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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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Warming‑induced changes of broccoli head to cauliflower‑like curd in Brassica oleracea are regulated by DNA methylation as revealed by methylome and transcriptome co‑profiling

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Molecular Horticulture 2022年第1期2卷 318-332页

作者： Zilei Yao Lu Yuan Ke Liu Tingjin Wang Bin Liu Yan Zhao Susheng Gan Liping Chen department of Horticulture College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA present address:College of Agronomy and biotechnology Yunnan Agricultural UniversityKunming 650201China

Increasingly warming temperature impacts on all aspects of growth and development in plants.Flower development is a complex process that is very sensitive to ambient temperature,and warming temperatures often lead to abnor-mal flower development and remarkably reduce the quality and yield of inflorescent vegetables and many other crops,which can be exemplified by Brassica oleracea cv.Green Harmony F1,a broccoli cultivar,whose floral develop-ment is ceased at inflorescence meristem(at 28℃)or floral primordium stage(at 22℃),forming a cauliflower-like curd(28℃)or intermediate curd(22℃)instead of normal broccoli head at 16℃.However,the underlying molecular regulatory mechanisms are not well understood.Here we report that warming temperature(28℃ or 22℃)induced hypermethylation of the genome,especially the promoter regions of such sets of genes as ribosome biogenesis-related and others,leading to the suppression of the apex-highly-expressed distinctive genes,subsequently resulting in the abnormal floral development,as revealed by methylome and transcriptome co-profiling.The regulation of warming-induced abnormal floral development in broccoli was further verified by the fact that the DNA methylation inhibitor 5-azacytidine(5-azaC)released the expression of genes from the warming temperature-induced suppres-sion,and restored the broccoli development to normalcy at warming temperature.The research provided new approaches to breeding broccoli and other crops for growing in wider or warmer temperature zones.

关键词： Brassica oleracea DNA methylation Floral development cessation Global warming Heat stress

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The boys are back in town: Rethinking the function of ribosomal DNA repeats in the genomic era

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Molecular Plant 2023年第3期16卷 514-516页

作者： Francesca B.Lopez Peter C.McKeown Antoine Fort Galina Brychkova Charles Spillane Genetics and biotechnology Laboratory Plant&AgriBiosciences Research Centre(PABC)Ryan InstituteUniversity of GalwayH91 REW4 GalwayIreland present address:department of Plant Biology and Genome Center University of CaliforniaDavisUC Davis Genome CenterDavisCA 95616USA

Next-generation sequencing technological advances,affording high-throughput,scalable,and fast assemblies,have enabled genome editing techniques that allow us to remove,insert,and modify genes for rapid and precise fun... 详细信息

关键词： remove precise function

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Britanin–a beacon of hope against gastrointestinal tumors?

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World Journal of Clinical Oncology 2024年第4期15卷 523-530页

作者： Agnieszka Kajdanek Damian Kołat Lin-Yong Zhao Mateusz Kciuk Zbigniew Pasieka Żaneta Kałuzińska-Kołat department of Biomedicine and Experimental Surgery Medical University of LodzLodz 90-136LodzkiePoland department of Functional Genomics Medical University of LodzLodz 90-752LodzkiePoland department of General Surgery&Laboratory of Gastric Cancer State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengdu 610041Sichuan ProvinceChina Gastric Cancer Center West China HospitalSichuan UniversityChengdu 610041Sichuan ProvinceChina department of Molecular biotechnology and Genetics University of LodzLodz 90-237LodzkiePoland

