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Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny

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Science China(Life Sciences) 2019年第2期62卷 203-214页

作者： Yurui Wang Chundi Wang Yaohan Jiang Laura A.Katz Feng Gao Ying Yan Institute of Evolution & Marine Biodiversity Ocean University of China Key Laboratory of Mariculture Ocean University of China Ministry of Education Department of Biological Sciences Smith College

Sequence-based approaches, such as analyses of ribosome DNA(rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities.However, recent studies demonstrate both r DNA copy number variation and intra-individual(intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA(SSU r DNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that:(i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa;(ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template;(iii)compared with the most common version, other variant sequences differ in only 1–3 nucleotides, likely generated during macronuclear(somatic) amplification;(iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses;(v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall,these analyses indicate the need for careful consideration of SSU r DNAvariation in analyses of the role of ciliates in ecosystems.

关键词： ciliates SSU rDNA sequence variation phylogenetic analyses rDNA copy number ecological significance

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Bioinformatics analyses of differentially expressed genes associated with spinal cord injury:a microarray-based analysis in a mouse model

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Neural Regeneration Research 2019年第7期14卷 1262-1270页

作者： Lei Guo Jing Lv Yun-Fei Huang Ding-Jun Hao Ji-Jun Liu Department of Spinal Surgery Honghui HospitalXi'an Jiaotong University Department of Clinical Laboratory Honghui HospitalXi'an Jiaotong University

Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioin

关键词： nerve regeneration spinal cord injury differentially expressed genes bioinformatics analyses Database for Annotation,Visualization and Integrated Discovery analysis inflammation Kyoto Encyclopedia of Genes and Genomes pathway microarray transcription factors neural regeneration

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Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses

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International Journal of Oral Science 2018年第4期10卷 263-272页

作者： Susan Yost Philip Stashenko Yoonhee Choi Maria Kukuruzinska Caroline A.Genco Andrew Salama Ellen O.Weinberg Carolyn D.Kramer Jorge Frias-Lopez Forsyth Institute 245 First StreetCambridgeMA 02142USA Boston University Henry M.Goldman School of Dental Medicine 100 East Newton StreetBostonMA 02118USA Department of Integrative Physiology and Pathobiology Tufts University School of Medicine136 Harrison AvenueBostonMA 02111USA Department of Oral Biology College of DentistryUniversity of Florida1395 Center DriveGainesvilleFL 32610-0424USA

Oral squamous cell carcinoma(OSCC) is the most prevalent and most commonly studied oral cancer. However, there is a void regarding the role that the oral microbiome may play in OSCC. Although the relationship between microbial community composition and OSCC has been thoroughly investigated, microbial profiles of the human microbiome in cancer are understudied. Here we performed a small pilot study of community-wide metatranscriptome analysis to profile mRNA expression in the entire oral microbiome in OSCC to reveal molecular functions associated with this disease. Fusobacteria showed a statistically significantly higher number of transcripts at tumour sites and tumour-adjacent sites of cancer patients compared to the healthy controls analysed. Regardless of the community composition, specific metabolic signatures were consistently found in disease. Activities such as iron ion transport, tryptophanase activity, peptidase activities and superoxide dismutase were over-represented in tumour and tumour-adjacent samples when compared to the healthy controls. The expression of putative virulence factors in the oral communities associated with OSCC showed that activities related to capsule biosynthesis, flagellum synthesis and assembly, chemotaxis, iron transport, haemolysins and adhesins were upregulated at tumour sites. Moreover, activities associated with protection against reactive nitrogen intermediates, chemotaxis, flagellar and capsule biosynthesis were also upregulated in non-tumour sites of cancer patients. Although they are preliminary, our results further suggest that Fusobacteria may be the leading phylogenetic group responsible for the increase in expression of virulence factors in the oral microbiome of OSCC patients.

