The exosome-mediated response can promote or restrain the diseases by regulating the intracellular pathways,making the exosome become an effective marker for diagnosis and therapeutic control at the single-cell level....The exosome-mediated response can promote or restrain the diseases by regulating the intracellular pathways,making the exosome become an effective marker for diagnosis and therapeutic control at the single-cell level.However,real-time analysis is hard to be achieved with traditional approaches because the exosomes usually need to be enriched by ultracentrifugation for a measurable signal-to-noise ratio.Recently developed label-free single-molecule imaging approaches may become an real-time quantitative tool for the analysis of single exosomes and related secretion behaviors of single living cells owing to their extreme sensitivity.展开更多
Polarimetric imaging has a wide range of applications for uncovering features invisible to human eyes and conventional imaging sensors.Chip-integrated,fast,cost-effective,and accurate full-Stokes polarimetric imaging ...Polarimetric imaging has a wide range of applications for uncovering features invisible to human eyes and conventional imaging sensors.Chip-integrated,fast,cost-effective,and accurate full-Stokes polarimetric imaging sensors are highly desirable in many applications,which,however,remain elusive due to fundamental material limitations.Here we present a chip-integrated Metasurface-based Full-Stokes Polarimetric Imaging sensor(MetaPolarIm)realized by integrating an ultrathin(~600 nm)metasurface polarization filter array(MPFA)onto a visible imaging sensor with CMOS compatible fabrication processes.The MPFA is featured with broadband dielectric-metal hybrid chiral metasurfaces and double-layer nanograting polarizers.This chip-integrated polarimetric imaging sensor enables single-shot full-Stokes imaging(speed limited by the CMOS imager)with the most compact form factor,records high measurement accuracy,dual-color operation(green and red)and a field of view up to 40 degrees.MetaPolarIm holds great promise to enable transformative applications in autonomous vision,industry inspection,space exploration,medical imaging and diagnosis.展开更多
Antibiotic-resistant bacteria severely threaten human health.Besides spontaneous mutations generated by endogenous factors,the resistance might also originate from mutations induced by certain antibiotics,such as the ...Antibiotic-resistant bacteria severely threaten human health.Besides spontaneous mutations generated by endogenous factors,the resistance might also originate from mutations induced by certain antibiotics,such as the fluoroquinolones.Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems.However,the relative contributions of these molecular mechanisms remain unclear,hindering understanding of the generation of resistant pathogens.Here,using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains,as well as those of the strains deficient for the mismatch repair(MMR)and the oxidative damage repair pathways,we find that the SOS response is the major mutagenesis contributor in mutation elevation,responsible for~30–50%of the total base-pair substitution(BPS)mutation-rate elevation upon treatment with sublethal levels of norfloxacin(0~50 ng/mL).We further estimate the significance of the effects on other mutational features of these mechanisms(i.e.,transversions,structural variations,and mutation spectrum)in E.coli using linear models.The SOS response plays a positive role in all three mutational features(mutation rates of BPSs,transversions,structural variations)and affects the mutational spectrum.The repair systems significantly reduce the BPS mutation rate and the transversion rate,regardless of whether antibiotics are present,while significantly increasing the structural variation rate in E.coli.Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis.展开更多
High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of ...High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring ones.Commercial library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples.With this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.展开更多
Perry L.McCarty passed away on June 4,at the age of 91.He was a revered leader in Environmental Engineering and Biotechnology.Dr.Perry L.McCarty passed away peacefully and with his family on June 4,2023.Perry was a wo...Perry L.McCarty passed away on June 4,at the age of 91.He was a revered leader in Environmental Engineering and Biotechnology.Dr.Perry L.McCarty passed away peacefully and with his family on June 4,2023.Perry was a world leader in Environmental Engineering,with special emphasis on Environmental Biotechnology,in which we form partnerships with microbial communities that provide services to make human society more sustainable.I was one of Perry’s Ph.D.students,and we worked together on research,service,and publishing throughout my career.I have deep and personal knowledge of how Perry and his students developed the fundamental principles that have allowed Environmental Biotechnology to flourish and advance humans’sustainability.展开更多
