focus on strategies that stabilize and contain the function of these populations within target environments. To this end, recent advancements have created layered sensing circuits that can compute cell survival, genetic contexts that are less susceptible to mutation, burden, and resource control circuits, and methods for population variability reduction. These tools expand the potential for real-world deployment of complex microbial systems by enhancing their environmental robustness and functional stability in the face of unpredictable host response and evolutionary pressure.
Science Translational Medicine · 2025
Ze Mi、Juan Chen、Zhe-Wen Zhang 等
The efficacy of immunotherapy in colorectal cancer (CRC) hinges upon a comprehensive understanding of how the immune system interacts with tumor cells within the colorectal microenvironment. Mature tertiary lymphoid structures (mTLSs) are associated with an increased objective response rate, progression-free survival, and overall survival in patients with CRC. Thus, it has been suggested that increasing mTLSs in the context of CRC could improve patient outcomes. However, no established method to specifically induce TLS maturation within and around tumor sites is available. To address this gap in technology, we engineered a Salmonella typhimurium strain, SLCVNP20009, to express tumor necrosis factor (TNF) superfamily member 14 (TNFSF14, also called LIGHT). This strain colonized tumors and released LIGHT, which then formed a ligand-receptor pair with herpes virus entry mediator (HVEM) to induce a powerful cellular immune response. Furthermore, this engineered microbe modulated the proportions of intestinal innate lymphoid cells (ILCs), which serve an anti-infection role in innate immunity. Mice that were deficient in HVEM or ILC3 exhibited fewer mTLSs, a greater bacterial burden, and increased mortality in two different models of CRC. Thus, this engineered microbe with enhanced immunogenic properties demonstrated the potential to stimulate mTLS-associated antitumor immune responses in the colon and was well tolerated in vivo. Our results indicate that LIGHT-HVEM signaling on group 3 ILCs (ILC3s) is crucial for mTLS formation and T cell-mediated antitumor immunity in CRC and additionally suggest a synbiotic-based therapeutic approach for the management of CRC.
Data in brief · 2023
Satwinder Singh、Feng Hou、Ruili Wang
Automatic speech recognition (ASR) has been an active area of research. Training with large annotated datasets is the key to the development of robust ASR systems. However, most available datasets are focused on high-resource languages like English, leaving a significant gap for low-resource languages. Among these languages is Punjabi, despite its large number of speakers, Punjabi lacks high-quality annotated datasets for accurate speech recognition. To address this gap, we introduce three labeled Punjabi speech datasets: Punjabi Speech (real speech dataset) and Google-synth/CMU-synth (synthesized speech datasets). The Punjabi Speech dataset consists of read speech recordings captured in various environments, including both studio and open settings. In addition, the Google-synth dataset is synthesized using Google's Punjabi text-to-speech cloud services. Furthermore, the CMU-synth dataset is created using the Clustergen model available in the Festival speech synthesis system developed by CMU. These datasets aim to facilitate the development of accurate Punjabi speech recognition systems, bridging the resource gap for this important language.
Research of Scientia Naturalis · 2025
Ardiaz Azhar、Livia Alves、Raul Gomez
The pervasive environmental pollution caused by petroleum-based plastics has catalyzed the search for sustainable alternatives. Bioplastics, derived from renewable biomass, offer a promising solution, yet their production can be inefficient and compete with food resources. Synthetic biology provides powerful tools to engineer microorganisms for the high-yield production of bioplastics like polyhydroxyalkanoates (PHA) from non-food feedstocks. This study aimed to conduct a comprehensive life cycle assessment (LCA) to quantify and compare the environmental impacts of PHA produced via a synthetically engineered microbial platform against conventional polyethylene terephthalate (PET). A "cradle-to-grave" LCA methodology was employed, encompassing feedstock cultivation, fermentation, polymer extraction, and end-of-life scenarios including landfilling and industrial composting. The results revealed that the synthetic biology-driven PHA exhibited a 65% lower global warming potential and a 70% reduction in non-renewable energy use compared to PET. However, it showed higher impacts in eutrophication and land use, linked to its lignocellulosic feedstock origins. The end-of-life analysis confirmed the significant advantage of PHA’s biodegradability. This study concludes that while synthetic biology-driven bioplastics offer substantial benefits in carbon footprint and fossil fuel dependency, a holistic view is crucial.
eLife · 2021
Oskar Staufer、Jacqueline A De Lora、Eleonora Bailoni 等
Employing concepts from physics, chemistry and bioengineering, 'learning-by-building' approaches are becoming increasingly popular in the life sciences, especially with researchers who are attempting to engineer cellular life from scratch. The SynCell2020/21 conference brought together researchers from different disciplines to highlight progress in this field, including areas where synthetic cells are having socioeconomic and technological impact. Conference participants also identified the challenges involved in designing, manipulating and creating synthetic cells with hierarchical organization and function. A key conclusion is the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives.
