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Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation

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Journal of Molecular Cell biology 2015年第4期7卷 366-382页

作者： Nickolai A.Tchurikov Daria M.Fedoseeva Dmitri v.Sosin Anastasia v.Snezhkina Nataliya v.Melnikova Anna v.Kudryavtseva Yuri v.Kravatsky Olga v.Kretova Department of Epigenetic Mechanisms of Gene Expression Regulation Engelhardt Institute of Molecular BiologyMoscow 119334Russia Group of Postgenomic Studies Engelhardt Institute of Molecular BiologyMoscow 119334Russia Laboratory of DNA-Protein Interactions Engelhardt Institute of Molecular BiologyMoscow 119334Russia

DNA double-strand breaks(DSBs)are involved in many cellular mechanisms,including replication,transcription,and genome *** recent observation that hot spots of DSBs in human chromosomes delimit DNA domains that possess coordinately expressed genes suggests a strong relationship between the organization of transcription patterns and hot spots of *** this study,we performed mapping of hot spots of DSBs in a human 43-kb ribosomal DNA(rDNA)repeated *** observed that rDNA units corresponded to the most fragile sites in human chromosomes and that these units possessed at least nine specific regions containing clusters of extremely frequently occurring DSBs,which were located exclusively in non-coding intergenic spacer(IGS)*** hot spots of DSBs corresponded to only a specific subset of DNase-hypersensitive sites,and coincided with CTCF,PARP1,and HNRNPA2B1 binding sites,and H3K4me3 *** rDNA-4C data indicate that the regions of IGS containing the hot spots of DSBs often form contacts with specific regions in different chromosomes,including the pericentromeric regions,as well as regions that are characterized by H3K27ac and H3K4me3 marks,CTCF binding sites,ChIA-PET and RIP signals,and high levels of *** data suggest a strong link between chromosome breakage and several different mechanisms of epigenetic regulation of gene expression.

关键词： double-strand breaks fragile sites rDNA IGS PARP1 HNRNPA2B1 4C

Copper-induced liver fibrosis affects the behavior of bone marrow cells in primary culture

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Frontiers in biology 2017年第4期12卷 271-279页

作者： Anatoliy I. Bozhkov Eugeniy G. Ivanov Yuliya A. Kuznetsova Svetlana L. Ohiienko Anastasiya Yu. Bondar 1. Research institute of biology of v.N. Karazin Kharkov National University sq. Svobody 4 61022 Kharkov Ukraine

BACKGROUND： The present study investigated the effects （LMCC）, which were administered per os, on the differentiation, of rats in primary culture. of low-molecular-weight components of bovine colostrum growth, and survival of cells obtained from the bone marrow METHODS： Bone marrow cells （BMCs） were obtained from both the rat femurs and were cultured in medium 199 supplemented with antibiotics （8% streptomycin and 8% gentamycin） and 20% inactivated fetal calf serum. In addition, the number of BMCs was counted and their morphotypes were determined. RESULTS： Animals were treated with copper （Cu） sulfate to induce liver fibrosis. Subsequent treatment with LMCC eliminated growth inhibition and normalized the bodyweight and temperature of animals with Cu-induced liver fibrosis. The number of lymphocytes in the bone marrow of animals with Cu-induced liver fibrosis was significantly higher than that in the bone marrow of control animals. The number ofneutrophils in untreated animals with liver fibrosis and LMCC-treated animals with liver fibrosis was lower than that in control animals. Neutrophils obtained from untreated animals with liver fibrosis and LMCC-treated animals with liver fibrosis underwent two-times faster degradation in vitro than neutrophils obtained from control animals. CONCLUSIONS： Our results indicate that LMCC affects the distribution of different morphological types of BMCs but does not prevent their degradation in vitro, which was two-times faster than that of BMCs obtained from control animals.

