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Rationally designed synthetic peptide as versatile calibrant to improve the accuracy of protein sequence analysis using MALDI mass spectrometry

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Chinese Chemical Letters 2024年第3期35卷 214-220页

作者： Lingpeng Zhan Yanyi Huang Guanbo Wang Institute for Cell analysis Shenzhen Bay LaboratoryShenzhen 518132China biomedical Pioneering Innovation Center Peking UniversityBeijing 100871China

Matrix-assisted laser desorption/ionization(MALDI)mass spectrometry(MS)plays an indispensable role in analyzing protein covalent *** reliable identification of amino acid residues and modifications relies on the mass accuracy,which is highly dependent on ***,the accuracy provided by the currently available calibrants still needs further improvement in terms of compatibility with multiple tandem MS modes or ion polarity modes,calibratable range,and minimizing suppression of and interference with analyte *** aiming at developing a versatile calibrant to solve these problem,we designed a synthetic peptide format of calibrant R_x(GDP_n)_m(referred to as“Gly-Asp-Pro,GDP”)according to the chemical natures of amino acids and polypeptide fragmentation rules in tandem *** four types of amino acid residues selected and arranged through rational designs,a GDP peptide produces highly regulated fragments that give rise to evenly spaced signals in each tandem MS mode and is compatible with both positive and negative ion *** internal calibration,its regulated fragmentation pattern minimizes interference with analyte signals,and using a single peptide as the input minimizes suppression of the analyte *** demonstrated by analyses of proteins including monoclonal antibody and Aβ-42,these features allowed significant increase of the mass accuracy and precision,which improved sequence coverage and sequence resolution in sequence analyses(including de novo sequencing).This rational design strategy may also inspire further development of synthetic calibrants that benefit structural analysis of biomolecules.

关键词： Biomolecule design Synthetic peptide Protein sequencing Covalent structure De novo sequencing Mass spectrometry Gas-phase fragmentation

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An optimized method of culturing neurons based on polyacrylamide gel

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Biophysics Reports 2024年第1期10卷 41-47页

作者： Yongjing Qiao Jihong Gong Ziqi Jin Yiting Tu Xiaofei Yang Key laboratory of Cognitive Science Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment Laboratory of Membrane Ion Channels and Medicine College of Biomedical Engineering SouthCentral Minzu University

Substrate stiffness is a microenvironment with a certain stiffness constructed by the extracellular matrix and adjacent cells, which plays an important role in the growth and development of cells and tissue formation. Studies have indicated that the stiffness of the brain is about 0.1–1 kPa. The physiological and pathological processes of the nervous system are mediated by the substrate stiffness that the neurons suffer. However, how substrate stiffness regulates these processes remains to be studied. Culturing neurons on substrates with different stiffness in vitro is one of the best methods to study the role of stiffness in regulating neuronal development and activity. In this study, by changing the preparation time and the activation time of polyacrylamide gel, we provide an improved method that achieves a low toxic substrate environment for better primary neuron adhesion and development. Hope that this method is convenient for those studying the role of substrate stiffness in neurons.

关键词： Polyacrylamide gel Neuron culture Cell adhesion Neural cell development

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3D hand pose and shape estimation from monocular RGB via efficient 2D cues

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Computational Visual Media 2024年第1期10卷 79-96页

作者： Fenghao Zhang Lin Zhao Shengling Li Wanjuan Su Liman Liu Wenbing Tao Hubei Key laboratory of Medical Information analysis and Tumor Diagnosis&Treatment School of Biomedical EngineeringSouth Central Minzu UniversityWuhan430074China National Key laboratory of Science and Technology of Multi-spectral Information Processing School of Artificial Intelligence and AutomationHuazhong University of Science and TechnologyWuhan430074China