Enzyme commission(EC)numbers,which associate a protein sequence with the biochemical reactions it catalyzes,are essential for the accurate understanding of enzyme functions and cellular metabolism.Many ab initio compu...Enzyme commission(EC)numbers,which associate a protein sequence with the biochemical reactions it catalyzes,are essential for the accurate understanding of enzyme functions and cellular metabolism.Many ab initio computational approaches were proposed to predict EC numbers for given input protein sequences.However,the prediction performance(accuracy,recall,and precision),usability,and efficiency of existing methods decreased seriously when dealing with recently discovered proteins,thus still having much room to be improved.Here,we report HDMLF,a hierarchical dual-core multitask learning framework for accurately predicting EC numbers based on novel deep learning techniques.HDMLF is composed of an embedding core and a learning core;the embedding core adopts the latest protein language model for protein sequence embedding,and the learning core conducts the EC number prediction.Specifically,HDMLF is designed on the basis of a gated recurrent unit framework to perform EC number prediction in the multi-objective hierarchy,multitasking manner.Additionally,we introduced an attention layer to optimize the EC prediction and employed a greedy strategy to integrate and fine-tune the final model.Comparative analyses against 4 representative methods demonstrate that HDMLF stably delivers the highest performance,which improves accuracy and F1 score by 60%and 40%over the state of the art,respectively.An additional case study of tyrB predicted to compensate for the loss of aspartate aminotransferase aspC,as reported in a previous experimental study,shows that our model can also be used to uncover the enzyme promiscuity.Finally,we established a web platform,namely,ECRECer(https://ecrecer.biodesign.ac.cn),using an entirely could-based serverless architecture and provided an offline bundle to improve usability.展开更多
High-quality genome-scale metabolic models(GEMs)could play critical roles on rational design of microbial cell factories in the classical Design-Build-Test-Learn cycle of synthetic biology studies.Despite of the const...High-quality genome-scale metabolic models(GEMs)could play critical roles on rational design of microbial cell factories in the classical Design-Build-Test-Learn cycle of synthetic biology studies.Despite of the constant establishment and update of GEMs for model microorganisms such as Escherichia coli and Saccharomyces cerevisiae,high-quality GEMs for non-model industrial microorganisms are still scarce.Zymomonas mobilis subsp.mobilis ZM4 is a non-model ethanologenic microorganism with many excellent industrial characteristics that has been developing as microbial cell factories for biochemical production.Although five GEMs of Z.mobilis have been constructed,these models are either generating ATP incorrectly,or lacking information of plasmid genes,or not providing standard format file.In this study,a high-quality GEM iZM516 of Z.mobilis ZM4 was constructed.The information from the improved genome annotation,literature,datasets of Biolog Phenotype Microarray studies,and recently updated Gene-Protein-Reaction information was combined for the curation of iZM516.Finally,516 genes,1389 reactions,1437 metabolites,and 3 cell compartments are included in iZM516,which also had the highest MEMOTE score of 91%among all published GEMs of Z.mobilis.Cell growth was then predicted by iZM516,which had 79.4%agreement with the experimental results of the substrate utilization.In addition,the potential endogenous succinate synthesis pathway of Z.mobilis ZM4 was proposed through simulation and analysis using iZM516.Furthermore,metabolic engineering strategies to produce succinate and 1,4-butanediol(1,4-BDO)were designed and then simulated under anaerobic condition using iZM516.The results indicated that 1.68 mol/mol succinate and 1.07 mol/mol 1,4-BDO can be achieved through combinational metabolic engineering strategies,which was comparable to that of the model species E.coli.Our study thus not only established a high-quality GEM iZM516 to help understand and design microbial cell factories for economic biochemical production using Z.mobilis as the chassis,but also provided guidance on building accurate GEMs for other non-model industrial microorganisms.展开更多
Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group.As a prominent strain in the fields of agriculture and bioengineering,there is still a lack of co...Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group.As a prominent strain in the fields of agriculture and bioengineering,there is still a lack of comprehensive understanding regarding its metabolic capabilities,specifically in terms of central metabolism and substrate utilization.Therefore,further exploration and extensive studies are required to gain a detailed insight into these aspects.This study reconstructed a genome-scale metabolic network model for P.stutzeri A1501 and conducted extensive curations,including correcting energy generation cycles,respiratory chains,and biomass composition.The final model,iQY1018,was successfully developed,covering more genes and reactions and having higher prediction accuracy compared with the previously published model iPB890.The substrate utilization ability of 71 carbon sources was investigated by BIOLOG experiment and was utilized to validate the model quality.The model prediction accuracy of substrate utilization for P.stutzeri A1501 reached 90%.The model analysis revealed its new ability in central metabolism and predicted that the strain is a suitable chassis for the production of Acetyl CoA-derived products.This work provides an updated,high-quality model of P.stutzeri A1501for further research and will further enhance our understanding of the metabolic capabilities.展开更多
Hexavalent uranium(U(VI))can be immobilized by various microbes.The role of extracellular polymeric substances(EPS)in U(VI)immobilization has not been quantified.This work provides a model framework to quantify the co...Hexavalent uranium(U(VI))can be immobilized by various microbes.The role of extracellular polymeric substances(EPS)in U(VI)immobilization has not been quantified.This work provides a model framework to quantify the contributions of three processes involved in EPS-mediated U(VI)immobilization:adsorption,bioreduction and desorption.Loosely associated EPS was extracted from a pure bacterial strain,Klebsiella sp.J1,and then exposed to H_(2) and O_(2)(no bioreduction control)to immobilize U(VI)in batch experiments.U(VI)immobilization was faster when exposed to H_(2) than O_(2) and stabilized at 94%for H_(2) and 85%for O_(2),respectively.The non-equilibrium data from the H_(2) experiments were best simulated by a kinetic model consisting of pseudo-second-order adsorption(ka=2.87×10^(−3) g EPS·(mg U)^(−1)·min^(−1)),first-order bioreduction(kb=0.112 min−1)and first-order desorption(kd=7.00×10^(−3) min^(−1))and fitted the experimental data with R^(2) of 0.999.While adsorption was dominant in the first minute of the experiments with H_(2),bioreduction was dominant from the second minute to the 50th min.After 50 min,adsorption was negligible,and bioreduction was balanced by desorption.This work also provides the first set of equilibrium data for U(VI)adsorption by EPS alone.The equilibrium experiments with O_(2) were well simulated by both the Langmuir isotherm and the Freundlich isotherm,suggesting multiple mechanisms involved in the interactions between U(VI)and EPS.The thermodynamic study indicated that the adsorption of U(VI)onto EPS was endothermic,spontaneous and favorable at higher temperatures.展开更多
