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Transcriptomic analysis of Andrias davidianus meat and experimental validation for exploring its bioactive components as functional foods

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Food Science and Human Wellness 2024年第1期13卷 166-172页

作者： Changge Guan Zhenglin Tan shucheng li Yi Wang Naoyuki Yamamoto Chong Zhang Songjun Wang Junjie Chen Xinhui Xing Key Laboratory for Industrial Biocatalysis Ministry of Education of ChinaDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China School of life Science and Technology Tokyo Institute of TechnologyYokohama 226-0026Japan Sensing System Research Center National Institute of Advanced Industrial Science and TechnologyTsukuba 305-8565Japan Center for Synthetic and Systems Biology Tsinghua UniversityBeijing 100084China Henan Giant Salamander Protection and Development Association Luoyang 471000China Intelligent Computing Research Center Harbin Institute of TechnologyShenzhen 518071China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055China Institute of Biomedical Health Technology and Engineering Shenzhen Bay LaboratoryShenzhen 518067China

Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in ***,the progress of functional peptides mining was slow due to lack of reference genome and protein sequence *** this study,we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10703 coding DNA *** functional annotation and amino acid composition analysis,we have discovered various genes related to signal transduction,and 16 genes related to *** have also found vast variety of functional peptides through protein coding sequence(CDS)analysis by comparing the data obtained with the functional peptide ***-Pro-Ile predicted by the CDS analysis was released from the CGS meat through enzymatic hydrolysis,suggesting that our approach is *** study suggested that transcriptomic analysis can be used as a reference to guide polypeptide mining in CGS meat,thereby providing a powerful mining strategy for the bioresources with unknown genomic and proteomic sequences.

关键词： Chinese giant salamander Transcriptomic analysis Bioactive components Functional peptides mining

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Screening of Chinese giant salamander meat hydrolysates with DPP-IV inhibitory activity and systematic elucidation of their hypoglycemic functions in mouse model

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Food Science and Human Wellness 2024年

作者： shucheng li Changge Guan Yi Wang Haihong Chen Wei li Songjun Wang Chong Zhang Xin-Hui Xing Key Laboratory for Industrial Biocatalysis， Ministry of Education of China， Department of Chemical Engineering， Tsinghua University School of life Science and Technology， Tokyo Institute of Technology Institute of Biopharmaceutical and Health Engineering， Tsinghua Shenzhen International Graduate School Henan Giant Salamander Protection and Development Association Center for Synthetic and Systems Biology， Tsinghua University Institute of Biomedical Health Technology and Engineering， Shenzhen Bay Laboratory

Type 2 diabetes (T2D) presents a significant health challenge， underscoring the need for functional foods and nutraceutical hypoglycemic bioactive peptides for its prevention. This study investigates the potential of proteolytic hydrolysate from artificially cultivated Chinese giant salamander (CGS) meat， a rich protein source， as a preventive strategy for T2D. We produced a CGS meat hydrolysate (CGSh) and demonstrated its ability to inhibit the T2D drug target DPP-IV through in vitro assays. We identified five peptides (WRPPDH， WAPPSKD， IPDSPF， IPEMIF， and VPIAVPT) with high DPP-IV inhibitory activity in CGSh， suggesting its potential antidiabetic effects. In vivo experiments showed that CGSh effectively reduced insulin resistance in mice induced with a high-fat diet， as evidenced by a slower increase in blood glucose levels and a decreased HOMA-IR index. 16S rRNA sequencing analysis revealed that CGSh improved gut microbial homeostasis， promoting beneficial microorganisms and reducing harmful bacteria. Metabolomic analyses identified an increase in valeric acid levels and highlighted nine potential biomarker metabolites. By inhibiting metabolic pathways such as AGE-RAGE， CGSh may also prevent diabetic complications and reduce inflammation. These findings suggest that CGSh has a promising hypoglycemic effect， making it a potential functional food ingredient for T2D prevention and treatment.

