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Resolving the geometric structure of trastuzumab by mobility capillary electrophoresis and native mass spectrometry

Chinese Chemical Letters 2024年第3期35卷 221-225页

作者： Wenjing Zhang Jie Hong Lei Yang Zuqiang Xu Yu Xiang Wei Xu School of life science Beijing Institute of TechnologyBeijing 100081China

Available online Immunoglobulins G(IgGs)are Y-shaped globular proteins,however,their high flexibility and heterogeneity pose great challenges to their structure and conformation *** structure of IgG closely correlates to its biofunctions,such as the antibody escape of human immunodeficiency virus(HIV)could attribute to the distance mismatch between the ends of two Fab arms(antigen-binding sites)and envelope glycoprotein spikes on virion ***,we report the first use of mobility capillary electrophoresis(MCE)and native mass spectrometry(nMS)to resolve the internal geometric structure and conformation of an IgG(trastuzumab)in solution *** proteolysis,the ellipsoid dimensions of IgG and its subunits were measured by MCE-nMS *** was then reconstructed,in which the sizes and relative positions of these three subunits in three-dimensional space were *** was found that the two Fab arms have an angle of~102.1°and a distance of~11.0 nm between the two antigen-binding sites under native condition,and the Fc arm was tilted~16.0°towards one of the Fab *** was not on the plane of Fab-Fab,but has an angle of no larger than 103.1°.Under acidic environment(pH 3.0),each subunit of the IgG would unfold into larger dimensions,and the angles between these subunits also *** great potential for tumor imaging and therapy,the structure of F(ab')_(2)fragments was also measured and validated by molecular dynamic *** was found that the electrostatic force among these three subunits and steric hindrance stemming from Fc help maintaining the angle between two Fab arms.

关键词： Native mass spectrometry Mobility capillary electrophoresis Trastuzumab Protein structure Geometric structure

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Molecular cloning and functional analysis of two calcium associated cuticular protein genes in Neocaridina denticulata sinensis

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Journal of Oceanology and Limnology 2024年第5期42卷 1659-1672页

作者： Xi GAO Mengmeng DUAN Yuying SUN Jiquan ZHANG School of life sciences/Hebei Basic science Center for Biotic Interaction Hebei UniversityBaoding 071002China institute of life science and Green Development Hebei UniversityBaoding 071002China

The body surface of crustaceans is covered with a sturdy *** growth and development of crustaceans are realized through *** denticulata sinensis is a suitable candidate for crustacean scientific *** calcium-associated cuticular protein genes,named NdCAP-1 and NdCAP-2,were obtained from *** *** docking simulated the binding effect of both proteins and calcium ***-quantitative reverse transcription PCR results show that NdCAP-1 is expressed in D_(2-4) stage,NdCAP-2 expressed in D_(2-4) and A-B stages,and both were significantly expressed in the cephalothorax cuticle and ***,it was revealed that NdCAP-1 and NdCAP-2 are regulated by NdEcR-mediated 20 E signaling *** of NdCAP-1 and NdCAP-2 was observed to cause surface *** recombinant proteins(rNdCAP-1 and rNdCAP-2),obtained by prokaryotic expression,had calcium-binding and chitin-binding ability,inhibited formation of calcium carbonate *** results show that calcium-associated cuticular proteins play important roles in cuticle formation and calcification.

关键词： Neocaridina denticulata sinensis calcium-associated cuticular protein molting cycle RNAi calcium-binding ability

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Multi-region calcium imaging in freely behaving mice with ultra-compact head-mounted fluorescence microscopes

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National science Review 2024年第1期11卷 161-173页

作者： Feng Xue Fei Li Ke-ming Zhang Lufeng Ding Yang Wang Xingtao Zhao Fang Xu Danke Zhang Mingzhai Sun Pak-Ming Lau Qingyuan Zhu Pengcheng Zhou Guo-Qiang Bi Department of Precision Machinery and Precision Instruments University of Science and Technology of China Hefei National Laboratory for Physical sciences at the Microscale University of Science and Technology of China Interdisciplinary Center for Brain Information the Brain Cognition and Brain Disease Institute Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Faculty of life and Health sciences Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences School of life sciences University of Science and Technology of China institute of Semiconductors Chinese Academy of Sciences Department of Modern life sciences and Biotecnology Xiongan Institute of Innovation Xiongan New Area Shenzhen-Hong Kong institute of Brain science-Shenzhen Fundamental Research Institutions Suzhou institute for Advanced Research University of Science and Technology of China institute of Artiflcial Intelligence Hefei Comprehensive National Science Center

