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Genome-scale metabolic models applied for human health and biopharmaceutical engineering

Quantitative Biology 2023年第4期11卷 363-375页

作者： Feiran Li Yu Chen Johan Gustafsson Hao Wang YiWang Chong Zhang Xinhui Xing nstitute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina Key Laboratory of Quantitative Synthetic Biology Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina Department of Biology and Biological Engineering Chalmers University of TechnologyGothenburgSweden Key Laboratory for Industrial Biocatalysis Ministry of EducationInstitute of Biochemical EngineeringDepartment of Chemical EngineeringTsinghua University BeijingChina Center for Synthetic and Systems Biology Tsinghua UniversityBejingChina institute of biomedical Health Technology and Engineering Shenzhen Bay LaboratoryShenzhenChina

Over the last 15 years,genome-scale metabolic models(GEMs)have been reconstructed for human and model animals,such as mouse and rat,to systematically understand metabolism,simulate multicellular or multi-tissue interplay,understand human diseases,and guide cell factory design for biopharmaceutical protein production.Here,we describe how metabolic networks can be represented using stoichiometric matrices and well-defined constraints for flux simulation.Then,we review the history of GEM development for quantitative understanding of Homo sapiens and other relevant animals,together with their applications.We describe how model develops from H.sapiens to other animals and from generic purpose to precise context-specific simulation.The progress of GEMs for animals greatly expand our systematic understanding of metabolism in human and related animals.We discuss the difficulties and present perspectives on the GEM development and the quest to integrate more biological processes and omics data for future research and translation.We truly hope that this review can inspire new models developed for other mammalian organisms and generate new algorithms for integrating big data to conduct more in-depth analysis to further make progress on human health and biopharmaceutical engineering.

关键词： constraint-based modeling disease genome-scale metabolicmodel metabolism

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THz Wave Detection of Gap Defects Based on a Convolutional Neural Network Improved by a Residual Shrinkage Network

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CSEE Journal of Power and Energy Systems 2023年第3期9卷 1078-1089页

作者： Zhonghao Zhang Guozheng Peng Yuanpeng Tan Tianjiao Pu Liming Wang China Electric Power research institute Tsinghua shenzhen international Gradual School Shenzhen 518055China

Internal air gap is a serious type of defect in the insulation equipment,which threatens the safe operation of the power grid.In order to diagnose the position and thickness of the internal air gap,this paper proposes a terahertz wave detection method based on wavelet analysis and a CNN(convolution neural network)model.According to the time-frequency characteristics of the wavelet cluster,the calculation method of air gap depth is proposed.To determine the thickness of the internal air gap,the performances of several classification methods,such as waveform feature analysis,Bayes,MLP(Multi-layer Perceptron),SVM(Support Vector Machine)and CNN are compared.The results show that the CNN modified by a residual shrinkage network and SVM(CNN-RSN-SVM)has the best performance.By adjusting the parameters,the classification accuracy of the CNN-RSN-SVM model can be elevated to 98.91%.Furthermore,the 3D imaging method of air gap defect based on wavelet analysis and CNNRSN-SVM classification model is formed.

关键词： Convolutional neural network defect detection insulation equipment terahertz wave

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Injectable baicalin/F127 hydrogel with antioxidant activity for enhanced wound healing

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Chinese Chemical Letters 2020年第7期31卷 1817-1821页

作者： Guiting Liu Ziting Bao Jun Wu Key Laboratory of Sensing Technology and biomedical Instrument of Guangdong Province School of Biomedical Engineering.Sun Yat-sen UniversityGuangzhou 510006China research institute of Sun Yat-sen University in shenzhen Shenzhen 518057China

