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Industry 5.0—The Relevance and Implications of Bionics and Synthetic Biology Artical
Peter Sachsenmeier
Engineering 2016, Volume 2, Issue 2, Pages 225-229 doi: 10.1016/J.ENG.2016.02.015
Bionics (the imitation or abstraction of the “inventions of nature) and, to an even greater extent, synthetic biology, will be as relevant to engineering development and industry as the silicon chip was over the last 50 years. Chemical industries already use so-called “white biotechnology” for new processes, new raw materials, and more sustainable use of resources. Synthetic biology is also used for the development of second-generation biofuels and for harvesting the sun´s energy with the help of tailor-made microorganisms or biometrically designed catalysts. The market potential for bionics in medicine, engineering processes, and DNA storage is huge. “Moonshot” projects are already aggressively focusing on diseases and new materials, and a US-led competition is currently underway with the aim of creating a thousand new molecules. This article describes a timeline that starts with current projects and then moves on to code engineering projects and their implications, artificial DNA, signaling molecules, and biological circuitry. Beyond these projects, one of the next frontiers in bionics is the design of synthetic metabolisms that include artificial food chains and foods, and the bioengineering of raw materials; all of which will lead to new insights into biological principles. Bioengineering will be an innovation motor just as digitalization is today. This article discusses pertinent examples of bioengineering, particularly the use of alternative carbon-based biofuels and the techniques and perils of cell modification. Big data, analytics, and massive storage are important factors in this next frontier. Although synthetic biology will be as pervasive and transformative in the next 50 years as digitization and the Internet are today, its applications and impacts are still in nascent stages. This article provides a general taxonomy in which the development of bioengineering is classified in five stages (DNA analysis, bio-circuits, minimal genomes, protocells, xenobiology) from the familiar to the unknown, with implications for safety and security, industrial development, and the development of bioengineering and biotechnology as an interdisciplinary field. Ethical issues and the importance of a public debate about the consequences of bionics and synthetic biology are discussed.
Keywords： Bionics Synthetic biology Bio-engineering Biological sensors Biofuels Bio weapons Virtual evolution Protocells Xeno cells Economic significance Industry 5.0 Germany China
A Prospect on Research and Application of Natural Toxins
Chen Yisheng
Strategic Study of CAE 2003, Volume 5, Issue 2, Pages 16-19
Toxins are biogenic chemical substances with meaningful value. They display plentiful diversities in many aspects such as biogenity, chemical structure, biological activity, etc. Toxinology, a novel disciplinary subject , develops rapidly in recent decades, the advances in which are pushing effect on chemical biology, chemical ecology, biogenic syntheses, life science, environment science and medicine. It is noteworthy that the toxin research gives impetus to drug discovery. Numerous useful clinical medicines are natural toxins or them derivatives. Meanwhile, the information from toxin researches could provide valuable pharmacophoric pattern and structure motif for drug design. Furthermore, toxins are outstanding toos to explain and to search new target site of drugs.
Keywords： natural toxins diversity in natural toxins control of biological toxicosis biogenic syntheses chemical biology chemical ecology new drug research
Microbial Medicine Industry: Current Status and Future Trends
Yu Qing, Huang Tingting, Deng Zixin
Strategic Study of CAE 2021, Volume 23, Issue 5, Pages 69-78 doi: 10.15302/J-SSCAE-2021.05.009
The microbial sourced natural products possess diverse structures and excellent activities, implying great potentials for clinical application. This study systematically analyzes the current status of the microbial medicine industry in China and summarizes the development trends of the industry from the aspects of microbial strain resource utilization, excellent strain screening, fermentation process optimization, strain engineering, and new microbial medicine development. This aims to facilitate major breakthroughs and industrial upgrades for China’s microbial medicine industry. Although China’s microbial medicine industry has solid resource and technical foundations, it still lags behind the international advanced level. Considering the opportunities and challenges, we propose several suggestions for promoting China’s microbial medicine industry: constructing large-scale scientific facilities for microbial medicine, strengthening basic research and independent technology development, establishing a talent cultivation system, and formulating systematic industrial incentives.
