Assembly mechanisms and energy transfer pathways deciphered in the cryo-EM structure of spinach photosystem Ⅱ-LHCⅡ supercomplex

Funded by the National Natural Science Foundation of China(NSFC),Ministry of Science and Technology of China,and Chinese Academy of Sciences,ajoint team of three laboratories from the Institute of Biophysics of Chinese Academy of Sciences,led by Dr.Liu Zhenfeng(柳振峰),Dr.Zhang Xinzheng(章新政)and Dr.Li Mei(李梅)respectively,solved the structure of spinach photosystem II-LHCII supercom-

Analysis and Inverse Substructuring Computation on Dynamic Quality of Mechanical Assembly

Mechanical assembly has its own dynamic quality directly affecting the dynamic quality of whole product and should be considered in quality inspection and estimation of mechanical assembly. Based on functional relations between dynamic characteristics involved in mechanical assembly, the effects of assembling process on dynamic characteristics of substructural components of an assembly system are investigated by substructuring analysis. Assembly-coupling dynamic stiffness is clarified as the dominant factor of the effects and can be used as a quantitative measure of assembly dynamic quality. Two computational schemes using frequency response functions（FRFs） to determine the stiffness are provided and discussed by inverse substructuring analysis, including their applicable conditions and implementation procedure in application. Eigenvalue analysis on matrix-ratios of FRFs before and after assembling is employed and well validates the analytical outcomes and the schemes via both a lumped-parameter model and its analogic experimental counterpart. Applying the two schemes to inspect the dynamic quality provides the message of dynamic performance of the assembly system, and therefore improves conventional quality inspection and estimation of mechanical assembly in completeness.

Mechanically driven assembly of biomimetic 2D-material microtextures with bioinspired multifunctionality

Nature provides a wealth of bio-inspiration for advanced material research.Assembling various nanomaterials into biomimetic microtextures with bioinspired functionalities has spurred increasing research interests and facilitated technological advances in various applications.In recent years,two-dimensional materials(2DMs)have emerged as important building block units in the biomimicry field due to their distinct chemical,physical,electrical,electrochemical,and catalytic properties.In this review article,various mechanically driven assembly approaches are summarized to fabricate various genealogies of biomimetic 2DM microtextures with bio-inspired multifunctionality.First,sequential deformation strategies are discussed to programmably construct higher dimensional 2DM microtextures,ranging from wrinkles/crumples(one-time deformation)to multiscale hierarchies(multiple deformations).Next,the current progress using higher dimensional 2DM microtextures to imitate different biological structures and/or induce bio-inspired multifunctionality is systematically summarized.Four showcases of bio-inspiration and biomimicry using different 2DM nanosheets are highlighted:(1)wrinkle patterns of an earthworm that spur the design of strain sensors with programmable working ranges and sensitivities,(2)wrinkle appearance of a Shar-Pei dog that motivates the fabrication of stretchable energy storage devices,(3)hierarchical scale textures of a desert lizard that inspire cation-induced gelation platforms for 2DM aerogels,and(4)wrinkle skin of an elephant that influences the development of 2DM protective skin for soft robots.Finally,challenges and future opportunities of adopting 2DM nanosheets to assemble biomimetic microstructures with synergistic functionalities are discussed.

Assessing mechanisms for microbial taxa and community dynamics using process models

Disentangling the assembly mechanisms controlling community composition,structure,distribution,functions,and dynamics is a central issue in ecology.Although various approaches have been proposed to examine community assembly mechanisms,quanti-tative characterization is challenging,particularly in microbial ecology.Here,we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations.Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes,we tested the applicability of three ecological models:the consumer–resource model,the neutral model,and the combined model.Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions.The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated.In contrast,the neutral model showed the best performance for rare taxa.Our analysis further indicated that immigration rates decreased with taxa abundance and com-petitions between taxa were strongly correlated with phylogeny,but within a certain phylogenetic distance only.The determinism underlying taxa and community dynamics were quantitatively assessed,showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning.Given its mechanistic basis,the framework developed here is expected to be potentially applicable beyond microbial ecology.