Baicalin,extracted from traditional Chinese medicine Scutellaria baicalensis Georg,possesses multiple pharmacological activities and has great potential for chronic skin wound repair.However,the poor solubility and lack of suitable vehicles greatly limit its further application.Herein,we proposed a convenient and robust strategy,employing PBS solution as solvent,to enhance the solubility of baicalin.Furthermore,we constructed injectable baicalin/F127 hydrogels to study their application in skin wound treatment.The composition and temperature sensitivity of baicalin/Pluronic®F-127 hydrogels were confirmed by FTIR and rheological testing,respectively.In vitro release measurement indicated that the first order model was best fitted with the release profile of baicalin from hydrogel matrix.Besides,MTT assay,AO/EO staining assay as well as hemolytic activity test revealed the excellent cytocompatibility of baicalin/F127 hydrogels.Antioxidant activity assay demonstrated the cytoprotective activity of baicalin/F127 hydrogels against reactive oxygen species(ROS).Furthermore,the in vivo experiments exhibited the ability of baicalin/F127 hydrogel to accelerate wound healing.In conclusion,this novel injectable baicalin/F127 hydrogel should have bright application for chronic wound treatment.

关键词： Wound healing Hydrogel Baicalin Antioxidant Injectable

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VTwins:有限宏基因组样本推断疾病致病微生物特征

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Science Bulletin 2023年第22期68卷 2806-2816,M0006页

作者：孟庆仁周茜时硕肖景发马勤于军陈军康禹 CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences and China National Center for BioinformationBeijing 100101China School of Medicine Southern University of Science and TechnologyShenzhen 518055China National Clinical research Center for Infectious Diseases The Third People’s Hospital of ShenzhenThe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen 518100China international Cancer Center Shenzhen University Medical SchoolShenzhen 518055China Department of biomedical Informatics The Ohio State UniversityColumbus OH 43210USA University of Chinese Academy of Sciences Beijing 100190China

从高维、高变宏基因组数据中挖掘与疾病强关联的微生物特征是人体微生态研究的一大难题.受遗传学双生子研究的启发,本文开发了一种新型微生物特征挖掘算法——虚拟双胞胎(VTwins)算法.该算法通过将原始队列转化为具有相近的微生物组特... 详细信息

从高维、高变宏基因组数据中挖掘与疾病强关联的微生物特征是人体微生态研究的一大难题.受遗传学双生子研究的启发,本文开发了一种新型微生物特征挖掘算法——虚拟双胞胎(VTwins)算法.该算法通过将原始队列转化为具有相近的微生物组特征但分组不同的配对样本形成的配对队列来消除混淆因素的影响.结果显示,VTwins在识别因果特征的敏感性方面超过传统方法,并且将所需样本规模减小10倍,就可鉴定与疾病相关的微生物或代谢途径,并通过模拟和真实数据进行验证.与其他16种同类软件进行的基准测试进一步验证了VTwins在处理高维数据和挖掘宏基因组研究中的因果关系的能力和适用性.总体而言,VTwins可直接且强大地处理高变、高维数据,在宏基因组和其他组学数据的因果关系挖掘方面具有广阔的应用前景.VTwins的开源访问网址为https://***/mengqingren/VTwins.

关键词： Causality High-dimensional data Metagenome Differential abundance Paired cohort

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Applications and prospects of cryo-EM in drug discovery

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Military Medical research 2023年第6期10卷 848-861页