Keywords： microbial medicine development trend biological activity microbial metabolism synthetic biology
An Additive Manufacturing Approach that Enables the Field Deployment of Synthetic Biosensors Article
Daniel Wolozny, John R. Lake, Paul G. Movizzo, Zhicheng Long, Warren C. Ruder
Engineering 2019, Volume 5, Issue 1, Pages 173-180 doi: 10.1016/j.eng.2018.12.001
The tools of synthetic biology can be used to engineer living biosensors that report the presence of analytes. Although these engineered cellular biosensors have many potential applications for deployment outside of the lab, they are genetically modified organisms (GMOs) and are often considered dangerous. Mitigating the risk of releasing GMOs into the environment while enabling their use outside a laboratory is critical. Here, we describe the development of a biosensing system consisting of a synthetic biological circuit, which is engineered in Escherichia coli that are contained within a unique 3D-printed device housing. These GMOs detect the chemical quorum signal of Pseudomonas aeruginosa, an opportunistic pathogen. Using this device, the living biosensor makes contact with a specimen of interest without ever being exposed to the environment. Cells can be visually analyzed in the field within culture tubes, or returned to the lab for further analysis. Many biosensors lack the versatility required for deployment in the field, where many diseases can go undiagnosed due to a lack of resources and equipment. Our bioassay device utilizes 3D printing to create a portable, modular, and inexpensive device for the field deployment of living biosensors.
Keywords： Synthetic biology Additive manufacturing Biosensors
Lanqing Liu, Hong Liu, Wei Zhang, Mingdong Yao, Bingzhi Li, Duo Liu, Yingjin Yuan
Engineering 2019, Volume 5, Issue 2, Pages 287-295 doi: 10.1016/j.eng.2018.11.029
Engineering the biosynthesis of plant-derived natural products in microbes presents several challenges, especially when the expression and activation of the plant cytochrome P450 enzyme is required. By recruiting two enzymes—HpaB and HpaC—from several bacteria, we constructed functional 4-hydroxyphenylacetate 3-hydroxylase (4HPA3H) in Saccharomyces cerevisiae to take on a role similar to that of the plant-derived cytochrome P450 enzyme and produce caffeic acid. Along with a common tyrosine ammonia lyase (TAL), the different combinations of HpaB and HpaC presented varied capabilities in producing the target product, caffeic acid, from the substrate, L-tyrosine. The highest production of caffeic acid was obtained with the enzyme combination of HpaB from Pseudomonas aeruginosa and HpaC from Salmonella enterica, which yielded up to 289.4 ± 4.6 mg·L−1 in shake-flask cultivation. The compatibility of heterologous enzymes within a yeast chassis was effectively improved, as the caffeic acid production was increased by 40 times from the initial yield. Six key amino acid residues around the flavin adenine dinucleotide (FAD) binding domain in HpaB from Pseudomonas aeruginosa were distinguished from those other HpaBs, and might play critical roles in affecting enzyme activity. We have thus established an effective approach to construct a highly efficient yeast system to synthesize non-native hydroxylated phenylpropanoids.
Keywords： Saccharomyces cerevisiae Caffeic acid Heterologous enzyme Cytochrome P450 Synthetic biology
Study on the molecular characteristic in phlegm-dampness constitution
Wang Qi,Dong Jing,Wu Hongdong,Wang Dongpo,Yao Shilin,Ren Xiaojuan
Strategic Study of CAE 2008, Volume 10, Issue 7, Pages 100-103
To investigate the molecular mechanism for phlegm-dampness constitution,examining the genome DNA of peripheral blood cells of six phlegm-dampness constitution and six normal constitution by using Affymetrix GeneChip Mapping 500K Array.We had identified 442 genes with significant differences between the phlegm-dampness constitution and the normal constitution by using Affymetrix Gene Chip Human Genome U133 plus-2, base on research results of prophase, sieve the related gene and characteristics of single nucleotide polymorphisms( SNP) of phlegm-dampnessconstitution.5 related genes and 6 SNPs with significant differences were identified between the phlegm-dampness constitution and the normal constitution. Further biologianalysis on the genes identified between two constitution groups demonstrate that they are involved in enzyme activity,sterol transporter activity,participate in the biology process of lipid metabolism, cholesterol metabolic process,brown fat cell differentiation, gluconeogenesis and thermoregulation.These results indicate that the Molecular characteristic of phlegm-dampness constitution is related to metabolism disorder.
Keywords： phlegm-dampness constitution Genechip Mapping Array Molecular characteristic
A method for Absolute Protein Expression Quantity Measurement Employing Insulator RiboJ Article
Hongbin Yu, Zheng Wang, Hanyue Xu, Jiusi Guo, Qingge Ma, Xiangxu Mu, Yunzi Luo
Engineering 2018, Volume 4, Issue 6, Pages 881-887 doi: 10.1016/j.eng.2018.09.012
Measuring the absolute protein expression quantity for a specific promoter is necessary in the fields of both molecular biology and synthetic biology. The strength of a promoter is traditionally characterized by measuring the fluorescent intensity of the fluorescent protein downstream of the promoter. Until now, measurement of the absolute protein expression quantity for a promoter, however, has been unsuccessful in synthetic biology. The fact that the protein coding sequence influences the expression level for different proteins, and the inconvenience of measuring the absolute protein expression level, present a challenge to absolute quantitative measurement. Here, we introduce a new method that combines the insulator RiboJ with the standard fluorescence curve in order to measure the absolute protein expression quantity quickly; this method has been validated by modeling verification. Using this method, we successfully measured nine constitutive promoters in the Anderson promoter family. Our method provides data with higher accuracy for pathway design and is a straightforward way to standardize the strength of different promoters.
