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Investigating loss of heterozygosity in a SCRaMbLEd yeast genome

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Science China(Life Sciences) 2019年第6期62卷 868-869页

作者： Junbiao Dai shenzhen key laboratory of synthetic genomics and Center for synthetic genomics Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences

Loss of heterozygosity (LOH) is a phenomenon in which elimination of one parental genomic region occurs in interspecific hybrids. LOH is common in cancer (Deng et al., 1996;Koufos et al., 1985). However, genetic analy... 详细信息

关键词： Loss of heterozygosity elimination individual genomes

Inevitability or contingency: how many chromosomes do we really need?

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Science China(Life Sciences) 2019年第1期62卷 140-143页

作者： Shuangying Jiang Junbiao Dai shenzhen key laboratory of synthetic genomics and Center for synthetic genomics Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences

In an essay written by the evolutionary biologist Theodosius Dobzhansky in 1973,he pointed out that "Nothing in Biology Makes Sense Except in the Light of Evolution."An interesting phenomenon in biology is the presence of variable numbers of chromosomes in different *** several species,which possess multiple circular chromosomes or simply linear chromosomes (Baril et al. 1989;Suwanto and Kaplan,1989;Jumas-Bilak et al.,1998), most prokaryotes only possess one circular *** contrast,the genomes of eukaryotic species are usually packaged into linear chromosomes with numbers varying from one to hundreds (Crosland and Crozier,1986;Lukhtanov,2015).

关键词： Inevitability contingency evolutionary biologist

Long noncoding RNA XIST:Mechanisms for X chromosome inactivation,roles in sex-biased diseases,and therapeutic opportunities

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Genes & Diseases 2022年第6期9卷 1478-1492页

作者： Jianjian Li Zhe Ming Liuyi Yang Tingxuan Wang Gaowen Liu Qing Ma shenzhen key laboratory of synthetic genomics Guangdong Provincial Key Laboratory of Synthetic GenomicsCAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong 518055PR China

Sexual dimorphism has been reported in various human diseases including autoimmune diseases,neurological diseases,pulmonary arterial hypertension,and some types of cancers,although the underlying mechanisms remain poorly *** long noncoding RNA(lncRNA)X-inactive specific transcript(XIST)is involved in X chromosome inactivation(XCI)in female placental mammals,a process that ensures the balanced expression dosage of X-linked genes between *** is abnormally expressed in many sex-biased *** addition,escape from XIST-mediated XCI and skewed XCI also contribute to sex-biased ***,its expression or modification can be regarded as a biomarker for the diagnosis and prognosis of many sex-biased *** manipulation of XIST expression can inhibit the progression of some of these diseases in animal models,and therefore XIST has been proposed as a potential therapeutic *** this manuscript,we summarize the current knowledge about the mechanisms for XIST-mediated XCI and the roles of XIST in sex-biased diseases,and discuss potential therapeutic strategies targeting XIST.

关键词： Epigenetic regulation Long noncoding RNA Sex-biased diseases X chromosome inactivation XIST

Towards high-density storage of text and images into DNA by the“Xiao-Pang”codec system

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Science China(Life Sciences) 2023年第6期66卷 1447-1450页

作者： Mingwei Lu Yang Wang Wei Qiang Junting Cui Yu Wang Xiaoluo Huang Junbiao Dai shenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhen518055China shenzhen key laboratory of synthetic genomics Guangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen518055China

Dear Editor,The information about human civilization has been passed down through texts and *** to its remarkable property,DNA has been suggested as an excellent medium for the long-term storage of texts and *** systems to convert the data into A/T/C/G sequence and vice versa have become quite *** current well-known codec systems(Blawat et al.,2016;Church et al.,2012;Erlich and Zielinski,2017;Goldman et al.,2013;Grass et al.,2015)

关键词： images text system

Ratiometric fluorescence immunoassay of SARS-CoV-2 nucleocapsid protein via Si-FITC nanoprobe-based inner filter effect

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Nano Research 2023年第4期16卷 5383-5390页

