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Effects of multiple but low pesticide loads on aquatic fungal communities colonizing leaf litter

Journal of Environmental Sciences 2016年第8期28卷 116-125页

作者： Anne Talk Susanne Kublik Marie Uksa Marion Engel Rüdiger Berghahn Gerhard Welzl Michael Schloter Silvia Mohr Research unit Environmental genomics Helmholtz Zentrum München Umweltbundesamt

In the first tier risk assessment（RA） of pesticides, risk for aquatic communities is estimated by using results from standard laboratory tests with algae, daphnids and fish for single pesticides such as herbicides, fungicides, and insecticides. However, fungi as key organisms for nutrient cycling in ecosystems as well as multiple pesticide applications are not considered in the RA. In this study, the effects of multiple low pesticide pulses using regulatory acceptable concentrations（RACs） on the dynamics of non-target aquatic fungi were investigated in a study using pond mesocosm. For that, fungi colonizing black alder（Alnus glutinosa） leaves were exposed to multiple, low pulses of 11 different pesticides over a period of 60 days using a real farmer＇s pesticide application protocol for apple *** pond mesocosms served as treatments and 4 as controls. The composition of fungal communities colonizing the litter material was analyzed using a molecular fingerprinting approach based on the terminal Restriction Fragment Length Polymorphism（t-RFLP） of the fungal Internal Transcribed Spacer（ITS） region of the ribonucleic acid（RNA） gene（s）. Our data indicated a clear fluctuation of fungal communities based on the degree of leaf litter degradation. However significant effects of the applied spraying sequence were not observed. Consequently also degradation rates of the litter material were not affected by the treatments. Our results indicate that the nutrient rich environment of the leaf litter material gave fungal communities the possibility to express genes that induce tolerance against the applied pesticides. Thus our data may not be transferred to other fresh water habitats with lower nutrient availability.

关键词： Mixture toxicity Pesticides Regulatory acceptable concentration Fungal community structure Leaf litter degradation

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Latest notable achievements in genomics

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Science China(Life Sciences) 2012年第7期55卷 645-648页

作者： WU JiaYan XIAO JingFa YU Jun Key Laboratory of genomics Science and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China

Within the past 10 years, the progress of genomics development in China exhibited a frogleap in terms of scale, quality, organization, and international collaboration. Human genome study has entered a new phase of interdisciplinarity in the history of life science in China. The rise of genomics relied on the development of technology and its integration with other academic disciplines, particularly in the following three areas. First, DNA sequencing technology has been improving its productivity and efficiency at an exponential growth rate. Second, bioinformatics supports the system of data collection, administration, annotation,

关键词：基因组学 DNA测序技术成绩人类基因组生物信息学国际合作生命科学数据采集

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CTP Synthase Is Required for Optic Lobe Homeostasis in Drosophila

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Journal of Genetics and genomics 2015年第5期42卷 261-274页

作者： Ömür Y.Tastan Ji-Long Liu Medical Research Council Functional genomics unit Department of PhysiologyAnatomy and GeneticsUniversity of Oxford

CTP synthase （CTPsyn） is a metabolic enzyme responsible for the de novo synthesis of the nucleotide CTE Several recent studies have shown that CTPsyn forms filamentous subcellular structures known as cytoophidia in bacteria, yeast, fruit flies and humans. However, it remains elusive whether and how CTPsyn and cytoophidia play a role during development. Here, we show that cytoophidia are abundant in the neuroepithelial stem cells in Drosophila optic lobes. Optic lobes are underdeveloped in CTPsyn mutants as well as in CTPsyn RNAi. Moreover, overexpressing CTPsyn impairs the development of optic lobes, specifically by blocking the transition from neuro- epithelium to neuroblast. Taken together, our results indicate that CTPsyn is critical for optic lobe homeostasis in Drosophila.

