A flexible,modular and versatile functional part assembly toolkit for gene cluster engineering in Streptomyces

Streptomyces has enormous potential to produce novel natural products(NPs)as it harbors a huge reservoir of uncharacterized and silent natural product biosynthetic gene clusters(BGCs).However,the lack of efficient gene cluster engineering strategies has hampered the pace of new drug discovery.Here,we developed an easy-to-use,highly flexible DNA assembly toolkit for gene cluster engineering.The DNA assembly toolkit is compatible with various DNA assembling approaches including Biobrick,Golden Gate,CATCH,yeast homologous recombination-based DNA assembly and homing endonuclease-mediated assembly.This compatibility offers great flexibility in handling multiple genetic parts or refactoring large gene clusters.To demonstrate the utility of this toolkit,we quantified a library of modular regulatory parts,and engineered a gene cluster(act)using characterized promoters that led to increased production.Overall,this work provides a powerful part assembly toolkit that can be used for natural product discovery and optimization in Streptomyces.

Ionic Liquid-Enhanced Assembly of Nanomaterials for Highly Stable Flexible Transparent Electrodes

The controlled assembly of nanomaterials has demon-strated significant potential in advancing technological devices.However,achieving highly efficient and low-loss assembly technique for nanomate-rials,enabling the creation of hierarchical structures with distinctive func-tionalities,remains a formidable challenge.Here,we present a method for nanomaterial assembly enhanced by ionic liquids,which enables the fabrication of highly stable,flexible,and transparent electrodes featuring an organized layered structure.The utilization of hydrophobic and non-volatile ionic liquids facilitates the production of stable interfaces with water,effectively preventing the sedimentation of 1D/2D nanomaterials assembled at the interface.Furthermore,the interfacially assembled nanomaterial monolayer exhibits an alternate self-climbing behavior,enabling layer-by-layer transfer and the formation of a well-ordered MXene-wrapped silver nanowire network film.The resulting composite film not only demonstrates exceptional photoelectric performance with a sheet resistance of 9.4Ωsq^(-1) and 93%transmittance,but also showcases remarkable environmental stability and mechanical flexibility.Particularly noteworthy is its application in transparent electromagnetic interference shielding materials and triboelectric nanogenerator devices.This research introduces an innovative approach to manufacture and tailor functional devices based on ordered nanomaterials.

Self-assembly of tau fragments as a key pathologic event in tauopathies

Tau protein is encoded by the microtubuleassociated protein tau(MAPT)gene and stabilizes microtubules in the neurons.Tau has unique biophysical properties that make it both highly water-soluble and positively charged.Although tau is an intrinsically disordered protein lacking defined secondary structures,it can acquire highly organized-sheet structures and stack into a filamentous inclusion such as a paired helical filament(PHF).

A telomere-to-telomere genome assembly of Zhonghuang 13,a widely-grown soybean variety from the original center of Glycine max

Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.

An Improved Chromosome-Level Genome Assembly and Annotation of Belted Beard Grunt(Hapalogenys analis)

Hapalogenys analis(order Lobotiformes)is an economically and ecologically significant fish species.It is a typical sedentary rocky reef fish and is primarily found in the northern Pacific Ocean.Here,we used Hi-C and PacBio sequencing technique to assemble a high-quality,chromosome-level genome for this species.The 539 Mb genome had a contig N50 with a size of 3.43 Mb,while 755 contigs clustered into 24 chromosomal groups with an anchoring rate of 99.02%.Of the total genomic sequence,132.74Mb(24.39%)were annotated as repeat elements.A total of 21360 protein-coding genes were identified,of which 20787 genes(97.32%)were successfully annotated to public databases.The BUSCO evaluation indicated that 96.90%of the total orthologous genes were matched.The phylogenetic tree representing H.analis and 14 other bony fish species indicated that the H.analis genome contained 364 expanded gene families related to olfactory receptor activity,compared with the common ancestor of H.analis and Sciaenidae.Comparative genomic analysis further identified 3584 contracted gene families.Branch-site modeling identified 277 genes experiencing positive selection,which may facilitate the adaptation to rocky reef environments.The genome reported here is helpful for ecological and evolutionary studies of H.analis.

