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Transcriptome assembly of Modiolus modiolus and comparative analysis with Bathymodiolus platifrons

Acta Oceanologica Sinica 2018年第8期37卷 38-45页

作者： MENG Jie YANG Mei XU Fei LI Xinzheng LI Li CAS Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of Sciences(CAS)Qingdao 266071China Laboratory for Marine Fisheries and Aquaculture Qingdao National Laboratory for Marine Science and TechnologyQingdao 266071China National and Local Joint Engineering Laboratory of Ecological Mariculture Institute of OceanologyChinese Academy of SciencesQingdao 266071China Center for Ocean Mega-Science Chinese Academy of SciencesQingdao 266071China Institute of Oceanology Chinese Academy of SciencesQingdao 266071China University of Chinese Academy of Sciences Beijing 100039China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266071China

The genetic basis for bivalves＇ adaptation and evolution is not well understood. Even few studies have focused on the mechanism of molluscan molecular evolution between the coastal intertidal zone and deep-sea *** our studies, we first conducted the transcritpome assembly of Modiolus modiolus mussels living in coastal intertidal zones. Also, we conducted transcriptome comparison analyses between M. modiolus and Bathymodiolus platifrons living in hydrothermal vents and cold methane/sulfide-hydrocarbon seeps. De novo assemblies of the clean reads yielded a total of 182 476 and 156 261 transcripts with N50 values of 1 769 and 1 545 in M. modiolus and B. platifrons. A total of 27 868 and 23 588 unigenes were identified, which also displayed the similar GO representation patterns. Among the 10 245 pairs of putative orthologs, we identified 26 protein-coding genes under strong positive selection（Ka/Ks〉1） and 12 genes showing moderate positive selection（0.5

关键词： mollusc transcriptome comparision positive selection stress adaptation

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Belgica antarctica(Diptera: Chironomidae): A natural modelorganism for extreme environments

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Insect Science 2022年第1期29卷 2-20页

作者： Iryna Kozeretska Svitlana Serga Pavlo Kovalenko Volodymyr Gorobchyshynand Peter Convey National Antarctic Scientific Center of Ukraine 01601Taras Shevchenko blv.16KyivUkraine Taras Shevchenko National Universityof Kyiv Department General and Medical Genetics01601Volodymyrska str.64/13KyivUkraine State Institution«Institute for Evolu-tionary Ecology of the National Academy of Sciences of Ukraine» Department of Population Dynamics03143Lebedeva str.37KyivUkraine and4British Antarctic SurveyNERCHigh CrossMadingley RoadCambridge CB30ETUnited Kingdom

Belgica antarctica(Diptera:Chironomidae),a brachypterous midge endemicto the maritime Antarctic,was first described in *** more than a century of study,a vast amount of information has been compiled on the species(3750000 Google searchresults as of January 10,2021),encompassing its ecology and biology,life cycle and re-production,polytene chromosomes,physiology,biochemistry and,increasingly,***2014,***’s genome was sequenced,further boosting *** develop-mental stages can be cultured successfully in the *** together,this wealthof information allows the species to be viewed as a natural model organism for studies ofadaptation and function in extreme environments.

关键词： Belgica antarctica Chironomidae stress adaptation Antarctica

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A first order system model of fracture healing

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2005年第9期6卷 926-930页

作者：王小平张先龙李柱国喻鑫罡 School of Mechanical Engineering Shanghai Jiaotong University Shanghai 200030 China Department of Orthopaedics Shanghai Sixth People’s HospitalShanghai 200233 China

A first order system model is proposed for simulating the influence of stress stimulation on fracture strength during fracture healing. To validate the model, the diaphyses of bilateral tibiae in 70 New Zealand rabbits were osteotomized and fixed with rigid plates and stress-relaxation plates, respectively. stress shielding rate and ultimate bending strength of the healing bone were measured at 2 to 48 weeks postoperatively. Ratios of stress stimulation and fracture strength of the healing bone to those of intact bone were taken as the system input and output. The assumed first order system model can approximate the experimental data on fracture strength from the input of stress stimulation over time, both for the rigid plate group and the stress-relaxation plate group, with different system parameters of time constant and gain. The fitting curve indicates that the effect of mechanical stimulus occurs mainly in late stages of healing. First order system can model the stress adaptation process of fracture healing. This approach presents a simple bio-mathematical model of the relationship between stress stimulation and fracture strength, and has the potential to optimize planning of functional exercises and conduct parametric studies.

关键词： First order system Fracture healing stress adaptation Simulation

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Expression Profiling and Structural Characterization of Micro RNAs in Adipose Tissues of Hibernating Ground Squirrels

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Genomics, Proteomics & Bioinformatics 2014年第6期12卷 284-291页

作者： Cheng-Wei Wu Kyle K.Biggar Kenneth B.Storey Department of Biology Carleton University Biochemistry Department Schulich School of Medicine and DentistryWestern University

