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Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

Science China(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige Hu Michael H Perlin David Danko Jun Lu Manuela Oliveira Johannes Werner Maria M Zambrano Maria A Sierra Olayinka O Osuolale PawełŁabaj Nicolás Rascovan Nur Hazlin Hazrin-Chong Soojin Jang Haruo Suzuki Marina Nieto-Caballero Bharath Prithiviraj Patrick K H Lee Agnieszka Chmielarczyk Anna Różańska Yongxiang Zhao Lan Wang Christopher E Mason Tieliu Shi Center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Department of Biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill Cornell Medicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine New York 10065USA Department of Pulmonary Medicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em Saúde Universidade do PortoPorto 4050-290Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto 4200-465Portugal Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal High Performance and Cloud Computing Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany Corporación Corpogen Research Center Bogotá110311Colombia Applied Environmental Metagenomics and Infectious Diseases Research(AEMIDR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria Maopolska centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-Marseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Department of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of Environment and Information Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of Colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn College of the City University of New York Brooklyn 11210USA School of Energy and Environment City University of Hong KongHong Kong 999077China Department of Microbiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments.To address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based methodology.Our findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical conditions.We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel antibiotics.Our study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

关键词： urban environment metagenome antibiotic resistance resistance diversity biosynthetic gene clusters

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Terahertz time-domain spectroscopy and micro-cavity components for probing samples: a review

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Frontiers of Information Technology & Electronic Engineering 2019年第5期20卷 591-607页

作者： Lin CHEN Deng-gao LIAO Xu-guang GUO Jia-yu ZHAO Yi-ming ZHU Song-lin ZHUANG Shanghai Key Lab of Modern Optical System University of Shanghai for Science and Technology Shanghai 200093 China Shanghai Cooperation innovation centre of Terahertz Spectroscopy and Imaging Technology Shanghai 200093 China Cooperative innovation Center of Terahertz Science University of Electronic Science and Technology Chengdu 611731 China

We give a brief review of the developments in terahertz time-domain spectroscopy(THz-TDS) systems and microcavity components for probing samples in the University of Shanghai for Science and Technology. The broadband terahertz(THz) radiation sources based on GaAs m-i-n diodes have been investigated by applying high electric fields. Then, the free space THz-TDS and fiber-coupled THz-TDS systems produced in our lab and their applications in drug/cancer detection are introduced in detail. To further improve the signal-to-noise ratio(SNR) and enhance sensitivity, we introduce three general micro-cavity approaches to achieve tiny-volume sample detection, summarizing our previous results about their characteristics, performance, and potential applications.

关键词： Terahertz (THz) time-domain spectroscopy Micro-cavity Metal holes array Waveguide cavities Spoof localized surface plasmons (LSPs)

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Hotspots and frontiers of the relationship between gastric cancer and depression:A bibliometric study

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World Journal of Gastroenterology 2023年第46期29卷 6076-6088页

作者： Jia-Yu Liu Ji-Qi Zheng Cheng-Liang Yin Wen-Pei Tang Jian-Ning Zhang Department of Neurosurgery The First Medical CentreChinese PLA General HospitalBeijing 100853China School of Health Humanities Peking UniversityBeijing 100191China Medical Big Data Research Center Medical Innovation Research Division of Chinese PLA General HospitalBeijing 100853China National Engineering Research Center for Medical Big Data Application Technology Chinese PLA General HospitalBeijing 100853China

BACKGROUND A significant relationship between gastric cancer(GC)and depression has been found in the last 20 years.However,there is no comprehensive information that helps researchers find popular and potential research directions on GC and depression.AIM To determine the research status and hotspots by bibliometric analysis of relevant publications on the relationship between GC and depression.METHODS We used the Web of Science Core Collection to search and collate the literature on GC and depression from 2000 to 2022 on 31 May,2023.Then,visualization analysis was performed using VOSviewer software(version 1.6.19)and the Bibliometrix package in R software.RESULTS We retrieved 153 pertinent publications from 2000 to 2022.The annual publication count showed an overall upward trend.China had the most prominent publications and significant contributions to this field(n=64,41.83%).Before 2020,most studies focused on“the effect of GC on the development and progression of depression in patients.”The latest research trends indicate that“the effect of depression on the occurrence and development of GC and its mechanism”will receive more attention in the future.CONCLUSION The study of“the effect of depression on the occurrence and development of GC and its mechanism”has emerged as a novel research theme over the past two years,which may become a research hotspot in this field.This study provides new insights into the hotpots and frontiers of the relationship between GC and depression,potentially guiding researchers toward hot research topics in the future.

