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Reconstructing cell lineage trees with genomic barcoding:approaches and applications

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Journal of Genetics and Genomics 2024年第1期51卷 35-47页

作者： Zizhang Li Wenjing Yang Peng Wu Yuyan Shan Xiaoyu Zhang Feng Chen Junnan Yang Jian-Rong Yang Advanced Medical Technology Center The First Affiliated HospitalZhongshan School of MedicineSun Yat-sen UniversityGuangzhouGuangdong 510080China Department of Genetics and Biomedical Informatics Zhongshan School of MedicineSun Yat-sen UniversityGuangzhouGuangdong 510080China Key Laboratory of Tropical Disease Control Ministry of EducationSun Yat-sen UniversityGuangzhouGuangdong 510080China

In multicellular organisms,developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree(CLT).The reconstruction of the CLT has long been a major goal in developmental biology and other related fields.Recent technological advancements,especially those in editable genomic barcodes and single-cell high-throughput sequencing,have sparked a new wave of experimental methods for reconstructing CLTs.Here we review the existing experimental approaches to the reconstruction of CLT,which are broadly categorized as either image-based or DNA barcode-based methods.In addition,we present a summary of the related literature based on the biological insight pro-vided by the obtained CLTs.Moreover,we discuss the challenges that will arise as more and better CLT data become available in the near future.Genomic barcoding-based CLT reconstructions and analyses,due to their wide applicability and high scalability,offer the potential for novel biological discoveries,especially those related to general and systemic properties of the developmental process.

关键词： Cell lineage tree Developmental regulation biotechnology Computational biology

Strategies on biosynthesis and production of bioactive compounds in medicinal plants

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Chinese Herbal Medicines 2024年第1期16卷 13-26页

作者： Miaoxian Guo Haizhou Lv Hongyu Chen Shuting Dong Jianhong Zhang Wanjing Liu Liu He Yimian Ma Hua Yu Shilin Chen Hongmei Luo Key Lab of Chinese Medicine Resources Conservation State Administration of Traditional Chinese Medicine of ChinaInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China Engineering Research Center of Chinese Medicine Resource Ministry of EducationBeijing 100193China Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou 311121China Chengdu University of Traditional Chinese Medicine Chengdu 611137China

Medicinal plants are a valuable source of essential medicines and herbal products for healthcare and disease therapy.Compared with chemical synthesis and extraction,the biosynthesis of natural products is a very promising alternative for the successful conservation of medicinal plants,and its rapid development will greatly facilitate the conservation and sustainable utilization of medicinal plants.Here,we summarize the advances in strategies and methods concerning the biosynthesis and production of natural products of medicinal plants.The strategies and methods mainly include genetic engineering,plant cell culture engineering,metabolic engineering,and synthetic biology based on multiple“OMICS”technologies,with paradigms for the biosynthesis of terpenoids and alkaloids.We also highlight the biosynthetic approaches and discuss progress in the production of some valuable natural products,exemplifying compounds such as vindoline(alkaloid),artemisinin and paclitaxel(terpenoids),to illustrate the power of biotechnology in medicinal plants.

关键词： biosynthetic strategies biotechnology natural products medicinal plants synthetic biology

biotechnology ofα-linolenic acid in oilseed rape(Brassica napus)using FAD2 and FAD3 from chia(Salvia hispanica)

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Journal of Integrative Agriculture 2023年第12期22卷 3810-3815页

作者： XUE Yu-fei Inkabanga Tseke ALAIN YIN Neng-wen JIANG Jia-yi ZHAO Yan-ping LU Kun LI Jia-na DING Yan-song ZHANG Shi-qing CHAI You-rong Integrative Science Center of Germplasm Creation in Western China(Chongqing)Science City and Southwest University/Chongqing Key Laboratory of Crop Quality Improvement/College of Agronomy and biotechnology Southwest UniversityChongqing 400715P.R.China Engineering Research Center of South Upland Agriculture Ministry of Education/Academy of Agricultural SciencesSouthwest UniversityChongqing 400715P.R.China Faculty of Agricultural Sciences National Pedagogic University(UPN)Kinshasa 8815D.R.Congo

