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Base editor-mediated large-scale screening of functional mutations in bacteria for industrial phenotypes

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Science China(Life Sciences) 2024年第5期67卷 1051-1060页

作者： Yaomeng Yuan Xihao Liao Shuang Li Xin-Hui Xing chong zhang MOE Key Laboratory for Industrial Biocatalysis Institute of Biochemical EngineeringDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055China Institute of Biomedical Health Technology and Engineering Shenzhen Bay LaboratoryShenzhen 440300China Center for Synthetic and Systems Biology Tsinghua UniversityBeijing 100084China

Base editing,the targeted introduction of point mutations into cellular DNA,holds promise for improving genome-scale functional genome screening to single-nucleotide *** efforts in prokaryotes,however,remain confined to loss-of-function screens using the premature stop codons-mediated gene inactivation library,which falls far short of fully releasing the potential of base ***,we developed a base editor-mediated functional single nucleotide variant screening pipeline in Escherichia *** constructed a library with 31,123 sgRNAs targeting 462 stress response-related genes in ***,and screened for adaptive mutations under isobutanol and furfural selective *** by the screening results,we successfully identified several known and novel functional *** pipeline might be expanded to the optimization of other phenotypes or the strain engineering in other microorganisms.

关键词： base editor high-throughput large-scale screening Escherichia coli functional mutation

Development of multi-functional anchorage support dynamic-static coupling performance test system and its application

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International Journal of Mining Science and Technology 2024年第3期34卷 339-349页

作者： Qi Wang Shuo Xu Bei Jiang chong zhang Zhe Sun Jingxuan Liu Cailin Jiao State Key Laboratory for Tunnel Engineering China University of Mining&Technology-BeijingBeijing 100083China Research Center of Geotechnical and Structural Engineering Shandong UniversityJinan 250061China

In underground engineering with complex conditions,the bolt(cable)anchorage support system is in an environment where static and dynamic stresses coexist,under the action of geological conditions such as high stresses and strong disturbances and construction conditions such as the application of high *** is essential to study the support components performance under dynamic-static coupling *** on this,a multi-functional anchorage support dynamic-static coupling performance test system(MAC system)is developed,which can achieve 7 types of testing functions,including single component performance,anchored net performance,anchored rock performance and so *** bolt and cable mechanical tests are conducted by MAC system under different prestress *** results showed that compared to the non-prestress condition,the impact resistance performance of prestressed bolts(cables)is significantly *** the prestress range of 50–160 k N,the maximum reduction rate of impact energy resisted by different types of bolts is 53.9%–61.5%compared to non-prestress *** the prestress range of 150–300 k N,the impact energy resisted by high-strength cable is reduced by76.8%–84.6%compared to non-prestress *** MAC system achieves dynamic-static coupling performance test,which provide an effective means for the design of anchorage support system.

关键词： Anchorage support system Development of test system Dynamic-static coupling test Combined stress

Noise-Tolerant ZNN-Based Data-Driven Iterative Learning Control for Discrete Nonaffine Nonlinear MIMO Repetitive Systems

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IEEE/CAA Journal of Automatica Sinica 2024年第2期11卷 344-361页

作者： Yunfeng Hu chong zhang Bo Wang Jing Zhao Xun Gong Jinwu Gao Hong Chen State Key Laboratory of Automotive Simulation and Control Jilin UniversityJilin UniversityChangchun 130025China College of Communication Engineering Jilin UniversityJilin UniversityChangchun 130025China Department of Electromechanical Engineering University of MacaoMacao 999078China School of Artificial Intelligence Jilin UniversityChangchun 130012China IEEE College of Electronics and Information Engineering Tongji UniversityShanghai 200092China

