Biofunctionalized semiconductor quantum dots for virus detection

Virus is a kind of microorganism and possesses simple structure and contains one nucleic acid,which must be replicated using the host cell system.It causes large-scale infectious diseases and poses serious threats to the health,social well-being,and economic conditions of millions of people worldwide.Therefore,there is an urgent need to develop novel strategies for accurate diagnosis of virus infection to prevent disease transmission.Quantum dots(QDs)are typical fluorescence nanomaterials with high quantum yield,broad absorbance range,narrow and size-dependent emission,and good stability.QDs-based nanotechnology has been found to be effective method with rapid response,easy operation,high sensitivity,and good specificity,and has been widely applied for the detection of different viruses.However,until now,no systematic and critical review has been published on this important research area.Hence,in this review,we aim to provide a comprehensive coverage of various QDs-based virus detection methods.The fundamental investigations have been reviewed,including information related to the synthesis and biofunctionalization of QDs,QDs-based viral nucleic acid detection strategies,and QDs-based immunoassays.The challenges and perspectives regarding the potential application of QDs for virus detection is also discussed.

Enabling technology and core theory of synthetic biology

Synthetic biology provides a new paradigm for life science research(“build to learn”)and opens the future journey of biotechnology(“build to use”).Here,we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology,including synthesis and assembly of a genome,DNA storage,gene editing,molecular evolution and de novo design of function proteins,cell and gene circuit engineering,cell-free synthetic biology,artificial intelligence(AI)-aided synthetic biology,as well as biofoundries.We also introduce the concept of quantitative synthetic biology,which is guiding synthetic biology towards increased accuracy and predictability or the real rational design.We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.

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

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 infection.Herein,a ratiometric fluorescence enzyme-linked immunosorbent assay(ELISA)was developed using Si-fluorescein isothiocyanate nanoparticles(FITC NPs)for detecting SARSCoV-2 nucleocapsid(N)protein.Si-FITC NPs were prepared by a one-pot hydrothermal method using 3-aminopropyl triethoxysilane(APTES)-FITC as the Si source.This method did not need post-modification and avoided the reduction in quantum yield and stability.The 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 effect.In ELISA,an immunocomplex was formed by the recognition of capture antibody/N protein/reporter antibody.ALP-linked secondary antibody bound to the reporter antibody and induced pNPP hydrolysis to specifically quench Si fluorescence in Si-FITC NPs.The 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 serum.Moreover,this proposed method can accurately distinguish coronavirus disease 2019(COVID-19)and non-COVID-19 patient samples.Therefore,this simple,sensitive,and accurate method can be applied for the early diagnosis of SARS-CoV-2 virus infection.

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

Coronavirus disease 2019(COVID-19)highlights the importance of rapid and reliable diagnostic assays for the management of virus transmission.Here,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 reaction.Si-FITC NPs showed two distinct peaks,Si fluorescence atλem=385 nm and FITC fluorescence atλem=490 nm.In the presence of KMnO_(4),Si fluorescence was decreased and FITC fluorescence was enhanced.Briefly,in the presence of N protein,catalase(CAT)-linked secondary antibody/reporter antibody/N protein/capture antibody immunocomplexes were formed on microplates.Subsequently,hydrogen peroxide(H_(2)O_(2))and Si-FITC NPs/KMnO_(4)were injected into the microplate together.The decomposition of H_(2)O_(2)by CAT resulted in remaining of KMnO_(4),which changed the fluorescence intensity ratio of Si-FITC NPs.The 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/mL.The N protein concentration can be accurately determined in human serum.Furthermore,the COVID-19 and non-COVID-19 patients were distinguishable by this method.Therefore,the ratiometric fluorescent immunoassay can be used for SARS-CoV-2 infection diagnosis with a high sensitivity and selectivity.

