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Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies

Synthetic and Systems Biotechnology 2022年第3期7卷 965-971页

作者： Suying Liu Jiaofang Huang Chen Zhang lihua wang Chunhai Fan Chao Zhong Division of Physical Biology and Bioimaging Center Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghaiChina University of Chinese Academy of Sciences BeijingChina School of Physical Science and Technology ShanghaiTech UniversityShanghaiChina State Key Laboratory of Bioreactor Engineering East China University of Science and TechnologyShanghaiChina Institute of Physics Swiss Federal Institute of Technology Lausanne(EPFL)LausanneSwitzerland The Interdisciplinary Research Center Shanghai Advanced Research InstituteChinese Academy of SciencesZhangjiang LaboratoryShanghaiChina School of Chemistry and Chemical Engineering Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina Center for Materials Synthetic Biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina

Bacterial communities form biofilms on various surfaces by synthesizing a cohesive and protective extracellular matrix,and these biofilms protect microorganisms against harsh environmental *** subtilis is a widely used experimental species,and its biofilms are used as representative models of beneficial ***,*** biofilms are known to be rich in extracellular polymeric substances(EPS)and other biopolymers such as DNA and proteins like the amyloid protein TasA and the hydrophobic protein *** materials,which form an interconnected,cohesive,three-dimensional polymer network,provide the mechanical stability of biofilms and mediate their adherence to surfaces among other functional ***,we explored how genetically-encoded components specifically contribute to regulate the growth status,mechanical properties,and antibiotic resistance of *** biofilms,thereby establishing a solid empirical basis for understanding how various genetic engineering efforts are likely to affect the structure and function of *** noted discrete contributions to biofilm morphology,mechanical properties,and survival from major biofilm components such as EPS,TasA and *** example,EPS plays an important role in maintaining the stability of the mechanical properties and the antibiotic resistance of biofilms,whereas BslA has a significant impact on the resolution that can be obtained for printing *** work provides a deeper understanding of the internal interactions of biofilm components through systematic genetic *** thus not only broadens the application prospects of beneficial biofilms,but also serves as the basis of future strategies for targeting and effectively removing harmful biofilms.

关键词： Bacillus subtilis Biofilms Synthetic biology Living materials Environmental tolerance

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Human RNA Modifications Disease Database(HRMDD):A web resource for the molecular and clinical landscape of RNA modifications in human diseases

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Genes & Diseases 2023年第4期10卷 1157-1160页

作者： Jianjian wang Lifang Li Hanxiao Zhou Shuang Li Liting Tian Xinyue wang Danyang Li Yue Yin Shangwei Ning lihua wang Department of Neurology The Second Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang 150081China College of Bioinformatics Science and Technology Harbin Medical UniversityHarbinHeilongjiang 150081China

Here,we developed a comprehensive web-searchable database,designated as Human RNA Modifications Disease Database(HRMDD,http://***/HRMDD/***).RNA modification(RM)is an important mechanism of epigenetic *** the evolution of both experimental technologies and computational methods,major progress has been made in identifying the genomic locations and distributions of various RM types throughout the transcriptome.^(1)

关键词： web Database Human

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RNA2Immune:A Database of Experimentally Supported Data Linking Non-coding RNA Regulation to The Immune System

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Genomics, Proteomics & Bioinformatics 2023年第2期21卷 283-291页

作者： Jianjian wang Shuang Li Tianfeng wang Si Xu Xu wang Xiaotong Kong Xiaoyu Lu Huixue Zhang Lifang Li Meng Feng Shangwei Ning lihua wang Department of Neurology The Second Affiliated Hospital of Harbin Medical UniversityHarbin 150081China College of Bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081China