关键词： CTP synthase Cytoophidium Drosophila Central nervous system Neuroepithelial stem cell

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Plant genomic resources at National genomics Data Center:assisting in data-driven breeding applications

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aBIOTECH 2024年第1期5卷 94-106页

作者： Dongmei Tian Tianyi Xu Hailong Kang Hong Luo Yanqing Wang Meili Chen Rujiao Li Lina Ma Zhonghuang Wang Lili Hao Bixia Tang Dong Zou Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang Shuhui Song National genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among *** various efforts in genomic data archiving,integrative analysis and value-added curation,the National genomics Data Center(NGDC),which is a part of the China National Center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database *** dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research ***,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application *** intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

关键词： Plant-omics data Data repositories Data integration Knowledgebase Plant genomics

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Innovations in functional genomics and molecular breeding of pea:exploring advances and opportunities

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aBIOTECH 2024年第1期5卷 71-93页

作者： Baizhi Chen Yan Shi Yuchen Sun Lu Lu Luyao Wang Zijian Liu Shifeng Cheng Agricultural genomics Institute at Shenzhen(AGIS) Chinese Academy of Agricultural Sciences(CAAS)ShenzhenChina

The garden pea(Pisum sativum L.)is a significant cool-season legume,serving as crucial food sources,animal feed,and industrial raw *** advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea ***,the release of the pea reference genome has enhanced our understanding of plant architecture,symbiotic nitrogen fixation(SNF),flowering time,floral organ development,seed development,and stress ***,a considerable gap remains between pea functional genomics and molecular *** review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

关键词： Pea Genome study Agronomic traits Breeding

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In silico analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells

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World Journal of Gastroenterology 2025年第3期31卷 84-102页

作者： Patricia de la Cruz-Ojeda Ester Parras-Martínez Raquel Rey-Pérez Jordi Muntané Functional genomics of Solid Tumors Laboratory Centre de Recherche des CordeliersParis 75006France Department of Oncology Surgery Cell Therapy and Organ TransplantationInstitute of Biomedicine of SevilleVirgen del Rocio University HospitalSeville 41013Spain Biomedical Research Center for Hepatic and Digestive Diseases CIBERehdMadrid 28029Spain Department of Medical Physiology and Biophysics University of SevilleSeville 41009Spain

BACKGROUND Hepatocellular carcinoma(HCC)is the most common subtype of primary liver cancer with varied incidence and epidemiology *** is still a recommended treatment for a large proportion of patients with advanced *** patterns of treatment responsiveness have been identified in differentiated hepatoblastoma HepG2 cells and metastatic HCC SNU449 *** To define the long non-codingRNA-microRNA-mRNA(lncRNA-miRNA-mRNA)predicted signatures related to selected hallmarks of cancer(apoptosis,autophagy,cell stress,cell dedifferentiation and invasiveness)in RNAseq studies using Sorafenib-treated HepG2 and SNU449 *** available software analyses allowed us to establish the lncRNA-miRNA-mRNA regulatory axes following treatment in HepG2 and SNU449 *** HepG2 and SNU449 cells were treated with Sorafenib(10μmol/L)for 24 *** RNA,including small and long RNA,was extracted with a commercial miRNeasy *** was carried out for the identification of changes in lncRNA-miRNA-mRNA regulatory *** MALAT,THAP9-AS1 and SNGH17 appeared to coordinately regulate miR-374b-3p and miR-769-5p that led to upregulation of SMAD7,TIRARP,TFAP4 and FAXDC2 in HepG2 ***12,EPB41 L4A-AS1,LINC01578,SNHG12 and GAS5 interacted with let-7b-3p,miR-195-5p and VEGFA in SNU449 *** axes MALAT1/hsamir-374b-3p/SMAD7 and MALAT1/hsa-mir-769-5p/TFAP4 were of high relevance for Sorafenib response in HepG2 cells,whereas PVT1/hsa-miR-195-5p/VEGFA was responsible for the differential response of SNU449 cells to Sorafenib *** Critical lncRNAs acting as sponges of miRNA were identified that regulated mRNA expression,whose proteins mainly increased the antitumor effectiveness of the treatment(SMAD7,TIRARP,TFAP4,FAXDC2 and ADRB2).However,the broad regulatory axis leading to increased VEGFA expression may be related to the side effect of Sorafenib in SNU449 cells.