Optimization of Fixture Number in Large Thin-Walled Parts Assembly Based on IPSO

There are lots of researches on fixture layout optimization for large thin-walled parts.Current researches focus on the positioning problem,i.e.,optimizing the positions of a constant number of fixtures.However,how to determine the number of fixtures is ignored.In most cases,the number of fixtures located on large thin-walled parts is determined based on engineering experience,which leads to huge fixture number and extra waste.Therefore,this paper constructs an optimization model to minimize the number of fixtures.The constraints are set in the optimization model to ensure that the part deformation is within the surface profile tolerance.In addition,the assembly gap between two parts is also controlled.To conduct the optimization,this paper develops an improved particle swarm optimization(IPSO)algorithm by integrating the shrinkage factor and adaptive inertia weight.In the algorithm,particles are encoded according to the fixture position.Each dimension of the particle is assigned to a sub-region by constraining the optional position range of each fixture to improve the optimization efficiency.Finally,a case study on ship curved panel assembly is provided to prove that our method can optimize the number of fixtures while meeting the assembly quality requirements.This research proposes a method to optimize the number of fixtures,which can reduce the number of fixtures and achieve deformation control at the same time.

Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

Engineering vascularized organotypic tissues via module assembly

Adequate vascularization is a critical determinant for the successful construction and clinical implementation of complex organotypic tissue models. Currently, low cell and vessel density and insufficient vascular maturation make vascularized organotypic tissue construction difficult,greatly limiting its use in tissue engineering and regenerative medicine. To address these limitations, recent studies have adopted pre-vascularized microtissue assembly for the rapid generation of functional tissue analogs with dense vascular networks and high cell density. In this article, we summarize the development of module assembly-based vascularized organotypic tissue construction and its application in tissue repair and regeneration, organ-scale tissue biomanufacturing, as well as advanced tissue modeling.

Experimental Study on the Electrochemical Performance of PEMFC under Different Assembly Forces

Proton exchange membrane fuel cell(PEMFC)is of paramount significance to the development of clean energy.The components of PEMFC are assembled using many pairs of nuts and bolts.The assembly champing bolt torque is critical to the electrochemical performance and mechanical stability of PEMFC.In this paper,a PEMFC with the threechannel serpentine flow field was used and studied.The different assembly clamping bolt torques were applied to the PEMFC in three uniform assembly bolt torque and six non-uniform assembly bolt torque conditions,respectively.And then,the electrochemical performance experiments were performed to study the effect of the assembly bolt torque on the electrochemical performance.The test results show that the assembly bolt torque significantly affected the electrochemical performance of the PEMFC.In uniform assembly bolt torque conditions,the maximal power density increased initially as the assembly bolt torque increased,and then decreased on further increasing the assembly torque.It existed the optimum assembly torque which was found to be 3.0 N·m in this work.In non-uniform assembly clamping bolt torque conditions,the optimum electrochemical performance appeared in the condition where the assembly torque of each bolt was closer to be 3.0 N·m.This could be due to the change of the contact resistance between the gas diffusion layer and bipolar plate and mass transport resistance for the hydrogen and oxygen towards the catalyst layers.This work could optimize the assembly force conditions and provide useful information for the practical PEMFC stack assembly.

A telomere-to-telomere genome assembly of Hongyingzi,a sorghum cultivar used for Chinese Baijiu production

Sorghum(Sorghum bicolor(L.)Moench)is a world cereal crop used in China for producing Baijiu,a distilled spirit.We report a telomere-to-telomere genome assembly of the Baijiu cultivar Hongyingzi,HYZ-T2T,using ultralong reads.The 10 chromosome pairs contained 33,462 genes,of which 93%were functionally annotated.The 20 telomeres and 10 centromeric regions on the HYZ-T2T chromosomes were predicted and two consecutive large inversions on chromosome 2 were characterized.A 65-gene reconstruction of the metabolic pathway of tannins,the flavor substances in Baijiu,was performed and may advance the breeding of sorghum cultivars for Baijiu production.

Virtual Assembly Collision Detection Algorithm Using Backpropagation Neural Network

As computer graphics technology continues to advance,Collision Detection(CD)has emerged as a critical element in fields such as virtual reality,computer graphics,and interactive simulations.CD is indispensable for ensuring the fidelity of physical interactions and the realism of virtual environments,particularly within complex scenarios like virtual assembly,where both high precision and real-time responsiveness are imperative.Despite ongoing developments,current CD techniques often fall short in meeting these stringent requirements,resulting in inefficiencies and inaccuracies that impede the overall performance of virtual assembly systems.To address these limitations,this study introduces a novel algorithm that leverages the capabilities of a Backpropagation Neural Network(BPNN)to optimize the structural composition of the Hybrid Bounding Volume Tree(HBVT).Through this optimization,the research proposes a refined Hybrid Hierarchical Bounding Box(HHBB)framework,which is specifically designed to enhance the computational efficiency and precision of CD processes.The HHBB framework strategically reduces the complexity of collision detection computations,thereby enabling more rapid and accurate responses to collision events.Extensive experimental validation within virtual assembly environments reveals that the proposed algorithm markedly improves the performance of CD,particularly in handling complex models.The optimized HBVT architecture not only accelerates the speed of collision detection but also significantly diminishes error rates,presenting a robust and scalable solution for real-time applications in intricate virtual systems.These findings suggest that the proposed approach offers a substantial advancement in CD technology,with broad implications for its application in virtual reality,computer graphics,and related fields.

