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Transcriptional profile in response to ionizing radiation at low dose in Deinococcus radiodurans

Progress in Natural Science:Materials International 2007年第5期17卷 529-536页

作者： Chen huan, Xu Zhenjian , Tian Bing , Chen Weiwei , hu Songnian and hua Yuejin (Institute of Nuclear-Agricultural Science, Zhejiang University, Hangzhou 310029, China james D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China) Institute of Nuclear-Agricultural Science Zhejiang University Hangzhou 310029 China james D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 310008 China Beijing Institute of Genomics Chinese Academy of Sciences Beijing 101300 China

The genome-wide transcription profile of Deinococcus radiodurans cells was investigated after treatment with low dose irradiation (2 kGy). From the expression profile, we found that the process of DNA repair was induced in order, i.e. genes involved in base excision repair, nucleotide excision repair and single-strand annealing were induced immediately after ionizing radiation, and genes for recombination repair, including recA, recD and recQ were then activated. Especially, recD and recQ were specifically induced at low dose irradiation, and this phenomenon informed us that these two genes would play a certain role in anti-oxidation. Some genes such as ddrA and ssb were activated during the whole repair phase. Furthermore, the response of oxidative stress-related genes under low dose irradiation showed a different pattern from that of the acute high-level irradiation, many anti-oxidative genes were induced to scavenge reactive oxygen species directly, other associated systems also changed their expression patterns during the recovery time, such as iron metabolism systems, intracellular mutagenic precursors sanitize systems. These characteristics indicate that there is a powerful and orderly recovery process in Deinococcus radiodurans.

关键词： Deinococcus radiodurans microarry oxidative stress ionizing radiation.

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贾湖遗址人骨的元素分析

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人类学学报 2005年第2期24卷 158-165页

作者：胡耀武 james H.Burton 王昌燧中国科学院研究生院人文学院社科系北京100049 Laboratory for Archaeological Chemistry Department of Anthropology University of Wisconsin-Madison

古代人类食谱分析是生物考古重要组成部分,我国在此方面尚缺乏较为系统的研究。本文利用微量元素分析方法,对河南舞阳贾湖遗址人骨进行了元素分析,根据骨中log(Sr Ca)、log(Ba Ca)的变化,揭示了贾湖先民生活方式从狩猎、采集至稻作农业... 详细信息

古代人类食谱分析是生物考古重要组成部分,我国在此方面尚缺乏较为系统的研究。本文利用微量元素分析方法,对河南舞阳贾湖遗址人骨进行了元素分析,根据骨中log(Sr Ca)、log(Ba Ca)的变化,揭示了贾湖先民生活方式从狩猎、采集至稻作农业和家畜驯养的发展过程。同时指出,样品249的log(Sr Ca)、log(Ba Ca)异常,当与其迁徙活动相关。

关键词：贾湖遗址人骨微量元素分析组成部分生物考古古代人类生活方式发展过程稻作农业谱分析迁徙

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A Comprehensive Transcriptomic Analysis of Infant and Adult Mouse Ovary

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Genomics, Proteomics & Bioinformatics 2014年第5期12卷 239-248页

作者： Linlin Pan Wei Gong Yuanyuan Zhou Xiaonuan Li Jun Yu Songnian hu james D. Watson Institute of Genome Sciences Zhejiang University CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