Over the last 50 years,the explosive adoption of modern agricultural practices has led to an enormous increase in the emission of non-biodegradable and highly biotoxic ions into the hydrosphere.Excess intake of such i...Over the last 50 years,the explosive adoption of modern agricultural practices has led to an enormous increase in the emission of non-biodegradable and highly biotoxic ions into the hydrosphere.Excess intake of such ions,even essential trace elements such as Cu^(2+)and F^(-),can have serious consequences on human health.Therefore,to ensure safe drinking water and regulate wastewater discharge,photoelectrochemical(PEC)online sensors were developed,with advantages such as low energy consumption,inherent miniaturization,simple instrumentation,and fast response.However,there is no publicly available systematic review of the recent advances in PEC ion sensors available in the literature since January 2017.Thus,this review covers the various strategies that have been used to enhance the sensitivity,selectivity,and limit of detection for PEC ion sensors.The photoelectrochemically active materials,conductive substrates,electronic transfer,and performance of various PEC sensors are discussed in detail and divided into sections based on the measurement principle and detected ion species.We conclude this review by highlighting the challenges and potential future avenues of research associated with the development of novel high-performance PEC sensors.展开更多
Flat optics presents a new path to control the phase, amplitude, and polarization state of light with ultracompact devices. Here we demonstrate chip-integrated metasurface devices for polarization detection of mid-inf...Flat optics presents a new path to control the phase, amplitude, and polarization state of light with ultracompact devices. Here we demonstrate chip-integrated metasurface devices for polarization detection of mid-infrared light with arbitrary polarization states. Six high-performance microscale linear and circular polarization filters based on vertically stacked plasmonic metasurfaces(with total thickness <600 nm) are integrated on the same chip to obtain all four Stokes parameters of light with high accuracy. The device designs can be tailored to operate at any wavelength in the mid-infrared spectral region and are feasible for on-chip integration with mid-infrared(mid-IR) photodetectors and imager arrays. Our work will enable on-chip mid-IR polarimeters and polarimetric imaging systems, which are highly desirable for many applications, such as clinical diagnosis, target detection, and space exploration.展开更多
The quantification and effects of system pH value on the interactions between Pb(II) and the biopolymer in activated sludge were investigated. The biopolymer had two protein-like fluorescence peaks (Ex/Em = 280 nm1...The quantification and effects of system pH value on the interactions between Pb(II) and the biopolymer in activated sludge were investigated. The biopolymer had two protein-like fluorescence peaks (Ex/Em = 280 nm1326-338 nm for peak A; Ex/Em = 220-230 nm/324-338 nm for peak B). The fluorescence intensities of peak B were higher than those of peak A. The fluorophores of both peaks could be largely quenched by Pb(ll), and the quencher dose for peak B was about half of that for peak A. The modified Stern-Volmer equation well depicted the fluorescence quenching titration. The quenching constant (Ka) values for both peaks decreased with rising system pH value, and then sharply decreased under alkaline conditions. It could be attributed to that the alkaline conditions caused the reduction of available Pb(II) due to the occurrence of Pb(OH)2 sediments. The Ka values of peak B were bigger than those for peak A at the same system pH values. Accordingly, the aromatic proteins (peak B) played a key role in the interactions between metal ions and the biopolymer.展开更多
Conformational dynamics contribute importantly to enzyme catalysis,such that targeted conformational constraint may affect catalysis.Firefly luciferases undergo extensive structural change during catalysis;key residue...Conformational dynamics contribute importantly to enzyme catalysis,such that targeted conformational constraint may affect catalysis.Firefly luciferases undergo extensive structural change during catalysis;key residues form a hydrophobic pocket,excluding water and enabling maximally energetic light production.Point mutants almost always luminesce at longer wavelengths(lower energy)than the wild type.Conformational constraint,using dipeptide analogue 3 at a position critical for optimized excited state structure,produced luciferase emission at a shorter wavelength by∼10 nm.Incomparison,introduction of conformationally constrained analogues 4,5,or 7 afforded luciferases emitting at longer wavelengths,while a related unconstrained luciferase(analogue 6)exhibited wild-type emission.The constrained luciferases tested were more stable than the wild type.Protein modeling demonstrated that the“inside”or“outside”orientation of the conformationally constrained dipeptide led to the shorter or longer emission wavelength,respectively.More broadly,these results suggest that local conformational constraint can control specific elements of enzyme behavior,both in vitro and in vivo.This represents the first example of studying enzyme function by introducing conformationally constrained dipeptides at a specific protein position.The principles discovered here in luciferase modification will enable studies to control the wavelength emission and photophysical properties of modified luciferases.展开更多