关键词： bone marrow cells bone marrow colostntm liver fibrosis

The fate of the herbicide propanil in plants of the littoral zone of the Three Gorges Reservoir(TGR),China

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Journal of Environmental Sciences 2016年第10期28卷 24-33页

作者： Zhongli Chen Andreas Schaffer institute for Environmental Research(biology v) RWTH Aachen UniversityAachen 52074Germany. Nanjing University School of the Environment Nanjing 210023China Chongqing University College of Resource and Eavironmental ScienceChongqing 400030China

The anti-seasonal hydrology with 30 m water fluctuations in the Three Gorges Reservoir(TGR)of China attracts growing environmental and ecological *** investigated the biotransformation of the herbicide propanil in plants dominating in the littoral zone of the TGR by applying the 14C-ring-labeled herbicide into non-aseptic hydroponic plant systems(Cynodon dactylon,Nelumbo nucifera and Bidens pilosa),aseptic plants(Lemna minor and Lemna gibba)and cell suspension cultures(*** and ***).(1)Propanil absorbed in plants of the hydroponic systems was(12.46±1.63)%of applied radioactivity(AR)(***),(52.36±6.38)%(***)and(76.55±6.07)%(***),*** 14C-residues in the plant extractable fractions and the corresponding media were confirmed by radio-Thin Layer Chromatography(TLC),radio-High Performance Liquid Chromatography(HPLC)and Gas Chromatography-Electron Ionization Mass Spectrometry(GC-EIMS)as propanil,3,4-dichloroaniline(DCA)and N-(3,4-dichlorophenyl)-β-D-glucopyranosylamine(Glu-DCA).(2)About 8%of AR was taken up by both aseptic plants,from which 7.0%of AR was extracted and identified also as propanfl,DCA and Glu-DCA.(3)Concerning cell suspension cultures,(39.22±9.39)%of AR was absorbed by *** after 72 hr,whereas the accumulated 14C-propanil by *** cell suspension culture amounted to(65.04±1.72)%after 7 *** identified compounds in cell cultures are consistent with those in the tested *** of the pesticide residues in the intact plants were un-extractable,which are recognized as the end of the detoxificafion *** therefore consider these plants as suitable for the phytoremediation of the herbicide propanil in the TGR region.

关键词： Three Gorges Reservoir(TGR) Propanil Plant degradation Non-extractable residues(NER)

Eyes of diff ering colors in Alvinocaris longirostris from deep-sea chemosynthetic ecosystems: genetic and molecular evidence of its formation mechanism

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Journal of Oceanology and Limnology 2021年第1期39卷 282-296页

作者： Qian XIN Min HUI Chaolun LI Zhongli SHA institute of Oceanology Chinese Academy of SciencesQingdao 266071China Center for Ocean Mega-Science Chinese Academy of SciencesQingdao 266071China Laboratory for marine biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China University of Chinese Academy of Sciences Beijing 100049China

Coloration is an important phenotypic trait for multiple adaptive *** is interesting to fi nd white-eye(AW)and orange-eye(AO)phenotypes in the shrimp Alvinocaris longirostris inhabiting the deep-sea cold seep and hydrothermal vent areas of the northwestern Pacifi *** comparative transcriptome analyses,1491 diff erentially expressed genes(DEGs)were identified between AW and *** them,many DEGs were associated with immunity,antioxidation,and detoxifi *** signifi cant enzyme encoding genes,xanthine dehydrogenase,and tryptophan oxidase involved in pigment biosynthesis pathways were up-regulated in AW and AO,respectively,which might be related to the diff erences of white and orange eye ***,single nucleotide polymorphism(SNP)calling detected that genotypes of 28 SNP distributing in 14 unigenes were completely diff erent between AW and ***,there were three and two non-synonymous mutations in immune genes crustin Pm5 and antimicrobial peptide,*** indicate that the diff erence in eye color is probably resulted from immune response to variable micro-environmental stressors encountered in the dispersal process of the shrimps,such as symbiotic microbes,pathogens,and toxic substances,and might be genetically fi xed at *** suggested pathway preliminarily explained the formation mechanism of diff erent eye phenotypes in Alvinocaridid shrimps,providing a basis for further study on adaptive evolution of eyes in deep-sea chemosynthetic faunas.