Ovary development is a complex process involving numerous genes. A well-developed ovary is essential for females to keep fertility and reproduce offspring. In order to gain a better insight into the molecular mechanisms related to the process of mammalian ovary development, we performed a comparative transcriptomic analysis on ovaries isolated from infant and adult mice by using next-generation sequencing technology （SOLID）. We identified 15,454 and 16,646 trans- criptionally active genes at the infant and adult stage, respectively. Among these genes, we also identified 7021 differentially expressed genes. Our analysis suggests that, in general, the adult ovary has a higher level of transcriptomic activity. However, it appears that genes related to primordial follicle development, such as those encoding Figla and Nobox, are more active in the infant ovary, whereas expression of genes vital for follicle development, such as Gdj~, Bmp4 and Bmpl5, is upreg- ulated in the adult. These data suggest a dynamic shift in gene expression during ovary development and it is apparent that these changes function to facilitate follicle maturation, when additional func- tional gene studies are considered. Furthermore, our investigation has also revealed several impor- tant functional pathways, such as apoptosis, MAPK and steroid biosynthesis, that appear to be much more active in the adult ovary compared to those of the infant. These findings will provide a solid foundation for future studies on ovary development in mice and other mammals and help to expand our understanding of the complex molecular and cellular events that occur during postnatal ovary development.

关键词： Folliculogenesis Postnatal ovary develop-ment Transcriptome RNA-seq

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A Probe Into The Relation Between The Cooperative Principle And The Politeness Principle

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四川文理学院学报 1997年第3期 81-87页

作者： hu Shangtian 达县师范高等专科学校师资科长、讲师

*** 1967,***,Americanphilosopher and linguist,proposed theCooperative Principle(***)in theWilliam james lectures delivered at *** new theory brings about agreat development in the concept ofconversational implicature,and has beenattached great attention to in the *** critics set such high value uponthe notion that they regard it as abreakthrough in *** CP helps

关键词： In A Probe Into The Relation Between The Cooperative Principle And The Politeness Principle

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The community structure and microbial linkage of rumen protozoa and methanogens in response to the addition of tea seed saponins in the diet of beef cattle

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Journal of Animal Science and Biotechnology 2021年第1期12卷 272-281页

作者： Cui Tan Carlos A.Ramírez-Restrepo Ali Mujtaba Shah Rui hu Matt Bell Zhisheng Wang Chris McSweeney Institute of Animal Nutrition Sichuan Agricultural UniversityChengdu 611130SichuanChina Commonwealth Scientific and Industrial Research Organisation CSIRO Agriculture and FoodAustralian Tropical Sciences and Innovation PrecinctJames Cook UniversityTownsville QLD 4811Australia Present address:CR Eco-efficient Agriculture Consultancy(CREAC) 46 Bilbao PlaceBushland Beach QLD 4818Australia Department of Livestock Production Shaheed Benazir Bhutto University of Veterinary and Animal SciencesSakrandSindh 67210Pakistan “Low Carbon Breeding Cattle and Safety Production” University Key Laboratory of Sichuan ProvinceYa’an 625014SichuanChina School of Biosciences University of NottinghamSutton BoningtonLoughborough LE125RDUK CSIRO Agriculture Queensland BioScience PrecinctSt LuciaBrisbane QLD 4067Australia.

Background: This study investigated changes in rumen protozoal and methanogenic communities, along with the correlations among microbial taxa and methane(CH_4) production of six Belmont Red Composite beef steers fed tea seed saponins(TSS). Animals were fed in three consecutive feeding periods, a high-grain basal diet for 14 d(BD period) then a period of progressive addition of TSS to the basal diet up to 30 g/d for 20 d(TSS period), followed by the basal diet for 13 d without TSS(BDP post-control period).Results: The study found that TSS supplementation decreased the amount of the protozoal genus Entodinium and increased Polyplastron and Eudiplodinium genera. During BDP period, the protozoa community of steers did not return to the protozoal profiles observed in BD period, with higher proportions of Metadinium and Eudiplodinium and lower Isotricha. The addition of TSS was found to change the structure of methanogen community at the subgenus level by decreasing the abundance of methanogens in the SGMT clade and increasing the abundance of methanogens in the RO clade. The correlation analysis indicated that the abundance of SGMT clade methanogens were positively correlated with Isotricha, and Isotricha genus and SGMT clade methanogens were positively correlated with CH_4 production. While RO clade were positively correlated with the proportion of Metadinium genus, which was negatively correlated with CH_4 ***: These results suggest that different genera of rumen protozoa ciliates appear to be selectively inhibited by TSS, and the change in methanogen community at the subgenus level may be due to the mutualistic relationships between methanogens and rumen ciliates.

