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The role of aromatic residues in controlling the supramolecular chirality of short amphiphilic peptides

Nano research 2023年第10期16卷 12230-12237页

作者： Hao Qi Kai Qi Jie Li Chunyong He Mingrui Liao Xuzhi Hu Yurong Zhao Yubin Ke Chunqiu Zhang Jun Zhang Jiqian Wang jian r.lu Hai Xu Department of Biological and Energy Chemical Engineering China University of Petroleum(East China)Qingdao 266580China College of Life Science Nankai UniversityTianjin 300071China Spallation Neutron Source Science Center Chinese Academy of Sciences(CAS)Dongguan 523803China Institute of High Energy Physics Chinese Academy of SciencesBeijing 100049China Biological Physics Group Department of Physics and AstronomyThe University of ManchesterManchester M139PLUK School of Material Science and Engineering China University of Petroleum(East China)Qingdao 266580China

Although the relationship between molecular and supramolecular chirality remains elusive,the existing results have demonstrated the vital role of hydrophilic motifs in controlling the supramolecular handedness of peptide nanofibrils compared with hydrophobic ***,unlike conventional hydrophobic residues,we speculate that aromatic hydrophobic residues are mostly likely to play a unique role in regulating the supramolecular handedness because theπ–πstacking interactions of their side chains are directional like hydrogen bonding and can direct high levels of self-assembly due to the geometric confining of aromatic *** confirm this hypothesis,we here design a series of amphiphilic short peptides,with their hydrophobic motifs being composed of aromatic *** short lengths not only favor their structural stability,synthesis,and sequence variation but also enable us to readily link their molecular and supramolecular *** the combination of experiments and theoretical simulations,we demonstrate that the peptides containing L-form aromatic residues form left-handed nanofibrils while those containing D-form aromatic residues assemble into right-handed ones,irrespective of the chirality of their C-terminal hydrophilic *** calculations revealed that the stacking of aromatic side chains betweenβ-strands directed the twisting direction of theβ-sheets formed,with L-and D-form phenylalanine side chains stacking in a clockwise and anti-clockwise way,and more ordered and stronger aromatic stacking for homochiral peptides facilitated the formation of nanofibrils with a marked tubular *** study has bridged the knowledge gap in our understanding of how aromatic residues affect the supramolecular chirality of short peptides.

关键词： amphiphilic short peptide molecular chirality supramolecular handedness aromatic residue π–πstacking

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recent development of peptide self-assembly

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Progress in Natural Science:Materials International 2008年第6期18卷 653-660页

作者： Xiubo Zhao,Fang Pan,jian r.lu*Biological Physics Group,School of Physics and Astronomy,The University of Manchester,Schuster Building,Oxford road,Manchester M13 9PL,UK Biological Physics Group School of Physics and Astronomy The University of Manchester Schuster Building Oxford Road Manchester M13 9PL UK

Amino acids are the building blocks to build peptides and *** development in peptide synthesis has however enabled us to mimic this natural process by preparing various long and short peptides possessing dierent conformations and biological *** self-assembly of short designed peptides into molecular nanostructures is becoming a growing interest in ***-assembled peptides exhibit several attractive features for applications in tissue regeneration,drug delivery,biological surface engineering as well as in food science,cosmetic industry and *** aim of this review is to introduce the readers to a number of represen-tative studies on peptide self-assembly.

关键词： Peptides Self-assembly Biomaterials AFM SEM DLS Neutron reflection

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Patterning the neuronal cells via inkjet printing of self-assembled peptides on silk scaffolds

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Progress in Natural Science:Materials International 2020年第5期30卷 686-696页

作者： Weizhen Sun Yi Zhang David A.Gregory Ana Jimenez-Franco Mhd Anas Tomeh Songwei Lv Jiqian Wang John W.Haycock jian r.lu Xiubo Zhao Department of Chemical and Biological Engineering University of Sheffield Department of Materials Science & Engineering University of Sheffield School of Pharmacy Changzhou University Centre for Bioengineering and Biotechnology China University of Petroleum East China School of Physics and Astronomy University of Manchester