It is common that 2,4,6-trichlorophenol (TCP) coexists with nitrate or nitrite in industrial wastewaters. In this work, simultaneous reductive dechlorination of TCP and denitrification of nitrate or nitrite competed...It is common that 2,4,6-trichlorophenol (TCP) coexists with nitrate or nitrite in industrial wastewaters. In this work, simultaneous reductive dechlorination of TCP and denitrification of nitrate or nitrite competed for electron donor, which led to their mutual inhibition. All inhibitions could be relieved to a certain degree by augmenting an organic electron donor, but the impact of the added electron donor was strongest for TCP. For simultaneous reduction ofTCP together with nitrate, TCP's removal rate value increased 75% and 150%, respectively, when added glucose was increased from 0.4 mmol· L^-1 to 0.5 mmol· L^-1 and to 0.76 mmol· L^-1 For comparison, the removal rate for nitrate increased by only 25% and 114% for the same added glucose. The relationship between their initial biodegradation rates versus their initial concentrations could be represented well with the Monod model, which quantified their half-maximum-rate concentration (Ks value), and Ks values for TCP, nitrate, and nitrite were larger with simultaneous reduction than independent reduction. The increases in Ks are further evidence that competition for the electron donor led to mutual inhibition. For bioremediation of wastewater containing TCP and oxidized nitrogen, both reduction reactions should proceed more rapidly if the oxidized nitrogen is nitrite instead of nitrate and if readily biodegradable electron acceptor is augmented.展开更多
Benzotriazole (BTA) is an emerging contaminant that also is a recalcitrant compound. Sequential and intimate coupling of UV-photolysis with biodegradation were investigated for their impacts on BTA removal and miner...Benzotriazole (BTA) is an emerging contaminant that also is a recalcitrant compound. Sequential and intimate coupling of UV-photolysis with biodegradation were investigated for their impacts on BTA removal and mineralization in aerobic batch experiments. Special attention was given to the role of its main photolytic products, which were aminophenol (AP), formic acid (FA), maleic acid (MA), and phenazine (PHZ). Experiments with sequential coupling showed that BTA biodegradation was accelerated by photolytic pretreatment up to 9 min, but BTA biodegradation was slowed with longer photolysis. FA and MA accelerated BTA biodegradation by being labile electron-donor substrates, but AP and PHZ slowed the rate because of inhibition due to their competition for intracellular electron donor. Because more AP and PHZ accumulated with increasing photolysis time, their inhibitory effects began to dominate with longer photolysis time. Intimately coupling photolysis with biodegradation relieved the inhibition effect, because AP and PHZ were quickly biodegraded and did not accumulate, which accentuated the beneficial effect of FA and MA.展开更多
Many plant disease resistance(R)genes function specifically in reaction to the presence of cognate effectors from a pathogen.Xanthomonas oryzae pathovar oryzae(Xoo)uses transcription activator-like effectors(TALes)to ...Many plant disease resistance(R)genes function specifically in reaction to the presence of cognate effectors from a pathogen.Xanthomonas oryzae pathovar oryzae(Xoo)uses transcription activator-like effectors(TALes)to target specific rice genes for expression,thereby promoting host susceptibility to bacterial blight.Here,we report the molecular characterization of Xa7,the cognate R gene to the TALes AvrXa7 and PthXo3,which target the rice major susceptibility gene SWEET14.Xa7 was mapped to a unique 74-kb region.Gene expression analysis of the region revealed a candidate gene that contained a putative AvrXa7 effector binding element(EBE)in its promoter and encoded a 113-amino-acid peptide of unknown function.Genome editing at the Xa7 locus rendered the plants susceptible to avrXa7-carrying Xoo strains.Both AvrXa7 and PthXo3 activated a GUS reporter gene fused with the EBE-containing Xa7 promoter in Nicotiana benthamiana.The EBE of Xa7 is a close mimic of the EBE of SWEET14 for TALe-induced disease susceptibility.Ectopic expression of Xa7 triggers cell death in N.benthamiana.Xa7 is prevalent in indica rice accessions from 3000 rice genomes.Xa7 appears to be an adaptation that protects against pathogen exploitation of SWEET14 and disease susceptibility.展开更多
基金National Institute of General Medical Sciences of the National Institutes of Health Grant[Grant No.R01GM107165].
文摘The exosome-mediated response can promote or restrain the diseases by regulating the intracellular pathways,making the exosome become an effective marker for diagnosis and therapeutic control at the single-cell level.However,real-time analysis is hard to be achieved with traditional approaches because the exosomes usually need to be enriched by ultracentrifugation for a measurable signal-to-noise ratio.Recently developed label-free single-molecule imaging approaches may become an real-time quantitative tool for the analysis of single exosomes and related secretion behaviors of single living cells owing to their extreme sensitivity.
基金supported in part by NSF under Grant No.2048230 and 1809997DOE under Grant No.DE-EE0008999+1 种基金Device fabrication and characterization in the Center for Solid State Electronics Research(CSSER)LeRoy Eyring Center for Solid State Science(LE-CSSS)at Arizona State University was supported,in part,by NSF contract ECCS-1542160.
