铁皮石斛多糖与Toll样受体4互作机制的计算模拟

为研究铁皮石斛多糖(Dendrobium officinale polysaccharide,DOP)具有免疫活性片段的结构特征及与Toll样受体4(Toll⁃like receptor 4,TLR4)的相互作用机制,基于对TLR4结合腔的亲疏水性分析,将DOP寡糖的分为疏水片段筛选和亲水片段筛选,通过分子对接和分子动力学模拟,分析作用最强的DOP片段的结构特征及与TLR4的相互作用机制。结果表明,找到作用最强的DOP七糖片段,具有与经典底物脂多糖相似的结合模式,其中疏水性四糖片段结合在疏水结合腔,亲水性三糖片段结合在电正性区域。具有潜在免疫活性的铁皮石斛多糖可以由乙酰基修饰的疏水四糖片段和没有乙酰基修饰的亲水三糖片段组成,主要通过氢键和疏水作用与TLR4进行相互作用,发挥免疫活性。

Real-Time analysis of exosome secretion of single cells with single molecule imaging

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.

Chip-integrated metasurface full-Stokes polarimetric imaging sensor

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.

Contribution of the SOS response and the DNA repair systems to norfloxacin induced mutations in E.coli

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.

An integrative protocol for one‑step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data

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.

In memory of Perry L. McCarty, seminal founder of Environmental Biotechnology

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.

Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework

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.

Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories

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.

Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501

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.

Contributions of adsorption, bioreduction and desorption to uranium immobilization by extracellular polymeric substances

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.

Recent advances in photoelectrochemical sensors for detection of ions in water

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.

多约束代谢网络模型的研究进展

基于约束的基因组尺度代谢网络模型(genome-scale metabolic models,GEMs)分析已被广泛应用于代谢表型的预测。而实际细胞中代谢速率除计量学约束外,还受到酶资源可用性和反应热力学可行性等其他因素影响,在GEMs中整合酶资源约束或者热力学约束构建多约束代谢网络模型可以进一步缩小优化解空间,提升细胞表型预测的准确性。文中主要对近年来多约束模型的研究进展进行了综述,介绍了不同多约束模型的构建方法,以及其在研究基因敲除影响、预测可行途径和提供代谢瓶颈信息等方面的应用。将多种约束条件进一步与代谢模型整合,可更准确地预测细胞代谢的瓶颈和关键调控改造靶点,从而为工业菌种代谢工程改造提供精确的设计指导。

基于图论和约束优化的异源代谢途径设计方法及应用

构建高产高附加值产品的微生物细胞工厂是代谢工程的研究目标之一,设计高效的产品合成途径是实现这一目标的重要方式。不同微生物底盘因其代谢能力有所差异,故而可以利用的底物和生产的产品范围有限。为了扩大其生产能力,需要进行代谢途径从无到有的设计。传统代谢工程基于经验进行异源途径设计的方式低效且无法确保结果的全面性,而系统生物学技术的蓬勃发展,为途径设计提供了新的方法。异源代谢途径设计方法主要包括基于图论的途径设计和基于约束优化的途径设计,这些方法利用包含丰富代谢反应信息的数据库,通过图论搜索策略或约束算法,计算出多条产品合成途径,进而筛选出最优途径指导菌株改造。本文将对途径设计所依赖的数据库、途径设计算法及其在代谢工程中的应用进行详细介绍,并讨论现有算法在实际应用中存在的不足和挑战,为研究者选择不同方法进行产品合成途径设计提供指导。

基于图论的代谢网络中流通代谢物处理新方法

使用图论方法对基因组尺度代谢网络进行途径搜索是目前途径设计中最常用的方法之一。然而,由于流通代谢物(如H^(+)、H_(2)O、CO_(2)和ATP等)的影响,图论搜索得到的途径在生物学上经常是不可行的。虽然前人提出了一些方法对流通代谢物进行处理,但均存在一些问题,目前还没有标准的处理方法。文中基于流通代谢物在反应中作为转移磷酸等功能基团转移载体的特性,提出了一种对流通代谢物成对处理的方法,并将其按照其在功能基团转移中发挥的作用进行优先级排序,以保证每个反应都有对应的代谢物连接,进而通过程序实现自动化处理。与已有其他方法处理结果的比较表明,这种流通代谢物成对排序处理的方法可以排除掉生物学不可行的途径,从而提高途径搜索的准确性,为利用图论方法进行途径设计和可视化提供更好的支撑。

Chip-integrated plasmonic flat optics for mid-infrared full-Stokes polarization detection

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.

Interactions between metal ions and the biopolymer in activated sludge： quantification and effects of system pH value

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.

Local Conformational Constraint of Firefly Luciferase Can Affect the Energy of Bioluminescence and Enzyme Stability

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.

Competition for electrons between reductive dechlorination and denitrification

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.

Comparison of sequential with intimate coupling o photolysis and biodegradation for benzotriazole

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.

The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen

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.