关键词： Gastric cancer Depression Bibliometric analysis Visualization Web of Science

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Antibody variable region engineering for improving cancer immunotherapy

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cancer Communications 2022年第9期42卷 804-827页

作者： Hantao Lou Xuetao Cao Ludwig Institute of cancer Research University of OxfordOxford OX37DRUK Chinese Academy for Medical Sciences Oxford Institute Nuffield Department of MedicineUniversity of OxfordOxford OX37FZUK Department of Immunology Centre for ImmunotherapyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesBeijing 100005P.R.China

The efficacy and specificity of conventional monoclonal antibody(mAb)drugs in the clinic require further improvement.Currently,the development and application of novel antibody formats for improving cancer immunotherapy have attracted much attention.Variable region-retaining antibody fragments,such as antigen-binding fragment(Fab),single-chain variable fragment(scFv),bispecific antibody,and bi/trispecific cell engagers,are engineered with humanization,multivalent antibody construction,affinity optimization and antibody masking for targeting tumor cells and killer cells to improve antibody-based therapy potency,efficacy and specificity.In this review,we summarize the application of antibody variable region engineering and discuss the future direction of antibody engineering for improving cancer therapies.

关键词： antibody engineering bi/trispecific killer engager cancer immunotherapy chimeric antigen receptor-T(CAR-T)cell nanobody natural killer(NK)cell scFv

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Engineering osteoblastic metastases to delineate the adaptive response of androgen-deprived prostate cancer in the bone metastatic microenvironment

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Bone Research 2019年第2期7卷 157-170页

作者： Nathalie Bock Ali Shokoohmand Thomas Kryza Joan Rohl Jonelle Meijer Phong A. Tran Colleen C. Nelson Judith A. Clements Dietmar W. Hutmacher School of Biomedical Sciences Faculty of Health and Australian Prostate Cancer Research Centre (APCRC-Q)Institute of Health and Biomedical Innovation (IHBI)Queensland University of Technology (QUT)BrisbaneQLD 4000Australia Translational Research Institute (TRI) WoolloongabbaQLD 4102Australia centre in Regenerative Medicine QUTKelvin GroveQLD 4059Australia Bone and Joint Disorders Program School of ChemistryPhysics and Mechanical EngineeringScience and Engineering Faculty (SEF)QUTBrisbaneQLD 4000Australia Australian Research Council (ARC) Training centre in Additive Biomanufacturing QUTKelvin GroveQLD 4059Australia

While stromal interactions are essential in cancer adaptation to hormonal therapies,the effects of bone stroma and androgen deprivation on cancer progression in bone are poorly understood.Here,we tissue-engineered and validated an in vitro microtissue model of osteoblastic bone metastases,and used it to study the effects of androgen deprivation in this microenvironment.The model was established by culturing primary human osteoprogenitor cells on melt electrowritten polymer scaffolds,leading to a mineralized osteoblast-derived microtissue containing,in a 3D setting,viable osteoblastic cells,osteocytic cells,and appropriate expression of osteoblast/osteocyte-derived mRNA and proteins,and mineral content.Direct co-culture of androgen receptordependent/ independent cell lines (LNCaP,C4-2B,and PC3) led cancer cells to display functional and molecular features as observed in vivo.Co-cultured cancer cells showed increased affinity to the microtissues,as a function of their bone metastatic potential.Cocultures led to alkaline phosphatase and collagen-I upregulation and sclerostin downregulation,consistent with the clinical marker profile of osteoblastic bone metastases.LNCaP showed a significant adaptive response under androgen deprivation in the microtissues,with the notable appearance of neuroendocrine transdifferentiation features and increased expression of related markers (dopa decarboxylase,enolase 2).Androgen deprivation affected the biology of the metastatic microenvironment with stronger upregulation of androgen receptor,alkaline phosphatase,and dopa decarboxylase,as seen in the transition towards resistance.The unique microtissues engineered here represent a substantial asset to determine the involvement of the human bone microenvironment in prostate cancer progression and response to a therapeutic context in this microenvironment.