关键词： Cell culture Hepatocellular carcinoma Non-coding RNA RNAseq Sorafenib

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An online coronavirus analysis platform from the National genomics Data Center

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Zoological Research 2020年第6期41卷 705-708页

作者： Zheng Gong Jun-Wei Zhu Cui-Ping Li Shuai Jiang Li-Na Ma Bi-Xia Tang Dong Zou Mei-Li Chen Yu-Bin Sun Shu-Hui Song Zhang Zhang Jing-Fa Xiao Yong-Biao Xue Yi-Ming Bao Zheng-Lin Du Wen-Ming Zhao China National Center for Bioinformation&National genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

DEAR EDITOR,Since the first reported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in December 2019,coronavirus disease 2019(COVID-19)has become a global pandemic,spreading to more than 200 countries and regions *** continued research progress and virus detection,SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate.

关键词： acute respiratory continued

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May the Force Be with You: Metabolism of Arginine and Pyrimidines

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Journal of Genetics and genomics 2015年第5期42卷 179-180页

作者： Ji-Long Liu Medical Research Council Functional genomics unit Department of Physiology Anatomy and Genetics University of Oxford

＂Why do arginine and pyrimidines have to be considered together？＂ This was the question I asked when I was invited by Barbara Zimmermann to attend the 23rd Intemational Conference on Arginine and Pyrimidines （ICAP） three years ago. The meeting was held in the summer of 2012 at Bogota, Columbia, known as the ＂the Athens of South America＂. I am not alone in wanting to know more about the relationship between arginine and pyrimidines. Last summer, when ! was organising the next ICAP meeting at Oxford （Aughey et al., 2014）, one of my colleagues asked me, ＂Why such a weird name for a conference？＂ I am not sure if I had given her a satisfying answer and I was enthused to find out what the reasons may be.

关键词： ICAP Metabolism of Arginine and Pyrimidines May the Force Be with You CPS

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mTOR-S6K1 pathway mediates cytoophidium assembly

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Journal of Genetics and genomics 2019年第2期46卷 65-74页

作者： Zhe Sun Ji-Long Liu School of Life Science and Technology ShanghaiTech University MRC Functional genomics unit Department of Physiology Anatomy and Genetics University of Oxford

CTP synthase(CTPS), the rate-limiting enzyme in de novo CTP biosynthesis, has been demonstrated to assemble into evolutionarily conserved filamentous structures, termed cytoophidia, in Drosophila, bacteria, yeast and mammalian cells. However, the regulation and function of the cytoophidium remain elusive. Here, we provide evidence that the mechanistic target of rapamycin(mTOR) pathway controls cytoophidium assembly in mammalian and Drosophila cells. In mammalian cells, we find that inhibition of mTOR pathway attenuates cytoophidium formation. Moreover, CTPS cytoophidium assembly appears to be dependent on the mTOR complex 1(mTORC1) mainly. In addition, knockdown of the mTORC1 downstream target S6 K1 can inhibit cytoophidium formation, while overexpression of the constitutively active S6 K1 reverses mTOR knockdown-induced cytoophidium disassembly. Finally, reducing m TOR protein expression results in a decrease of the length of cytoophidium in Drosophila follicle ***, our study connects CTPS cytoophidium formation with the mTOR signaling pathway.

关键词： mTOR Cytoophidium CTP synthase Colorectal cancer cell Drosophila

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Rice genomics: over the Past Two Decades and into the Future

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genomics, Proteomics & Bioinformatics 2018年第6期16卷 397-404页

作者： Shuhui Song Dongmei Tian Zhang Zhang Songnian Hu Jun Yu BIG Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future.

关键词： Rice genome Genomic diversity Heterosis Domestication

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