α-Linolenic acid(ALA,18:3Δ9,12,15)is an essential fatty acid for humans since it is the precursor for the biosynthesis of omega-3 long-chain polyunsaturated fatty acids(LC-PUFA).Modern people generally suffer from deficiency of ALA because most staple food oils are low or lack ALA content.Biotechnological enrichment of ALA in staple oil crops is a promising strategy.Chia(Salvia hispanica)has the highest ALA content in its seed oil among known oil crops.In this study,the FAD2 and FAD3 genes from chia were engineered into a staple oil crop,oilseed rape(Brassica napus),via Agrobaterium tumefaciens-mediated transformation of their LP4-2A fusion gene construct driven by the seed-specific promoter P_(NapA).In seeds of T0,T1,and T2 lines,the average ALA contents were 20.86,23.54,and 24.92%,respectively,which were 2.21,2.68,and 3.03 folds of the non-transformed controls(9.42,8.78,and 8.22%),respectively.The highest seed ALA levels of T0,T1,and T2 plants were 38.41,35.98,and 39.19%respectively,which were 4.10-4.77 folds of the respective controls.FA-pathway enzyme genes(BnACCD,BnFATA,BnSAD,BnSCD,BnDGAT1,BnDGAT2,and BnDGAT3)and positive regulatory genes(BnWRI1,BnLEC1,BnL1L,BnLEC2,BnABI3,BnbZIP67,and BnMYB96)were all significantly up-regulated.In contrast,BnTT1,BnTT2,BnTT8,BnTT16,BnTTG1,and BnTTG2,encoding negative oil accumulation regulators but positive secondary metabolism regulators,were all significantly down-regulated.This means the foreign ShFAD2-ShFAD3 fusion gene,directly and indirectly,remodeled both positive and negative loci of the whole FA-related network in transgenic B.napus seeds.

关键词： biotechnology α-linolenic acid oilseed rape(Brassica napus) FAD2 FAD3 chia(Salvia hispanica)

Emerging biotechnology applications in natural product and synthetic pharmaceutical analyses

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Acta Pharmaceutica Sinica B 2022年第11期12卷 4075-4097页

作者： Shilin Chen Zheng Li Sanyin Zhang Yuxin Zhou Xiaohe Xiao Pengdi Cui Binjie Xu Qinghe Zhao Shasha Kong Yuntao Dai Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China State Key Laboratory of Component Traditional Chinese Medicine College of Pharmaceutical Engineering of Traditional Chinese MedicineHaihe Laboratory of Modern Chinese MedicineTianjin University of Traditional Chinese MedicineTianjin 301617China Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese MedicineChengdu 611137China China Military Institute of Chinese Medicine Fifth Medical Center of Chinese PLA General HospitalBeijing 100039China

Pharmaceutical analysis is a discipline based on chemical, physical, biological, and information technologies. At present, biotechnological analysis is a short branch in pharmaceutical analysis;however, bioanalysis is the basis and an important part of medicine. Biotechnological approaches can provide information on biological activity and even clinical efficacy and safety, which are important characteristics of drug quality. Because of their advantages in reflecting the overall biological effects or functions of drugs and providing visual and intuitive results, some biotechnological analysis methods have been gradually applied to pharmaceutical analysis from raw material to manufacturing and final product analysis,including DNA super-barcoding, DNA-based rapid detection, multiplex ligation-dependent probe amplification, hyperspectral imaging combined with artificial intelligence, 3D biologically printed organoids,omics-based artificial intelligence, microfluidic chips, organ-on-a-chip, signal transduction pathwayrelated reporter gene assays, and the zebrafish thrombosis model. The applications of these emerging biotechniques in pharmaceutical analysis have been discussed in this review.