关键词： Engineering osteoblastic metastases the adaptive response metastatic microenvironment

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Young Yum pill inhibits inflammatory mediators and nuclear factor-kappa B signaling in lipopolysaccharide-stimulated RAW 264.7 macrophages

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Journal of Traditional Chinese Medicine 2019年第5期39卷 624-631页

作者： Yin Chengle Muhammad Jahangir Hossen Anfernee Kai-Wing Tse Su Tao Fu Xiuqiong Li Ting Guo Hui Zhu Peili Li Junkui Chou Jiyao Wang Yaping Yu Zhiling centre for cancer and Inflammation Research School of Chinese Medicine Hong Kong Baptist UniversityHong KongChina Research and Development centre for Natural Health Products Hong Kong Baptist University Shenzhen Research Institute and Continuing EducationShenzhen 518057China centre for cancer and Inflammation Research School of Chinese MedicineHong Kong Baptist University Hong KongChina

OBJECTIVE: To investigate the effect of Young Yum pill (YYP) on inflammatory mediators in cultured RAW 264.7 cells and elucidate the nuclear factor- kappa B (NF-κB)-related mechanism behind the action. METHODS: YYP was extracted with 95% ethanol Lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages were used to evaluate the effect of YYP on inflammatory mediators. Production of nitric oxide (NO) and prostaglandin E2 (PGE2) were measured by Griess test and enzyme-linked immunosorbent assay, respectively. The levels of genes and proteins involved in the generation of inflammatory mediators were examined using real-time polymerase chain reaction and Western blotting, respectively. RESULTS: YYP dose-dependently suppressed LPS-induced production of NO, PGE2 and tumor necrosis factor-α(TNF-α), and elevation of mRNA and protein levels of inducible NO synthase and cyclooxygenase- 2 in RAW 264.7 macrophages. These observations were associated with decreased NF-κB p65 phosphorylation and nuclear localization, enhanced Akt (protein kinase B) phosphorylation, as well as reduced inhibitor of κB (IκB)α degradation and IκB kinase α/β phosphorylation. CONCLUSION: The present study demonstrated an inhibitory effect of YYP on the NF-κB-regulated inflammatory mediators NO, PGE2 and TNF-α in LPS-stimulated RAW 264.7 macrophages, providing a pharmacological basis for the use of YYP in treating inflammatory disorders.

关键词： Inflammation NF-kappa B Lipopolysaccharides RAW 264.7 cells Macrophages Young Yum pill

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Low-Cost and Scalable Platform with Multiplexed Microwell Array Biochip for Rapid Diagnosis of COVID-19

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Research 2021年第1期2021卷 94-102页

作者： Yang Wang Kaiju Li Gaolian Xu Chuan Chen Guiqin Song Zaizai Dong Long Lin Yu Wang Zhiyong Xu Mingxia Yu Xinge Yu Binwu Ying Yubo Fan Lingqian Chang Jia Geng Beijing Advanced innovation Center for Biomedical Engineering Key Laboratory for Biomechanics and MechanobiologySchool of Biological Science and Medical EngineeringBeihang UniversityBeijing 100083China Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation CenterChengdu 610041China Nano Biomedical Research centre School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai 200030China Wuhan Chain Medical Labs WuhanHubei 430011China Department of Clinical Laboratory Zhongnan Hospital of Wuhan UniversityWuhanHubei 430071China Department of Biomedical Engineering City University of Hong KongChina

Sensitive detection of SARS-CoV-2 is of great importance for inhibiting the current pandemic of COVID-19.Here,we report a simple yet efficient platform integrating a portable and low-cost custom-made detector and a novel microwell array biochip for rapid and accurate detection of SARS-CoV-2.The instrument exhibits expedited amplification speed that enables colorimetric read-out within 25 minutes.A polymeric chip with a laser-engraved microwell array was developed to process the reaction between the primers and the respiratory swab RNA extracts,based on reverse transcriptase loop-mediated isothermal amplification(RT-LAMP).To achieve clinically acceptable performance,we synthesized a group of six primers to identify the conserved regions of the ORF1ab gene of SARS-CoV-2.Clinical trials were conducted with 87 PCR-positive and 43 PCRnegative patient samples.The platform demonstrated both high sensitivity(95.40%)and high specificity(95.35%),showing potentials for rapid and user-friendly diagnosis of COVID-19 among many other infectious pathogens.