Aiming at the tracking problem of a class of discrete nonaffine nonlinear multi-input multi-output(MIMO) repetitive systems subjected to separable and nonseparable disturbances, a novel data-driven iterative learning control(ILC) scheme based on the zeroing neural networks(ZNNs) is proposed. First, the equivalent dynamic linearization data model is obtained by means of dynamic linearization technology, which exists theoretically in the iteration domain. Then, the iterative extended state observer(IESO) is developed to estimate the disturbance and the coupling between systems, and the decoupled dynamic linearization model is obtained for the purpose of controller synthesis. To solve the zero-seeking tracking problem with inherent tolerance of noise,an ILC based on noise-tolerant modified ZNN is proposed. The strict assumptions imposed on the initialization conditions of each iteration in the existing ILC methods can be absolutely removed with our method. In addition, theoretical analysis indicates that the modified ZNN can converge to the exact solution of the zero-seeking tracking problem. Finally, a generalized example and an application-oriented example are presented to verify the effectiveness and superiority of the proposed process.

关键词： Adaptive control control system synthesis data-driven iterative learning control neurocontroller nonlinear discrete time systems

Diabetic retinopathy identification based on multi-sourcefree domain adaptation

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International Journal of Ophthalmology(English edition) 2024年第7期17卷 1193-1204页

作者： Guang-Hua zhang Guang-Ping Zhuo Zhao-Xia zhang Bin Sun Wei-Hua Yang Shao-chong zhang School of Big Data Intelligent Diagnosis&Treatment Industry Taiyuan UniversityTaiyuan 030032Shanxi ProvinceChina Shanxi Key Laboratory of Intelligent Optimization Computing and Blockchain Technology Taiyuan Normal UniversityTaiyuan 030619Shanxi ProvinceChina Shanxi Eye Hospital Taiyuan 030002Shanxi ProvinceChina College of Computer Science and Technology Taiyuan Normal UniversityTaiyuan 030619Shanxi ProvinceChina Shenzhen Eye Institute Shenzhen Eye HospitalJinan UniversityShenzhen 518040Guangdong ProvinceChina

AIM:To address the challenges of data labeling difficulties,data privacy,and necessary large amount of labeled data for deep learning methods in diabetic retinopathy(DR)identification,the aim of this study is to develop a source-free domain adaptation(SFDA)method for efficient and effective DR identification from unlabeled ***:A multi-SFDA method was proposed for DR *** method integrates multiple source models,which are trained from the same source domain,to generate synthetic pseudo labels for the unlabeled target ***,a softmax-consistence minimization term is utilized to minimize the intra-class distances between the source and target domains and maximize the inter-class *** is performed using three color fundus photograph datasets(APTOS2019,DDR,and EyePACS).RESULTS:The proposed model was evaluated and provided promising results with respectively 0.8917 and 0.9795 F1-scores on referable and normal/abnormal DR identification *** demonstrated effective DR identification through minimizing intra-class distances and maximizing inter-class distances between source and target ***:The multi-SFDA method provides an effective approach to overcome the challenges in DR *** method not only addresses difficulties in data labeling and privacy issues,but also reduces the need for large amounts of labeled data required by deep learning methods,making it a practical tool for early detection and preservation of vision in diabetic patients.

关键词： diabetic retinopathy multisource-free domain adaptation pseudo-label generation softmaxconsistence minimization

Bibliometric analysis of hotspots and trends of global myopia research

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International Journal of Ophthalmology(English edition) 2024年第5期17卷 940-950页

作者： Xing-Yang Wu Hui-Hui Fang Yan-Wu Xu Yan-Ling zhang Shao-chong zhang Wei-Hua Yang Shenzhen Eye Institute Shenzhen Eye HospitalJinan UniversityShenzhen 518040Guangdong ProvinceChina School of Future Technology South China University of TechnologyGuangzhou 510641Guangdong ProvinceChina