作者： Kong-Fu Zhu Chuang Yuan Yong-Ming Du Kai-Lei Sun Xiao-Kang Zhang Horst Vogel Xu-Dong Jia Yuan-Zhu Gao Qin-Fen Zhang Da-Ping Wang Hua-Wei Zhang Department of biomedical Engineering Southern University of Science and TechnologyShenzhen 518055GuangdongChina Department of Biochemistry and Molecular Biology School of Basic Medical SciencesPeking UniversityBeijing 100191China Department of Structural Biology St.Jude Children’s Research HospitalMemphisTN 38105USA Center for Protein Science and Crystallography School of Life SciencesFaculty of ScienceChinese University of Hong KongHong Kong 999077China Interdisciplinary Center for Brain Information the Brain Cognition and Brain Disease InstituteShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055GuangdongChina Faculty of Life and Health Sciences Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055GuangdongChina shenzhen-Hong Kong institute of Brain Science-shenzhen Fundamental research Institutions Shenzhen 518055GuangdongChina shenzhen institute of Advanced Technology Chinese Academy of SciencesShenzhen 518055GuangdongChina State Key Lab for Biocontrol School of Life SciencesSun Yat-Sen UniversityGuangzhou 510275China Cryo‑EM Facility Center Southern University of Science and TechnologyShenzhen 518055GuangdongChina Department of Orthopedics Shenzhen Intelligent Orthopaedics and Biomedical Innovation PlatformGuangdong Provincial Research Center for Artifcial Intelligence and Digital Orthopedic TechnologyShenzhen Second People’s HospitalThe First Affiliated Hospital of Shenzhen UniversityShenzhen 518000GuangdongChina Guangdong Provincial Key Laboratory of Advanced Biomaterials Southern University of Science and TechnologyShenzhen 518055GuangdongChina

Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time-and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy(cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence(AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of mediumresolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.

关键词： Cryo-electron microscopy(cryo-EM) Drug discovery Structure-based drug design Fragment-based drug discovery Proteolysis targeting chimeras Drug repurposing Artificial intelligence(AI)

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Advances in antioxidative nanozymes for treating ischemic stroke

再生工程(英文)

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再生工程(英文) 2023年第1期4卷 95-102页

作者： Jingyang Shan Xia Liu Xiuping Li Yunru Yu Bin Kong Lijie Ren Department of Neurology Shenzhen Institute of Translational MedicineThe First Affiliated Hospital of Shenzhen UniversityShenzhen Second People’s HospitalGuangdong Key Laboratory for Biomedical Measurements and Ultrasound ImagingNational-Regional Key Technology Engineering Laboratory for Medical UltrasoundSchool of Biomedical EngineeringShenzhen University Medical SchoolShenzhen 518060China Pharmaceutical Sciences Laboratory Åbo Akademi UniversityTurku 20520Finland

Ischemic stroke is one of the most common public diseases that increase mortality.In the ischemic brain,blood flow restoration can cause the generation of excess reactive oxygen species(ROS).Endogenous anti-oxidases in the living system,including catalase(CAT)and superoxide dismutase(SOD),can consume the excess ROS by catalysis to regulate inflammation.However,these natural enzymes are difficult to be widely used in the treatment of stroke.Taking advantages of high stability,low cost,and long-term storage,antioxidative nanozymes-mediated treatments have been proven as a promising method against ischemic stroke.To highlight the progress,we summarize the advances in nanozymes with the antioxidative ability for treating ischemic stroke.It is believed that such a promising therapeutic strategy of antioxidative nanozymes will significantly contribute to the field of ischemic stroke.We expect that antioxidative nanozymes will play significant roles in both basic research and clinical applications.

关键词： Nanozymes Reactive oxygen species Antioxidative ability Blood brain barrier Ischemic stroke

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Progress and perspectives of in situ polymerization method for lithium-based batteries

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Interdisciplinary Materials 2023年第4期2卷 609-634页

作者： Guanyou Xiao Hao Xu Chen Bai Ming Liu Yan-Bing He institute of Materials research(IMR) Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina

The application of lithium-based batteries is challenged by the safety issues of leakage and flammability of liquid electrolytes.Polymer electrolytes(PEs)can address issues to promote the practical use of lithium metal batteries.However,the traditional preparation of PEs such as the solution-casting method requires a complicated preparation process,especially resulting in side solvents evaporation issues.The large thickness of traditional PEs reduces the energy density of the battery and increases the transport bottlenecks of lithium-ion.Meanwhile,it is difficult to fill the voids of electrodes to achieve good contact between electrolyte and electrode.In situ polymerization appears as a facile method to prepare PEs possessing excellent interfacial compatibility with electrodes.Thus,thin and uniform electrolytes can be obtained.The interfacial impedance can be reduced,and the lithium-ion transport throughput at the interface can be increased.The typical in situ polymerization process is to implant a precursor solution containing monomers into the cell and then in situ solidify the precursor under specific initiating conditions,and has been widely applied for the preparation of PEs and battery assembly.In this review,we focus on the preparation and application of in situ polymerization method in gel polymer electrolytes,solid polymer electrolytes,and composite polymer electrolytes,in which different kinds of monomers and reactions for in situ polymerization are discussed.In addition,the various compositions and structures of inorganic fillers,and their effects on the electrochemical properties are summarized.Finally,challenges and perspectives for the practical application of in situ polymerization methods in solid-state lithium-based batteries are reviewed.

关键词： in situ polymerization interface compatibility lithium-based batteries polymer electrolytes

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Black phosphorus-based photothermal therapy with aCD47-mediated immune checkpoint blockade for enhanced cancer immunotherapy

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Light(Science & Applications) 2020年第1期9卷 479-493页

作者： Zhongjian Xie Minhua Peng Ruitao Lu Xiangying Meng Weiyuan Liang Zhongjun Li Meng Qiu Bin Zhang Guohui Nie Ni Xie Han Zhang Paras N.Prasad Shenzhen International Institute for Biomedical Research Shenzhen 518116 GuangdongPR China shenzhen institutes of Advanced Technology Chinese Academy of SciencesShenzhen 518055 GuangdongPR China School of Basic Medical Sciences Guangzhou Medical UniversityGuangzhou 511436 GuangdongPR China Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province Institute of Microscale Optoelectronicsand Otolaryngology Department and Biobank of the First Affiliated HospitalShenzhen Second People’s HospitalHealth Science CenterShenzhen UniversityShenzhen 518060PR China Key Laboratory of Marine Chemistry Theory and Technology(Ocean University of China) Ministry of EducationQingdao 266100PR China Department of Chemistry Institute for LasersPhotonicsand BiophotonicsUniversity at BuffaloStateUniversity of New YorkBuffaloNYUSA

Here,we describe a combination strategy of black phosphorus(BP)-based photothermal therapy together with anti-CD47 antibody(aCD47)-based immunotherapy to synergistically enhance cancer treatment.Tumour resistance to immune checkpoint blockades in most cancers due to immune escape from host surveillance,along with the initiation of metastasis through immunosuppressive cells in the tumour microenvironment,remains a significant challenge for cancer immunotherapy.aCD47,an agent for CD47/SIRPαaxis blockade,induces modest phagocytic activity and a low response rate for monotherapy,resulting in failures in clinical trials.We showed that BP-mediated ablation of tumours through photothermal effects could serve as an effective strategy for specific immunological stimulation,improving the inherently poor immunogenicity of tumours,which is particularly useful for enhancing cancer immunotherapy.BP in combination with aCD47 blockade activates both innate and adaptive immunities and promotes local and systemic anticancer immune responses,thus offering a synergistically enhanced effect in suppression of tumour progression and in inducing abscopal effects for inhibition of metastatic cancers.Our combination strategy provides a promising platform in which photothermal agents could help to enhance the therapeutic efficacy of immunotherapy.