关键词： instrument diagnosis specificity

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Gene editing applications to modulate crop flowering time and seed dormancy

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aBIOTECH 2020年第4期1卷 233-245页

作者： Olena Kishchenko Yuzhen Zhou Satyvaldy Jatayev Yuri Shavrukov Nikolai Borisjuk Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake School of Life SciencesHuaiyin Normal UniversityHuai’anChina Jiangsu Collaborative innovation centre of Regional Modern Agriculture and Environmental Protection Huaiyin Normal UniversityHuai’anChina Institute of Cell Biology and Genetic Engineering NAS of UkraineKievUkraine Faculty of Agronomy S.Seifullin Kazakh AgroTechnical UniversityNur-SultanKazakhstan College of Science and Engineering Biological SciencesFlinders UniversityAdelaideAustralia

Gene editing technologies such as CRISPR/Cas9 have been used to improve many agricultural traits,from disease resistance to grain quality.Now,emerging research has used CRISPR/Cas9 and other gene editing technologies to target plant reproduction,including major areas such as flowering time and seed dormancy.Traits related to these areas have important implications for agriculture,as manipulation of flowering time has multiple applications,including tailoring crops for regional adaptation and improving yield.Moreover,understanding seed dormancy will enable approaches to improve germination upon planting and prevent pre-harvest sprouting.Here,we summarize trends and recent advances in using gene editing to gain a better understanding of plant reproduction and apply the resulting information for crop improvement.

关键词： Genome editing CRISPR/Cas9 Flowering time Florigen Seed dormancy

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Surveillance of patients following surgery with curative intent for colorectal cancer

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World Journal of Gastroenterology 2007年第28期13卷 3816-3823页

作者： Steven Gan Katherine Wilson Paul Hollington Department of Surgery St George HospitalGray StreetKogarahNSW 2217Australia Department of Surgery Flinders Medical CentreFlinders DriveBedford Park 5042AdelaideAustralia

Surveillance after resection of colorectal cancer with curative intent is an important component of post- operative care. Clinical review, imaging, colonoscopy, and cost to the community are among significant issues to consider in planning a surveillance regime. This review aims to identify the available evidence for the use of surveillance and its individual components. The literature pertaining to follow-up of patients following potentially curative surgery for colorectal cancer was reviewed in order to formulate a summary of the wide range of clinical practice. There is evidence of improved survival of patients undergoing more intense follow-up compared with those having minimal surveillance, with an estimated overall 5-year gain of up to 10%. The efficacy of individual components of follow-up regimes remains unclear, but an overall package of 'intensive' follow-up including clinical review, liver imaging, and colonoscopy appears to be of benefit. It is cost-effective and can be specialist or community-based.

关键词：结肠直肠癌肿瘤学结肠镜检查手术监督

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Optimal sequencing of chemotherapy with chemoradiotherapy based on TNM stage classification and EBV DNA in locoregionally advanced nasopharyngeal carcinoma

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cancer Communications 2019年第1期39卷 576-578页

作者： Li-Ting Liu Melvin L.K.Chua Yungan Tao Lin-Quan Tang Hai-Qiang Mai Sun Yat-sen University cancer Center State Key Laboratory of Oncology in South China Collaborative innovation Center for cancer Medicine Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou 510060GuangdongP.R.China Department of Nasopharyngeal Carcinoma Sun Yat-sen University Cancer Center651 Dongfeng Road EastGuangzhou 510060GuangdongP.R.China Divisions of Radiation Oncology and Medical Sciences National Cancer Centre SingaporeSingapore 169610Singapore Oncology Academic Programme Duke-National University of Singapore Medical SchoolSingapore 169857Singapore.5 Institute Gustave-Roussy94800 VillejuifFrance

Main text In the past decades,there have been several studies con-cerning the efficacy of sequencing of chemotherapy on disease control and survival in locoregionally advanced(LA)nasopharyngeal carcinoma(NPC).The addition of concurrent cisplatin to radiotherapy has demonstrated survival improvements that are attributable to both dis-tant metastasis and locoregional control.Specific to the latter,the advent of intensity-modulated radiotherapy has resulted in superior tumor control given the bet-ter dosimetry compared to conventional techniques[1].However,distant recurrence still occurs in 20-30%patients and accounts for the main cause of death.To address this,several groups have explored the advantages of adding neoadjuvant chemotherapy(NACT)or adju-vant chemotherapy(ACT)to the backbone of concurrent chemoradiotherapy(CCRT).

关键词： chemotherapy nasopharyngeal metastasis

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