The patterning of neuronal cells and guiding neurite growth are important for neuron tissue engineering and cell-based biosensors. In this paper, inkjet printing has been employed to pattern self-assembled I3QGK peptide nanofibers on silk substrates for guiding the growth of neuron-like PC12 cells. Atomic force microscopy(AFM)confirmed the dynamic self-assembly of I3QGK into nanofiber structures. The printed self-assembled peptide strongly adheres to regenerated silk fibroin(rSF) substrates through charge-charge interactions. It was observed that in the absence of I3QGK, PC12 cells exhibited poor attachment to rSF films, while for rSF surfaces coated or printed with peptide nanofibers, cellular attachment was significantly improved in terms of both cell density and morphology. AFM results revealed that peptide nanofibers can promote the generation of axons and terminal buttons of PC12 cells, indicating that I3QGK nanofibers not only promote cellular attachment but also facilitate differentiation into neuronal phenotypes. Inkjet printing allows complex patterning of peptide nanofibers onto rSF substrates, which enabled us to engineer cell alignment and provide an opportunity to direct axonal development in vitro. The live/dead assay showed that printed I3QGK patterns exhibit no cytotoxicity to PC12 cells demonstrating potential for future nerve tissue engineering applications.

关键词： Neurobiology Micro-patterning Inkjet printing Self-assembling peptides PC12 cells

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Progress of vegetation modelling and future research prospects

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Science China Earth Sciences 2024年第9期67卷 2718-2738页

作者： Siqi LI Xu ZHANG Zhengyao lu jian NI jianhua lu State Key Laboratory of Tibetan Plateau Earth System Resources and Environment(TPESRE)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China College of resources and Environment University of Chinese Academy of SciencesBeijing 100049China British Antarctic Survey Cambridge CB30ETUnited Kingdom Department of Physical Geography and Ecosystem Science Lund UniversityLund 22362Sweden College of Life Sciences Zhejiang Normal UniversityJinhua 321004China School of Atmospheric Sciences Sun Yat-sen University and Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)Zhuhai 519082China

Terrestrial vegetation is a crucial component of the Earth system,and its changes not only represent one of the most distinct aspects of climate change but also exert significant feedback within the climate system by exchanging energy,moisture,and carbon *** quantitatively and mechanistically study climate-vegetation feedback,numerical vegetation models have been developed on the theory of ecophysiological constraints on plant functional *** models eventually can simulate vegetation distribution and succession across different spatial and temporal scales,and associated terrestrial carbon cycle processes by categorizing vegetation into biomes according different plant functional types and their associated environmental *** we review the developing history of vegetation models and provide recent advances and future *** 21st century,static vegetation models,as developed statistical models,can only simulate equilibrated characteristics of vegetation *** last several decades,Dynamic Global Vegetation Models(DGVMs)have been developed to simulate instantaneous responses of vegetation to climate change and associated dynamics,and can be coupled with Earth system models to investigate interactions among atmosphere,ocean,and *** are also widely applied to investigate the dynamics accounting for changes in the geographic distribution patterns of land surface vegetation at different spatial and temporal scales and to assess the impacts of terrestrial carbon and water fluxes and land use *** suggest that future vegetation modeling could integrate with machine learning,and explore vegetation transient response and feedback as well as impacts of process hierarchies and human activities on climate and ecosystem.

关键词： Vegetation models DGVMs Ecosystems Plant functional types Plant functional traits

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Evolutionary mechanisms and practical significance of reproductive success and clonal diversity in unisexual vertebrate polyploids

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Science China(Life Sciences) 2024年第3期67卷 449-459页

作者： Meng lu Li Zhou jian-Fang Gui State Key Laboratory of Freshwater Ecology and Biotechnology Hubei Hongshan Laboratorythe Innovation Academy of Seed DesignInstitute of HydrobiologyChinese Academy of SciencesWuhan 430072China University of Chinese Academy of Sciences Beijing 100049China

Unisexual reproduction is generally relevant to polyploidy, and unisexual vertebrates are often considered an evolutionary “dead end” due to the accumulation of deleterious mutations and absence of genetic diversity. However, some unisexual polyploids have developed strategies to avoid genomic decay, and thus provide ideal models to unveil unexplored evolutionary mechanisms, from the reproductive success to clonal diversity creation. This article reviews the evolutionary mechanisms for overcoming meiotic barrier and generating genetic diversity in unisexual vertebrates, and summarizes recent research advancements in the polyploid Carassius complex. Gynogenetic gibel carp(Carassius gibelio) is a unique amphitriploid that has undergone a recurrent autotriploidy and has overcome the bottleneck of triploid sterility via gynogenesis. recently, an efficient strategy in which ploidy changes, including from amphitriploid to amphitetraploid, then from amphitetraploid to novel amphitriploid, drive unisexual-sexual-unisexual reproduction transition and clonal diversity has been *** on this new discovery, multigenomic reconstruction biotechnology has been used to breed a novel strain with superior growth and stronger disease resistance. Moreover, a unique reproduction mode that combines both abilities of ameiotic oogenesis and sperm-egg fusion,termed as ameio-fusiongensis, has been discovered, and it provides an efficient approach to synthesize sterile allopolyploids. In order to avoid ecological risks upon escape and protect the sustainable property rights of the aquaculture seed industry, a controllable fertility biotechnology approach for precise breeding is being developed by integrating sterile allopolyploid synthesis and gene-editing *** review provides novel insights into the origin and evolution of unisexual vertebrates and into the attempts being made to exploit new breeding biotechnologies in aquaculture.