Estimating 3D hand shape from a single-view RGB image is important for many ***,the diversity of hand shapes and postures,depth ambiguity,and occlusion may result in pose errors and noisy hand *** full use of 2D cues such as 2D pose can effectively improve the quality of 3D human hand shape *** this paper,we use 2D joint heatmaps to obtain spatial details for robust pose *** also introduce a depth-independent 2D mesh to avoid depth ambiguity in mesh regression for efficient hand-image *** method has four cascaded stages:2D cue extraction,pose feature encoding,initial reconstruction,and reconstruction ***,we first encode the image to determine semantic features during 2D cue extraction;this is also used to predict hand joints and for ***,during the pose feature encoding stage,we use a hand joints encoder to learn spatial information from the joint ***,a coarse 3D hand mesh and 2D mesh are obtained in the initial reconstruction step;a mesh squeeze-and-excitation block is used to fuse different hand features to enhance perception of 3D hand ***,a global mesh refinement stage learns non-local relations between vertices of the hand mesh from the predicted 2D mesh,to predict an offset hand mesh to fine-tune the reconstruction *** and qualitative results on the FreiHAND benchmark dataset demonstrate that our approach achieves state-of-the-art performance.

关键词： hand 3D reconstruction deep learning image features 3D mesh

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RGS22 maintains the physiological function of ependymal cells to prevent hydrocephalus

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Science China Life Sciences 2024年

作者： Xue Pang Lin Gu Qiu-Ying Han Jia-Qing Xing Ming Zhao Shao-Yi Huang Jun-Xi Yi Jie Pan Hao Hong Wen Xue Xue-Qing Zhou Zhi-Hui Su Xin-Ran Zhang Li-Ming Sun Shao-Zhen Jiang Dan Luo Ling Chen Zheng-Jie Wang Yu Yu Tian Xia Xue-Min Zhang Ai-Ling Li Tao Zhou Hong Cai Tao Li Nanhu laboratory National Center of Biomedical Analysis School of Basic Medical Sciences Fudan University Department of Basic Medical Sciences School of Medicine Tsinghua University

Ependymal cells line the wall of cerebral ventricles and ensure the unidirectional cerebrospinal fluid （CSF） flow by beating their motile cilia coordinately. The ependymal denudation or ciliary dysfunction causes hydrocephalus. Here, we report that the deficiency of regulator of Gprotein signaling 22 （RGS22） results in severe congenital hydrocephalus in both mice and rats. Interestingly, RGS22 is specifically expressed in ependymal cells within the brain. Using conditional knock-out mice, we further demonstrate that the deletion of Rgs22 exclusively in nervous system is sufficient to induce hydrocephalus. Mechanistically, we show that Rgs22 deficiency leads to the ependymal denudation and impaired ciliogenesis. This phenomenon can be attributed to the excessive activation of lysophosphatidic acid receptor （LPAR） signaling under Rgs22–/–condition, as the LPAR blockade effectively alleviates hydrocephalus in Rgs22–/–rats. Therefore, our findings unveil a previously unrecognized role of RGS22 in the central nervous system, and present RGS22 as a potential diagnostic and therapeutic target for hydrocephalus.

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Microenvironment responsive pod-structured astaxanthin nanocarrier for ameliorating inflammatory bowel disease

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Chinese Chemical Letters 2024年第7期35卷 360-366页

作者： Jingting Wang Yuanyuan Chen Linlin Han Shasha Xia Xingyao Zhang Peng Xue Yuejun Kang Jian Ming Zhigang Xu Key laboratory of Luminescence analysis and Molecular Sensing Ministry of EducationSchool of Materials and Energy&Chongqing Engineering Research Center for Micro-Nano Biomedical Materials and DevicesSouthwest UniversityChongqing 400715China College of Food Science Southwest UniversityChongqing 400715China State Key laboratory of Chemo/Biosensing and Chemometrics Hunan UniversityChangsha 410082China