作者： Guobin Mao Yang Yang Shijie Cao Silu Ye Yifang Li Wei Zhao Hongwei An Yingxia Liu Junbiao Dai Yingxin Ma CAS key laboratory of Quantitative Engineering Biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Guangxi University of Chinese Medicine Nanning 530001China shenzhen key laboratory of Pathogen and Immunity National Clinical Research Center for infectious diseaseState Key Discipline of Infectious DiseaseShenzhen Third People’s HospitalSecond Hospital Affiliated to Southern University of Science and TechnologyShenzhen 518112China

The global pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)virus has necessitated rapid,easy-to-use,and accurate diagnostic methods to monitor the virus ***,a ratiometric fluorescence enzyme-linked immunosorbent assay(ELISA)was developed using Si-fluorescein isothiocyanate nanoparticles(FITC NPs)for detecting SARSCoV-2 nucleocapsid(N)***-FITC NPs were prepared by a one-pot hydrothermal method using 3-aminopropyl triethoxysilane(APTES)-FITC as the Si *** method did not need post-modification and avoided the reduction in quantum yield and *** p-nitrophenyl(pNP)produced by the alkaline phosphatase(ALP)-mediated hydrolysis of pnitrophenyl phosphate(pNPP)could quench Si fluorescence in Si-FITC NPs via the inner filter *** ELISA,an immunocomplex was formed by the recognition of capture antibody/N protein/reporter ***-linked secondary antibody bound to the reporter antibody and induced pNPP hydrolysis to specifically quench Si fluorescence in Si-FITC *** change in fluorescence intensity ratio could be used for detecting N protein,with a wide linearity range(0.01-10.0 and 50-300 ng/mL)and low detection limit(0.002 ng/mL).The concentration of spiked SARS-CoV-2 N protein could be determined accurately in human ***,this proposed method can accurately distinguish coronavirus disease 2019(COVID-19)and non-COVID-19 patient ***,this simple,sensitive,and accurate method can be applied for the early diagnosis of SARS-CoV-2 virus infection.

关键词： Si-fluorescein isothiocyanate(FITC)nanoparticles ratiometric fluorescent probe severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) inner filter effect enzyme-linked immunosorbent assay(ELISA)

Improving cooperativity of transcription activators by oligomerization domains in mammalian cells

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synthetic and Systems Biotechnology 2023年第1期8卷 114-120页

作者： Xinmao Chen Ziming Liu Chunbo Lou Ying Guan Qi Ouyang Yanhui Xiang School of Physics Peking UniversityBeijing100871China Department of Chemical Engineering Tsinghua UniversityBeijing100871China Center for Cell and Gene Circuit Design CAS Key Laboratory of Quantitative Engineering BiologyGuangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055China

Cooperative activation is critical for the applications of synthetic biology in mammalian *** this study,we have developed cooperative transcription factor by fusing oligomerization domain in mammalian ***,we demonstrated that two oligomerized domains(CI434 and CI)successfully improved transcription factor cooperativity in bacterial cells but failed to increase cooperativity in mammalian cells,possibly because the additional mammalian activation domain disrupted their oligomerization ***,we chose a different type of oligomerized domain(CarHC),whose ability to oligomerize is not dependent on its C-terminal domains,to fuse with a transcription factor(RpaR)and activation domain(VTR3),forming a potential cooperative transcription activator RpaR-CarH-VTR3 for mammalian regulatory *** with RpaR-VTR3,the cooperativity of RpaR-CarH-VTR3 was significantly improved with higher Hill coefficient and a narrower input range in the inducible switch system in mammalian ***,a mathematical model based on statistical mechanics model was developed and the simulation results supported the hypothesis that the tetramer of the CarH domain in mammalian cells was the reason for the cooperative capacity of RpaR-CarH-VTR3.

关键词： activation narrow cooperative

Biodegradation of aromatic pollutants meets synthetic biology

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synthetic and Systems Biotechnology 2021年第3期6卷 153-162页

作者： Liang Xiang Guoqiang Li Luan Wen Cong Su Yong Liu Hongzhi Tang Junbiao Dai CAS key laboratory of Quantitative Engineering Biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055PR China State key laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240PR China

Ubiquitously distributed microorganisms are natural decomposers of environmental ***,because of continuous generation of novel recalcitrant pollutants due to human activities,it is difficult,if not impossible,for microbes to acquire novel degradation mechanisms through natural *** biology provides tools to engineer,transform or even re-synthesize an organism purposefully,accelerating transition from unable to able,inefficient to efficient degradation of given pollutants,and therefore,providing new solutions for environmental *** this review,we described the pipeline to build chassis cells for the treatment of aromatic pollutants,and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different ***,we discussed challenges and opportunities for future research in this field.