To investigate the circuit-level neural mechanisms of behavior, simultaneous imaging of neuronal activity in multiple cortical and subcortical regions is highly desired. Miniature head-mounted microscopes offer the capability of calcium imaging in freely behaving animals. However, implanting multiple microscopes on a mouse brain remains challenging due to space constraints and the cumbersome weight of the ***, we present TINIscope, a Tightly Integrated Neuronal Imaging microscope optimized for electronic and opto-mechanical design. With its compact and lightweight design of 0.43 g, TINIscope enables unprecedented simultaneous imaging of behavior-relevant activity in up to four brain regions in ***-of-concept experiments with TINIscope recorded over 1000 neurons in four hippocampal subregions and revealed concurrent activity patterns spanning across these regions. Moreover, we explored potential multi-modal experimental designs by integrating additional modules for optogenetics, electrical stimulation or local field potential recordings. Overall, TINIscope represents a timely and indispensable tool for studying the brain-wide interregional coordination that underlies unrestrained behaviors.

关键词： miniature microscope multiple sites calcium imaging multimodal integration hippocampus

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Replacement of fish meal with cottonseed protein concentrate in Chinese mitten crab(Eriocheir sinensis): Nutrient digestibility, growth performance, free amino acid profile, and expression of genes related to nutrient metabolism

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Animal Nutrition 2024年第2期17卷 447-462页

作者： Xinting Liu Danyang Zou Yizhu Wang Yutong Zhuang Yang Liu Yanyu Li Zhenzhu Sun Chaoxia Ye Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring Institute of Modern Aquaculture Science and Engineering School of Life Science South China Normal University

This study aimed to investigate the application of cottonseed protein concentrate(CPC) in Chinese mitten crabs(Eriocheir sinensis). First, the apparent digestibility coefficient(ADC) of CPC, fish meal and soybean meal were compared in crabs(21.72 ± 0.33 g). The protein ADC of CPC was 90.42%, which was significantly higher than that of soybean meal(83.16%)(P < 0.05). The ADC of Phe, Cys and Glu of CPC were significantly higher than those of fish meal, while the ADC of Ile, Leu, Lys, Met, Thr and Ala of CPC were significantly lower(P < 0.05). Second, we investigated the effects of fish meal substitution by CPC on growth performance, free amino acid profile, and expression of genes related to nutrient metabolism in crabs. Six diets were formulated by replacing 0%, 15%, 30%, 45%, 60% and 75% fish meal with CPC, namely FM, CPC15, CPC30, CPC45, CPC60, and CPC75. A total of 630 crabs(1.68 ± 0.00 g) were randomly divided into 18 tanks(3 tanks per group) and fed 3 times daily for 9 weeks. Results showed that CPC75 group significantly reduced growth performance, feed conversion efficiency, and free Ile, Leu, Lys, Met, and Thr contents in muscle(P < 0.05). The contents of free amino acids(Arg, His, Ile, Leu, Lys, Met, Phe, Thr, Val,Ala, Cys, Glu, Gly, Ser and Tyr) in hepatopancreas decreased linearly with the increase of dietary CPC level(P < 0.05). The substitution of more than 45% fish meal with CPC significantly decreased the concentration of delicious amino acids(Ala, Glu and Gly) in hepatopancreas(P < 0.05), which might adversely affect crab flavor. The expression of genes related to antioxidant capacity, protein transport, TOR pathway and lipid metabolism was significantly downregulated by increasing dietary CPC level(P < 0.05). In conclusion, based on the quadratic regression analysis of FCR and PER, the optimal replacement levels of fish meal with CPC in crab diet containing 35% fish meal were 32.36% and 35.38%, respectively. It is recommended that Ile, Leu and Thr be

关键词： Eriocheir sinensis Cottonseed protein concentrate Digestibility Amino acid TOR signaling pathway

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Structural insights into AtABCG25,an angiosperm-specific abscisic acid exporter

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Plant Communications 2024年第1期5卷 284-295页

作者： Jian Xin Yeling Zhou Yichun Qiu He Geng Yuzhu Wang Yi Song Jiansheng Liang Kaige Yan Department of Chemical Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China institute of Plant and Food science Department of BiologySchool of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Max Planck institute of Molecular Plant Physiology Potsdam-GolmGermany institute for Biological Electron Microscopy Southern University of Science and TechnologyShenzhenGuangdongChina