Anti-inflammatory drugs targeting inflammatory bowel disease(IBD)have attracted considerable attention but still face low therapeutic outcomes and frequent side ***(ATX),a natural ketone,possesses potent antioxidant and anti-inflammatory ***,it faces problems such as poor water solubility,photothermal instability,and low ***,we employed a supramolecular encapsulation strategy to create a nanoscale oral delivery system for ATX(referred to as FC-ATX NPs)by coupling fucoidan(FUC)with chitosan oligosaccharides(COS).The obtained FC-ATX NPs exhibited a particular“bean pod”structure with uniform size,good encapsulation efficiency,excellent physical and chemical stability,pH-triggered intestinal targeted slow-release properties,and potent antioxidant *** vitro cell culture experiments showed that FC-ATX NPs promoted cellular uptake and scavenged excessive intracellular reactive oxygen species(ROS).In mouse models of colitis,FC-ATX NPs enhanced the drug absorption of intestinal epithelial cells and effectively accumulated at the site of *** work provides an efficient approach to enhance the bioavailability of ATX and has excellent application potential as an oral targeted delivery system for colitis therapy.

关键词： Oral administration Astaxanthin Nanocarrier Anti-oxidant activity Colon targeting

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Designed imidazole-based supramolecular catalysts for accelerating oxidation/hydrolysis cascade reactions

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Nano Research 2024年第6期17卷 4916-4923页

作者： Yuanxi Liu Wenjie Xu Shichao Xu Haifeng Wu Baoli Zhang Li Song Zhen-Gang Wang State Key laboratory of Organic-Inorganic Composites Key Lab of Biomedical Materials of Natural Macromolecules(Ministry of Education)Beijing Laboratory of Biomedical MaterialsCollege of Materials Science and EngineeringBeijing University of Chemical TechnologyBeijing 100029China National Synchrotron Radiation laboratory CAS Center for Excellence in NanoscienceUniversity of Science and Technology of ChinaHefei 230029China

Reconstructing enzymatic active sites presents a significant challenge due to the intricacies involved in achieving enzyme-like scaffold folding and spatial arrangement of essential functional *** is also a growing interest in building biocatalytic networks,wherein multiple enzymatic active sites are localized within a single artificial system,allowing for cascaded *** this work,we report the self-assembly of imidazole or its derivatives with fluorenylmethyloxycarbonyl-modified histidine and Cu2+to fabricate a supramolecular catalyst,which possesses catechol oxidase-like dicopper center with multiple imidazole as the coordination *** electron microscopy,low-temperature X-band continuous-wave electron paramagnetic resonance,K-edge X-ray absorption spectra/the extended X-ray absorption fine structure analysis,and density functional theory modeling were used for the structural characterization of the *** phenol derivatives and the dissolved oxygen were used as the substrates,with the addition of 4-aminoantipyrine to generate a red adduct with a maximum absorbance at 510 nm,for obtaining time-dependent absorbance change curves and estimating the *** results reveal that the addition of imidazole synergistically accelerates the oxidative activity about 10-fold and the hydrolysis activity about 14-fold than fluorenylmethyloxycarbonyl modified-histidine/Cu2+.The supramolecular nanoassembly also exhibits the ability to catalyze oxidation/hydrolysis cascade reactions,converting 2′,7′-dichlorofluorescin diacetate into 2′,7′-*** process can be regulated through the methylation of the imidazole component at various *** work may contribute to the design of advanced biomimetic catalysts,and shed light on early structural models of the active sites of the primitive copper-dependent enzymes.

