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
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
Whole-genome duplication(WGD)events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms.In the present study,the newly sequenced genome of a g...Whole-genome duplication(WGD)events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms.In the present study,the newly sequenced genome of a giant ciliated protist,Stentor roeselii,provides an opportunity for the analysis of the collinearity and retention of reciprocal best-hit genes between two Stentor species.As a main result,we have unveiled a previously undetected ancient WGD event shaping the genome of its congener,Stentor coeruleus,a model protist used in cytological and evolutionary studies.Genomes of two congeners,S.coeruleus and S.roeselii,are compared and analyzed,revealing that:(i)the former exhibits a much higher retention rate of colinear-gene pairs(28%)than does S.roeselii,and in S.coeruleus,75%of genes that have a RBH hit in S.roeselii,have paralogs with high amino-acid identity,consistent with a WGD event in the lineage leading to S.coeruleus;(ii)the S.roeselii genome possesses extremely short intergenic regions,implying that the lengths of intergenic regions are under strong selection;(iii)the unique characteristics of introns may have been shaped in the common ancestor of heterotrichs;(iv)gene families that play a role in activities of multiple protein kinases and voltage-gated ion channels expanded rapidly in the ancestor of both taxa,possibly relating to the remarkable regenerative ability in Stentor.This study offers new insights into the evolutionary dynamics of ciliate genomes,with implications for understanding of the processes underlying the evolution of genomic complexity.展开更多
Bioluminescence is routinely used to track cellular and molecular features in vivo.This technique relies upon the enzymatic oxidation of a small molecule to produce a photon of light.However,most bioluminescent probes...Bioluminescence is routinely used to track cellular and molecular features in vivo.This technique relies upon the enzymatic oxidation of a small molecule to produce a photon of light.However,most bioluminescent probes exhibit suboptimal tissue penetrance,limiting applications in some preclinical models.We aimed to develop red-shifted tools for more sensitive,deep tissue imaging.Toward this end,we were inspired by the cell-compatible and red-emitting chromophore present in common fluorescent proteins(FPs).We synthesized two firefly luciferin analogues(FPLucs)based on the fluorescent motif.The probes produced>650 nm light,with peak emission values of 701 and 699 nm,making them amenable for tissue imaging.We further identified more optimal luciferases for processing FPLucs,using a combination of Rosetta-guided design and screening.When incubated with the analogues,the engineered luciferases exhibited improved light outputs compared to native firefly luciferase.The designer luciferase-luciferin pairs could also be readily detected in tissue mimics.Continued development of these and other fluorophore-inspired luciferins will expand applications of bioluminescence imaging.展开更多
With the advancement of industry and bio-agriculture,the effective management of CO_(2) has emerged as a critical challenge for humanity.This study systematically explores multiple CO_(2) assimilation pathways using t...With the advancement of industry and bio-agriculture,the effective management of CO_(2) has emerged as a critical challenge for humanity.This study systematically explores multiple CO_(2) assimilation pathways using the comb-FBA algorithm,aiming to identify efficient artificial carbon fixation pathways.By extracting 49 CO_(2) and HCO3involved reactions and combining them with 6,529 reactions from MetaCyc,we constructed the computational set for analysis.These 16 core reactions give rise to 136 carbon fixation pathways for single C2 targets(such as acetyl-CoA,glyoxylate,and oxalate)and 576 carbon fixation pathways for single C3 targets(including glyceraldehyde-3-phosphate or pyruvate).Based on these core reactions,we identified four principal carbon fixation modes.Through systematic assessments,we identified 12 promising CO_(2) fixation pathways,each comprising no more than 20 reaction steps and demonstrating thermodynamic feasibility.Through further analysis of enzyme oxygen sensitivity and availability,we identified three novel and promising pathways.By examining metabolite conversion relationships,we also identified alternative carbon fixation reaction modules,offering flexibility for pathway optimization and experimental design.In conclusion,this study provides a diverse library of artificial carbon fixation pathways,demonstrating the power of the comb-FBA algorithm in designing carbon assimilation pathways and laying the foundation for more efficient CO_(2) fixation strategies.展开更多
Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable c...Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable contributions of genomic resources such as ParameciumDB,genomic data are still mostly limited to species in and near the P.aurelia group.This study addresses this gap by HiFi sequencing,assembling,and annotating the macronuclear genomes of five rare Paramecium species:P.calkinsi,P.duboscqui,P.nephridiatum,P.putrinum,and P.woodruffi.These genomes enable a comprehensive exploration of genomic diversity,genome evolution,and phylogenomic relationships within the genus Paramecium.The genome sizes range from 47.78 to 113.16 Mb,reflecting unexpected variation in genomic content,and genic features differ from those of other reported Paramecium genomes,such as larger intron sizes and higher GC content.Nonetheless,the de novo assemblies indicate that macronuclear genomes of all Paramecium are highly streamlined,with~77%being protein-coding gene regions.Based on gene-duplication depths,synonymous mutations in paralogs,and phylogenomic relationships,we discovered that the five species experienced at least three whole-genome duplication(WGD)events,independent of those previously found in the P.aurelia complex.Using all available WGD data for Paramecium,we further explore the paralog dynamics after WGD events by modeling.This study contributed to a more comprehensive and deeper understanding of genome architecture and evolution in Paramecium.展开更多
Nowadays,biological databases are playing an increasingly critical role in biological research.Myceliophthora thermophila is an excellent thermophilic fungal chassis for industrial enzyme production and plant biomass-...Nowadays,biological databases are playing an increasingly critical role in biological research.Myceliophthora thermophila is an excellent thermophilic fungal chassis for industrial enzyme production and plant biomass-based chemical synthesis.The lack of a dedicated public database has made access to and reanalysis of M.thermophila data difficult.To bridge this gap,we developed MTD(https://mtd.biodesign.ac.cn/),a cloud-based omics database and interactive platform for M.thermophila.MTD integrates comprehensive genome annotations,sequence-based predictions,transcriptome data,curated experimental descriptions,and bioinformatics analysis tools,offering a comprehensive,one-stop solution with a‘top-down’search strategy to streamline M.thermophila research.The platform supports data reproduction,rapid querying,and in-depth mining of existing tran-scriptome datasets.Based on analyses using data and tools in MTD,we identified shifts in metabolic allocation in a glucoamylase hyperproduction strain of M.thermophila,highlighting changes in fatty acid biosynthesis and amino acids biosynthesis pathways,which provide new insights into the underlying phenotypic alterations.As a pioneering resource,MTD marks a key advancement in M.thermophila research and sets the model for developing similar databases for other species.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
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
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
Melatonin is a biogenic amine that can be found in plants,animals and microorganism.The metabolic pathway of melatonin is different in various organisms,and biosynthetic endogenous melatonin acts as a molecular signal...Melatonin is a biogenic amine that can be found in plants,animals and microorganism.The metabolic pathway of melatonin is different in various organisms,and biosynthetic endogenous melatonin acts as a molecular signal and antioxidant protection against external stress.Microbial synthesis pathways of melatonin are similar to those of animals but different from those of plants.At present,the method of using microorganism fermentation to produce melatonin is gradually prevailing,and exploring the biosynthetic pathway of melatonin to modify microorganism is becoming the mainstream,which has more advantages than traditional chemical synthesis.Here,we review recent advances in the synthesis,optimization of melatonin pathway.L-tryptophan is one of the two crucial precursors for the synthesis of melatonin,which can be produced through a four-step reaction.Enzymes involved in melatonin synthesis have low specificity and catalytic efficiency.Site-directed mutation,directed evolution or promotion of cofactor synthesis can enhance enzyme activity and increase the metabolic flow to promote microbial melatonin production.On the whole,the status and bottleneck of melatonin biosynthesis can be improved to a higher level,providing an effective reference for future microbial modification.展开更多