AIM:To gain insights into the global research hotspots and trends of ***:Articles were downloaded from January 1,2013 to December 31,2022 from the Science Core Database website and were mainly statistically analyzed by bibliometrics ***:A total of 444 institutions in 87 countries published 4124 *** 2013 and 2022,China had the highest number of publications(n=1865)and the highest H-index(61).Sun Yat-sen University had the highest number of publications(n=229)and the highest H-index(33).Ophthalmology is the main category in related *** from 2020 to 2022 highlight keywords of options and reference,child health(pediatrics),myopic traction mechanism,public health,and machine learning,which represent research ***:Myopia has become a hot research *** and Chinese institutions have the strongest academic influence in the field from 2013 to *** main driver of myopic research is still medical or *** study highlights the importance of public health in addressing the global rise in myopia,especially its impact on children’s *** present,a unified theoretical system is still *** surgical and therapeutic solutions must be proposed for people with different characteristics to manage and intervene refractive *** addition,the benefits of artificial intelligence(AI)models are also reflected in disease monitoring and prediction.

关键词： bibliometric analysis myopia global trends

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

One stone two birds:electrochemical and colorimetric dual-mode biosensor based on copper peroxide/covalent organic framework nanocomposite for ultrasensentive norovirus detection

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Food Science and Human Wellness 2024年第2期13卷 920-931页

作者： Guobao Ning Quanmei Duan Huan Liang Huifang Liu Min Zhou Chunlan Chen chong zhang Hui Zhao Canpeng Li School of Chemical Science and Technology Yunnan UniversityKunming 650091China Laboratory for Conservation and Utilization of Bio-resource Yunnan UniversityKunming 650091China Kunming Customs Technology Center Kunming 650228China

Norovirus(NoV)is regarded as one of the most common causes of foodborne diarrhea in the *** is urgent to identify the pathogenic microorganism of the diarrhea in short *** this work,we developed an electrochemical and colorimetric dual-mode detection for NoV based on the excellent dual catalytic properties of copper peroxide/COF-NH_(2)nanocomposite(CuO_(2)@COF-NH_(2)).For the colorimetric detection,NoV can be directly detected by the naked eye based on CuO_(2)@COF-NH_(2)as a laccase-like nonazyme using“peptide-NoV-antibody”recognition *** colorimetric assay displayed a wide and quality linear detection range from 1 copy/mL to 5000 copies/mL of NoV with a low limit of detection(LOD)of 0.125 copy/*** the electrochemical detection of NoV,CuO_(2)@COF-NH_(2)showed an oxidation peak of copper ion from Cu^(+)to Cu^(2+)using“peptide-NoV-antibody”recognition *** electrochemical assay showed a linear detection range was 1-5000 copies/mL with a LOD of 0.152 copy/***'s worthy to note that this assay does not need other electrical signal molecule,which provide the stable and sensitive electrochemial detection for *** electrochemical and colorimetric dual-mode detection was used to detect NoV in foods and faceal samples,which has the potential for improving food safety and diagnosing of NoV-infected diarrhea.

关键词： Norovirus Specific peptides Electrochemical and colorimetric assay Dual-mode Copper peroxide/covalent organic framework

Intelligent diagnosis of retinal vein occlusion based on color fundus photographs

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International Journal of Ophthalmology(English edition) 2024年第1期17卷 1-6页

作者： Yu-Ke Ji Rong-Rong Hua Sha Liu Cui-Juan Xie Shao-chong zhang Wei-Hua Yang Eye Hospital Nanjing Medical UniversityNanjing 210000Jiangsu ProvinceChina College of Electronic Information Engineering Nanjing University of Aeronautics and AstronauticsNanjing 210000Jiangsu ProvinceChina Shenzhen Eye Institute Shenzhen Eye HospitalJinan UniversityShenzhen 518000Guangdong ProvinceChina