关键词： Beef steers Methane Methanogen Protozoa Tea seed saponin

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现代宇宙学的奠基人——james Peebles

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科学通报 2019年第36期64卷 3784-3788页

作者：胡彬北京师范大学天文系

2019年10月8日,瑞典诺贝尔评审委员会将今年的物理学奖颁发给3位天体物理学家james Peebles,Michel Mayor和Didier Queloz.其中james Peebles(图1)的获奖理由是他对物理宇宙学理论建立的贡献;而后两位科学家是由于发现首个绕类日恒星运... 详细信息

2019年10月8日,瑞典诺贝尔评审委员会将今年的物理学奖颁发给3位天体物理学家james Peebles,Michel Mayor和Didier Queloz.其中james Peebles(图1)的获奖理由是他对物理宇宙学理论建立的贡献;而后两位科学家是由于发现首个绕类日恒星运行的系外行星而获奖.相比于后两位获奖者,Peebles获得的更像是一个终身成就奖.鉴于笔者的研究方向同为理论宇宙学,在这里谨结合自身的研究经历谈一谈Peebles对现代宇宙学的贡献.

关键词： Nobel Prize cosmology cosmic mircowave background cosmic large scale structure formation

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High-brightness polarized light-emitting diodes

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Light(Science & Applications) 2012年第1期1卷 72-78页

作者： Elison Matioli Stuart Brinkley Kathryn M Kelchner Yan-Ling hu Shuji Nakamura Steven DenBaars james Speck Claude Weisbuch Department of Electrical Engineering and Computer Science Massachusetts Institute of TechnologyCambridgeMAUSA Department of Electrical and Computer Engineering University of CaliforniaSanta BarbaraCAUSA Materials Department University of CaliforniaSanta BarbaraCAUSA Laboratoire de Physique de la Matie`re Condense´e CNRSEcole PolytechniquePalaiseauFrance

Light-emitting diodes are becoming the alternative for future general lighting applications,with huge energy savings compared to conventional light sources owing to their high efficiency and *** light sources would largely enhance the efficiency in a number of applications,such as in liquid-crystal displays,and also greatly improve contrast in general illumination due to the reduction in indirect ***,we demonstrate light-emitting diodes presenting high-brightness polarized light emission by combining the polarization-preserving and directional extraction properties of embedded photonic-crystals applied to non-polar gallium nitride.A directional enhancement of up to 1.8-fold was observed in the total polarized light emission together with a high polarization degree of 88.7%at 465 *** discuss the mechanisms of polarized light emission in non-polar gallium nitride and the photonic-crystal design rules to further increase the light-emitting diode *** work could open the way to polarized white-light emitters through their association with polarization-preserving down-converting phosphors.

关键词： GaN LEDs m-plane polarized light

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SARS-CoV-2 Epitopes following Infection and Vaccination Overlap Known Neutralizing Antibody Sites

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Research 2022年第2期2022卷 71-84页