关键词： profiles analyses

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Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains

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Journal of Integrative Plant Biology 2020年第2期62卷 201-217页

作者： Pengfei Dong Xiaoyu Tu Haoxuan Li Jianhua Zhang Donald Grierson Pinghua Li Silin Zhong State Key Laboratory of Agrobiotechnology School of Life SciencesThe Chinese University of Hong KongHong KongChina Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Zhejiang UniversityHangzhou 310058China State Key Laboratory of Crop Biology College of AgronomyShandong Agricultural UniversityTai’an 271018China

Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation,which is best studied in the mammalian models.Using in situ Hi-C,we have compared the 3D chromatin architectures of rice mesophyll and endosperm,foxtail millet bundle sheath and mesophyll,and maize bundle sheath,mesophyll and endosperm tissues.We found that their global A/B compartment partitions are stable across tissues,while local A/B compartment has tissue-specific dynamic associated with differential gene expression.Plant domains are largely stable across tissues,while new domain border formations are often associated with transcriptional activation in the region.Genes inside plant domains are not conserved across species,and lack significant co-expression behavior unlike those in mammalian TADs.Although we only observed chromatin loops between gene islands in the large genomes,the maize loop gene pairs’syntenic orthologs have shorter physical distances in small genome monocots,suggesting that loops instead of domains might have conserved biological function.Our study showed that plants’chromatin features might not have conserved biological functions as the mammalian ones.

关键词： plant chromatin domains Tissue-specific Hi-C analyses rice

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Mathematical analyses of the GPS receiver interference tolerance and mean time to loss lock

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Defence Technology（防务技术） 2019年第3期15卷 440-449页

作者： Ehab M.Shaheen Sherif A.Elgamel Electronic Warfare Department Military Technical College

In this paper, novel mathematical expressions are derived for the Global Positioning System (GPS) receiver interference tolerance in the presence of different types of interference signals such as: continuous wave interference, narrowband interference, partial band interference, broadband interference, match spectrum interference and pulse interference. Also, in this paper the mean time to loss lock is determined in order to analyse the mentioned interferences effect on the GPS receiver. These derived analytical expressions are validated with the aid of extensive simulation experiments.

关键词： Mathematical analyses GPS receiver interference tolerance

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analyses of p-^(11)B,p-^(11)C and d-^(11)C Reactions

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Chinese journal of nuclear physics 1995年第1期17卷 60-66页

作者： Shen Qing-biao Zhang Jing-shang Han Yin-lu Bai Xi-xiang (China Institute of Atomic Energy,P.O.Box 275(41),Beijing 102413) 中国原子能科学院北京

Aiming at the production of 11C radioactive beam,various nuclear data ofp+11B reaction at incident proton energies spanning 1-25 MeV were obtained by calcu-lation with quasiquantum multistep direct （QMSD） theory and Hauser-Feshbach （HF）theory.The calculations basically agree with the experimental data.The angular distri-butions in lab frame of 11C produced in the reversed geometry reaction 1H(11B,11C)nwere deduced.The cross sections of p+11C and d+11C reactions induced by 11C beamwere also predicted.The results show that the experimental measurement for 11C+d re-action is more feasible than for 11C+p reaction at HI-13 tandem accelerator.

关键词： 11C Radioactive beam analyses

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Theory and Implementation of Sensitivity analyses Based on Their Algebraic Representation in the Graph Model

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Journal of Systems Science and Systems Engineering 2019年第5期28卷 580-601页

作者： Jinshuai Zhao Haiyan Xu Keith W.Hipel Baohua Yang College of Economics and Management Nanjing University of Aeronautics and Astronautics Nanjing 211106 China College of Computer Science and Technology Jiangsu Normal University Xuzhou 221116 China Department of Systems Design Engineering University of Waterloo Waterloo Canada School of Business Jiangsu Normal University Xuzhou 221116 China

Sensitivity analyses based on an algebraic representation in the graph model for conflict resolution (GMCR) are generalized for ascertaining the robustness of stability results by varying decision makers' preference ranking.The ordinal preferences in GMCR are advantageous to carry out sensitivity analyses with respect to systematically identifying the influence of preference alterations upon the four basic stabilities consisting of Nash stability,general metarationality,symmetric metarationality and sequential stability.The proposed algebraic representation of the four basic stabilities is not only effective and convenient for computer implementation of sensitivity analysis,but also makes it easier to understand the meaning of the four stabilities when compared with the existing matrix representation.Further,these sensitivity analyses results are embedded into the latest version of the decision support system NUAAGMCR,which can be used to study real-world conflicts.To illustrate how these contributions to sensitivity analyses can be applied in practice and provide valuable strategic insights,they are used to investigate the civil war conflict in South Sudan.