Keywords： RiboJ Promoter measurement Synthetic biology
Albert Stuart Reece
Engineering 2023, Volume 26, Issue 7, Pages 16-16 doi: 10.1016/j.eng.2022.07.011
The central dogma of biology holds that the transcription of DNA into RNA and the translation of RNA into proteins forms the primary axis of biological activity [1]. Following major advances in the description of the complex glycan and lipid chains that are added onto these basic building blocks, the glycome and lipidome have recently been added to this doctrine as an exciting new extension named the ‘‘paracentral dogma” [2]. However, it has been pointed out that biological systems can include many layers, which are described in modern omics technology platforms relating to both cell-intrinsic and cell-extrinsic layers of control, including metabolomic, microbiomic, immunological, epigenomic, epitranscriptomic, proteomic and phosphoproteomic layers [3].
It is well known that stem and progenitor cells have a metabolism that is based on glycolysis and glutaminolysis [4]. Although this provides less energy to the cell than oxidative phosphorylation, it suffices for these cells’ needs, since such cells are generally relatively quiescent and normally suppress energy-intensive processes such as genome duplication and transcription. Moreover, it has been shown that the high intracellular lactate levels involved in such states not only inhibits the key gatekeeper enzymes of oxidative phosphorylation (i.e., pyruvate dehydrogenase and carnitine palmitoyl acyltransferase) but also actually covalently modifies them by lactylation in order to maintain this inhibited metabolic–epigenomic state [5]. In addition, intermediate metabolism and nutrients are the source of the very extensive library of post-translational modifications to DNA, RNA, and proteins, as well as supplying cellular energy for many of the required reactions. Hence, the metabolic state locks in and reinforces the epigenomic state, and the metabolome and epigenome thereby play mutually reinforcing roles. This self-reinforcing coordination explains why it is so difficult to generate induced pluripotent cells and is a contributory explanation for why the described protocols typically have such low cellular yields.
These concepts become even more important when it is considered that cancer cells are de-differentiated, similarly rely on glycolysis and glutaminolysis, and are similarly metabolically–epigenomically–genomically synchronized. The disruption of this metabolic system is a key focus of mechanistic cancer research.
These important considerations imply that the descriptive and predictive power of the newly described ‘‘paracentral dogma” of biology may be usefully and meaningfully extended by including the metabolome, along with the genome, transcriptome, proteome, glycome, and lipidome, to describe cell-intrinsic regulation—not only in terms of another omics analytical layer but also as a fully predictive and interactive partner in the symphonic-like multilayer coordination that evidently comprises cellular regulatory layering.
Artificial Intelligence Cracks a 50-Year-Old Grand Challenge in Biology
Sean O´Neill
Engineering 2021, Volume 7, Issue 6, Pages 706-708 doi: 10.1016/j.eng.2021.04.003
Engineering DNA Materials for Sustainable Data Storage Using a DNA Movable-Type System Article
Zi-Yi Gong, Li-Fu Song, Guang-Sheng Pei, Yu-Fei Dong, Bing-Zhi Li, Ying-Jin Yuan
Engineering 2023, Volume 29, Issue 10, Pages 130-136 doi: 10.1016/j.eng.2022.05.023
DNA molecules are green materials with great potential for high-density and long-term data storage. However, the current data-writing process of DNA data storage via DNA synthesis suffers from high costs and the production of hazards, limiting its practical applications. Here, we developed a DNA movable-type storage system that can utilize DNA fragments pre-produced by cell factories for data writing. In this system, these pre-generated DNA fragments, referred to herein as "DNA movable types," are used as basic writing units in a repetitive way. The process of data writing is achieved by the rapid assembly of these DNA movable types, thereby avoiding the costly and environmentally hazardous process of de novo DNA synthesis. With this system, we successfully encoded 24 bytes of digital information in DNA and read it back accurately by means of high-throughput sequencing and decoding, thereby demonstrating the feasibility of this system. Through its repetitive usage and biological assembly of DNA movable-type fragments, this system exhibits excellent potential for writing cost reduction, opening up a novel route toward an economical and sustainable digital data-storage technology.