Non-coding RNAs(ncRNAs),such as microRNAs(miRNAs),long non-coding RNAs(lncRNAs),and circular RNAs(circRNAs),have emerged as important regulators of the immune system and are involved in the control of immune cell biology,disease pathogenesis,as well as vaccine responses.A repository of ncRNA-immune associations will facilitate our understanding of ncRNA-dependent mechanisms in the immune system and advance the development of therapeutics and prevention for immune ***,we describe a comprehensive database,RNA2Immune,which aims to provide a high-quality resource of experimentally supported database linking ncRNA regulatory mechanisms to immune cell function,immune disease,cancer immunology,and *** current version of RNA2Immune documents 50,433 immune-ncRNA associations in 42 host species,including(1)6690 ncRNA associations with immune functions involving 31 immune cell types;(2)38,672 ncRNA associations with 348 immune diseases;(3)4833 ncRNA associations with cancer immunology;and(4)238 ncRNA associations with vaccine responses involving 26 vaccine types targeting 22 ***2Immune provides a user-friendly interface for browsing,searching,and downloading ncRNA-immune system ***,RNA2Immune provides important information about how ncRNAs influence immune cell function,how dysregulation of these ncRNAs leads to pathological consequences(immune diseases and cancers),and how ncRNAs affect immune responses to vaccines.

关键词： ncRNA Immune cell Immune disease Cancer immunology Vaccine

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Dynamical investigation of tunable magnetism in Au@Ni-carbide nanocrystals by a combined soft and hard X-ray absorption spectroscopy

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Nano Research 2022年第5期15卷 4320-4326页

作者： Weifeng Huang Jianxin Kang Tingwen Chen Dawei Pang lihua wang Hang Wei Changchun Yang Dongfeng Zhang Lin Guo College of Chemistry and Chemical Engineering Inner Mongolia UniversityHohhot 010021China School of Electronic Engineering Jiujiang UniversityJiujiang 332005China School of Chemistry Beihang UniversityBeijing 100191China Institute of Microstructure and Property of Advanced Materials Beijing University of TechnologyBeijing 100124China

Nickel based magnetic nanocrystals have been widely applied in magnetic and catalytic *** magnetic properties of nickel can be easily obtained via non-magnetic doping or phase ***,phase transformation from face centered cubic(fcc)to hexagonal close packed(hcp)induced magnetism adjustment of Ni are always confused with nickel carbide(Ni_(3)C),due to the similar atomic structures of hcp-Ni and ***,we present series of Au@Ni-carbide magnetic materials achieved from the controlled carbonation of Au@Ni core-shell structures,whose magnetism is tunable by adjusting the amount of carbon in the Ni ***-situ hard X-ray absorption spectroscopy(XAS)at the metal K edge and soft XAS at both metal L edge and carbon K edge provide solid evidence for the carbonation process from fcc-Ni to Ni_(x)C,rather than phase transformation to *** investigation reveals that the magnetism of the hybrids is mainly contributed from the residual *** result represents an accurate and effective way to distinguish hexagonal Ni_(3)C from hcp-Ni,and provides the pathway to control magnetism of Ni-based materials for applications.

关键词： X-ray absorption spectroscopy soft X-ray absorption spectroscopy carbide nickel carbonation process magnetism

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The enzyme-amplified amperometric DNA sensor using an electrodeposited polymer redox mediator

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Science China Chemistry 2009年第6期52卷 746-750页

作者： ZHANG LanYong WAN Ying ZHANG Jiong LI Di wang lihua SONG ShiPing FAN ChunHai Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800China

A highly sensitive method for the detection of a breast cancer-associated BRCA-1 gene is reported. The detection is based on a classical sandwich-type assay using horseradish peroxidase (HRP) as a catalytic label and electrodeposited Os2+/3+ conducting polymer (PAA-PVI-Os) as a redox mediator. Target DNA could be detected by the HRP-catalyzed reduction of H2O2, leading to a limit of detection as low as 10 fM.

关键词： DNA detection conducting polymer HRP electrochemistry

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MaBEL1 regulates banana fruit ripening by activating cell wall and starch degradation-related genes

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Journal of Integrative Plant Biology 2023年第9期65卷 2036-2055页

作者： Zunyang Song Xiaoyang Zhu Xiuhua Lai Hangcong Chen lihua wang Yulin Yao Weixin Chen Xueping Li Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China Ministry of EducationCollege of HorticultureSouth China Agricultural UniversityGuangzhou 510642China Key Laboratory of Food Processing Technology and Quality Control in Shandong Province College of Food Science and EngineeringShandong Agricultural UniversityTai'an 271018China