关键词： biotechnology Pharmaceutical analysis Rawmaterials Manufacturing control Quality analysis

White biotechnology and the production of bio-products

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Systems Microbiology and Biomanufacturing 2022年第3期2卷 413-429页

作者： Masoumeh Kordi Robab Salami Parisa Bolouri Nasser Delangiz Behnam Asgari Lajayer Eric D.van Hullebusch Department of Plant Sciences and biotechnology Faculty of Life Sciences&BiotechnologyShahid Beheshti UniversityTehranIran Department of Genetic and Bioengineering BiotechnologyYeditepe UniversityIstambulTurkey Department of Plant biotechnology and Breeding Faculty of AgricultureUniversity of TabrizTabrizIran Department of Soil Science Faculty of AgricultureUniversity of TabrizTabrizIran Institut de Physique du Globe de Paris CNRSUniversitéde Paris75005 ParisFrance

White biotechnology uses enzymes and microorganisms to produce value-added chemicals from renewable sources.White biotechnology provides valuable components for the food,pharmaceutical,agricultural sectors as well as other industries.Metabolic diversity in fungi,yeast,and bacteria can be exploited to produce food additives and other industrial products.This is an interesting topic for those interested in screening and metabolic testing of microorganisms,industrial biotechnology,fermentation technology,and the biological products research community.The use of microbial-derived compounds has a long history in the food industry,and compounds such as flavorings,essential amino acids,poly-unsaturated fatty acids,organic acids,gelling,etc.can be obtained from microbial sources.Also,the role of microbes in human health and well-being cannot be ignored.Microbes produce primary metabolites such as vitamins,nucleotides,and amino acids,as well as secondary metabolites.These secondary metabolites are used to make many drugs.In agriculture,microbes are also used to make fertilizers and biological pesticides.This paper reviews the types of bio-products obtained through biotechnology and the barriers and challenges of white biotechnology.

关键词： Microorganisms biotechnology Industry Food Pharmaceutical White biotechnology

Mesenchymal stem cell differentiation and usage for biotechnology applications:tissue engineering and food manufacturing

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Biomaterials Translational 2022年第1期3卷 17-23页

作者： Dafna Benayahu Department of Cell and Developmental Biology Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael

Recent advances in the field of stem cell research now enable their utilisation for biotechnology applications in regenerative medicine and food tech.The first use of stem cells as biomedical devices employed a combination of cells and scaffold to restore,improve,or replace damaged tissues and to grow new viable tissue for replacement organs.This approach has also been adopted to replace meat production in the food industry.Mesenchymal stem cells are the source material used to induce cells to differentiate into the desired lineage.These technologies require mass propagation and rely on supplying the regulatory factors that direct differentiation.Mesenchymal stem cells can differentiate into fibroblastic and skeletal cells;fibroblastic/chondrogenic/osteogenic/myogenic and adipogenic lineages.Each differentiation fate requires specific key molecular regulators and appropriate activation conditions.Stem cell commitment determination involves a concerted effort of coordinated activation and silencing of lineage-specific genes.Transcription factors which bind gene promoters and chromatin-remodelling proteins are key players in the control process of lineage commitment and differentiation from embryogenesis through adulthood.Consequently,a major research challenge is to characterise such molecular pathways that coordinate lineage-specific differentiation and function.Revealing the mechanisms of action and the main factors will provide the knowledge necessary to control activation and regulation to achieve a specific lineage.Growing cells on a scaffold is a support system that mimics natural tissue and transduces the appropriate signals of the tissue niche for appropriate cellular function.The outcome of such research will deepen the understanding of cell differentiation to promote and advance the biotech,allowing the cell expansion required for their usage in therapy or the development of food tech.