Structural color printings have broad applications due to their advantages of long-term sustainability,eco-friendly manufacturing,and ultra-high resolution.However,most of them require costly and time-consuming fabric...Structural color printings have broad applications due to their advantages of long-term sustainability,eco-friendly manufacturing,and ultra-high resolution.However,most of them require costly and time-consuming fabrication processes from nanolithography to vacuum deposition and etching.Here,we demonstrate a new color printing technology based on polymer-assisted photochemical metal deposition(PPD),a room temperature,ambient,and additive manufacturing process without requiring heating,vacuum deposition or etching.The PPD-printed silver films comprise densely aggregated silver nanoparticles filled with a small amount(estimated<20%volume)of polymers,producing a smooth surface(roughness 2.5 nm)even better than vacuum-deposited silver films(roughness 2.8 nm)at~4 nm thickness.Further,the printed composite films have a much larger effective refractive index n(~1.90)and a smaller extinction coefficient k(~0.92)than PVD ones in the visible wavelength range(400 to 800 nm),therefore modulating the surface reflection and the phase accumulation.The capability of PPD in printing both ultra-thin(~5 nm)composite films and highly reflective thicker film greatly benefit the design and construction of multilayered Fabry–Perot(FP)cavity structures to exhibit vivid and saturated colors.We demonstrated programmed printing of complex pictures of different color schemes at a high spatial resolution of~6.5μm by three-dimensionally modulating the top composite film geometries and dielectric spacer thicknesses(75 to 200 nm).Finally,PPD-based color picture printing is demonstrated on a wide range of substrates,including glass,PDMS,and plastic,proving its broad potential in future applications from security labeling to color displays.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
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
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 by the Science & Technology Innovation Project of Laoshan Laboratory(LSKJ202203203)the National Science Foundation of China (32270558)+4 种基金the National Institutes of Health Grant (R35-GM122566-01)the National Science Foundation (DEB-1927159, DBI-2119963)the Moore and Simons Foundations (735927)the Young Taishan Scholar Program of Shandong Provincethe Project of Outstanding Young Innovative Team in Higher Education Institutions of Shandong Province (2023KJ038).
文摘Whole-genome duplication(WGD)events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms.In the present study,the newly sequenced genome of a giant ciliated protist,Stentor roeselii,provides an opportunity for the analysis of the collinearity and retention of reciprocal best-hit genes between two Stentor species.As a main result,we have unveiled a previously undetected ancient WGD event shaping the genome of its congener,Stentor coeruleus,a model protist used in cytological and evolutionary studies.Genomes of two congeners,S.coeruleus and S.roeselii,are compared and analyzed,revealing that:(i)the former exhibits a much higher retention rate of colinear-gene pairs(28%)than does S.roeselii,and in S.coeruleus,75%of genes that have a RBH hit in S.roeselii,have paralogs with high amino-acid identity,consistent with a WGD event in the lineage leading to S.coeruleus;(ii)the S.roeselii genome possesses extremely short intergenic regions,implying that the lengths of intergenic regions are under strong selection;(iii)the unique characteristics of introns may have been shaped in the common ancestor of heterotrichs;(iv)gene families that play a role in activities of multiple protein kinases and voltage-gated ion channels expanded rapidly in the ancestor of both taxa,possibly relating to the remarkable regenerative ability in Stentor.This study offers new insights into the evolutionary dynamics of ciliate genomes,with implications for understanding of the processes underlying the evolution of genomic complexity.
基金the U.S.National Institutes of Health(R01 GM107630 to J.A.P.)the Paul G.Allen Frontiers Group. A.E.M.-M. was supported by a George Hewitt Medical Research Postdoctoral Fellowship+3 种基金Some experiments were performed at the Laser Spectroscopy Laboratories (LSL) at UCIDr. Donald Caldwell and Dr. Martinthe members of the Prescher lab for helpful discussions, members of the Weiss and Martin laboratories (UCI) for providing equipment and reagentsBioRender (https://biorender.com/)。
文摘Bioluminescence is routinely used to track cellular and molecular features in vivo.This technique relies upon the enzymatic oxidation of a small molecule to produce a photon of light.However,most bioluminescent probes exhibit suboptimal tissue penetrance,limiting applications in some preclinical models.We aimed to develop red-shifted tools for more sensitive,deep tissue imaging.Toward this end,we were inspired by the cell-compatible and red-emitting chromophore present in common fluorescent proteins(FPs).We synthesized two firefly luciferin analogues(FPLucs)based on the fluorescent motif.The probes produced>650 nm light,with peak emission values of 701 and 699 nm,making them amenable for tissue imaging.We further identified more optimal luciferases for processing FPLucs,using a combination of Rosetta-guided design and screening.When incubated with the analogues,the engineered luciferases exhibited improved light outputs compared to native firefly luciferase.The designer luciferase-luciferin pairs could also be readily detected in tissue mimics.Continued development of these and other fluorophore-inspired luciferins will expand applications of bioluminescence imaging.