关键词： alvinocaridid shrimps cold seep and hydrothermal vent diff erentially expressed genes eye color single nucleotide polymorphism(SNP)mutation transcriptome

New species in Aspergillus section Fumigati from reclamation sites in Wyoming (U.S.A.) and revision of A. viridinutans complex

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Fungal Diversity 2014年第1期64卷 253-274页

作者： Alena Nováková vit Hubka Zuzana Dudová Tetsuhiro Matsuzawa Alena Kubátová Takashi Yaguchi Miroslav Kolařík biology Centre AS CR v.v.i.Institute of Soil BiologyNa Sádkách 737005ČeskéBudějoviceCzech Republic Laboratory of Physiology and Genetics of Fungi Institute of Microbiology AS CRv.v.iVídeňská108314220 Prague 4Czech Republic Department of Botany Faculty of ScienceCharles University in PragueBenátská212801 Prague 2Czech Republic Medical Mycology Research Center Chiba University1-8-1InohanaChuo-kuChiba 260-8673Japan

The Aspergillus viridinutans complex includes morphologically similar,soil-inhabiting *** its species boundaries have not been fully defined,many isolates from the complex have been isolated as opportunistic human and animal *** the present study,these species were dominant in spoil sites subjected to various types of reclamation management after coal *** species were characterised using two different PCR-fingerprinting methods,sequence data from the β-tubulin(benA)and calmodulin(caM)genes,macro-and micromorphology(optical and scanning electron microscopy),maximum growth temperatures and mating *** addition,RNA polymerase II gene(RPB2),actin(act1)and ITS sequences were deposited for the ex-type isolates of newly described *** mating experiment results,phylogenetic analyses and ascospore morphology suggested the presence of five species in the *** *** aureolus(*** aureola)was the only homothallic *** species,***,***(***)and *** ***.,were heterothallic and their morphologically distinguishable teleomorph was induced by systematic mating *** viridinutans *** to be a very rare species and was represented only by the ex-type isolate in which the MAT1-1 locus was *** viridinutans and *** were typified in accordance with the rules of the new botanical *** species outside the *** complex isolated from the reclamation sites were *** and *** as well as two new sister species,*** *** *** *** were closely related each to other and to *** new species are phylogenetically distant from all anamorphic species and resemble ***,*** and *** in micromorphology and are distinguishable from each other by the slower growth of *** on all tested ***,no isolate from the

关键词： Aspergillus fumigatus Heterothallic species MAT locus Neosartorya udagawae PCR fingerprinting Soil fungi

Enhancement of the ‘tractor-beam’ pulling force on an optically bound structure

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Light(Science & Applications) 2017年第1期6卷 136-141页

作者： Jana Damková Lukáš Chvátal Jan Ježek Jindřich Oulehla Oto Brzobohatý Pavel Zemánek institute of Scientific Instruments of the CAS v.v.i.Královopolská147Brno 61264Czech Republic

Recently,increasing attention has been devoted to mastering a new technique of optical delivery of micro-objects tractorbeam’1–*** beams have uniform intensity profiles along their propagation direction and can exert a negative force that,in contrast to the familiar pushing force associated with radiation pressure,pulls the scatterer toward the light *** was experimentally observed that under certain circumstances,the pulling force can be significantly enhanced6 if a non-spherical scatterer,for example,a linear chain of optically bound objects10–12,is optically *** we demonstrate that motion of two optically bound objects in a tractor beam strongly depends on theirs mutual distance and spatial *** configuration-dependent optical forces add extra flexibility to our ability to control matter with *** these interactions opens the door to new applications involving the formation,sorting or delivery of colloidal self-organized structures.

关键词： beam scatter mutual

Pharmacological and Predicted Activities of Natural Azo Compounds

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Natural Products and Bioprospecting 2017年第1期7卷 151-169页

作者： valery M.Dembitsky Tatyana A.Gloriozova vladimir v.Poroikov National Scientific Center of marine biology 17 Palchevsky Str.VladivostokRussia 690041 institute of Biomedical Chemistry MoscowRussia 119121

This paper describes research on natural azo compounds isolated from fungi,plant,bacteria,and *** than 120 biologically active diazene containing alkaloids demonstrate confirmed pharmacological activity,including antitumor,antimicrobial,and antibacterial *** structures,origin,and biological activities of azo compounds are *** the computer program PASS,some structure–activity relationship new activities are also predicted,pointing toward possible new applications of these *** article emphasizes the role of natural azo compounds as an important source of drug prototypes and leads for drug discovery.