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基于RBF-PSO算法的潜艇尾部结构噪声优化

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噪声与振动控制 2024年第1期44卷 199-204页

作者：李舒成张冠军柯昱照武汉理工大学船海与能源动力工程学院武汉430063 武汉理工大学高性能船舶技术教育部重点实验室武汉430063

针对潜艇尾部结构噪声突出问题,选取潜艇尾部桨轴艇耦合模型为研究对象,以潜艇尾部质量为约束条件,以纵向、横向激励力下的水下潜艇尾部辐射声功率级为优化目标,设计以尾壳板厚度、T型材结构参数(面板宽、腹板高、面板厚度、腹板厚度)... 详细信息

针对潜艇尾部结构噪声突出问题,选取潜艇尾部桨轴艇耦合模型为研究对象,以潜艇尾部质量为约束条件,以纵向、横向激励力下的水下潜艇尾部辐射声功率级为优化目标,设计以尾壳板厚度、T型材结构参数(面板宽、腹板高、面板厚度、腹板厚度)为设计变量的均匀试验设计,采用径向基函数(Radia Basis Function,RBF)神经网络构建反映设计变量与优化目标之间映射关系的代理模型,使用粒子群算法(Particle Swarm Optimization,PSO)对潜艇尾部噪声进行多目标优化。研究表明:纵向激励下潜艇尾部水下辐射声功率合成级降低3.79 dB,横向激励下潜艇尾部水下辐射声功率合成级降低1.55 d B,潜艇尾部质量降低3.424 t。将RBF-PSO算法应用于潜艇尾部结构低频噪声优化问题效果较好,可以为潜艇的结构噪声优化提供指导。

关键词：声学 RBF神经网络粒子群算法潜艇尾部噪声优化

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Orbitofrontal cortex action of 5-hydroxytryptamine and its receptor in an acute forced swimming stress-induced depression model

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Neural Regeneration Research 2009年第7期4卷 530-535页

作者： Huipeng li Fengli An shucheng An College of life Science Shaanxi Normal University Xi'an 710062 Shaanxi Province China

BACKGROUND： The orbitofrontal cortex （OFC） is a brain region closely associated with emotion. 5-hydroxytryptamine （5-HT） has been shown to be involved in human depression. OBJECTIVE： To investigate OFC actions and mechanisms of 5-HT and 5-HT1A receptor （5-HT1AR） in stress-induced depression.DESIGN, TIME AND SETTING： A randomized, controlled, animal experiment was performed at Laboratory of Neurobiology, College of life Science, Shaanxi Normal University between May 2006 and March 2008. MATERIALS： 5-HT, p-chlorophenylalanine （PCPA, an inhibitor to tryptophan hydroxylase） and spiperone （5-HT1AR antagonist） were provided by Sigma, USA; rabbit anti-rat 5-HT1AR antibody was provided by Tianjin Haoyang Biological Manufacture. METHODS： A total of 40 male Sprague Dawley rats, aged 3 months, were randomly divided into five groups： control, model, 5-HT, spiperone ＋ 5-HT, and PCPA, with 8 rats in each group. Except for control group, rats in the other four groups were used to establish depression models by forced swimming for 15 minutes. At 30 minutes before forced swimming test, 0.5 pL of 5-HT （12.5 pg/pL）, PCPA （20 pg/pL）, spiperone （1.3 pg/pL）＋ 5-HT （12.5 pg/pL, 10 minutes later）, and saline were respectively injected into the OFC of 5-HT, PCPA, spiperone ＋ 5-HT, and model groups, respectively. The control group received a saline microinjection into the OFC.MAIN OUTCOME MEASURES： Forced swimming and open field tests were employed to measure animal behaviors, and immunohistochemistry was used to analyze 5-HT1AR expression in the OFC, cingulate cortex, and piriform cortex. RESULTS：（1） Compared with the model group, 5-HT microinjection into the OFC prominently reduced immobility time in the forced swimming test and rearing in open field test （P 〈 0.05）; locomotion and grooming in open field test were increased, although there was no significance （P 〉 0.05）. Furthermore, following PCPA microinjection into the OFC （PCPA ＋ forced swimming stress）, immobility time in f