基金supported by the Strategic Priority Research Pro-gram of the Chinese Academy of Sciences(XDC0120201)the National Natural Science Foundation of China(12326611).
文摘With the advancement of industry and bio-agriculture,the effective management of CO_(2) has emerged as a critical challenge for humanity.This study systematically explores multiple CO_(2) assimilation pathways using the comb-FBA algorithm,aiming to identify efficient artificial carbon fixation pathways.By extracting 49 CO_(2) and HCO3involved reactions and combining them with 6,529 reactions from MetaCyc,we constructed the computational set for analysis.These 16 core reactions give rise to 136 carbon fixation pathways for single C2 targets(such as acetyl-CoA,glyoxylate,and oxalate)and 576 carbon fixation pathways for single C3 targets(including glyceraldehyde-3-phosphate or pyruvate).Based on these core reactions,we identified four principal carbon fixation modes.Through systematic assessments,we identified 12 promising CO_(2) fixation pathways,each comprising no more than 20 reaction steps and demonstrating thermodynamic feasibility.Through further analysis of enzyme oxygen sensitivity and availability,we identified three novel and promising pathways.By examining metabolite conversion relationships,we also identified alternative carbon fixation reaction modules,offering flexibility for pathway optimization and experimental design.In conclusion,this study provides a diverse library of artificial carbon fixation pathways,demonstrating the power of the comb-FBA algorithm in designing carbon assimilation pathways and laying the foundation for more efficient CO_(2) fixation strategies.
基金supported by the Laoshan Laboratory(LSKJ202203203)the National Natural Science Foundation of China(31961123002,32270435 and 32471688)+1 种基金the National Institutes of Health(R35-GM122566-01)the National Science Foundation(DBI-2119963,DEB-1927159 and 1911449).
文摘Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable contributions of genomic resources such as ParameciumDB,genomic data are still mostly limited to species in and near the P.aurelia group.This study addresses this gap by HiFi sequencing,assembling,and annotating the macronuclear genomes of five rare Paramecium species:P.calkinsi,P.duboscqui,P.nephridiatum,P.putrinum,and P.woodruffi.These genomes enable a comprehensive exploration of genomic diversity,genome evolution,and phylogenomic relationships within the genus Paramecium.The genome sizes range from 47.78 to 113.16 Mb,reflecting unexpected variation in genomic content,and genic features differ from those of other reported Paramecium genomes,such as larger intron sizes and higher GC content.Nonetheless,the de novo assemblies indicate that macronuclear genomes of all Paramecium are highly streamlined,with~77%being protein-coding gene regions.Based on gene-duplication depths,synonymous mutations in paralogs,and phylogenomic relationships,we discovered that the five species experienced at least three whole-genome duplication(WGD)events,independent of those previously found in the P.aurelia complex.Using all available WGD data for Paramecium,we further explore the paralog dynamics after WGD events by modeling.This study contributed to a more comprehensive and deeper understanding of genome architecture and evolution in Paramecium.
基金funded by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDC0110300)the National Key R&D Program of China(2023YFC3403602 and 2022YFC2106000)+2 种基金National Natural Science Foundation of China(32300529,32270100,and 32271481)the Innovation Fund of Haihe Laboratory of Synthetic Biology(22HHSWSS00014)the Tianjin Synthetic Biotechnology Inno-vation Capacity Improvement Project(TSBICIP-PTJJ-007-12).