关键词： enzyme mimic self-assembly supramolecular catalyst cascade reactions

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Self-shrinking supramolecular nanoparticles syndicate energy suppression and NIR-II mild photothermal amplification of mitochondrial oxidative stress for breast cancer therapy

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Nano Research 2024年第5期17卷 4314-4328页

作者： Hongmei Liu Jiming Xu Mengjie Ye Hengbo Zhang Linlin Han Jingting Wang Peng Xue Yuejun Kang Zhigang Xu Key laboratory of Luminescence analysis and Molecular Sensing Ministry of EducationSchool of Materials and Energy&Chongqing Engineering Research Center for Micro-Nano Biomedical Materials and DevicesSouthwest UniversityChongqing 400715China Key laboratory of Laser Technology and Optoelectronic Functional Materials of Hainan Province College of Chemistry and Chemical EngineeringHainan Normal UniversityHaikou 571158China Yibin Academy of Southwest University Yibin 644000China

Photothermal therapy(PTT)may lead to healthy tissue damage,tumor metastasis,and recurrence,which makes mild photothermal therapy(mild PTT)stand ***,overcoming heat resistance,insufficient therapeutic effect,and poor photothermal conversion efficiency has become new ***,we report a dynamic supramolecular nanocarrier formed from amide-sericin and aldehyde-polyhydroxy glucan(denoted as SDA),the loose cavity of which can be filled by using the pharmaceutical combination of lonidamine(LND)and NIR-II photothermal agent of IR-1061,producing SDLI with a tighter inner hole,smaller and uniform particle size and excellent stability due to multiple pulling ***,the intricate internal network structure prevents the hydrophobic IR-1061 from forming aggregates in the small cavity,and the photothermal conversion efficiency(PCE)can reach 48.9%.At the acidic tumor microenvironment of pH 6.5,the controlled release of LND can solve the problem of heat resistance of NIR-II mild PTT and significantly improve the therapeutic effect of NIR-II mild ***,SDLI also shows a reasonable tumor inhibition rate,so the synergistic strategy of inhibiting tumor energy metabolism and NIR-II mild PTT to magnify mitochondrial oxidative stress,continuous cell stress state-induced immunogenic cell death to promote the induction of tumor apoptosis is proposed to achieve more effective cancer treatment.

关键词： self-shrinkage dynamic supramolecular nanoparticles tumor energy metabolism NIR-II mild photothermal therapy mitochondrial oxidative stress

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Discovery of TK-642 as a highly potent,selective,orally bioavailable pyrazolopyrazine-based allosteric SHP2 inhibitor

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Acta Pharmaceutica Sinica B 2024年第8期14卷 3624-3642页

作者： Kai Tang Shu Wang Siqi Feng Xinyu Yang Yueyang Guo Xiangli Ren Linyue Bai Bin Yu Hong-Min Liu Yihui Song School of Pharmaceutical Sciences&Key laboratory of Advanced Drug Preparation Technologies Ministry of EducationZhengzhou UniversityZhengzhou 450001China College of Chemistry Pingyuan LaboratoryState Key Laboratory of Antiviral DrugsZhengzhou UniversityZhengzhou 450001China Tianjian laboratory of Advanced biomedical Sciences Institute of Advanced Biomedical SciencesZhengzhou UniversityZhengzhou 450000China State Key laboratory of Pharmaceutical Biotechnology Nanjing UniversityNanjing 210023China

Src homology-2-containing protein tyrosine phosphatase 2(SHP2)is a promising therapeutic target for cancer *** this work,we presented the structure-guided design of 5,6-fused bicyclic allosteric SHP2 inhibitors,leading to the identification of pyrazolopyrazine-based TK-642 as a highly potent,selective,orally bioavailable allosteric SHP2 inhibitor(SHP2WT IC_(50)=2.7 nmol/L)with favorable pharmacokinetic profiles(F=42.5%;t_(1/2)=2.47 h).Both dual inhibition biochemical assay and docking analysis indicated that TK-642 likely bound to the“tunnel”allosteric site of ***-642 could effectively suppress cell proliferation(KYSE-520 cells IC_(50)=5.73μmol/L)and induce apoptosis in esophageal cancer cells by targeting the SHP2-mediated AKT and ERK signaling ***,oral administration of TK-642 also demonstrated effective anti-tumor effects in the KYSE-520 xenograft mouse model,with a T/C value of 83.69%.Collectively,TK-642 may warrant further investigation as a promising lead compound for the treatment of esophageal cancer.