Banana is a typical subtropical fruit, sensitive to chilling injuries and prone to softening ***, the underlying regulatory mechanisms of the softening disorder caused by cold stress remain obscure. Herein, we found that BEL1-LIKE HOMEODOMAIN transcription factor 1(MaBEL1)and its associated proteins regulate the fruit softening and ripening process. The transcript and protein levels of MaBEL1 were up-regulated with fruit ripening but severely repressed by the chilling stress. Moreover, the MaBEL1 protein interacted directly with the promoters of the cell wall and starch degradation-related genes, such as MaAMY3, MaXYL32, and MaEXP-A8. The transient overexpression of MaBEL1 alleviated fruit chilling injury and ripening disorder caused by cold stress and promoted fruit softening and ripening of “Fenjiao” banana by inducing ethylene production and starch and cell wall degradation. The accelerated ripening was also validated by the ectopic overexpression in ***, MaBEL1-silencing aggravated the chilling injury and ripening disorder and repressed fruit softening and ripening by inhibiting ethylene production and starch and cell wall degradation. MaABI5-like and MaEBF1, the two positive regulators of the fruit softening process,interacted with MaBEL1 to enhance the promoter activity of the starch and cell wall degradationrelated genes. Moreover, the F-box protein MaEBF1 does not modulate the degradation of MaBEL1, which regulates the transcription of MaABI5-like protein. Overall, we report a novel MaBEL1-MaEBF1-MaABI5-like complex system that mediates the fruit softening and ripening disorder in “Fenjiao” bananas caused by cold stress.

关键词： cold stress fruit ripening interaction MaBEL1 softening disorder transcriptional regulation

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In situ atomic-scale observation of dislocation behaviors in twin-structured Pt nanocrystals

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Science China(Technological Sciences) 2021年第3期64卷 599-604页

作者： GUO YiZhong SUN Tao FU LiBo HAO LongHu HUANG Ming WEI RuJian LUO JunFeng HE Xin wang XingQuan XIONG XiaoDong wang lihua HAN XiaoDong Beijing Key Lab of Microstructure and Property of Advanced Materials Institute of Microstructure and Properties of Advanced MaterialsBeijing University of TechnologyBeijing 100124China Grikin Advanced Materials CO. LTD.Beijing 102200China

The deformation mechanisms of twin-structured metallic materials have attracted great *** previous theoretical predictions have suggested that the repulsive force of the twin boundary(TB)can significantly affect the deformation of twinstructured metals,it remains unclear whether this prediction applies to experimental *** this paper,the atomic-scaled deformation process of twin-structured Pt nanocrystals was in situ observed using our home-made device in a high-resolution transmission electron *** have shown that the plastic deformation of the twin-structured Pt nanocrystals was governed by full dislocation generation as well as Lomer dislocation(LD)lock formation and *** LD locks were destructed,these full dislocations tended to move towards the surface of the *** findings revealed that due to the ultra-high repulsive force of TB on dislocation,there was no dislocation-TB reaction during the *** findings can enrich our understanding of the dislocation behaviors of twin-structured nanocrystals.

关键词： deformation mechanism repulsive force twin boundary dislocations in situ

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Recognizing single phospholipid vesicle collisions on carbon fiber nanoelectrode

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Science China Chemistry 2017年第11期60卷 1474-1480页

作者： Yueyue Zhang Min Li Zhenhua Li Qian Li Ali Aldalbahi Jiye Shi lihua wang Chunhai Fan Xiaolei Zuo Division of Physical Biology Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai 201800China University of Chinese Academy of Sciences Beijing 100049China Chemistry Department King Saud UniversityRiyadh 11451Saudi Arabia

We recognize the stochastic collisions of dopamine contained phospholipid vesicle on carbon fiber nanoelectrode, extending the observation of discrete collision events on nanoelectrode to biologically relevant analytes. To decrease noise interference to the technique, the dimensions of nanoelectrode was systematically investigated and optimized. Scanning electron microscopy(SEM) further supported the comparable sizes of nanoelectrode and vesicles(~100 nm in diameter). Vesicles collision and rupture on the surface of nanoelectrode led to the dopamine release from vesicles, which could be electrochemically oxidized to dopamine-o-quinone and detected via voltammetry. The comparable size of the nanoelectrode with vesicles and fast voltammetry allowed differentiation of single collision events from the current magnitudes and peak widths in the electrochemical collision experiments, which shows the efficacy of the method to characterize vesicle samples. This work provides a foundation upon which quantitative sensor technology might be built for the detection of dopamine contained vesicles with high spatial and temporal resolution.