关键词： unisexual vertebrates polyploidy reproduction transition clonal diversity precise breeding genomic reconstruction controllable fertility

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Intelligent geochemical interpretation of mass chromatograms:Based on convolution neural network

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Petroleum Science 2024年第2期21卷 752-764页

作者： Kai-Ming Su Jun-Gang lu jian Yu Zi-Xing lu Shi-Jia Chen Hubei Key Laboratory of Petroleum Geochemistry and Environment Wuhan430100HubeiChina College of resources and Environment Yangtze UniversityWuhan430100HubeiChina School of Geoscience and Technology Southwest Petroleum UniversityChengdu610500SichuanChina Changqing Oilfield Company PetroChinaXi'an710021ShaanxiChina

Gas chromatography-mass spectrometry(GC-MS)is an extremely important analytical technique that is widely used in organic *** is the only approach to capture biomarker features of organic matter and provides the key evidence for oil-source correlation and thermal maturity ***,the conventional way of processing and interpreting the mass chromatogram is both timeconsuming and labor-intensive,which increases the research cost and restrains extensive applications of this *** overcome this limitation,a correlation model is developed based on the convolution neural network(CNN)to link the mass chromatogram and biomarker features of samples from the Triassic Yanchang Formation,Ordos Basin,*** this way,the mass chromatogram can be automatically *** research first performs dimensionality reduction for 15 biomarker parameters via the factor analysis and then quantifies the biomarker features using two indexes(*** and PMI)that represent the organic matter thermal maturity and parent material type,***,training,interpretation,and validation are performed multiple times using different CNN models to optimize the model structure and hyper-parameter setting,with the mass chromatogram used as the input and the obtained MI and PMI values for supervision(label).The optimized model presents high accuracy in automatically interpreting the mass chromatogram,with r2values typically above 0.85 and0.80 for the thermal maturity and parent material interpretation results,*** significance of this research is twofold:(i)developing an efficient technique for geochemical research;(ii)more importantly,demonstrating the potential of artificial intelligence in organic geochemistry and providing vital references for future related studies.

关键词： Organic geochemistry Biomarker Mass chromatographic analysis Automated interpretation Convolution neural network Machine learning

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Echo State Network Based on Improved Knowledge Distillation for Edge Intelligence

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Chinese Journal of Electronics 2024年第1期33卷 101-111页

作者： jian ZHOU Yuwen jianG Lijie XU lu ZHAO Fu XIAO College of Computer Nanjing University of Posts and Telecommunications jiangsu High Technology research Key Laboratory for Wireless Sensor Networks

Echo state network(ESN) as a novel artificial neural network has drawn much attention from time series prediction in edge intelligence. ESN is slightly insufficient in long-term memory, thereby impacting the prediction performance. It suffers from a higher computational overhead when deploying on edge devices. We firstly introduce the knowledge distillation into the reservoir structure optimization, and then propose the echo state network based on improved knowledge distillation(ESN-IKD) for edge intelligence to improve the prediction performance and reduce the computational overhead. The model of ESN-IKD is constructed with the classic ESN as a student network, the long and short-term memory network as a teacher network, and the ESN with double loop reservoir structure as an assistant network. The student network learns the long-term memory capability of the teacher network with the help of the assistant network. The training algorithm of ESN-IKD is proposed to correct the learning direction through the assistant network and eliminate the redundant knowledge through the iterative pruning. It can solve the problems of error learning and redundant learning in the traditional knowledge distillation process. Extensive experimental simulation shows that ESN-IKD has a good time series prediction performance in both long-term and short-term memory, and achieves a lower computational overhead.