Britanin is a bioactive sesquiterpene lactone known for its potent anti-inflammatory and anti-oxidant properties.It also exhibits significant anti-tumor activity,suppressing tumor growth in vitro and in vivo.The current body of research on Britanin includes thirty papers predominantly related to neoplasms,the majority of which are gastrointestinal tumors that have not been summarized before.To drive academic debate,the present paper reviews the available research on Britanin in gastrointestinal tumors.It also outlines novel research directions using data not directly concerned with the digestive system,but which could be adopted in future gastrointestinal research.Britanin was found to counteract liver,colorectal,pancreatic,and gastric tumors,by regulating proliferation,apoptosis,autophagy,immune response,migration,and angiogenesis.As confirmed in pancreatic,gastric,and liver cancer,its most commonly noted molecular effects include nuclear factor kappa B and B-cell lymphoma 2 downregulation,as well as Bcl-2-associated X protein upregulation.Moreover,it has been found to induce the Akt kinase and Forkhead box O1 axis,activate the AMP-activated protein kinase pathway,elevate interleukin-2 and peroxisome proliferator-activated receptor-γlevels,reduce interleukin-10,as well as downregulate matrix metalloproteinase-9,Twist family bHLH transcription factor 1,and cyclooxygenase-2.It also inhibits Myc–HIF1αinteraction and programmed death ligand 1 transcription by interrupting the Ras/RAF/MEK/ERK pathway and mTOR/P70S6K/4EBP1 signaling.Future research should aim to unravel the link between Britanin and acetylcholinesterase,mast cells,osteolysis,and ischemia,as compelling data have been provided by studies outside the gastrointestinal context.Since the cytotoxicity of Britanin on noncancerous cells is significantly lower than that on tumor cells,while still being effective against the latter,further in-depth studies with the use of animal models are merited.The compound exhibits pleiotropic biological activity and offers

关键词： Britanin Sesquiterpene lactones Chemotherapeutics Gastrointestinal tumors In vitro In vivo

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An integrative protocol for one‑step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data

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Marine Life Science & Technology 2023年第4期5卷 564-572页

作者： Jiahao Ni Jiao Pan Yaohai Wang Tianhao Chen Xinshi Feng Yichen Li Tongtong Lin Michael Lynch Hongan Long Weiyi Li Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China Laboratory for Marine Biology and biotechnology Laoshan LaboratoryQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA department of Biology Indiana UniversityBloomingtonIN 47401USA present address:SLAC National Accelerator Laboratory Stanford UniversityStanford 94305USA

High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring ones.Commercial library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples.With this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.

关键词： Amplicon library preparation Lab-made protocol Long-primer PCR Cost efficiency

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Distinctive and complementary roles of E2F transcription factors during plant replication stress responses

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Molecular Plant 2023年第8期16卷 1269-1282页

作者： Maherun Nisa Thomas Eekhout Clara Bergis Jose-Antonio Pedroza-Garcia Xiaoning He Christelle Mazubert Ilse Vercauteren Toon Cools Rim Brik-Chaouche Jeannine Drouin-Wahbi Layla Chmaiss David Latrasse Catherine Bergounioux Klaas Vandepoele Moussa Benhamed Lieven De Veylder Cécile Raynaud Universite Paris-Saclay CNRSINRAEUniversite EvryInstitute of Plant Sciences Paris-Saclay(IPS2)91190 Gif-sur-YvetteFrance Universite de Paris Cite CNRSINRAEInstitute of Plant Sciences Paris-Saclay(IPS2)91190 Gif-sur-YvetteFrance department of Plant biotechnology and bioinformatics Ghent University9052 GhentBelgium Center for Plant Systems Biology VIB9052 GhentBelgium present address:Plant Molecular and Cellular Biology Laboratory Salk Institute for Biological StudiesLa JollaCA 92037USA

Survival of living organisms is fully dependent on their maintenance of genome integrity,being permanently threatened by replication stress in proliferating cells.Although the plant DNA damage response(DDR)regulator SOG1 has been demonstrated to cope with replication defects,accumulating evidence points to other pathways functioning independent of SOG1.Here,we report the roles of the Arabidopsis E2FA and EF2B transcription factors,two well-characterized regulators of DNA replication,in plant response to replication stress.Through a combination of reverse genetics and chromatin immunoprecipitation approaches,we show that E2FA and E2FB share many target genes with SOG1,providing evidence for their involvement in the DDR.Analysis of double-and triple-mutant combinations revealed that E2FB,rather than E2FA,plays the most prominent role in sustaining plant growth in the presence of replication defects,either operating antagonistically or synergistically with SOG1.Conversely,SOG1 aids in overcoming the replication defects of E2FA/E2FB-deficient plants.Collectively,our data reveal a complex transcriptional network controlling the replication stress response in which E2Fs and SOG1 act as key regulatory factors.