文摘Nowadays,biological databases are playing an increasingly critical role in biological research.Myceliophthora thermophila is an excellent thermophilic fungal chassis for industrial enzyme production and plant biomass-based chemical synthesis.The lack of a dedicated public database has made access to and reanalysis of M.thermophila data difficult.To bridge this gap,we developed MTD(https://mtd.biodesign.ac.cn/),a cloud-based omics database and interactive platform for M.thermophila.MTD integrates comprehensive genome annotations,sequence-based predictions,transcriptome data,curated experimental descriptions,and bioinformatics analysis tools,offering a comprehensive,one-stop solution with a‘top-down’search strategy to streamline M.thermophila research.The platform supports data reproduction,rapid querying,and in-depth mining of existing tran-scriptome datasets.Based on analyses using data and tools in MTD,we identified shifts in metabolic allocation in a glucoamylase hyperproduction strain of M.thermophila,highlighting changes in fatty acid biosynthesis and amino acids biosynthesis pathways,which provide new insights into the underlying phenotypic alterations.As a pioneering resource,MTD marks a key advancement in M.thermophila research and sets the model for developing similar databases for other species.
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 R&D Program of China(2021YFC2100900)National Nature Science Foundation of China(32100062)+1 种基金Youth Innovation Promotion Association,CAS(2020182)Tianjin Synthetic Biotechnology Inno-vation Capacity Improvement Project(TSBICIP-CXRC-029).
文摘Melatonin is a biogenic amine that can be found in plants,animals and microorganism.The metabolic pathway of melatonin is different in various organisms,and biosynthetic endogenous melatonin acts as a molecular signal and antioxidant protection against external stress.Microbial synthesis pathways of melatonin are similar to those of animals but different from those of plants.At present,the method of using microorganism fermentation to produce melatonin is gradually prevailing,and exploring the biosynthetic pathway of melatonin to modify microorganism is becoming the mainstream,which has more advantages than traditional chemical synthesis.Here,we review recent advances in the synthesis,optimization of melatonin pathway.L-tryptophan is one of the two crucial precursors for the synthesis of melatonin,which can be produced through a four-step reaction.Enzymes involved in melatonin synthesis have low specificity and catalytic efficiency.Site-directed mutation,directed evolution or promotion of cofactor synthesis can enhance enzyme activity and increase the metabolic flow to promote microbial melatonin production.On the whole,the status and bottleneck of melatonin biosynthesis can be improved to a higher level,providing an effective reference for future microbial modification.
基金support from National Science Foundation under grant no.1838443,1809997,and 1947753supported,in part,by NSF grant no.ECCS-1542160.
文摘Structural color printings have broad applications due to their advantages of long-term sustainability,eco-friendly manufacturing,and ultra-high resolution.However,most of them require costly and time-consuming fabrication processes from nanolithography to vacuum deposition and etching.Here,we demonstrate a new color printing technology based on polymer-assisted photochemical metal deposition(PPD),a room temperature,ambient,and additive manufacturing process without requiring heating,vacuum deposition or etching.The PPD-printed silver films comprise densely aggregated silver nanoparticles filled with a small amount(estimated<20%volume)of polymers,producing a smooth surface(roughness 2.5 nm)even better than vacuum-deposited silver films(roughness 2.8 nm)at~4 nm thickness.Further,the printed composite films have a much larger effective refractive index n(~1.90)and a smaller extinction coefficient k(~0.92)than PVD ones in the visible wavelength range(400 to 800 nm),therefore modulating the surface reflection and the phase accumulation.The capability of PPD in printing both ultra-thin(~5 nm)composite films and highly reflective thicker film greatly benefit the design and construction of multilayered Fabry–Perot(FP)cavity structures to exhibit vivid and saturated colors.We demonstrated programmed printing of complex pictures of different color schemes at a high spatial resolution of~6.5μm by three-dimensionally modulating the top composite film geometries and dielectric spacer thicknesses(75 to 200 nm).Finally,PPD-based color picture printing is demonstrated on a wide range of substrates,including glass,PDMS,and plastic,proving its broad potential in future applications from security labeling to color displays.
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 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.