关键词： Knowledge engineering Training Performance evaluation Computational modeling Time series analysis Artificial neural networks reservoirs

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Two-layer Lagrange-based relay network topology and trajectory design for solar system explorations

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Science China(Information Sciences) 2024年第6期67卷 342-358页

作者： Jun CAO jian JIAO Hao LIU rongxing lu Qinyu ZHANG Guangdong Provincial Key Laboratory of Aerospace Communication and Networking Technology Harbin Institute of Technology (Shenzhen) Faculty of Computer Science (FCS) University of New Brunswick

Exploration targeting outer planets and even the edge of the solar system is an emerging direction for the deep-space exploration in the next decades. To address this challenge, a novel two-layer Lagrangebased relay network topology is proposed in this study. Specifically, we utilize the Sun-Mars and Sun-Saturn Lagrange points(LPs) L4 and L5 to build a two-layer backbone relay network, which ensures continuous and high-efficiency communication capability for the exploration of the solar system. Furthermore, we utilize the planetary gravity assist and design the transfer trajectory of backbone relays with the help of planetary celestial body motion equations and Kepler's laws. Moreover, we conduct link budget analysis for multihop relay transmission under Gamma-Gamma distribution, shadowed rician fading, and additive white Gaussian noise channels in several typical exploration scenarios and validate that the LP relays can effectively support future deep-space exploration missions.

关键词： deep-space communication Lagrangian points backbone relay network transfer trajectory relay selection

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An aptamer-driven DNA nanodevice for improved delivery of synthetic immunostimulants

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Nano research 2024年第10期17卷 9078-9083页

作者： Dejie lu Zhenghan Di Lele Li jian Zhao Li Zheng Guangxi Engineering Center in Biomedical Materials for Tissue and Organ regeneration Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and ApplicationGuangxi Key Laboratory of Regenerative MedicineThe First Affiliated Hospital of Guangxi Medical UniversityGuangxi Medical UniversityNanning 530021China CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and TechnologyBeijing 100190China

Efficient delivery of therapeutics to immune cells remains a formidable challenge for cancer *** this work,we demonstrate that an aptamer-driven DNA nanodevice,constructed through linkage of a synthetic immunostimulant(Toll-like receptor 9 agonist:CpG motif)to an aptamer,could significantly enhance the immunostimulatory activity by facilitating the uptake and retention of therapeutics in *** administration of the DNA nanodevice results in efficient tumor growth inhibition in both breast cancer and melanoma mouse *** studies suggest that the DNA nanodevice leads to reeducation of tumor-associated macrophages and ultimately to reversing the tumor immune *** strategy for aptamer-mediated and vehicle-free delivery of immunostimulatory oligonucleotides provides a potential platform for cancer immunotherapy.

关键词： aptamer immunostimulatory oligonucleotides DNA nanodevice tumor-associated macrophages cancer therapy

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Occurrence and possible sources of antibiotic resistance genes in seawater of the South China Sea

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Frontiers of Environmental Science & Engineering 2024年第9期18卷 27-38页

作者： jian lu Jun Wu Cui Zhang jianhua Wang Xia He CAS Key Laboratory of Coastal Environmental Processes and Ecological remediation Yantai Institute of Coastal Zone Research(YIC)Chinese Academy of Sciences(CAS)Shandong Key Laboratory of Coastal Environmental ProcessesYICCASYantai 264003China Yantai research Institute Harbin Engineering UniversityYantai 264006China College of Environmental Science and Engineering Guilin University of TechnologyGuilin 541006China

Antibiotic resistance genes(ArGs)might have great effect on ecological security and human *** are important reservoirs that receive tremendous amounts of pollutants ***,information on the proliferation of ArGs in seawater is still *** study performed field sampling to investigate the occurrence and distribution of ArGs in seawater of the South China Sea,which is the deepest and largest sea in *** results showed that the total absolute abundances of ArGs in seawater samples ranged from 2.1×10^(3)to 2.3×10^(4)copies/mL,with an of 5.0×10^(3)copies/mL and a range of 2.2×10^(3)–1.8×10^(4)copies/mL for those with mobile genetic elements(MGEs).Genes resistant to multidrug,aminoglycoside,tetracycline,and fluoroquinolone antibiotics accounted for 77.3%–88.6%of total ArGs in *** and Cyanobacteria represented 32.1%–56.2%and 30.4%–49.5%of microbial community,***_MIT9313 and Clade_la were the prevalent genera in seawater of the South China *** co-occurrence relationship existed among ArGs,MGEs,and *** activities had critical influence on ArGs and *** wastewater,wastewater treatment plant effluent,sewage,aquaculture tailwater,and runoff were determined as the important sources of ArGs in seawater of the South China Sea based on positive matrix factorization analysis.

关键词： The South China Sea Antibiotic resistance genes Mobile genetic element Source apportionment

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