关键词： Sensitivity analyses algebraic expression graph model ordinal preference conflict resolution

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Entropy resistance analyses of a two-stream parallel flow heat exchanger with viscous heating

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Chinese Physics B 2013年第8期22卷 361-364页

作者：程雪涛梁新刚 Key Laboratory for Thermal Science and Power Engineering of Ministry of Education School of Aerospace Tsinghua University

Heat exchangers are widely used in industry, and analyses and optimizations of the performance of heat exchangers are important topics. In this paper, we define the concept of entropy resistance based on the entropy generation analyses of a one-dimensional heat transfer process. With this concept, a two-stream parallel flow heat exchanger with viscous heating is analyzed and discussed. It is found that the minimization of entropy resistance always leads to the maximum heat transfer rate for the discussed two-stream parallel flow heat exchanger, while the minimizations of entropy generation rate, entropy generation numbers, and revised entropy generation number do not always.

关键词： entropy generation minimization heat exchanger entropy resistance analyses

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Numerical analyses and experiment investigations of an annular micro gas turbine power system using fuels with low heating values

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Science China(Technological Sciences) 2009年第12期52卷 3565-3579页

作者： YANG ChunHsiang LEE ChengChia HSIAO JenHao CHEN ChiunHsun Department of Mechanical Engineering ‘National’Chiao Tung University

This study investigates the effects of using fuels with low heating values on the performance of an annular micro gas turbine(MGT)experimentally and numerically.The MGT used in this study is MW-54, whose original fuel is liquid(Jet A1).Its fuel supply system is re-designed to use biogas fuel with low heating value(LHV).The purpose is to reduce the size of a biogas distributed power supply system and to enhance its popularization.This study assesses the practicability of using fuels with LHVs by using various mixing ratios of methane(CH4)and carbon dioxide(CO2).Prior to experiments,the corresponding simulations,aided by the commercial code CFD-ACE+,were carried out to investigate the cooling effect in a perforated combustion chamber and combustion behavior in an annular MGT when LHV gas was used.The main purposes are to confirm that there are no hot spots occurring in the liners and the exhaust temperatures of combustor are lower than 700°C when MGT is operated under different conditions.In experiments,fuel pressure and mass flow rate,turbine rotational speed,generator power output,and temperature distribution were measured to analyze MGT performance.Experimental results indicate that the presented MGT system operates successfully under each tested condition when the minimum heating value of the simulated fuel is approximately 50%of pure methane.The power output is around 170 W at 85000 r/min as 90%CH4 with 10%CO2 is used and 70 W at 60000 r/min as 70%CH4 with 30%CO2 is used.When a critical limit of 60%CH4 is used,the power output is extremely low. Furthermore,the best theoretical Brayton cycle efficiency for such MGT is calculated as 23%according to the experimental data while LHV fuel is used.Finally,the numerical results and experiment results reveal that MGT performance can be improved further and the possible solutions for performance im- provement are suggested for the future studies.

关键词： numerical analyses experiment investigations annular micro gas turbine low heating values

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The application analyses for primary spectrum pyrometer

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Science China(Physics,Mechanics & Astronomy) 2007年第6期50卷 753-765页

作者： FU TaiRan1,CHENG XiaoFang2 & ZHONG MaoHua1 1 China Academy of Safety Science & Technology,Beijing 100029,China 2 Department of Thermal Science and Energy Engineering,University of Science and Technology of China,Hefei 230026,China China Academy of Safety Science & Technology Beijing China Department of Thermal Science and Energy Engineering University of Science and Technology of China Hefei China

In the applications of primary spectrum pyrometry,based on the dynamic range and the minimum sensibility of the sensor,the application issues,such as the measurement range and the measurement partition,were investigated through theoretical analyses. For a developed primary spectrum pyrometer,the theoretical predictions of measurement range and the distributions of measurement partition were presented through numerical simulations. And the measurement experiments of high-temperature blackbody and standard temperature lamp were processed to further verify the above theoretical analyses and numerical results. Therefore the research in the paper provides the helpful supports for the applications of primary spectrum pyrometer and other radiation pyrometers.

关键词： primary spectrum pyrometry, radiation temperature measurement, temperature, emissivity, measurement range, measurement partition In the applications of primary spectrum pyrometry, based on the dynamic range and the minimum sensibility of the sensor, the application issues, such as the measurement range and the measurement partition, were investigated through theoretical analyses. For a developed primary spectrum pyrometer, the theoretical predictions of measurement range and the distributions of measurement partition were presented through numerical simulations. And the measurement experiments of high-temperature blackbody and standard temperature lamp were processed to further verify the above theoretical analyses and numerical results. Therefore the research in the paper provides the helpful supports for the applications of primary spectrum pyrometer and other radiation pyrometers.……

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