关键词： biotechnology chromatin remodelling differentiation gene expression mesenchymal cells

The Effects of Disruptive Thinking on the Food Industry*

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Advances in Bioscience and biotechnology 2024年第6期15卷 360-379页

作者： Omotola Oluwakemi Dairo Bernard Boamah Bekoe Faculty of Business and Law Anglia Ruskin University Cambridge UK College of Education and Liberal Art Wilmington University Delaware USA College of Management Science Hohai University Nanjing China

This study aimed to understand disruptive thinking and how its ideas can change the food industry. This was achieved by identifying, studying, and understanding the impacts, current trends, and different disruptive ideas and innovations emerging in the food industry. The study was conducted through interpretive research philosophy by carrying out secondary data collection processes, where both qualitative and quantitative information was presented. Deductive approaches were also selected to apply existing theories and models, which were used to construct research hypotheses and present detailed findings. The study finds that, with disruptive thinking, enhancements in the product life cycle, new flavors, and improvements in food packaging have been possible. The supply chain, which is always considered a complex part of the food industry, has been streamlined, offering greater transparency and real-time tracking and improving quality control across distribution systems.

关键词： Disruptive Thinking Food Industry Supply Chain Lab-Grown Meat biotechnology

Biosafety and biosecurity in the era of biotechnology:The Middle East region

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Journal of Biosafety and Biosecurity 2022年第2期4卷 130-145页

作者： Laith AL-Eitan Malek Alnemri Department of biotechnology and Genetic Engineering Jordan University of Science and TechnologyIrbid 22110Jordan

biotechnology became a paradigm-shifting science among all subfields of biology.The benefits of biotechnology have reached many practical fields,whether human health,animal,and/or agricultural.However,wherever there is a biotechnology practice,there is an associated biohazard with it,and its negative impact may reach all living entities including humans.Therefore,the cooperation of the leading institutions in this field has culminated in creating the concepts and applications of biosafety and biosecurity.The countries of the Middle East are considered biotechnology-practicing and have shown a clear acceptance to this field.But unfortunately,the Middle East region is one that is facing the most multichallenges,which would constitute real and noticeable concern at the local and international levels.Such challenges represented by wars and armed conflicts,deteriorating economic conditions,the large number of refugees,and the spread of many epidemics.Thus,limiting the region’s ability to deal with the surrounding biological hazards and struggling the way to the one health concept.Therefore,this article aims to shed light on the activities of the Middle East countries in the field of biotechnology and to address potential biological threats,whether natural such as the spread of viruses,or intentional such as biological attacks and bioterrorism.The article also shows the capacity of the countries of the region in the field of biosafety and biosecurity based on available information.Accordingly,some countries are lacking the required level of preparedness to face potential biological threats.Multi-institutional and international cooperation between the concerned countries will significantly enhance the capacity of the region in biosafety and biosecurity to meet the level of biological risk.Search methodology:wide range of related keywords(based on the section)combined with the name of the region,or one country individually have been searched using available search engines and databases such as google scholar and PubMed.A

关键词： Biosafety Biosecurity biotechnology Bioterrorism Biological weapons Middle east Viruses

The Application of biotechnology in Medicinal Plants Breeding Research in China

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Chinese Journal of Integrative Medicine 2015年第7期21卷 551-560页

作者：黄和平栗进才黄璐琦汪电雷黄鹏聂久胜 School of Pharmacy Anhui University of Chinese Medicine National Resource Center for Chinese Materia Medica China Academy of Chinese Medical Sciences Department of Pharmacy Bozhou Vocational and Technical College

Breeding is not only an important area of medicinal plants research but also the foundation for the superior varieties acquirement of medicinal plants. The rise of modem biotechnology provides good opportunities and new means for medicinal plants breeding research in China. biotechnology shows its technical advantages and new development prospects in breeding of new medicinal plants varieties with high and stable yield, good quality, as well as stress-resistance. In this paper, we describe recent advances, problems, and development prospects about the application of modem biotechnology in medicinal plants breeding research in China.

关键词： biotechnology medicinal plants breeding application China