关键词： immunotherapy cancer mediated

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Engineering biocompatible TeSex nano-alloys as a versatile theranostic nanoplatform

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National Science Review 2021年第6期8卷 148-159页

作者： Xiang Ling Zhaokui Jin Qi Jiang Xiaotao Wang Bin Wei Zhongchang Wang Yangsen Xu Tianye Cao Jonathan W.Engle Weibo Cai Chenliang Su Qianjun He international Collaborative Laboratory of 2D Materials for Optoelectronic Science & Technology Engineering Technology Research Center for 2D Materials Information Functional Devices and Systems of Guangdong ProvinceInstitute of Microscale OptoelectronicsShenzhen University Guangdong Provincial Key Laboratory of biomedical Measurements and Ultrasound Imaging National-Regional Key Technology Engineering Laboratory for Medical UltrasoundSchool of Biomedical EngineeringHealth Science CenterShenzhen University Department of Quantum and Energy Materials International Iberian Nanotechnology Laboratory (INL) Departments of Radiology and Medical Physics University of Wisconsin-Madison

Photothermal nanotheranostics, especially in the near infrared II(NIR-II) region, exhibits a great potential in precision and personalized medicine, owing to high tissue penetration of NIR-II light.NIR-II-photothermal nanoplatforms with high biocompatibility as well as high photothermal effect are urgently needed but rarely reported so far. Te nanomaterials possess high absorbance to NIR-II light but also exhibit high cytotoxicity, impeding their biomedical applications. In this work, the controllable incorporation of biocompatible Se into the lattice of Te nanostructures is proposed to intrinsically tune their inherent cytotoxicity and enhance their biocompatibility, developing TeSexnano-alloys as a new kind of theranostic nanoplatform. We have uncovered that the cytotoxicity of Te nanomaterials primarily derives from irreversible oxidation stress and intracellular imbalance of organization and energy, and can be eliminated by incorporating a moderate proportion of Se(x = 0.43). We have also discovered that the as-prepared TeSexnano-alloys have extraordinarily high NIR-II-photothermal conversion efficiency(77.2%),64Cu coordination and computed tomography contrast capabilities, enabling high-efficacy multimodal photothermal/photoacoustic/positron emission tomography/computed tomography imaging-guided NIR-II-photothermal therapy of cancer. The proposed nano-alloying strategy provides a new route to improve the biocompatibility of biomedical nanoplatforms and endow them with versatile theranostic functions.

关键词： nanomedicine nano-alloys photothermal therapy cancer nanotheranostics biomedical imaging

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Recent advances in the development of nanomedicines for the treatment of ischemic stroke

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Bioactive Materials 2021年第9期6卷 2854-2869页

作者： Xing Tian Taojian Fan Wentian Zhao Ghulam Abbas Bo Han Ke Zhang Nan Li Ning Liu Weiyuan Liang Hao Huang Wen Chen Bing Wang Zhongjian Xie Key Laboratory of Xinjiang Phytomedicine Resource and Utilization Ministry of EducationCollege of PharmacyShihezi UniversityShihezi832002China institute of Microscale Optoelectronics Collaborative Innovation Centre for Optoelectronic Science&TechnologyKey Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Physics and Optoelectronic EngineeringShenzhen Key Laboratory of Micro-Nano Photonic Information TechnologyGuangdong Laboratory of Artificial Intelligence and Digital Economy(SZ)Shenzhen UniversityShenzhen518060PR China Shenzhen International Institute for Biomedical Research 518116ShenzhenGuangdongChina

Ischemic stroke is still a serious threat to human life and health,but there are few therapeutic options available to treat stroke because of limited blood-brain penetration.The development of nanotechnology may overcome some of the problems related to traditional drug development.In this review,we focus on the potential applications of nanotechnology in stroke.First,we will discuss the main molecular pathological mechanisms of ischemic stroke to develop a targeted strategy.Second,considering the important role of the blood-brain barrier in stroke treatment,we also delve mechanisms by which the blood-brain barrier protects the brain,and the reasons why the therapeutics must pass through the blood-brain barrier to achieve efficacy.Lastly,we provide a comprehensive review related to the application of nanomaterials to treat stroke,including liposomes,polymers,metal nanoparticles,carbon nanotubes,graphene,black phosphorus,hydrogels and dendrimers.To conclude,we will summarize the challenges and future prospects of nanomedicine-based stroke treatments.

关键词： Stroke Nanomaterials Blood-brain barrier

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