Cellular hormone homeostasis is essential for precise spatial and temporal signaling responses and *** acid(ABA)plays pivotal roles in orchestrating various developmental and stress re-sponses and confersfitness benefits over ecological and evolutionary timescales in terrestrial *** ABA level is regulated by complex processes,including biosynthesis,catabolism,and ***25 is thefirst ABA exporter identified through genetic screening and affects diverse ABA *** the structural basis of ABA export by ABCG25 is critical for further manipulations of ABA homeostasis and *** used cryo-electron microscopy to elucidate the structural dynamics of AtABCG25 and successfully characterized different states,including apo AtABCG25,ABA-bound AtABCG25,and ATP-bound AtABCG25(E232Q).Notably,AtABCG25 forms a homodimer that fea-tures a deep,slit-like cavity in the transmembrane domain,and we precisely characterized the critical residues in the cavity where ABA *** binding triggers closure of the nucleotide-binding domains and conformational transitions in the transmembrane *** show that AtABCG25 belongs to a conserved ABCG subfamily that originated during the evolution of *** subfamily neofunctionalized to regulate seed germination via the endosperm,in concert with the evolution of this angio-sperm-specific,embryo-nourishing ***,thesefindings provide valuable insights into the intricate substrate recognition and transport mechanisms of the ABA exporter AtABCG25,paving the way for genetic manipulation of ABA homeostasis and plantfitness.

关键词： AtABCG25 abscisic acid ABC transporters cryo-EM structure

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Inhibition mechanisms of CRISPR-Cas9 by AcrⅡA25.1 and AcrⅡA32

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science China(life sciences) 2024年第9期67卷 1781-1791页

作者： Jianlin Zheng Yuwei Zhu Tengjin Huang Wenbo Gao Jiale He Zhiwei Huang HIT Center for life sciences School of Life Science and TechnologyHarbin Institute of TechnologyHarbin 150080China Westlake Center for Genome Editing Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou 310024China

In the ongoing arms race between bacteria and bacteriophages,bacteriophages have evolved anti-CRISPR proteins to counteract bacterial CRISPR-Cas ***,AcrⅡA25.1 and AcrⅡA32 have been found to effectively inhibit the activity of Spy Cas9 both in bacterial and human ***,their molecular mechanisms remain ***,we report the cryo-electron microscopy structures of ternary complexes formed by AcrⅡA25.1 and AcrⅡA32 bound to Spy Cas9-sg *** structural analysis and biochemical experiments,we revealed that AcrⅡA25.1 and AcrⅡA32 recognize a novel,previously-unidentified anti-CRISPR binding site on Spy *** found that both AcrⅡA25.1 and AcrⅡA32 directly interact with the WED domain,where they spatially obstruct conformational changes of the WED and PI domains,thereby inhibiting Spy Cas9 from recognizing protospacer adjacent motif(PAM)and unwinding double-stranded *** addition,they may inhibit nuclease activity by blocking the dynamic conformational changes of the Spy Cas9 surveillance *** summary,our data elucidate the inhibition mechanisms of two new anti-CRISPR proteins,provide new strategies for the modulation of Spy Cas9 activity,and expand our understanding of the diversity of anti-CRISPR protein inhibition mechanisms.

关键词： anti-CRISPR cryo-EM Spy Cas9 AcrⅡA25.1 AcrⅡA32 inhibiton

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Brain-inspired chaotic spiking backpropagation

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National science Review 2024年第6期11卷 169-179页

作者： Zijian Wang Peng Tao Luonan Chen Key Laboratory of Systems Health science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of Sciences Key Laboratory of Systems Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Guangdong institute of Intelligence science and Technology Pazhou Laboratory(Huangpu)

Spiking neural networks(SNNs) have superior energy efficiency due to their spiking signal transmission,which mimics biological nervous systems, but they are difficult to train effectively. Although surrogate gradient-based methods offer a workable solution, trained SNNs frequently fall into local minima because they are still primarily based on gradient dynamics. Inspired by the chaotic dynamics in animal brain learning, we propose a chaotic spiking backpropagation(CSBP) method that introduces a loss function to generate brain-like chaotic dynamics and further takes advantage of the ergodic and pseudo-random nature to make SNN learning effective and robust. From a computational viewpoint, we found that CSBP significantly outperforms current state-of-the-art methods on both neuromorphic data sets(***-CIFAR10 and DVS-Gesture) and large-scale static data sets(e.g. CIFAR100 and Image Net) in terms of accuracy and robustness. From a theoretical viewpoint, we show that the learning process of CSBP is initially chaotic, then subject to various bifurcations and eventually converges to gradient dynamics,consistently with the observation of animal brain activity. Our work provides a superior core tool for direct SNN training and offers new insights into understanding the learning process of a biological brain.