关键词： single vesicle carbon fiber nanoelectrode high resolution electrochemical detection

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Genetically encoded X-ray cellular imaging for nanoscale protein localization

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National Science Review 2020年第7期7卷 1218-1227页

作者： Huating Kong Jichao Zhang Jiang Li Jian wang Hyun-Joon Shin Renzhong Tai Qinglong Yan Kai Xia Jun Hu lihua wang Ying Zhu Chunhai Fan Bioimaging Center Shanghai Synchrotron Radiation FacilityZhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Canadian Light Source Inc. University of Saskatchewan Pohang Accelerator Laboratory POSTECH School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and Shanghai Key Laboratory for Nucleic Acids Chemistry and NanomedicineInstitute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University

Spatial resolution defines the physical limit of microscopes for probing biomolecular localization and interactions in cells. Whereas synchrotron-based X-ray microscopy(XRM) represents a unique approach for imaging a whole cell with nanoscale resolution due to its intrinsic nanoscale resolution and great penetration ability, existing approaches to label biomolecules rely on the use of exogenous tags that are multi-step and error-prone. Here, we repurpose engineered peroxidases as genetically encoded X-ray-sensitive tags(GXET) for site-specific labeling of protein-of-interest in mammalian cells. We find that 3,3-diaminobenzidine(DAB) polymers that are in-situ catalytically formed by fusion-expressed peroxidases are visible under XRM. Using this new tag, we imaged the protein location associated with the alteration of a DNA-methylation pathway with an ultra-high resolution of 30 nanometers. Importantly, the excellent energy resolution of XRM enables multicolor imaging using different peroxidase tags. The development of GXET enlightens the way to nanoscopic imaging for biological studies.

关键词： synchrotron-based X-ray microscopy cellular imaging nanoscale protein localization genetically encoded X-ray tags 3,3-diaminobenzidine polymers

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Study of the inflammatory activating process in the early stage of Fusobacterium nucleatum infected PDLSCs

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International Journal of Oral Science 2023年第1期15卷 113-126页

作者： Yushang wang lihua wang Tianyong Sun Song Shen Zixuan Li Xiaomei Ma Xiufeng Gu Xiumei Zhang Ai Peng Xin Xu Qiang Feng Department of Implantology School and Hospital of StomatologyCheeloo College of MedicineShandong University&Shandong Key Laboratory of Oral Tissue Regeneration&Shandong Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinanChina Department of Human Microbiome School and Hospital of StomatologyCheeloo College of MedicineShandong University&Shandong Key Laboratory of Oral Tissue Regeneration&Shandong Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinanChina Department of Orthodontics School and Hospital of StomatologyCheeloo College of MedicineShandong University&Shandong Key Laboratory of Oral Tissue Regeneration&Shandong Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinanChina State key laboratory of microbial technology Shandong UniversityQingdaoChina

Fusobacterium nucleatum(***)is an early pathogenic colonizer in periodontitis,but the host response to infection with this pathogen remains *** this study,we built an *** infectious model with human periodontal ligament stem cells(PDLSCs)and showed that *** could inhibit proliferation,and facilitate apoptosis,ferroptosis,and inflammatory cytokine production in a dose-dependent *** *** adhesin Fad A acted as a proinflammatory virulence factor and increased the expression of interleukin(IL)-1β,IL-6 and *** study showed that Fad A could bind with PEBP1 to activate the Raf1-MAPK and IKK-NF-κB signaling ***-course RNA-sequencing analyses showed the cascade of gene activation process in PDLSCs with increasing durations of *** ***κB1 and NFκB2 upregulated after 3 h of ***-infection,and the inflammatory-related genes in the NF-κB signaling pathway were serially elevated with *** computational drug repositioning analysis,we predicted and validated that two potential drugs(piperlongumine and fisetin)could attenuate the negative effects of ***,this study unveils the potential pathogenic mechanisms of *** and the host inflammatory response at the early stage of *** infection.

关键词： inflammatory drugs PDL

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