关键词： depression orbitofrontal cortex 5-hydroxytryptamine forced swimming test open field test

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茉莉酸甲酯对猕猴桃果实抗葡萄座腔菌过程中能量代谢和膜脂代谢的影响

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中国农业科学 2024年第7期57卷 1377-1393页

作者：肖刘华康乃慧李树成郑致远罗绕绕陈金印陈明向妙莲江西农业大学农学院/江西省果蔬采后处理关键技术与质量安全协同创新中心/江西省果蔬保鲜与无损检测重点实验室

【背景】由葡萄座腔菌(Botryosphaeria dothidea)引起的软腐病是猕猴桃果实贮藏期的重要病害，对猕猴桃产业造成了严重的经济损失。茉莉酸甲酯(MeJA)是一类广泛存在于植物体内的生物信号分子，前期研究发现MeJA能够有效诱导猕猴桃果实抵... 详细信息

【背景】由葡萄座腔菌(Botryosphaeria dothidea)引起的软腐病是猕猴桃果实贮藏期的重要病害，对猕猴桃产业造成了严重的经济损失。茉莉酸甲酯(MeJA)是一类广泛存在于植物体内的生物信号分子，前期研究发现MeJA能够有效诱导猕猴桃果实抵御***的侵染。【目的】分析MeJA对果实能量代谢和膜脂代谢的影响，深入解析MeJA介导的猕猴桃果实抗病机理。【方法】以‘红阳’猕猴桃(Actinidia chinensis ***)为试验材料，分3组进行试验：接种组(Inoculation)，果实不经过MeJA处理，但接种***;MeJA+接种组(MeJA+inoculation)，果实经过0.1 mmol·L-1MeJA熏蒸处理24 h并接种***；对照组(Control)，不作任何处理，即未经MeJA处理且不接种***。所有果实于培养箱((20±1)℃、相对湿度90%—95%)中贮藏8 d。利用2,7-二氯二氢荧光素乙酰乙酸(H2DCFDA)染色分析果实活性氧(ROS)积累情况，测定丙二醛(MDA)含量和相对电导率，分析磷脂酶D(PLD)、脂肪酶(LPS)、脂氧合酶(LOX)、琥珀酸脱氢酶(SDH)、苹果酸脱氢酶(MDH)、H+-ATP酶(H+-ATPase)、Ca2+-ATP酶(Ca2+-ATPase)和细胞色素C氧化酶(CCO)活性及其相应基因的表达，利用高效液相色谱仪(HPLC)检测三磷酸腺苷(ATP)、二磷酸腺苷(ADP)、单磷酸腺苷(AMP)、草酰乙酸和延胡索酸的含量，并对接种组和MeJA+接种组猕猴桃果实膜脂代谢和能量代谢指标进行相关性分析。【结果】与接种组相比，MeJA处理抑制了接种***果实中活性氧(ROS)的过量累积，减缓了膜脂过氧化程度，并有效降低了PLD、LPS和LOX活性及AcLOXs、AcPLD和AcLPS的表达，但提高了SDH、MDH、H+-ATPase、Ca2+-ATPase和CCO的活性及AcSDH、AcMDH、AcH+-ATPase、AcCa2+-ATPase和AcCCO转录水平，促进了ATP、ADP、草酰乙酸和延胡索酸的产生，延缓了果实能荷的下降，保障了果实抵御病原菌所需的能量。相关性分析表明，猕猴桃果实膜脂代谢与ROS的积累呈正相关，而与能荷呈负相关。【结论】MeJA诱导猕猴桃果实对***的抗性与其调控果实能量水平和减缓ROS参与的膜脂代谢进程有关。

关键词：茉莉酸甲酯猕猴桃果实葡萄座腔菌诱导抗性能量代谢膜脂代谢

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Feasible and reliable quantification of mRNA in Arabidopsis thaliana using optical thin-film biosensor chips