文摘Polarimetric imaging has a wide range of applications for uncovering features invisible to human eyes and conventional imaging sensors.Chip-integrated,fast,cost-effective,and accurate full-Stokes polarimetric imaging sensors are highly desirable in many applications,which,however,remain elusive due to fundamental material limitations.Here we present a chip-integrated Metasurface-based Full-Stokes Polarimetric Imaging sensor(MetaPolarIm)realized by integrating an ultrathin(~600 nm)metasurface polarization filter array(MPFA)onto a visible imaging sensor with CMOS compatible fabrication processes.The MPFA is featured with broadband dielectric-metal hybrid chiral metasurfaces and double-layer nanograting polarizers.This chip-integrated polarimetric imaging sensor enables single-shot full-Stokes imaging(speed limited by the CMOS imager)with the most compact form factor,records high measurement accuracy,dual-color operation(green and red)and a field of view up to 40 degrees.MetaPolarIm holds great promise to enable transformative applications in autonomous vision,industry inspection,space exploration,medical imaging and diagnosis.
基金supported by Laoshan Laboratory(LSKJ202203203)the National Natural Science Foundation of China(31961123002,32270435)+3 种基金the Fundamental Research Funds for the Central Universities(202161064)the Young Taishan Scholars Program of Shandong Province(tsqn201812024)the Natural Science Foundation of Shandong Province(ZR2023QC191)the National Institutes of Health award(R35-GM122566).
文摘Antibiotic-resistant bacteria severely threaten human health.Besides spontaneous mutations generated by endogenous factors,the resistance might also originate from mutations induced by certain antibiotics,such as the fluoroquinolones.Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems.However,the relative contributions of these molecular mechanisms remain unclear,hindering understanding of the generation of resistant pathogens.Here,using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains,as well as those of the strains deficient for the mismatch repair(MMR)and the oxidative damage repair pathways,we find that the SOS response is the major mutagenesis contributor in mutation elevation,responsible for~30–50%of the total base-pair substitution(BPS)mutation-rate elevation upon treatment with sublethal levels of norfloxacin(0~50 ng/mL).We further estimate the significance of the effects on other mutational features of these mechanisms(i.e.,transversions,structural variations,and mutation spectrum)in E.coli using linear models.The SOS response plays a positive role in all three mutational features(mutation rates of BPSs,transversions,structural variations)and affects the mutational spectrum.The repair systems significantly reduce the BPS mutation rate and the transversion rate,regardless of whether antibiotics are present,while significantly increasing the structural variation rate in E.coli.Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis.
基金supported by the National Natural Science Foundation of China(31961123002,31872228)the Fundamental Research Funds for the Central Universities of China(202041001)+1 种基金the Young Taishan Scholars Program of Shandong Province(tsqn201812024)the National Science Foundation(DEB-1927159).
文摘High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring ones.Commercial library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples.With this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.
文摘Perry L.McCarty passed away on June 4,at the age of 91.He was a revered leader in Environmental Engineering and Biotechnology.Dr.Perry L.McCarty passed away peacefully and with his family on June 4,2023.Perry was a world leader in Environmental Engineering,with special emphasis on Environmental Biotechnology,in which we form partnerships with microbial communities that provide services to make human society more sustainable.I was one of Perry’s Ph.D.students,and we worked together on research,service,and publishing throughout my career.I have deep and personal knowledge of how Perry and his students developed the fundamental principles that have allowed Environmental Biotechnology to flourish and advance humans’sustainability.
基金the National Key Research and Development Program of China(2020YFA0908300)the National Natural Science Foundation of China(32201242)+2 种基金the Youth Innovation Promotion Association CAS,Innovation fund of Haihe Laboratory of Synthetic Biology(22HHSWSS00021)Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project(TSBICIP-PTJS-001,TSBICIP-CXRC-018,and TSBICIP-PTJJ-007)the China Postdoctoral Science Foundation(2022M713328).
文摘Enzyme commission(EC)numbers,which associate a protein sequence with the biochemical reactions it catalyzes,are essential for the accurate understanding of enzyme functions and cellular metabolism.Many ab initio computational approaches were proposed to predict EC numbers for given input protein sequences.However,the prediction performance(accuracy,recall,and precision),usability,and efficiency of existing methods decreased seriously when dealing with recently discovered proteins,thus still having much room to be improved.Here,we report HDMLF,a hierarchical dual-core multitask learning framework for accurately predicting EC numbers based on novel deep learning techniques.HDMLF is composed of an embedding core and a learning core;the embedding core adopts the latest protein language model for protein sequence embedding,and the learning core conducts the EC number prediction.Specifically,HDMLF is designed on the basis of a gated recurrent unit framework to perform EC number prediction in the multi-objective hierarchy,multitasking manner.Additionally,we introduced an attention layer to optimize the EC prediction and employed a greedy strategy to integrate and fine-tune the final model.Comparative analyses against 4 representative methods demonstrate that HDMLF stably delivers the highest performance,which improves accuracy and F1 score by 60%and 40%over the state of the art,respectively.An additional case study of tyrB predicted to compensate for the loss of aspartate aminotransferase aspC,as reported in a previous experimental study,shows that our model can also be used to uncover the enzyme promiscuity.Finally,we established a web platform,namely,ECRECer(https://ecrecer.biodesign.ac.cn),using an entirely could-based serverless architecture and provided an offline bundle to improve usability.