Designing Membrane Electrode Assembly for Electrochemical CO_(2)Reduction:a Review

Currently, the electrochemical CO_(2) reduction reaction (CO_(2) RR) can realize the resource conversion of CO_(2) , which is a promising approach to carbon resource use. Important advancements have been made in exploring the CO_(2) RR performance and mechanism because of the rational design of electrolyzer systems, such as H-cells, flow cells, and catalysts. Considering the future development direction of this technology and large-scale application needs, membrane electrode assembly (MEA) systems can improve energy use efficiency and achieve large-scale CO_(2) conversion, which is considered the most promising technology for industrial applications. This review will concentrate on the research progress and present situation of the MEA component structure. This paper begins with the composition and construction of a gas diff usion electrode. Then, the application of ion-exchange membranes in MEA is introduced. Furthermore, the eff ects of pH and the anion and cation of the anolyte on MEA performance are explored. Additionally, we present the anode reaction type in MEA. Finally, the challenges in this field are summarized, and upcoming trends are projected. This review should offer researchers a clearer picture of MEA systems and provide important, timely, and valuable insights into rational electrolyzer design to facilitate further development of CO_(2) electrochemical reduction.

Response and assembly of abundant and rare taxa in Zaopei under different combination patterns of Daqu and pit mud:from microbial ecology to Baijiu brewing microecosystem

The quality and aroma of strong-flavor Baijiu are mainly dependent on Daqu,pit mud(PM),and the interaction of both.However,little is known about how their combination patterns affect the microbiome and metabolome of Zaopei,especially the metabolic function of rare taxa.Here,an experiment on industrial size was designed to assess the effects of 6 combinations(3 kinds of Daqu×2 kinds of PM)on the composition and assembly of different taxa,as well as the flavor profile.The results showed that Zaopei's microbiota was composed of a few abundant taxa and enormous rare taxa,and rare bacterial and abundant fungal subcommunities were significantly affected by combination patterns.The assembly processes of abundant/rare taxa and bacterial/fungal communities were distinct,and environmental changes mediated the balance between stochastic and deterministic processes in rare bacteria assembly.Furthermore,specific combination patterns improved the flavor quality of Zaopei by enhancing the interspecies interaction,which was closely related to rare taxa,especially rare bacteria.These findings highlighted that rare bacteria might be the keystone in involving community interaction and maintaining metabolic function,which provided a scientific foundation for better understanding and regulating the brewing microbiota from the viewpoint of microbial ecology.

Digital Twin Modeling and Simulation Optimization of Transmission Front and Middle Case Assembly Line

As the take-off of China’s macro economy,as well as the rapid development of infrastructure construction,real estate industry,and highway logistics transportation industry,the demand for heavy vehicles is increasing rapidly,the competition is becoming increasingly fierce,and the digital transformation of the production line is imminent.As one of themost important components of heavy vehicles,the transmission front andmiddle case assembly lines have a high degree of automation,which can be used as a pilot for the digital transformation of production.To ensure the visualization of digital twins(DT),consistent control logic,and real-time data interaction,this paper proposes an experimental digital twin modeling method for the transmission front and middle case assembly line.Firstly,theDT-based systemarchitecture is designed,and theDT model is created by constructing the visualization model,logic model,and data model of the assembly line.Then,a simulation experiment is carried out in a virtual space to analyze the existing problems in the current assembly line.Eventually,some improvement strategies are proposed and the effectiveness is verified by a new simulation experiment.

Design and assembly of a nested imaging X-ray telescope for the Hot Universe Baryon Surveyor mission

The Hot Universe Baryon Surveyor (HUBS) mission will carry a nested X-ray telescope capable of observing an energy range from 0.5 keV to 2 keV to study hot baryon evolution. In this paper, we report the latest progress in the design and construction of nested X-ray telescopes which were designed to use a three-stage conic-approximation type assembly to simplify the manufacturing process. The mirror substrate is made using the thermal glass slumping method, with mirrors characterized by a root-mean-square roughness of 0.3 nm, with expected high reflectivity and good thermal stability. We also discuss methods of telescope construction and conduct a deformation analysis of the manufactured mirror. The in situ measurement system program is developed to guide the telescope assembly process.