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Journal of Genetics and Genomics 2010年第5期37卷 341-346页

作者： Sulan Bai Fan Wang Zhen Zhang shucheng li Jie Zhang Yaochuan Zhang College of life Sciences Capital Normal University Beijing 100048 China Beijing Vocational College of Agriculture Beijing 102442 China

mRNA quantification is very important in molecular biological researches. Traditional spectrophotometric method cannot distinguish DNA, rRNA and tRNA species from mRNA. Northern blot can be used for mRNA quantification but is known to be time consuming. To rapidly detect mRNA levels, we developed an optical thin-film biosensor chip based method, to quantify mRNA in samples. After total RNA was extracted, the mRNA with poly（A） tails was reverse transcribed with oligo（dT）20 primers and dNTPs mixed with digoxigenin（DIG）-11-dUTE The transcribed first strand cDNA was hybridized with oligo（dA）20 nucleotide probes spotted on optical thin-film biosensor chips. Excess first strand cDNA, single-strand RNA, and mis-matched DNA/DNA hybrids were removed by washing. The perfect-matched DNA/DNA hybrid was detected with anti-DIG-AP （alkaline phosphatase） conjugate and then incubated with NBT/BCIP substrate for color development. The range of the color is from purplish red to blue, according to the cDNA mass deposited on chip sur- face. Detection of mRNA levels from Arabidopsis samples proved that this method is feasible for mRNA quantification, and has great potential for application in mRNA quantification in various organisms.

关键词： mRNA quantification optical thin-film biosensor chip assay

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A new MaterialGo database and its comparison with other high-throughput electronic structure databases for their predicted energy band gaps

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Science China(Technological Sciences) 2019年第8期62卷 1423-1430页

作者： JIE JianShu WENG MouYi li ShunNing CHEN Dong li shucheng XIAO WeiJi ZHENG JiaXin PAN Feng Wang linWang School of Advanced Materials Peking University Shenzhen Graduate School Shenzhen 518055 China Materials Science Division Lawrence Berkeley National Laboratory Berkeley 94720 USA

Recently, many high-throughput calculation materials databases have been constructed and found wide applications. However, a database is only useful if its content is reliable and sufficiently accurate. It is thus of paramount importance to gauge the reliabilities and accuracies of these databases. Although many properties have been predicted accurately in these databases,electronic band gap is well known to be underestimated by traditional density functional theory(DFT) calculations under local density approximation(LDA), which becomes a challenging problem for materials database building. Here, we introduce MaterialGo(http://***/***), a new database calculating the band structures of crystals using both Perdew-Burke-Ernzerhof(PBE) exchange-correlation functional and Heyd-Scuseria-Ernzerhof(HSE) hybrid *** different PBE databases, it is found that their band gaps are consistent when no U parameter is used for transition metal d-state or heavy element f-state to correct their self-interaction error, but rather different when PBE+U are used, mostly because of the different values of U used in different database. HSE calculations under standard parameters will give larger band gaps that are closer to experiment. Based on the high-throughput HSE calculations over 10000 crystal structures, we might have a better understanding of the relationship between crystal structures and electronic structures, which will help us to further explore material genome science and engineering.

关键词： high-throughput hybrid functional calculation database

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A descriptor of “material genes”: Effective atomic size in structural unit of ionic crystals

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Science China(Technological Sciences) 2019年第5期62卷 849-855页

作者： CHEN Dong li ShunNing JIE JianShu li SiBai ZHENG ShiSheng WENG MouYi YU ChangCheng li shucheng CHEN DaJun PAN Feng School of Advanced Materials Shenzhen Graduate School Peking University