AIM:To develop an artificial intelligence(AI)diagnosis model based on deep learning(DL)algorithm to diagnose different types of retinal vein occlusion(RVO)by recognizing color fundus photographs(CFPs).METHODS:Totally 914 CFPs of healthy people and patients with RVO were collected as experimental data sets,and used to train,verify and test the diagnostic model of *** the images were divided into four categories[normal,central retinal vein occlusion(CRVO),branch retinal vein occlusion(BRVO),and macular retinal vein occlusion(MRVO)]by three fundus disease *** Transformer was used to build the RVO diagnosis model,and different types of RVO diagnosis experiments were *** model’s performance was compared to that of the ***:The accuracy of the model in the diagnosis of normal,CRVO,BRVO,and MRVO reached 1.000,0.978,0.957,and 0.978;the specificity reached 1.000,0.986,0.982,and 0.976;the sensitivity reached 1.000,0.955,0.917,and 1.000;the F1-Sore reached 1.000,0.9550.943,and 0.887 *** addition,the area under curve of normal,CRVO,BRVO,and MRVO diagnosed by the diagnostic model were 1.000,0.900,0.959 and 0.970,*** diagnostic results were highly consistent with those of fundus disease experts,and the diagnostic performance was ***:The diagnostic model developed in this study can well diagnose different types of RVO,effectively relieve the work pressure of clinicians,and provide help for the follow-up clinical diagnosis and treatment of RVO patients.

关键词： deep learning artificial intelligence Swin Transformer diagnostic model retinal vein occlusion color fundus photographs

Establishing the link between D-mannose and juvenile grass carp(Ctenopharyngodon idella):Improved growth and intestinal structure associated with endoplasmic reticulum stress,mitophagy,and apical junctional complexes

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Animal Nutrition 2024年第3期18卷 450-463页

作者： chong zhang Lin Feng Pei Wu Yang Liu Xiaowan Jin Hongmei Ren Hua Li Fali Wu Xiaoqiu Zhou Weidan Jiang Animal Nutrition Institute Sichuan Agricultural UniversityChengdu 611130China Fish Nutrition and Safety Production University Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengdu 611130China Key Laboratory of Animal Disease-Resistance Nutrition Ministry of EducationMinistry of Agriculture and Rural AffairsKey Laboratory of Sichuan ProvinceChengdu 611130China

D-mannose,essential for protein glycosylation,has been reported to have immunomodulatory effects and to maintain intestinal flora *** addition to evaluating growth performance,we examined the impact of D-mannose on the structure of epithelial cells and apical junction complexes in the animal *** 1800 grass carp(16.20±0.01 g)were randomly divided into six treatments with six replicates of 50 fish each and fed with six different levels of D-mannose(0.52,1.75,3.02,4.28,5.50 and 6.78 g/kg diet)for 70 *** study revealed that D-mannose increased feed intake(P 0.05).D-mannose supplementation at 1.75 g/kg increased crude protein content in fish and lipid production value(P<0.05).D-mannose supplementation at 4.28 g/kg increased intestinal length,intestinal weight and fold height of grass carp compared to the control group(P<0.05).This improvement may be attributed to the phosphomannose isomerase(PMI)-mediated enhancement of *** study found that D-mannose supplementation at 4.28 or 3.02 g/kg reduced serum diamine oxidase activity or D-lactate content(P<0.05)and improved cellular and intercellular structures for the first *** improvement of cellular redox homeostasis involves alleviating endoplasmic reticulum(ER)stress through the inositol-requiring enzyme 1(IRE1),RNA-dependent protein kinase-like ER kinase(PERK),and activating transcription factor 6(ATF6)signaling *** alleviation of ER stress may be linked to the phosphomannomutase(PMM)-mediated enhancement of protein *** addition,ubiquitin-dependent[PTEN-induced putative kinase 1(PINK1)/Parkin]and ubiquitin-independent[BCL2-interacting protein 3-like(BNIP3L),BCL2-interacting protein 3(BNIP3),and FUN14 domain containing 1(FUNDC1)]mitophagy may play a role in maintaining cellular redox *** enhancement of intercellular structures includes enhancing tight junction and adherent junction structures,which may be closely associated with the small Rho GTPase pr

关键词： Grass carp(Ctenopharyngodon idella) D-mannose Intestine structure Endoplasmic reticulum stress Mitophagy Apical junctional complex