MODELING METHOD FOR PRODUCT STRUCTURE MAPPING BASED ON REVERSE SOLVING OF LOCUS AND MOTION

Aiming at the problem of structure design in reverse-design of mechanism, a structure mapping method based on reverse solving of locus and motion （RSLM） is presented. The mechanism scheme meeting the requirements of geometric and structural features is obtained through RSLM. The element instance subsets related to component are established based on the element type mapping, pair structure type mapping and design knowledge mapping between components and elements layer by layer. The assembly position mapping of elements is established based on the topological structure information of mechanism scheme, and the product modeling of structure mapping is realized. The algorithm program and prototype system of product structure mapping based on RSLM are developed. Application samples show that the method implements the integration of scheme design, assembly design and structure design, and modeling for product structure mapping based on RSLM. The feasibility of assembly is analyzed in scheme design that contributes to reducing the design error, and raising the design efficiency and quality.

Microeukaryotic plankton community dynamics under ecological water replenishment:Insights from eDNA metabarcoding

Ecological water replenishment(EWR)is an important strategy for river restoration globally,but timely evaluation of its ecological effects at a large spatiotemporal scale to further adjust the EWR schemes is of great challenge.Here,we examine the impact of EWR on microeukaryotic plankton communities in three distinct river ecosystems through environmental DNA(eDNA)metabarcoding.The three ecosystems include a long-term cut-off river,a short-term connected river after EWR,and long-term connected rivers.We analyzed community stability by investigating species composition,stochastic and deterministic dynamics interplay,and ecological network robustness.We found that EWR markedly reduced the diversity and complexity of microeukaryotic plankton,altered their community dynamics,and lessened the variation within the community.Moreover,EWR disrupted the deterministic patterns of community organization,favoring dispersal constraints,and aligning with trends observed in naturally connected rivers.The shift from an isolated to a temporarily connected river appeared to transition community structuring mechanisms from deterministic to stochastic dominance,whereas,in permanently connected rivers,both forces concurrently influenced community assembly.The ecological network in temporarily connected rivers post-EWR demonstrated significantly greater stability and intricacy compared to other river systems.This shift markedly bolstered the resilience of the ecological network.The eDNA metabarcoding insights offer a novel understanding of ecosystem resilience under EWR interventions,which could be critical in assessing the effects of river restoration projects throughout their life cycle.

Insight into the Ebola virus nucleocapsid assembly mechanism： crystal structure of Ebola virus nucleoprotein core domain at 1.8 A resolution

Ebola virus （EBOV） is a key member of Filoviridae family and causes severe human infectious diseases with high morbidity and mortality. As a typical negative-sense single-stranded RNA （-ssRNA） viruses, EBOV possess a nucleocapsid protein （NP） to facilitate genomic RNA encapsidation to form viral ribonucleoprotein complex （RNP） together with genome RNA and polymerase, which plays the most essential role in virus proliferation cycle. However, the mechanism of EBOV RNP formation remains unclear. In this work, we solved the high resolution structure of core domain of EBOV NP. The polypeptide of EBOV NP core domain （NPcore） pos- sesses an N-lobe and C-lobe to clamp a RNA binding groove, presenting similarities with the structures of the other reported viral NPs encoded by the members from Mononegavirales order. Most strikingly, a hydrophobic pocket at the surface of the C-lobe is occupied by an a- helix of EBOV NPcore itself, which is highly conserved among filoviridae family. Combined with other bio- chemical and biophysical evidences, our results provides great potential for understanding the mechanism underlying EBOV RNP formation via the mobility of EBOV NP element and enables the development of antiviral therapies targeting EBOV RNP formation.