Evaluating Methods of Visual Assistance for Workers to Improve Quality and Usability in Individualized Kitchen Cabinet Assembly

In times of digitalisation, visual assistance systems in assembly are increasingly important. The design of these assembly systems needs to be highly complex to meet the requirements. Due to the increasing number of variants in production processes, as well as shorter innovation and product life cycles, assistance systems should improve quality and reduce complexity of assembly processes. However, many large kitchen manufacturers still assemble kitchen cabinets manually, due to the high variety of components, such as rails and fittings. This paper focuses on the analysis and evaluation of virtual assistance systems to improve quality and usability in individualised kitchen cabinet assembly processes at a large German manufacturer. A solution is identified and detailed.

Target-induced Trivalent G-quadruplex/hemin DNAzyme for Colorimetric Detection of Hg^(2+) Based on an Exonuclease III Assisted Catalytic Hairpin Assembly

Mercury ion(Hg^(2+)),a highly noxious of heavy metalion,has detrimental effects on the ecological environment and human health.Herein,we have developed an exonuclease III(Exo III)assisted catalytic hairpin assembly formation of a trivalent G-quadruplex/hemin DNAzyme for colorimetric detection of Hg^(2+).A hairpin DNA(Hr)was designed with thymine-Hg^(2+)-thymine pairs that catalyzed by Exo III is prompted to happen upon binding Hg^(2+).A released DNA fragment triggers the catalytic assembly of other three hairpins(H1,H2,and H3)to form many trivalent G-quadruplex/hemin DNA enzymes for signal output.The developed sensor shows a dynamic range from 2 pM to 2μM,with an impressively low detection limit of 0.32 pM for Hg^(2+)detection.Such a sensor also has good selectivity toward Hg^(2+)detection in the presence of other common metal ions.This strategy shows the great potential for visual detection with portable type.

Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis

Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions.Here,we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv.‘Hongyang’,named Hongyang v4.0,which is the first to achieve two de novo haploid-resolved haplotypes,HY4P and HY4A.HY4P and HY4A have a total length of 606.1 and 599.6 Mb,respectively,with almost the entire telomeres and centromeres assembled in each haplotype.In comparison with Hongyang v3.0,the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions,resulting in∼38.6–39.5 Mb extra sequences,which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A,respectively.Furthermore,our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres.Globally,centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer(Ach-CEN153)with different copy numbers among chromosomes.Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids,but also have genetic features for participation in the regulation of cell division.The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.

quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

A high-quality genome is the basis for studies on functional,evolutionary,and comparative genomics.The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences,along with the emergence of a new‘telomere-to-telomere(T2T)assembly’era.However,the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited.Here,we developed a user-friendly web toolkit,quarTeT,which currently includes four modules:AssemblyMapper,GapFiller,TeloExplorer,and CentroMiner.First,AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome.Then,GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences.Finally,TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome.These four modules can be used alone or in combination with each other for T2T genome assembly and characterization.As a case study,by adopting the entire modular functions of quarTeT,we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0,which was assembled with the addition of manual handling.Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods.Collectively,quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration.

Progress and perspective of single-atom catalysts for membrane electrode assembly of fuel cells

A fuel cell is an energy conversion device that can continuously input fuel and oxidant into the device through an electrochemical reaction to release electrical energy.Although noble metals show good activity in fuel cell-related electrochemical reactions,their ever-increasing price considerably hinders their industrial application.Improvement of atom utilization efficiency is considered one of the most effective strategies to improve the mass activity of catalysts,and this allows for the use of fewer catalysts,saving greatly on the cost.Thus,single-atom catalysts(SACs)with an atom utilization efficiency of 100%have been widely developed,which show remarkable performance in fuel cells.In this review,we will describe recent progress on the development of SACs for membrane electrode assembly of fuel cell applications.First,we will introduce several effective routes for the synthesis of SACs.The reaction mechanism of the involved reactions will also be introduced as it is highly determinant of the final activity.Then,we will systematically summarize the application of Pt group metal(PGM)and nonprecious group metal(non-PGM)catalysts in membrane electrode assembly of fuel cells.This review will offer numerous experiences for developing potential industrialized fuel cell catalysts in the future.