Micro RNAs（mi RNAs） are small non-coding RNAs that are important in regulating metabolic stress. In this study, we determined the expression and structural characteristics of 20 mi RNAs in brown（BAT） and white adipose tissue（WAT） during torpor in thirteen-lined ground squirrels. Using a modified stem-loop technique, we found that during torpor, expression of six mi RNAs including let-7a, let-7b, mi R-107, mi R-150, mi R-222 and mi R-31 was significantly downregulated in WAT（P 〈 0.05）, which was 16%–54% of euthermic non-torpid control squirrels,whereas expression of three mi RNAs including mi R-143, mi R-200 a and mi R-519 d was found to be upregulated by 1.32–2.34-fold. Similarly, expression of more mi RNAs was downregulated in BAT during torpor. We detected reduced expression of 6 mi RNAs including mi R-103 a, mi R-107, mi R-125 b, mi R-21, mi R-221 and mi R-31（48%–70% of control）, while only expression of mi R-138 was significantly upregulated（2.91 ± 0.8-fold of the control, P 〈 0.05）. Interestingly,mi RNAs found to be downregulated in WAT during torpor were similar to those dysregulated in obese humans for increased adipogenesis, whereas mi RNAs with altered expression in BAT during torpor were linked to mitochondrial b-oxidation. mi RPath target prediction analysis showed that mi RNAs downregulated in both WAT and BAT were associated with the regulation of mitogen-activated protein kinase（MAPK） signaling, while the mi RNAs upregulated in WAT were linked to transforming growth factor b（TGFb） signaling. Compared to mouse sequences, no unique nucleotide substitutions within the stem-loop region were discovered for the associated pre-mi RNAs for the mi RNAs used in this study, suggesting no structure-influenced changes in pre-mi RNA processing efficiency in the squirrel. As well, the expression of mi RNA processingenzyme Dicer remained unchanged in both tissues during torpor. Overall, our findings suggest that changes of mi RNA expression in adipose tissues may be l

关键词： Non-coding RNA Dicer Ground squirrel stress adaptation Hypometabolism

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Non-CG DNA methylation-deficiency mutations enhance mutagenesis rates during salt adaptation in cultured Arabidopsis cells

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stress Biology 2021年第1期1卷 144-155页

作者： Xiaohong Zhu Shaojun Xie Kai Tang Rajwant KKalia Na Liu Jinbiao Ma Ray ABressan Jian-Kang Zhu State Key Laboratory of Crop stress adaptation and Improvement School of Life SciencesHenan UniversityKaifengChina State Key Laboratory of Cotton Biology School of Life SciencesHenan UniversityKaifengChina Bioinformatics Core Purdue UniversityWest LafayetteIN 47907USA Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteIN 47907USA Central Arid Zone Research Institute Jodhpur 342003India State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhou 310021China State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and GeographyChinese Academy of Sciences 830011UrumqiChina Shanghai Center for Plant stress Biology Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200032China

Much has been learned about how plants acclimate to stressful environments,but the molecular basis of stress adaptation and the potential involvement of epigenetic regulation remain poorly ***,we examined if salt stress induces mutagenesis in suspension cultured plant cells and if DNA methylation affects the mutagenesis using whole genome resequencing *** generated suspension cell cultures from two Arabidopsis DNA methylation-deficient mutants and wild-type plants,and subjected the cultured cells to stepwise increases in salt stress intensity over 40 culture *** show that ddc(drm1 drm2 cmt3)mutant cells can adapt to grow in 175 mM NaCl-containing growth medium and exhibit higher adaptability compared to wild type Col-0 and nrpe1 cells,which can adapt to grow in only 125mM NaCl-containing growth *** treated nrpe1 and ddc cells but not wild type cells accumulate more mutations compared with their respective untreated *** is no enrichment of stress responsive genes in the list of mutated genes in salt treated cells compared to the list of mutated genes in untreated *** results suggest that DNA methylation prevents the induction of mutagenesis by salt stress in plant cells during stress adaptation.

关键词： Salt stress Cell suspension DNA methylation-deficient mutants stress-induced mutagenesis stress adaptation

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Histone demethylase Bcjarl regulating pathogenic development and virulence of the gray mold fungus Botrytis cinerea

Histone demethylase Bcjarl regulating pathogenic development...

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中国植物病理学会2019年学术年会

作者： Hou Jie Feng Huiqiang Chang Haowu Liu Yue Li Guihua Yang Song Sun Chenhao Zhang Mingzhe Yuan Ye Sun Jiao Zhang Hao Qin Qingming College of Plant Sciences Jilin University College of Forestry BeiHua University College of Computer Science and Technology Jilin University

Histone 3 Lysine 4（H3K4） demethylation is ubiquitous in organisms;however,the roles of H3K4 demethylase JARID1（Jar1）/KDM5 in the development and pathogenesis of fungal pathogens remain largely ***,we demonstrate that Jar1/KDM5 in Botrytis cinerea,the gray mold fungus,plays crucial roles in these *** BcJAR1 gene was deleted in *** wild-type strain B05.10 and was reintroduced into the BcJAR1 deletion mutant to generate the complemented strains via Agrobacterium tumefaciens-mediated transformation（ATMT） *** roles of BcJAR1 in the fungus development and pathogenesis were investigated using approaches of genetics,molecular/cell biology,pathogenicity and transcriptomic *** findings demonstrate that Bcjar1 is a H3K4 demethylase and is functionally equivalent to ScJhd2,the sole H3K4 demethylase in Saccharomyces cerevisiae that belongs to the ***1 regulates H3K4 me3 and H3K4 me2/me3 methylation levels during vegetative and pathogenic development,*** of BcJAR1 impairs conidiation,appressorium formation and stress adaptation;abolishes infection cushion（IC） formation and virulence,but promotes sclerotium production,of the △BcJar1 ***1 mediates reactive oxygen species（ROS） production and proper accumulation and assembly of Sep4,a virulence determinant that initiates infection structure（IFS） formation and host *** cAMP partially restored the ability of appressorium formation,but failed to rescue IC formation of the △Bcjar1 mutants,suggesting that cAMP can trigger processes that bypass the defect resulting from the absence of the histone ***1 orchestrates global expression of genes related to ROS production,stress response,carbohydrate transmembrane transport,secondary metabolites,etc.,which are required for conidiation,IFS formation,host penetration,and virulence of the gray mold *** work systematically elucidates BcJar1 functions and provides novel insights

关键词： Botrytis cinerea H3K4 demethylase JARID1(Jar1)/KDM5 stress adaptation infection structures development and pathogenesis septin protein Sep4 reactive oxygen species cAMP signaling

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