In vitro assembly of the bacterial actin protein MamK from ＇Candidatus Magnetobacterium casensis＇ in the phylum Nitrospirae

Magnetotactic bacteria （MTB）, a group of phylogeneti- cally diverse organisms that use their unique intracellular magnetosome organelles to swim along the Earth＇s magnetic field, play important roles in the biogeochemical cycles of iron and sulfur. Previous studies have revealed that the bacterial actin protein MamK plays essential roles in the linear arrangement of magnetosomes in MTB cells belonging to the Proteobacteria phylum. However, the molecular mechanisms of multi- ple-magnetosome-chain arrangements in MTB remain largely unknown. Here, we report that the MamK filaments from the uncultivated ＇Candidatus Magnetobacterium casensis＇ （Mcas） within the phylum Nitrospirae polymerized in the presence of ATP alone and were stable without obvious ATP hydrolysis-mediated disassembly. MamK in Mcas can convert NTP to NDP and NDP to NMP, showing the highest preference to ATP. Unlike its Magnetospirillum counterparts, which form a single magnetosome chain, or other bacterial actins such as MreB and ParM, the polymerized MamK from Mcas is independent of metal ions and nucleotides except for ATP, and is assembled into well-ordered filamentous bundles consisted of multiple filaments. Our results suggest a dynamically stable assembly of MamK from the uncultivated Nitrospirae MTB that synthesizes multiple magnetosome chains per cell, These findings further improve the current knowledge of biomineralization and organelle biogenesis in prokaryotic systems.

Relative position fitting based control strategy for thruster point assembly mechanism of electric propulsion

Purpose-Thruster point assembly mechanism(TPAM)of the electric propulsion system allows to adjust the thrust vector,sothat the thrust vectorisdirectedtothesatellitecenterof gravity(COG)during the satellite on-orbit working period.In this way the impact of disturbance torque caused by deviation of the thrust vector from the satellite COG during thruster ignition can be decreased.Therefore,the control accuracy of satellite is influenced directly by the control accuracy of TPAM.On the other hand,the on-orbit application of TPAM is restricted to the on-orbit computer resource.Therefore,the purpose of this paper is to design a control strategy for TPAM,and the strategy should not only be able to control the TPAM precisely but also be easily implemented by the on-board computer.Design/methodology/approach-First,the structure and work principle of TPAM are discussed,and the mathematical model based on D-H coordinate system is built for it.Then the fitting methods are utilized to design the control strategy of TPAM.Absolute position fitting-based control strategy and relative position fitting-based control strategy are designed,and the least squares algorithm is introduced for parameter selection.Findings-Simulations and tests are provided for the TPAM.Compared with the state-of-the-art PD controller,the proposed control strategy shows smaller overshoot and more simple realization.The experiment results are matched with the simulation results and both the experiment and simulation results show the validity of the proposed control strategies.Practical implications-The designed control strategies can be used for the TPAM of some satellite’s electric propulsion system.Originality/value-The mathematical model of the TPAM based on D-H coordinate system is given.The absolute position fitting-based control strategy and relative position fitting-based control strategy are proposed.Compared with existing methods,the two control strategies have more simple structure and smaller amount of computations.Furthermore,the relative position fitting-based control strategy achieves high precision with simple structure.

Assembly mechanism and energy transfer pathways of plant photosystem II-LHCII supercomplexes discovered through cryo-electron microscopy

Funded by the National Natural Science Foundation of China,Chinese Ministry of Science and Technology,and Chinese Academy of Sciences,ajoint team of three laboratories from the Institute of Biophysics of Chinese Academy of Sciences,namely Liu Zhenfeng’s(柳振峰),Zhang

Horizontal and vertical gene transfer drive sediment antibiotic resistome in an urban lagoon system

Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes(ARGs)in urban aquatic ecosystems.However,limited information is available concerning the ARG profiles and the forces responsible for their assembly in urban landscape lagoon systems.Here,we employed high-throughput quantitative PCR(HT-q PCR)to characterize the spatial variations of ARGs in surface and core sediments of Yundang Lagoon,China.The results indicated that the average richness and absolute abundance of ARGs were 11 and 53 times higher in the lagoon sediments as compared to pristine reference Tibetan lake sediments,highlighting the role of anthropogenic activities in ARG pollution.Co-occurrence network analysis indicated that various anaerobic prokaryotic genera belonging to Alpha-,Deltaproteobacteria,Bacteroidetes,Euryarchaeota,Firmicutes and Synergistetes were the potential hosts of ARGs.The partial least squares-path modeling(PLS-PM)analysis revealed positive and negative indirect effects of physicochemical factors and heavy metals on the lagoon ARG profiles,via biotic factors,respectively.The horizontal(mediated by mobile genetic elements)and vertical(mediated by prokaryotic communities)gene transfer may directly contribute the most to drive the abundance and composition of ARGs,respectively.Furthermore,the neutral community model demonstrated that the assembly of sediment ARG communities was jointly governed by deterministic and stochastic processes.Overall,this study provides novel insights into the diversity and distribution of ARGs in the benthic habitat of urban lagoon systems and underlying mechanisms for the spread and proliferation of ARGs.