作者： Li Yang Te Liang Lane M.Pierson Hongye Wang Jesse K.Fletcher Shu Wang Duran Bao Lii Zhang Zhen huang Wenshu Zheng Xiaomei Zhang Heewon Park Yuwen Li james E.Robinson Amy K.Fechan Christopher J.Lyon Jing Cao Lisa A.Morici Chenzhong Li Chad J.Roy Xiaobo Yu Tony hu Center for Cllular and Molecular Diagnostics Tulane University Schoo of Medicine1430 Tulane AveNew OrleansLA 70112USA Department of Biochemisty and Molecular Biology Tulane University School of Medicine1430 Tulane AveNew OrleansLA 70112USA Beijing Key Laboratory for Forest Pest Control Bejjing Foresiry UniersilyBeijing 10083.China State Key Laboratory of Proteommics Beijing Protcome Resarch CenterNattional Center for Protein Sciences-Beiing(PHOENIX Center)Beijing Institute of LijfeomicsBeijing 102206China Hayward Genetis Cener Department of PediatricsTulane Universily School of Medicine1430 Tulane AveNew OrleansLA 70112USA Department of Pediatrics Tulane Uhriversity School of Medicine1430 Ttulane AveNew OrleansLA 70112USA Infectious Disease Depariment Ochsner Clinic FoundationNew OrleansLA 70121USA Universty of Texas Souhwestern Medical Cener 5323 Harry Himes BlvdDallasTX 75390USA Department of Microbiology Imruolog Tulane Untiversity School of Medicine 1430 Tulane AveNew OrleansLA 70112USA Division of Microbiology Tulane National Primate Research Center18703 Three Rivers RoadCovingtonLA 70433USA

Identification of epitopes targeted following virus infection or vaccination can guide vaccine design and development of therapeutic interventions targeting functional sites,but can be ***,we employed peptide microarrays to map linear peptide epitopes(LPEs)recognized following SARS-CoV-2 infetion and *** detected by nonhuman primate(NHP)and patient IgMs after SARS-CoV-2 infection extensively overlapped,localized to functionally important virus regions,and aligned with reported neutralizing antibody binding *** LPE overlap occurred atfter infection and vaccination,with LPE clusters specifc to each stimulus,where strong and conserved LPEs mapping to sites known or likely to inhibit spike protein ***-specifc LPEs tended to map to sites known or likely to be afected by structural changes induced by the proline substitutions in the mRNA vaccine's S *** LPEs to regions of known functional importance in this manner may acelerate vaccine evaluation and discovery of targets for sile secific therapeutic interventions.

关键词： vaccine Antibody likely

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BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data

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Genomics, Proteomics & Bioinformatics 2011年第6期9卷 238-244页

作者： Tongwu Zhang Yingfeng Luo Kan Liu Linlin Pan Bing Zhang Jun Yu Songnlan hu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China james D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 31007 China

The emergence of next-generation sequencing （NGS） technologies has significantly improved sequencing throughput and reduced costs. However, the short read length, duplicate reads and massive volume of data make the data processing much more difficult and complicated than the first-generation sequencing technology. Al- though there are some software packages developed to assess the data quality, those packages either are not easily available to users or require bioinformatics skills and computer resources. Moreover, almost all the quality assessment software currently available didn＇t taken into account the sequencing errors when dealing with the du- plicate assessment in NGS data. Here, we present a new user-friendly quality assessment software package called BIGpre, which works for both Illumina and 454 platforms. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well. BIGpre is primarily written in Perl and integrates graphical capability from the statistics package R. This package produces both tabular and graphical summaries of data quality for sequencing datasets from Illumina and 454 platforms. Processing hundreds of millions reads within minutes, this package provides immediate diagnostic information for user to manipulate sequencing data for downstream analyses. BIGpre is freely available at http：//***/.

关键词： next-generation sequencing quality assessment duplicate reads sequencing error

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Particle deposition in a gas-finger propagating in a liquidfilled channel

Particle deposition in a gas-finger propagating in a liquidf...

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中国力学大会-2015

作者： Chen Yi-Cheng hu Yingying Tai Cheng-Feng Za-mankhan Parsa Lin San-Yih Filoche Marcel Grotberg james B. The Department of Biomedical Engineering the University of Michigan The Department of Aeronautics and Astronautics National Cheng Kung University Physique de la Matiere Condensee Ecole PolytechniqueCNRS

We investigate deposition of particles in a two-dimensional gas-finger.A finite volume method is used to discretize the continuity and Navier-Stokes equations in the moving frame(fixed at the gas-finger tip).The pressure correction-volume of fluid method is applied to solve the two-phase fluid *** Stokes drag force is used to calculate the particles motion and deposition in the two-phase flow.

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