关键词： Azo metabolites Alkaloids Fungi Plant Bacteria Sponges SAR

vertical microbial profiling of water column reveals prokaryotic communities and distribution features of Antarctic Peninsula

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Acta Oceanologica Sinica 2023年第9期42卷 90-100页

作者： Jiang Li Luying Zhao Xiaoqian Gu Chengxuan Li Qian Zhang Liping Fu Ao Zhang marine Biological Resources and Environment Center First Institute of OceanographyMinistry of Natural ResourcesQingdao 266061China Ministry of Natural Resources Key Labatary for Science&Technology of marine Ecosystems Qingdao 266061China CAS and Shandong Province Key Laboratory of Experimental marine biology Center for Ocean Mega-ScienceInstitute of OceanologyChinese Academy of SciencesQingdao 266071China College of Chemical Engineering Qingdao University of Science&TechnologyQingdao 266042China

Prokaryotic diversity and community composition in the water column of eight stations(63 samples) around the Antarctic Peninsula of the Southern Ocean were investigated. Through pyrosequencing of the v3–v4hypervariable regions of the 16S ribosomal RNA gene, we characterized 4 720 089 valid reads representing 48 188operational taxonomic units(OTUs, 97% similarity). The community was dominated by the phyla Pseudomonadota(original name: Proteobacteria, 47%), Oxyphotobacteria(26%), and Bacteroidota(original name: Bacteroidetes, 18%), which comprised an average of 91% of the total OTUs in all samples. The prokaryotic community composition varied vertically within the water column. Water column prokaryotic communities exhibited a clear depth profile, with higher microbial richness and higher diversity observed with increasing water depth. Cluster analysis of the community composition of water column samples exhibited a similar trend with depth. Correlation with environmental factors suggested distinct variation in prokaryotic community composition with changes in depth, salinity, temperature and dissolved oxygen levels. Functional prediction showed presence of active nitrogen, sulphur and methane metabolic cycles along the vertical transect of the studied region. These results will improve our knowledge of prokaryotic diversity and community composition at different depth of water column for better understanding of the microbial ecology and nutrient cycles in Antarctic Peninsula region of the Southern Ocean.

关键词： prokaryotic diversity 16S rRNA high-throughput sequencing(HTS) Southern Ocean

Deletion of the waaf gene affects O antigen synthesis and pathogenicity in vibrio parahaemolyticus from shellfish

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Food Science and Human Wellness 2022年第2期11卷 418-426页

作者： Feng Zhao Guoying Ding Qilong Wang Huihui Du Guosheng Xiao Deqing Zhou College of biology and food engineering Chongqing Three Gorges UniversityWanzhou 404100China Yellow Sea Fisheries Research institute Chinese Academy of Fishery SciencesLaboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266071China

vibrio parahaemolyticus is the main cause of foodborne gastroenteritis,which is widely distributed in shellfish and other *** *** are nonpathogenic,and only a few types,such as serotype O3:K6,are pathogenic,which is also the most prevalent strain in ***,the relationship between this serotype and pathogenicity has yet to be *** waaf gene is located in the O antigen synthesis gene ***,we constructed a waaf gene deletion mutant(i.e.,Δwaaf)of wild-type(WT)which isolated from shellfish serotype O3:K6 via chitin-mediated transformation *** then constructed theΔwaaf complementary strain(i.e.,C-△waaf)via the Escherichia coli S17λpir strain by *** basic physiological characteristics,adhesion to Caco2 cells,and pathogenicity of the WT,△waaf,and C-△waaf strains were *** curves showed no remarkable differences between the WT andΔwaaf ***,theΔwaaf strain non-reactive to O3 antisera and other 12 O-group antisera of ***,the number of flgella and extracellular polysaccharides decreased,the adhesion decreased,and the pathogenicity *** characteristics of the C-△waaf strain were similar to those of the WT strain These results indicated that the waaf gene is vital to the serotype in ***,and changes in O antigen could affect the pathogenicity of this *** study will be helpful to understand the pathogenic mechanism of ***.

关键词： vibrio parahaemolyticus waaf gene LPS O antigen Pathogenicity