关键词： replication stress E2F SOG1 cell cycle Arabidopsis

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Conservation and Diversification of the SHR-SCR- SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots

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Molecular Plant 2016年第8期9卷 1197-1209页

作者： Eun Kyung Yoon Souvik Dhar Mi-Hyun Lee Jae Hyo Song Shin Ae Lee Gyuree Kim Sejeong Jang Ji Won Choi Jeong-Eun Choe Jeong Hoe Kim Myeong Min Lee Jun Lim department of Systems biotechnology Konkuk University Seoul 05029 Korea department of Systems Biology Yonsei University Seoul 03722 Korea department of Biology Kyungpook National University Daegu 41566 Korea 4TheSe tlRors cotribCited equally/to ttats article present address: department of Agricultural biotechnology National Institute of Agricultural Sciences Jeonju 54874 Korea present address: department of Agricultural Biology National Institute of Agricultural Sciences Wanju 55365 Korea

Development of the functional endodermis of Arabidopsis thaliana roots is controlled, in part, by GRAS transcription factors, namely SHORT-ROOT （SHR）, SCARECROW （SCR）, and SCARECROW-LIKE 23 （SCL23）. Recently, it has been shown that the SHR-SCR-SCL23 regulatory module is also essential for spec- ification of the endodermis （known as the bundle sheath） in leaves. Nevertheless, compared with what is known about the role of the SHR-SCR-SCL23 regulatory network in roots, the molecular interactions of SHR, SCR, and SCL23 are much less understood in shoots. Here, we show that SHR forms protein com- plexes with SCL23 to regulate transcription of SCL23 in shoots, similar to the regulation mode of SCR expression. Our results indicate that SHR acts as master regulator to directly activate the expression of SCR and SCL23. In the SHR-SCR-SCL23 network, we found a previously uncharacterized negative feed- back loop whereby SCL23 modulates SHR levels. Through molecular, genetic, physiological, and morpho- logical analyses, we also reveal that the SHR-SCR-SCL23 module plays a key role in the formation of the endodermis （known as the starch sheath） in hypocotyls. Taken together, our results provide new insights into the regulatory role of the SHR-SCR-SCL23 network in the endodermis development in both roots and shoots.

关键词： endodermis gene regulatory network SHORT-ROOT SCARECROW SCARECROW-LIKE 23,transcription factor

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Mitochondrial Perturbation Negatively Affects Auxin Signaling

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Molecular Plant 2014年第7期7卷 1138-1150页

作者： Pavel Ivanov Kerchev Inge De Clercq Jordi Denecker Per Muihlenbock Robert Kumpf Long Nguyen Dominique Audenaert Wim Dejonghe Frank Van Breusegem department of Plant Systems Biology VIB Ghent University B-9052 Gent Belgium department of Plant biotechnology and bioinformatics Ghent University B-9052 Gent Belgium present address: department of Plant Protection Biology Swedish University of Agricultural Sciences SE-230 53 Alnarp Sweden VlB Compound Screening Facility B-9052 Gent Belgium

Mitochondria are crucial players in the signaling and metabolic homeostasis of the plant cell. The molecular components that orchestrate the underlying processes, however, are largely unknown. Using a chemical biology approach, we exploited the responsiveness of Arabidopsis UDP-glucosyltransferase-encoding UGT74E2 towards mitochondrial per- turbation in order to look for novel mechanisms regulating mitochondria-to-nucleus communication. The most potent inducers of UGT74E2 shared a （2-furyl）acrylate （FAA） substructure that negatively affected mitochondrial function and was identified before as an auxin transcriptional inhibitor. Based on these premises, we demonstrated that perturbed mitochondria negatively affect the auxin signaling machinery. Moreover, chemical perturbation of polar auxin transport and auxin biosynthesis was sufficient to induce mitochondrial retrograde markers and their transcript abundance was constitutively elevated in the absence of the auxin transcriptional activators ARF7 and ARF19.