基金the National Key Technology Research and Development Program of China(2018YFA0900300 and 2022YFA0911800)the National Natural Science Foundation of China(21978071 and U1932141)+3 种基金the Key Science and Technology Innovation Project of Hubei Province(2021BAD001)2022 Joint Projects between Chinese and CEEC’s Universities(202004)the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang Province(2018R01014)the Innovation Base for Introducing Talents of Discipline of Hubei Province(2019BJH021)。
文摘High-quality genome-scale metabolic models(GEMs)could play critical roles on rational design of microbial cell factories in the classical Design-Build-Test-Learn cycle of synthetic biology studies.Despite of the constant establishment and update of GEMs for model microorganisms such as Escherichia coli and Saccharomyces cerevisiae,high-quality GEMs for non-model industrial microorganisms are still scarce.Zymomonas mobilis subsp.mobilis ZM4 is a non-model ethanologenic microorganism with many excellent industrial characteristics that has been developing as microbial cell factories for biochemical production.Although five GEMs of Z.mobilis have been constructed,these models are either generating ATP incorrectly,or lacking information of plasmid genes,or not providing standard format file.In this study,a high-quality GEM iZM516 of Z.mobilis ZM4 was constructed.The information from the improved genome annotation,literature,datasets of Biolog Phenotype Microarray studies,and recently updated Gene-Protein-Reaction information was combined for the curation of iZM516.Finally,516 genes,1389 reactions,1437 metabolites,and 3 cell compartments are included in iZM516,which also had the highest MEMOTE score of 91%among all published GEMs of Z.mobilis.Cell growth was then predicted by iZM516,which had 79.4%agreement with the experimental results of the substrate utilization.In addition,the potential endogenous succinate synthesis pathway of Z.mobilis ZM4 was proposed through simulation and analysis using iZM516.Furthermore,metabolic engineering strategies to produce succinate and 1,4-butanediol(1,4-BDO)were designed and then simulated under anaerobic condition using iZM516.The results indicated that 1.68 mol/mol succinate and 1.07 mol/mol 1,4-BDO can be achieved through combinational metabolic engineering strategies,which was comparable to that of the model species E.coli.Our study thus not only established a high-quality GEM iZM516 to help understand and design microbial cell factories for economic biochemical production using Z.mobilis as the chassis,but also provided guidance on building accurate GEMs for other non-model industrial microorganisms.
基金funded by the National Key Research and Development Program of China(2018YFA0901400)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB0480000)+1 种基金Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects(TSBICIP-PTJS-001)Ministry of Science of China and Youth Innovation Promotion Association CAS(292023000018).
文摘Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group.As a prominent strain in the fields of agriculture and bioengineering,there is still a lack of comprehensive understanding regarding its metabolic capabilities,specifically in terms of central metabolism and substrate utilization.Therefore,further exploration and extensive studies are required to gain a detailed insight into these aspects.This study reconstructed a genome-scale metabolic network model for P.stutzeri A1501 and conducted extensive curations,including correcting energy generation cycles,respiratory chains,and biomass composition.The final model,iQY1018,was successfully developed,covering more genes and reactions and having higher prediction accuracy compared with the previously published model iPB890.The substrate utilization ability of 71 carbon sources was investigated by BIOLOG experiment and was utilized to validate the model quality.The model prediction accuracy of substrate utilization for P.stutzeri A1501 reached 90%.The model analysis revealed its new ability in central metabolism and predicted that the strain is a suitable chassis for the production of Acetyl CoA-derived products.This work provides an updated,high-quality model of P.stutzeri A1501for further research and will further enhance our understanding of the metabolic capabilities.
文摘Hexavalent uranium(U(VI))can be immobilized by various microbes.The role of extracellular polymeric substances(EPS)in U(VI)immobilization has not been quantified.This work provides a model framework to quantify the contributions of three processes involved in EPS-mediated U(VI)immobilization:adsorption,bioreduction and desorption.Loosely associated EPS was extracted from a pure bacterial strain,Klebsiella sp.J1,and then exposed to H_(2) and O_(2)(no bioreduction control)to immobilize U(VI)in batch experiments.U(VI)immobilization was faster when exposed to H_(2) than O_(2) and stabilized at 94%for H_(2) and 85%for O_(2),respectively.The non-equilibrium data from the H_(2) experiments were best simulated by a kinetic model consisting of pseudo-second-order adsorption(ka=2.87×10^(−3) g EPS·(mg U)^(−1)·min^(−1)),first-order bioreduction(kb=0.112 min−1)and first-order desorption(kd=7.00×10^(−3) min^(−1))and fitted the experimental data with R^(2) of 0.999.While adsorption was dominant in the first minute of the experiments with H_(2),bioreduction was dominant from the second minute to the 50th min.After 50 min,adsorption was negligible,and bioreduction was balanced by desorption.This work also provides the first set of equilibrium data for U(VI)adsorption by EPS alone.The equilibrium experiments with O_(2) were well simulated by both the Langmuir isotherm and the Freundlich isotherm,suggesting multiple mechanisms involved in the interactions between U(VI)and EPS.The thermodynamic study indicated that the adsorption of U(VI)onto EPS was endothermic,spontaneous and favorable at higher temperatures.