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

Dear Editor,The information about human civilization has been passed down through texts and images.Owing to its remarkable property,DNA has been suggested as an excellent medium for the long-term storage of texts and images.Codec systems to convert the data into A/T/C/G sequence and vice versa have become quite critical.The 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)

Whole genome engineering by synthesis

Whole genome engineering is now feasible with the aid of genome editing and synthesis tools. Synthesizing a genome from scratch allows modifications of the genomic structure and function to an extent that was hitherto not possible, which will finally lead to new insights into the basic principles of life and enable valuable applications. With several recent genome synthesis projects as examples, the technical details to synthesize a genome and applications of synthetic genome are addressed in this perspective. A series of ongoing or future synthetic genomics projects, including the different genomes to be synthesized in GPwrite, synthetic minimal genome, massively recoded genome, chimeric genome and synthetic genome with expanded genetic alphabet, are also discussed here with a special focus on theoretical and technical impediments in the design and synthesis process. Synthetic genomics will become a commonplace to engineer pathways and genomes according to arbitrary sets of design principles with the development of high-efficient, low-cost genome synthesis and assembly technologies.

Identification of long chain isoprenoid hydrocarbons from pyrolytic product of Dunaliella

In the pyrolytic research on Dunaliella salina cultured under natural conditions, abundant long chain regular isoprenoid hydrocarbons have been first detected and identified from algal pyrolytic product. Specially, the discovery of high abundant 2,6,10,14,18-pentamethyle-icosane indicated that regular iC25 probably originated from specific holophilic algae in hyper-

Efficient de novo assembly and modification of large DNA fragments

Synthetic genomics has provided new bottom-up platforms for the functional study of viral and microbial genomes.The construction of the large,gigabase(Gb)-sized genomes of higher organisms will deepen our understanding of genetic blueprints significantly.But for the synthesis and assembly of such large-scale genomes,the development of new or expanded methods is required.In 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 sequences.Our method,therefore,should provide a standard framework for producing long DNA molecules,which are critical materials for synthetic genomics and metabolic engineering.

Construction, characterization and application of a genomewide promoter library in Saccharomyces cerevisiae

Promoters are critical elements to control gene expression but could behave differently under various growth conditions. Here we report the construction of a genome-wide promoter library, in which each native promoter in Saccharomyces cerevisiae was cloned upstream of a yellow fluorescent protein （YFP） reporter gene. Nine libraries were arbitrarily defined and assembled in bacteria. The resulting pools of promoters could be prepared and transformed into a yeast strain either as centromeric plasmids or integrated into a genomic locus upon enzymatic treatment. Using fluorescence activated cell sorting, we classified the yeast strains based on YFP fluorescence intensity and arbitrarily divided the entire library into 12 bins, representing weak to strong promoters. Several strong promoters were identified from the most active bins and their activities were assayed under different growth conditions. Finally, these promoters were applied to drive the expression of genes in xylose utilization to improve fermentation efficiency. Together, this library could provide a quick solution to identify and utilize desired promoters under user-defined growth conditions.

Biodegradation of aromatic pollutants meets synthetic biology

Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants.However,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 evolution.Synthetic 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 bioremediation.In 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 level.Finally,we discussed challenges and opportunities for future research in this field.

Dissecting PCNA function with a systematically designed mutant library in yeast

Proliferating cell nuclear antigen (PCNA), encoded by POL30 in Saccharomyces cerevisiae, is a key component of DNA metabolism. Here, a library consisting of 304 PCNA mutants was designed and constructed to probe the contribution of each residue to the biological function of PCNA. Five regions with elevated sen sitivity to DNA damaging reagents were identified using high-throughput phe no type screening. Using a series of genetic and biochemical analyses, we demonstrated that one particular mutant, K168A, has defects in the DNA damage tolerance (DDT) pathway by disrupting the interaction between PCNA and Rad5. Subsequent domain analysis showed that the PCNA-Rad5 interaction is a prerequisite for the function of Rad5 in DDT. Our study not only provides a resource in the form of a library of versatile mutants to study the functions of PCNA, but also reveals a key residue on PCNA (K168) which highlights the importance of the PCNA-Rad5 interaction in the template switching (TS) pathway.