关键词： mitochondrial perturbation auxin signaling retrograde communication.

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The Formation of Anthocyanic Vacuolar Inclusions in Arabidopsis thaliana and Implications for the Sequestration of Anthocyanin Pigments

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Molecular Plant 2010年第1期3卷 78-90页

作者： Lucille Pourcel Niloufer G. Irani Yuhua LU Ken Riedl Steve Schwartz Erich Grotewold department of Plant Cellular and Molecular Biology and Plant biotechnology Center Ohio State University Columbus OH 43210 USA department of Food Science and Technology The Ohio State University Columbus OH 43210 USA present address: department of Plant Systems Biology Flanders Institute for Biotechnology and Department of Plant Biotechnology and Genetics GhentUniversity 9052 Ghent Belgium Current address: department of Chemistry Eastern Illinois University Charleston IL 61920 USA

Anthocyanins are flavonoid pigments that accumulate in the large central vacuole of most plants. Inside the vacuole, anthocyanins can be found uniformly distributed or as part of sub-vacuolar pigment bodies, the Anthocyanic Vacuolar Inclusions （AVIs）. Using Arabidopsis seedlings grown under anthocyanin-inductive conditions as a model to un- derstand how AVIs are formed, we show here that the accumulation of AVIs strongly correlates with the formation of cyanidin 3-glucoside （C3G） and derivatives. Arabidopsis mutants that fail to glycosylate anthocyanidins at the 5-0 position （Sgt mutant） accumulate AVIs in almost every epidermal cell of the cotyledons, as compared to wild-type seedlings, where only a small fraction of the cells show AVIs. A similar phenomenon is observed when seedlings are treated with vanadate. Highlighting a role for autophagy in the formation of the AVIs, we show that various mutants that interfere with the autophagic process （atg mutants） display lower numbers of AVIs, in addition to a reduced accumulation of anthocyanins. Interestingly, vanadate increases the numbers of AVIs in the atg mutants, suggesting that several pathways might participate in AVl formation. Taken together, our results suggest novel mechanisms for the formation of sub-vacuolar compartments capable of accumulating anthocyanin pigments.

关键词： Anthocyanin autophagy cyanidin 3-glucoside vacuolar inclusion vanadate.

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Calcineurin-B-Like Protein CBL9 Interacts with Target Kinase CIPK3 in the Regulation of ABA Response in Seed Germination

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Molecular Plant 2008年第2期1卷 238-248页

作者： Girdhar K. Pandey John J. Grant Yong Hwa Cheong Beom-Gi Kim Le Gong Li Sheng Luan department of Plant and Microbial Biology University of California Berkeley CA 94720 USA department of Plant Molecular Biology University of Delhi South Campus Benito Juarez Road New Delhi-110021 India present address: department of Bio-Environmental Science Sunchon National University Suncheon Jeonnam 540-742 Korea present address: department of Molecular Physiology and Biochemistry National institute of Agricultural Biotechnology Suwon 441-707 Korea

Calcium plays a vital role as a second messenger in many signaling pathways in plants. The calcineurin B-like proteins （CBLs） represent a family of plant calcium-binding proteins that function in calcium signaling by interacting with their interacting protein kinases （CIPKs）. In our previous study, we have reported a role for one of the CBLs （CBL9） and one of the CIPKs （CIPK3） in ABA signaling. Here, we have shown that CBL9 and CIPK3 physically and functionally interact with each other in regulating the ABA responses. The CBL9 and CIPK3 proteins interacted with each other in the yeast two- hybrid system and when expressed in plant cells. The double mutant cbl9cipk3 showed the similar hypersensitive response to ABA as observed in single mutants （cbl9 or cipk3）. The constitutively active form of CIPK3 genetically complemented the cbl9 mutant, indicating that CIPK3 function downstream of CBL9. Based on these findings, we conclude that CBL9 and CIPK3 act together in the same pathway for regulating ABA responses.

关键词： ABA calcium CBL CIPK osmotic stress signal transduction.

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