基金financial support from the National Natural Science Foundation of China(NSFC,Nos.52176178,51876018)Innovation Research Group of Universities in Chongqing(No.CXQT21035)+1 种基金Scientific and Technological Research Program of Chongqing Municipal Education Commission of China(No.KJZDM202201101)Chongqing Postgraduate Innovation Project(No.CYS22645)。
文摘Over the last 50 years,the explosive adoption of modern agricultural practices has led to an enormous increase in the emission of non-biodegradable and highly biotoxic ions into the hydrosphere.Excess intake of such ions,even essential trace elements such as Cu^(2+)and F^(-),can have serious consequences on human health.Therefore,to ensure safe drinking water and regulate wastewater discharge,photoelectrochemical(PEC)online sensors were developed,with advantages such as low energy consumption,inherent miniaturization,simple instrumentation,and fast response.However,there is no publicly available systematic review of the recent advances in PEC ion sensors available in the literature since January 2017.Thus,this review covers the various strategies that have been used to enhance the sensitivity,selectivity,and limit of detection for PEC ion sensors.The photoelectrochemically active materials,conductive substrates,electronic transfer,and performance of various PEC sensors are discussed in detail and divided into sections based on the measurement principle and detected ion species.We conclude this review by highlighting the challenges and potential future avenues of research associated with the development of novel high-performance PEC sensors.
基金U.S.Air Force(FA9550-16-1-0183)Directorate for Engineering(1542160,171141,1809997)+1 种基金National Science Foundation(NSF)(ECCS-1542160)Arizona State University
文摘Flat optics presents a new path to control the phase, amplitude, and polarization state of light with ultracompact devices. Here we demonstrate chip-integrated metasurface devices for polarization detection of mid-infrared light with arbitrary polarization states. Six high-performance microscale linear and circular polarization filters based on vertically stacked plasmonic metasurfaces(with total thickness <600 nm) are integrated on the same chip to obtain all four Stokes parameters of light with high accuracy. The device designs can be tailored to operate at any wavelength in the mid-infrared spectral region and are feasible for on-chip integration with mid-infrared(mid-IR) photodetectors and imager arrays. Our work will enable on-chip mid-IR polarimeters and polarimetric imaging systems, which are highly desirable for many applications, such as clinical diagnosis, target detection, and space exploration.
基金Acknowledgements This work was supported by the Foundation of State Key Laboratory of Pollution Control and Resource Reuse (Tongji University), China (No. PCRRE16019), the National Natural Science Foundation of China (Grant Nos. 51678422 and 51378368), Sheng Yun- Fei College Students Scientific and Technological Innovation Fund, China Scholarship Council (No. 201506260022), the National Science & Technology Pillar Program (No. 2013BAD21B03), and the higher school innovative engineering plan (111 Projec0.
文摘The quantification and effects of system pH value on the interactions between Pb(II) and the biopolymer in activated sludge were investigated. The biopolymer had two protein-like fluorescence peaks (Ex/Em = 280 nm1326-338 nm for peak A; Ex/Em = 220-230 nm/324-338 nm for peak B). The fluorescence intensities of peak B were higher than those of peak A. The fluorophores of both peaks could be largely quenched by Pb(ll), and the quencher dose for peak B was about half of that for peak A. The modified Stern-Volmer equation well depicted the fluorescence quenching titration. The quenching constant (Ka) values for both peaks decreased with rising system pH value, and then sharply decreased under alkaline conditions. It could be attributed to that the alkaline conditions caused the reduction of available Pb(II) due to the occurrence of Pb(OH)2 sediments. The Ka values of peak B were bigger than those for peak A at the same system pH values. Accordingly, the aromatic proteins (peak B) played a key role in the interactions between metal ions and the biopolymer.
基金supported by research grants R01GM12367 and R35GM140819 from the National Institutes of General Medical Sciences,NIH.
文摘Conformational dynamics contribute importantly to enzyme catalysis,such that targeted conformational constraint may affect catalysis.Firefly luciferases undergo extensive structural change during catalysis;key residues form a hydrophobic pocket,excluding water and enabling maximally energetic light production.Point mutants almost always luminesce at longer wavelengths(lower energy)than the wild type.Conformational constraint,using dipeptide analogue 3 at a position critical for optimized excited state structure,produced luciferase emission at a shorter wavelength by∼10 nm.Incomparison,introduction of conformationally constrained analogues 4,5,or 7 afforded luciferases emitting at longer wavelengths,while a related unconstrained luciferase(analogue 6)exhibited wild-type emission.The constrained luciferases tested were more stable than the wild type.Protein modeling demonstrated that the“inside”or“outside”orientation of the conformationally constrained dipeptide led to the shorter or longer emission wavelength,respectively.More broadly,these results suggest that local conformational constraint can control specific elements of enzyme behavior,both in vitro and in vivo.This represents the first example of studying enzyme function by introducing conformationally constrained dipeptides at a specific protein position.The principles discovered here in luciferase modification will enable studies to control the wavelength emission and photophysical properties of modified luciferases.