Investigating loss of heterozygosity in a SCRaMbLEd yeast genome

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 analysis of LOH has been mainly conducted based on predetermined features of individual genomes.

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

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 organisms.Besides 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 chromosome.In 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).

Studying bona fide SARS-CoV-2 biology in a BSL-2 biosafety environment using a split-virus-genome system

Dear Editor,Severe acute respiratory syndrome coronavirus 2(SARSCoV-2)was identified as the pathogen causing the coronavirus disease(COVID-19),which sometimes resulted in fatal pneumonia(Hu et al.,2021).SARS-CoV-2 is a biosafety level 3(BSL-3)pathogen,and the requirement for high containment conditions is a bottleneck for basic research on viral biology.To help general researchers who wish to study SARS-CoV-2 but do not have access to a BSL-3 facility,a system that(1)can mimic the real life cycle of the virus;(2)allows easy genetic manipulation;and(3)shows high biosafety in BSL-2 laboratory is required.

Whole genome synthesis： from poliovirus to synthetic yeast

About thirty years ago when the human genome project （HGP） was first proposed, there was widespread disagreement on whether it was worth spending $3 billion to sequence a genome with only 3% coding sequences, which was potentially with enormous errors due to technical limitations at the time [1].

Hydrocarbons pyrolysed from nannoplanktonic algae:An experimental organism system for study on the origin of petroleum and natural gas

Enukuania huxleyi is marine nanoplanktonic alga with calcify scale called coccolith om its cell surface.This ubiquitous species with the Lafgest biomass in marice forms gigantic blooms covering thousands

Unveiling degradation mechanism of PAHs by a Sphingobium strain from a microbial consortium

Polycyclic aromatic hydrocarbons(PAHs)are a class of persistent pollutants with adverse biological effects and pose a serious threat to ecological environments and human health.The previously isolated phenanthrene‐degrading bacterial consortium(PDMC)consists of the genera Sphingobium and Pseudomonas and can degrade a wide range of PAHs.To identify the degradation mechanism of PAHs in the consortium PDMC,metagenomic binning was conducted and a Sphingomonadales assembly genome with 100%completeness was obtained.Additionally,Sphingobium sp.SHPJ‐2,an efficient degrader of PAHs,was successfully isolated from the consortium PDMC.Strain SHPJ‐2 has powerful degrading abilities and various degradation pathways of high‐molecular‐weight PAHs,including fluoranthene,pyrene,benzo[a]anthracene,and chrysene.Two ring‐hydroxylating dioxygenases,five cytochrome P450s,and a pair of electron transfer chains associated with PAH degradation in strain SHPJ‐2,which share 83.0%–99.0%similarity with their corresponding homologous proteins,were identified by a combination of Sphingomonadales assembly genome annotation,reverse‐transcription quantitative polymerase chain reaction and heterologous expression.Furthermore,when coexpressed in Escherichia coli BL21(DE3)with the appropriate electron transfer chain,PhnA1B1 could effectively degrade chrysene and benzo[a]anthracene,while PhnA2B2 degrade fluoranthene.Altogether,these results provide a comprehensive assessment of strain SHPJ‐2 and contribute to a better understanding of the molecular mechanism responsible for the PAH degradation.

eeting report on Synthetic Biology Young Scholar Forum

On May 23 in 2015, the first Synthetic Biology Young Scholar Forum （SynBioYSF） was held at Tsinghua University in Beijing, China. This forum aimed to serve as a platform for synthetic biologists, especially early career scholars, to exchange and discuss recent advances and promote synthetic biology research in China. Drs. Zhen Xie and Junbiao Dai served as the secretary general and deputy secretary general in the first SynBioYSF organization committee, which included eleven young principle investigators in the field of synthetic biology. This forum attracted about 200 participants from more than 40 universities, institutes and enterprises. In this report, we summarized 19 invited presentations and 4 lightening talks in this forum.