Morphable three-dimensional electronic mesofliers capable of on-demand unfolding

Development of miniaturized three-dimensional(3 D)fliers with integrated functional components has important implications to a diverse range of engineering areas.Among the various active and passive miniaturized 3 D fliers reported previously,a class of 3 D electronic fliers inspired by wind-dispersed seeds show promising potentials,owing to the lightweight and noiseless features,aside from the stable rotational fall associated with a low falling velocity.While on-demand shape-morphing capabilities are essential for those 3 D electronic fliers,the realization of such miniaturized systems remains very challenging,due to the lack of fast-response 3 D actuators that can be seamlessly integrated with 3 D electronic fliers.Here we develop a type of morphable3 D mesofliers with shape memory polymer(SMP)-based electrothermal actuators,capable of large degree of actuation deformations,with a fast response(e.g.,~1 s).Integration of functional components,including sensors,controllers,and chip batteries,enables development of intelligent 3 D mesoflier systems that can achieve the on-demand unfolding,triggered by the processing of real-time sensed information(e.g.,acceleration and humidity data).Such intelligent electronic mesofliers are capable of both the low-air-drag rising and the low-velocity falling,and thereby,can be used to measure the humidity fields in a wide 3 D space by simple hand throwing,according to our demonstrations.The developed electronic mesofliers can also be integrated with other types of physical/chemical sensors for uses in different application scenarios.

Reprogrammable 3D Mesostructures Through Compressive Buckling of Thin Films with Prestrained Shape Memory Polymer

The mechanically guided assembly that relies on the compressive buckling of strate- gically patterned 2D thin films represents a robust route to complex 3D mesostructures in advanced materials and even functional micro-devices. Based on this approach, formation of complex 3D configurations with suspended curvy features or hierarchical geometries remains a challenge. In this paper, we incorporate the prestrained shape memory polymer in the 2D precur- sor design to enable local rolling deformations after the mechanical assembly through compressive buckling. A theoretical model captures quantitatively the effect of key design parameters on local rolling deformations. The combination of precisely controlled global buckling and local rolling expands substantially the range of accessible 3D configurations. The combined experimental and theoretical studies over a dozen of examples demonstrate the utility of the proposed strategy in achieving complex reprogrammable 3D mesostructures.

Peptoid-based hierarchically-structured biomimetic nanomaterials: Synthesis, characterization and applications

Peptoids(or poly-N-substituted glycines)are a promising class of bioinspired sequence-defined polymers due to their highly efficient synthesis,high chemical stability,enzyme hydrolysis resistance,and biocompatibility.By tuning the side chain chemistry of peptoids,it allows for precise control over sequences and achieving a large side-chain diversity.Due to these unique features,in the last several years,many amphiphilic peptoids were designed as highly tunable building blocks for the preparation of biomimetic nanomaterials with well-defined hierarchical structures and desired functionalities.Herein,we provide an overview of the recent achievements in this area by dividing them into the following three aspects.First,mica-and silica-templated peptoid selfassembly are summarized.The presence of inorganic substrates provides the guarantee of investigating their selfassembly mechanisms and interactions between peptoids and substrates using nanoscale characterization techniques,particularly in situ atomic force microscopy(AFM)and AFMbased dynamic force spectroscopy(AFM-DFS).Second,solution-phase self-assembly of peptoids into nanotubes and nanosheets is presented,as well as their self-repair properties.Third,the applications of peptoid-based nanomaterials are outlined,including the construction of catalytic nanomaterials as a template and cytosolic delivery as cargoes.