Keywords： 合成生物学 DNA信息存储 DNA活字存储系统 经济性DNA数据存储
Next-Generation Imaging: New Insights from Multicolor Microscopy in Liver Biology and Disease
Felix Heymann, Adrien Guillot, Moritz Peiseler, Frank Tacke
Engineering 2022, Volume 9, Issue 2, Pages 17-21 doi: 10.1016/j.eng.2021.06.015
Advances and Strategies for Controlling the Quality and Safety of Postharvest Fruit Review
Tong Chen, Dongchao Ji, Zhanquan Zhang, Boqiang Li, Guozheng Qin, Shiping Tian
Engineering 2021, Volume 7, Issue 8, Pages 1177-1184 doi: 10.1016/j.eng.2020.07.029
Fresh fruits are highly valued by consumers worldwide, owing to their delicious flavors, abundant nutrients, and health-promoting characteristics, and as such, fruits make up an important component of a healthy diet. The postharvest quality and safety of fresh fruit involve complex interactions among the fruit, environmental factors, and postharvest pathogens. Efficient regulation of fruit senescence and pathogen resistance, as well as disease-causing abilities of postharvest pathogens, is critical to understanding the fundamental mechanisms that underlie fruit quality and safety. This paper provides a comprehensive review of recent advances and currently available strategies for maintaining fruit quality and controlling major postharvest pathogens, mainly Botrytis cinerea and Penicillium expansum, which may promote sustainable and environmental-friendly development of the fruit industry.
Keywords： Fruit Postharvest Quality maintenance Safety
美国实验生物学会议（Experimental Biology Annual Meeting）
Conference Date: 6 Apr 2019
Conference Place: 美国/佛罗里达/奥兰多
Administered by: 美国实验生物学联合会(Federation of America Societies for Experimental Biology)
Conference Date: 20 Sep 2019
Conference Place: 上海闵行区
Administered by: 中国生物化学与分子生物学会分子系统生物学专业委员会、中国运筹学会计算系统生物学分会
2019全国植物生物学大会，National Congress of Plant Biology
Conference Date: 11 Oct 2019
Conference Place: 中国/四川/成都
Administered by: 中国植物学会、中国作物学会、中国细胞生物学学会、中国遗传学会、中国植物生理与植物分子生物学会
Title Author Date Type Operation
Industry 5.0—The Relevance and Implications of Bionics and Synthetic Biology
Peter Sachsenmeier
Journal Article
Microbial Medicine Industry: Current Status and Future Trends
Yu Qing, Huang Tingting, Deng Zixin
Journal Article
An Additive Manufacturing Approach that Enables the Field Deployment of Synthetic Biosensors
Daniel Wolozny, John R. Lake, Paul G. Movizzo, Zhicheng Long, Warren C. Ruder
Journal Article
Engineering the Biosynthesis of Caffeic Acid in Saccharomyces cerevisiae with Heterologous Enzyme Combinations
Lanqing Liu, Hong Liu, Wei Zhang, Mingdong Yao, Bingzhi Li, Duo Liu, Yingjin Yuan
Journal Article
Study on the molecular characteristic in phlegm-dampness constitution
Wang Qi,Dong Jing,Wu Hongdong,Wang Dongpo,Yao Shilin,Ren Xiaojuan
Journal Article
A method for Absolute Protein Expression Quantity Measurement Employing Insulator RiboJ
Hongbin Yu, Zheng Wang, Hanyue Xu, Jiusi Guo, Qingge Ma, Xiangxu Mu, Yunzi Luo
Journal Article
Extending the “Paracentral Dogma” of Biology with the Metabolome: Implications for Understanding Genomic–Glycomic–Metabolic–Epigenomic Synchronization
Albert Stuart Reece
Journal Article
Artificial Intelligence Cracks a 50-Year-Old Grand Challenge in Biology
Sean O´Neill
Journal Article
Engineering DNA Materials for Sustainable Data Storage Using a DNA Movable-Type System
Zi-Yi Gong, Li-Fu Song, Guang-Sheng Pei, Yu-Fei Dong, Bing-Zhi Li, Ying-Jin Yuan
Journal Article
Next-Generation Imaging: New Insights from Multicolor Microscopy in Liver Biology and Disease
Felix Heymann, Adrien Guillot, Moritz Peiseler, Frank Tacke
Journal Article
Advances and Strategies for Controlling the Quality and Safety of Postharvest Fruit
Tong Chen, Dongchao Ji, Zhanquan Zhang, Boqiang Li, Guozheng Qin, Shiping Tian
Journal Article
美国实验生物学会议（Experimental Biology Annual Meeting）
6 Apr 2019
Conference Information
第一届全国系统生物学大会
20 Sep 2019
Conference Information
2019全国植物生物学大会，National Congress of Plant Biology
11 Oct 2019
Conference Information
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