The atomic size of each element, described by the ionic radius, is one category of "material genes" and can facilitate our understanding of atomic arrangements in compounds. Most of the ionic radii currently used to measure the sizes of cations and anions in ionic crystals are derived from hard-sphere model based on the coordination numbers, or the soft-sphere model incorporating the effect of ionic polarization. Herein we take a first step towards a novel "effective atomic size"(EAS) model,which takes into consideration the impact of the types and number of neighboring atoms on the relationship between ionic radii and interatomic distances. Taking the binary compounds between Group IA/IIA and VIA/VIIA elements gathered from the latest databases as an example, we show that the proposed EAS model can yield excellent agreement between the predicted and the DFT-calculated interatomic distances, with deviation of less than 0.1 ?. A set of EAS radii for ionic crystals has been compiled and the role of coordination numbers, geometric symmetry and distortion of structural units has been examined. Thanks to its superior predictability, the EAS model can serve as a foundation to analyze the structure of newly-discovered compounds and to accelerate materials screening processes in the future works.

关键词： ionic radii interatomic distance effective atomic size coordination environment structural units

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Discovering unusual structures from exception using big data and machine learning techniques

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Science Bulletin 2019年第9期64卷 612-616页

作者： Jianshu Jie Zongxiang Hu Guoyu Qian Mouyi Weng Shunning li shucheng li Mingyu Hu Dong Chen Weiji Xiao Jiaxin Zheng lin-Wang Wang Feng Pan School of Advanced Materials Peking UniversityShenzhen Graduate School Materials Science Division Lawrence Berkeley National Laboratory

Recently, machine learning(ML) has become a widely used technique in materials science study. Most work focuses on predicting the rule and overall trend by building a machine learning model. However,new insights are often learnt from exceptions against the overall trend. In this work, we demonstrate that how unusual structures are discovered from exceptions when machine learning is used to get the relationship between atomic and electronic structures based on big data from high-throughput calculation database. For example, after training an ML model for the relationship between atomic and electronic structures of crystals, we find AgO2 F, an unusual structure with both Ag3+and O22à, from structures whose band gap deviates much from the prediction made by our model. A further investigation on this structure might shed light into the research on anionic redox in transition metal oxides of li-ion batteries.

关键词： Machine learning Gradient boosting decision tree Band gap Unusual structures

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CMN: a co-designed neural architecture search for efficient computing-in-memory-based mixture-of-experts

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Science China(Information Sciences) 2024年第10期67卷 100-114页

作者： Shihao HAN Sishuo liU shucheng DU Mingzi li Zijian YE Xiaoxin XU Yi li Zhongrui WANG Dashan SHANG Department of Electrical and Electronic Engineering The University of Hong Kong ACCESS-AI Chip Center for Emerging Smart Systems InnoHK Centers Key Lab of Fabrication Technologies for Integrated Circuits Chinese Academy of Sciences Laboratory of Microelectronics Devices and Integrated Technology Institute of MicroelectronicsChinese Academy of Sciences University of Chinese Academy of Sciences School of Microelectronics Southern University of Science and Technology

Artificial intelligence(AI) has experienced substantial advancements recently, notably with the advent of large-scale language models(LLMs) employing mixture-of-experts(MoE) techniques, exhibiting human-like cognitive skills. As a promising hardware solution for edge MoE implementations, the computing-in-memory(CIM) architecture collocates memory and computing within a single device, significantly reducing the data movement and the associated energy consumption. However, due to diverse edge application scenarios and constraints, determining the optimal network structures for MoE, such as the expert's location,quantity, and dimension on CIM systems remains elusive. To this end, we introduce a software-hardware co-designed neural architecture search(NAS) framework, CIM-based MoE NAS(CMN), focusing on identifying a high-performing MoE structure under specific hardware constraints. The results of the NYUD-v2 dataset segmentation on the RRAM(SRAM) CIM system reveal that CMN can discover optimized MoE configurations under energy, latency, and performance constraints, achieving 29.67×(43.10×) energy savings,175.44×(109.89×) speedup, and 12.24× smaller model size compared to the baseline MoE-enabled Visual Transformer, respectively. This co-design opens up an avenue toward high-performance MoE deployments in edge CIM systems.

关键词： mixture-of-experts computing-in-memory neural architecture search resistive random-access memory static random-access memory

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