关键词： Aromatic compounds synthetic biology Bioremediation Environmental pollution Microorganisms

Efficient de novo assembly and modification of large DNA fragments

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Science China(Life Sciences) 2022年第7期65卷 1445-1455页

作者： Shuangying Jiang Yuanwei Tang Liang Xiang Xinlu Zhu Zelin Cai Ling Li Yingxi Chen Peishuang Chen Yuge Feng Xin Lin Guoqiang Li Jafar Sharif Junbiao Dai CAS key laboratory of Quantitative Engineering Biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China RIKEN Center for Integrative Medical Sciences(IMS) Developmental Genetics LaboratoryYokohama 230-0045Japan

synthetic genomics has provided new bottom-up platforms for the functional study of viral and microbial *** construction of the large,gigabase(Gb)-sized genomes of higher organisms will deepen our understanding of genetic blueprints *** for the synthesis and assembly of such large-scale genomes,the development of new or expanded methods is *** this study,we develop an efficient pipeline for the construction of large DNA fragments sized 100 kilobases(kb)or above from scratches and describe an efficient method for“scar-free”engineering of the assembled *** method,therefore,should provide a standard framework for producing long DNA molecules,which are critical materials for synthetic genomics and metabolic engineering.

关键词： DNA assembly budding yeast large DNA fragments sequence modification DNA synthesis synthetic Biology

Ratiometric fluorescent Si-FITC nanoprobe for immunoassay of SARS-CoV-2 nucleocapsid protein

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Nano Research 2023年第2期16卷 2859-2865页

作者： Guobin Mao Silu Ye Wen Yin Yang Yang Xinghu Ji Jin He Yingxia Liu Junbiao Dai Zhike He Yingxin Ma CAS key laboratory of Quantitative Engineering Biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China State key laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China shenzhen key laboratory of Pathogen and Immunity National Clinical Research Center for Infectious DiseaseState Key Discipline of Infectious DiseaseShenzhen Third People's HospitalSecond Hospital Affiliated to Southern University of Science and TechnologyShenzhen 518112China College of Chemistry and Molecular Sciences Wuhan UniversityWuhan 430072China

Coronavirus disease 2019(COVID-19)highlights the importance of rapid and reliable diagnostic assays for the management of virus ***,we developed a one-pot hydrothermal method to prepare Si-FITC nanoparticles(NPs)for the fluorescent immunoassay of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)nucleocapsid protein(N protein).The synthesis of Si-FITC NPs did not need post-modification,which addressed the issue of quantum yield reduction during the coupling ***-FITC NPs showed two distinct peaks,Si fluorescence atλem=385 nm and FITC fluorescence atλem=490 *** the presence of KMnO_(4),Si fluorescence was decreased and FITC fluorescence was ***,in the presence of N protein,catalase(CAT)-linked secondary antibody/reporter antibody/N protein/capture antibody immunocomplexes were formed on ***,hydrogen peroxide(H_(2)O_(2))and Si-FITC NPs/KMnO_(4)were injected into the microplate *** decomposition of H_(2)O_(2)by CAT resulted in remaining of KMnO_(4),which changed the fluorescence intensity ratio of Si-FITC *** fluorescence intensity ratio correlated significantly with the N protein concentration ranging from 0.02 to 50.00 ng/mL,and the detection limit was 0.003 ng/mL,which was more sensitive than the commercial ELISA kit with a detection limit of 0.057 ng/*** N protein concentration can be accurately determined in human ***,the COVID-19 and non-COVID-19 patients were distinguishable by this ***,the ratiometric fluorescent immunoassay can be used for SARS-CoV-2 infection diagnosis with a high sensitivity and selectivity.

关键词： Si-FITC nanoparticles ratiometric fluorescent probe SARS-CoV-2 ELISA