Food Bioscience · 2026
Hui-Xin Zhao、Jian Ma、Rui Cao 等
暂无摘要
Journal of advanced research · 2024
Liwei Wu、Tingyu Ma、Chenxi Zang 等
BACKGROUND: Licorice is extensively and globally utilized as a medicinal herb and is one of the traditional Chinese herbal medicines with valuable pharmacological effects. Its therapeutic components primarily reside within its roots and rhizomes, classifying it as a tonifying herb. As more active ingredients in licorice are unearthed and characterized, licorice germplasm resources are gaining more and more recognition. However, due to the excessive exploitation of wild licorice resources, the degrading germplasm reserves fail to meet the requirements of chemical extraction and clinical application. AIM OF REVIEW: This article presents a comprehensive review of the classification and phylogenetic relationships of species in genus Glycyrrhiza, types of active components and their pharmacological activities, licorice omics, biosynthetic pathways of active compounds in licorice, and metabolic engineering. It aims to offer a unique and comprehensive perspective on Glycyrrhiza, integrating knowledge from diverse fields to offer a comprehensive understanding of this genus. It will serve as a valuable resource and provide a solid foundation for future research and development in the molecular breeding and synthetic biology fields of Glycyrrhiza. KEY SCIENTIFIC CONCEPTS OF REVIEW: Licorice has an abundance of active constituents, primarily triterpenoids, flavonoids, and polysaccharides. Modern pharmacological research unveiled its multifaceted effects encompassing anti-inflammatory, analgesic, anticancer, antiviral, antioxidant, and hepatoprotective activities. Many resources of Glycyrrhiza species remain largely untapped, and multiomic studies of the Glycyrrhiza lineage are expected to facilitate new discoveries in the fields of medicine and human health. Therefore, strategies for breeding high-yield licorice plants and developing effective biosynthesis methods for bioactive compounds will provide valuable insights into resource conservation and drug development. Metabolic engineering and microorganism-based green production provide alternative strategies to improve the production efficiency of natural products.
Scientia Sinica Vitae · 2025
Na Li、Ning Fu、Bing-Zhi Li 等
Lignin is the most abundant renewable carbon-neutral aromatic polymer resource in nature, serving as an ideal feedstock for the sustainable production of energy, chemicals, and materials. Currently, biological conversion represents one of the most promising pathways for lignin valorization. However, the structural heterogeneity of lignin hinders its valorization. Developing advanced strategies for directional lignin depolymerization and bioconversion is a cutting-edge research frontier. Emerging synthetic biology and artificial intelligence technologies provide novel approaches for enhancing lignin valorization. This review outlines the design principles of aromatic lignin depolymerization and conversion pathways, with a focus on three major routes for lignin valorization through synthetic bioman-ufacturing. Furthermore, prospects for lignin bioconversion research and applications empowered by synthetic biology and artificial intelligence are discussed.
Journal of theoretical biology · 2017
Wolfgang Halter、Jan Maximilian Montenbruck、Zoltan A Tuza 等
Reliable in silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and ribosomes on mRNA and DNA templates, respectively. By analyzing the convergence properties of this model based upon geometric considerations, we present additional insights into the dynamic mechanisms of the process of protein synthesis. Further, we demonstrate how this model can be used to evaluate the performance of synthetic gene circuits under different loading scenarios.
为什么值得关注
AI 辅助短评，基于标题和摘要整理该数据库整合化合物注释、专家整理的生物制造证据与文献通路，并提供计算预测候选通路，形成可追溯的知识框架，有助于跨研究比较与微生物生产策略的理性设计。但需注意：预测通路未经原文实验验证，专家整理证据的覆盖度（1054/74237）有限，数据库价值取决于后续更新与外部验证。