关键词： spiking neural networks surrogate gradient local minima backpropagation brain-inspired learning chaos

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Surface-phonon-polariton-enhanced photoinduced dipole force for nanoscale infrared imaging

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National science Review 2024年第5期11卷 227-235页

作者： Jian Li Junghoon Jahng Xuezhi Ma Jing Liang Xue Zhang Qianhao Min Xiao-Liang Wang Shuangjun Chen Eun Seong Lee Xing-Hua Xia State Key Lab of Analytical Chemistry for life science School of Chemistry and Chemical Engineering Nanjing University Hyperspectral Nano-Imaging Team Korea Research Institute of Standards and Science institute of Materials Research and Engineering Agency for ScienceTechnology and Research College of Materials science and Engineering Nanjing Tech University

The photoinduced dipole force(Pi DF) is an attractive force arising from the Coulombic interaction between the light-induced dipoles on the illuminated tip and the sample. It shows extreme sample-tip distance and refractive index dependence, which is promising for nanoscale infrared(IR) imaging of ultrathin samples. However, the existence of Pi DF in the mid-IR region has not been experimentally demonstrated due to the coexistence of photoinduced thermal force(Pi TF), typically one to two orders of magnitude higher than Pi DF. In this study, we demonstrate that, with the assistance of surface phonon polaritons, the Pi DF of c-quartz can be enhanced to surpass its Pi TF, enabling a clear observation of Pi DF spectra reflecting the properties of the real part of permittivity. Leveraging the detection of the Pi DF of phonon polaritonic substrate, we propose a strategy to enhance the sensitivity and contrast of photoinduced force responses in transmission images, facilitating the precise differentiation of the heterogeneous distribution of ultrathin samples.

关键词： surface phonon polariton photoinduced dipole force nanoscale infrared imaging ultrathin sample

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Structural engineering of antimicrobials for optimal broad-spectrum activity

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Green Chemical Engineering 2024年第4期5卷 473-482页

作者： Arunmozhiarasi Armugam Diane S.W.Lim Siti Nurhanna Riduan Shook Pui Chan Jerome Asugan Yugen Zhang institute of Bioengineering and Bioimaging institute of Sustainability for Chemicals Energy and Environment(ISCE2) Agency for Science Technology and Research (A*STAR) Diploma in Biomedical science School of Chemical and Life SciencesSingapore Polytechnic

Antimicrobial materials are a crucial component in eradicating and managing the spread of infectious *** are expected to act on a broad-spectrum of microbes, including emerging pathogens which could cause the next Disease X. Herein, we reassessed a series of antimicrobial imidazolium polymers on our shelves and uncovered extended functionality through dual modes of action. By redesigning their structures, a truly broadspectrum antimicrobial material with optimized activity against bacteria(G +ve, G-ve) and fungi, as well as enveloped and non-enveloped viruses was developed. We demonstrated that the imidazolium polymer exhibits dual modes of function against microbes: targeting the microbial membrane and binding DNA. The latter DNA binding affinity was found to be key against non-enveloped viruses. With this insight, we designed small molecule compounds that exhibited optimum broad-spectrum antimicrobial activity and excellent efficacy against ESKAPE group of pathogens that are responsible for some of the deadliest nosocomial infections worldwide. Our results could also shed light on the design of broad-spectrum antimicrobial compounds against Disease X.

关键词： Broad-spectrum Antimicrobial Polyimidazolium Structure-function Membrane active

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How variable progenitor clones construct a largely invariant neocortex

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National science Review 2024年第1期11卷 129-144页

作者： Zhongfu Shen Jiajun Yang Qiangqiang Zhang Kuiyu Wang Xiaohui Lv Xiaolin Hu Jian Ma Song-Hai Shi New Cornerstone science Laboratory IDG/McG overn Institute for Brain Research Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Department of Computer sciences Tsinghua University College of life sciences Nankai University Chinese institute for Brain Research

The neocortex contains a vast collection of diverse neurons organized into distinct layers. While nearly all neocortical neurons are generated by radial glial progenitors(RGPs), it remains largely unclear how a complex yet organized neocortex is constructed reliably and robustly. Here, we show that the division behavior and neuronal output of RGPs are highly constrained with patterned variabilities to support the reliable and robust construction of the mouse neocortex. The neurogenic process of RGPs can be well-approximated by a consistent Poisson-like process unfolding over time, producing deep to superficial layer neurons progressively. The exact neuronal outputs regarding layer occupation are variable; yet, this variability is constrained systematically to support all layer formation, largely reflecting the variable intermediate progenitor generation and RGP neurogenic entry and exit timing differences. Together, these results define the fundamental features of neocortical neurogenesis with a balanced reliability and variability for the construction of the complex neocortex.

关键词： neocortex radial glial progenitor intermediate progenitor neurogenesis clonal variability layer formation

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