关键词： Protein tyrosine phosphatase Pyrazolopyrazine SHP2 inhibitor Esophageal cancer

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Melittin enhanced intracellular trehalose with synergistic membrane stabilization of macromolecular protectants for cell cryopreservation

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Science China(Technological Sciences) 2024年第4期67卷 1160-1169页

作者： NIU QingJing GAO ShuHui ZHU KongYing REN LiXia YUAN XiaoYan School of Materials Science and Engineering Tianjin Key Laboratory of Composite and Functional MaterialsTianjin UniversityTianjin 300350China analysis and Measurement Center Tianjin UniversityTianjin 300072China

Cryopreservation plays an essential role in biobanking and cell therapy,but the physiological toxicity of traditional cryoprotectants such as glycerol and dimethyl sulfoxide(DMSO)has raised safety issues for biomedical ***,a nonreducing disaccharide that accumulates in desiccation-or cold-tolerant organisms,has been considered as a biocompatible ***,a naturally occurring membrane-active cationic peptide,melittin,was utilized to facilitate membraneimpermeable trehalose entry into cells for effective cell ***(ethylene glycol)and poly(vinyl pyrrolidone)were applied as macromolecular protectants to improve the stabilization of cell *** the optimal protocol,the postthaw recovery of human red blood cells in freezing bags at a hematocrit of~50%could achieve 82.9%with favorable cell morphologies and physiological ***,the cryosurvival of L929 fibroblasts reached 84.3%compared to the conventional method using 10%(v/v)*** short,this work by using trehalose and melittin provides a biocompatible solvent-free approach for long-term cryostorage of cells.

关键词： melittin intracellular trehalose membrane stabilization macromolecular protectants cell cryopreservation

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Synthesis and potential osteogenic applications of Wnt3a-loaded ZIF-8 nanoparticles

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Chinese Chemical Letters 2024年第3期35卷 399-405页

作者： Hengfei Wang Song Chen Zihan He Junyu Chen Zhou Zhu Qianbing Wan Jian Wang Xibo Pei State Key laboratory of Oral Diseases National Clinical Research Center for Oral DiseasesDepartment of ProsthodonticsWest China Hospital of StomatologySichuan UniversityChengdu 610041China Chongqing Key laboratory of Oral Diseases and biomedical Sciences Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationStomatological Hospital of Chongqing Medical UniversityChongqing 400016China

The Wnt signaling pathway plays a critical role in bone homeostasis,and the related protein therapy strategies have been reported to have great potential in osseointegration;however,they face formidable challenges such as complex external environments and unavoidable protein *** this work,we report a novel approach combining the synthesis of metal–organic frameworks(MOFs)and protein encapsulation in a one-pot process based on zeolitic imidazolate framework-8(ZIF-8)and Wnt3a protein,with improved biomechanical behavior and enhanced protein biological *** combination was designed to enhance the Wnt3a protein function through the improved chemical stability provided by the ZIF-8 ***,the zinc ions contained in the ZIF-8 crystals induced bone homeostasis,further favoring the *** results showed that the Wnt3a protein-loaded ZIF-8 crystals served as efficient drug delivery vehicles to promote osteogenesis,preventing protein *** particular,Wnt3a-loaded ZIF-8 nanoparticles(Wnt3a@ZIF-8 NPs)had higher efficacy on bone marrow mesenchymal stem cells(BMSCs)than ZIF-8 NPs or Wnt3a proteins,contributing to the osteogenesis through ZIF-8 crystals and intracellular Wnt3a proteins released from Wnt3a@ZIF-8 ***,polymerase chain reaction(PCR)analysis showed that the osteogenic pathways were ***,the present one-pot process can open up new avenues to develop signaling protein-delivery systems for applications in protein therapy strategies.

关键词： Metal–organic frameworks Nanoparticle Drug release Osteogenesis Bone defects

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