基金Acknowledgements The authors acknowledge the financial support of the ability construction project of local Colleges and Universities in Shanghai (No. 16070503000), Special Fund of State Key Joint Laboratory of Environment Simulation and Pollution Control (No. 16K10ESPCT), Shanghai Gaofeng & Gaoyuan Project for University Academic Program Development, and the United States National Science Foundation (No. O651794).
文摘It is common that 2,4,6-trichlorophenol (TCP) coexists with nitrate or nitrite in industrial wastewaters. In this work, simultaneous reductive dechlorination of TCP and denitrification of nitrate or nitrite competed for electron donor, which led to their mutual inhibition. All inhibitions could be relieved to a certain degree by augmenting an organic electron donor, but the impact of the added electron donor was strongest for TCP. For simultaneous reduction ofTCP together with nitrate, TCP's removal rate value increased 75% and 150%, respectively, when added glucose was increased from 0.4 mmol· L^-1 to 0.5 mmol· L^-1 and to 0.76 mmol· L^-1 For comparison, the removal rate for nitrate increased by only 25% and 114% for the same added glucose. The relationship between their initial biodegradation rates versus their initial concentrations could be represented well with the Monod model, which quantified their half-maximum-rate concentration (Ks value), and Ks values for TCP, nitrate, and nitrite were larger with simultaneous reduction than independent reduction. The increases in Ks are further evidence that competition for the electron donor led to mutual inhibition. For bioremediation of wastewater containing TCP and oxidized nitrogen, both reduction reactions should proceed more rapidly if the oxidized nitrogen is nitrite instead of nitrate and if readily biodegradable electron acceptor is augmented.
基金Acknowledgements The authors acknowledge the financial support of the ability construction project of local Colleges and Universities in Shanghai (16070503000), Special Fund of State Key Joint Laboratory of Environment Simulation and Pollution Control (16K10ESPCT), Shanghai Gaofeng & Gaoyuan Project for University Academic Program Development (A-9103- 15-065004), and the United States National Science Foundation (0651794).
文摘Benzotriazole (BTA) is an emerging contaminant that also is a recalcitrant compound. Sequential and intimate coupling of UV-photolysis with biodegradation were investigated for their impacts on BTA removal and mineralization in aerobic batch experiments. Special attention was given to the role of its main photolytic products, which were aminophenol (AP), formic acid (FA), maleic acid (MA), and phenazine (PHZ). Experiments with sequential coupling showed that BTA biodegradation was accelerated by photolytic pretreatment up to 9 min, but BTA biodegradation was slowed with longer photolysis. FA and MA accelerated BTA biodegradation by being labile electron-donor substrates, but AP and PHZ slowed the rate because of inhibition due to their competition for intracellular electron donor. Because more AP and PHZ accumulated with increasing photolysis time, their inhibitory effects began to dominate with longer photolysis time. Intimately coupling photolysis with biodegradation relieved the inhibition effect, because AP and PHZ were quickly biodegraded and did not accumulate, which accentuated the beneficial effect of FA and MA.
基金supported by the United States Department of Agriculture National Institute of Agriculture and Food(2017-67013-26521 to B.Y.)the National Science Foundation(1238189 to F.F.W.,V.P.B.,and B.Y.,1741090 to F.F.W.)subawards to University of Missouri and University of Florida from the Heinrich Heine University Düsseldorf funded by the Bill&Melinda Gates Foundation[OPP1155704](B.Y.and F.F.W.).
文摘Many plant disease resistance(R)genes function specifically in reaction to the presence of cognate effectors from a pathogen.Xanthomonas oryzae pathovar oryzae(Xoo)uses transcription activator-like effectors(TALes)to target specific rice genes for expression,thereby promoting host susceptibility to bacterial blight.Here,we report the molecular characterization of Xa7,the cognate R gene to the TALes AvrXa7 and PthXo3,which target the rice major susceptibility gene SWEET14.Xa7 was mapped to a unique 74-kb region.Gene expression analysis of the region revealed a candidate gene that contained a putative AvrXa7 effector binding element(EBE)in its promoter and encoded a 113-amino-acid peptide of unknown function.Genome editing at the Xa7 locus rendered the plants susceptible to avrXa7-carrying Xoo strains.Both AvrXa7 and PthXo3 activated a GUS reporter gene fused with the EBE-containing Xa7 promoter in Nicotiana benthamiana.The EBE of Xa7 is a close mimic of the EBE of SWEET14 for TALe-induced disease susceptibility.Ectopic expression of Xa7 triggers cell death in N.benthamiana.Xa7 is prevalent in indica rice accessions from 3000 rice genomes.Xa7 appears to be an adaptation that protects against pathogen exploitation of SWEET14 and disease susceptibility.