Browsing by Author "Zhang, Yan"

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    Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages
    Mian, M. A. Rouf; Zhang, Yan; Wang, Zeng-Yu; Zhang, Ji-Yi; Cheng, Xiaofei; Chen, Lei; Chekhovskiy, Konstantin; Dai, Xinbin; Mao, Chunhong; Cheung, Foo; Zhao, Xuechun; He, Ji; Scott, Angela D.; Town, Christopher D.; May, Gregory D. (2008-03-04)
    Background Tall fescue (Festuca arundinacea Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence tag (EST) database developed from nine cDNA libraries representing tissues from different plant organs, developmental stages, and abiotic stress factors. The results of inter-library and library-specific in silico expression analyses of these ESTs are also reported. Results A total of 41,516 ESTs were generated from nine cDNA libraries of tall fescue representing tissues from different plant organs, developmental stages, and abiotic stress conditions. The Festuca Gene Index (FaGI) has been established. To date, this represents the first publicly available tall fescue EST database. In silico gene expression studies using these ESTs were performed to understand stress responses in tall fescue. A large number of ESTs of known stress response gene were identified from stressed tissue libraries. These ESTs represent gene homologues of heat-shock and oxidative stress proteins, and various transcription factor protein families. Highly expressed ESTs representing genes of unknown functions were also identified in the stressed tissue libraries. Conclusion FaGI provides a useful resource for genomics studies of tall fescue and other closely related forage and turf grass species. Comparative genomic analyses between tall fescue and other grass species, including ryegrasses (Lolium sp.), meadow fescue (F. pratensis) and tetraploid fescue (F. arundinacea var glaucescens) will benefit from this database. These ESTs are an excellent resource for the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) PCR-based molecular markers.
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    An attenuated Lassa vaccine in SIV-infected rhesus macaques does not persist or cause arenavirus disease but does elicit Lassa virus-specific immunity
    Zapata, Juan Carlos; Poonia, Bhawna; Bryant, Joseph; Davis, Harry; Ateh, Eugene; George, Lanea; Crasta, Oswald R.; Zhang, Yan; Slezak, Tom; Jaing, Crystal; Pauza, C. D.; Goicochea, Marco; Moshkoff, Dmitry; Lukashevich, Igor S.; Salvato, Maria S. (2013-02-12)
    Background Lassa hemorrhagic fever (LHF) is a rodent-borne viral disease that can be fatal for human beings. In this study, an attenuated Lassa vaccine candidate, ML29, was tested in SIV-infected rhesus macaques for its ability to elicit immune responses without instigating signs pathognomonic for arenavirus disease. ML29 is a reassortant between Lassa and Mopeia viruses that causes a transient infection in non-human primates and confers sterilizing protection from lethal Lassa viral challenge. However, since the LHF endemic area of West Africa also has high HIV seroprevalence, it is important to determine whether vaccination could be safe in the context of HIV infection. Results SIV-infected and uninfected rhesus macaques were vaccinated with the ML29 virus and monitored for specific humoral and cellular immune responses, as well as for classical and non-classical signs of arenavirus disease. Classical disease signs included viremia, rash, respiratory distress, malaise, high liver enzyme levels, and virus invasion of the central nervous system. Non-classical signs, derived from profiling the blood transcriptome of virulent and non-virulent arenavirus infections, included increased expression of interferon-stimulated genes (ISG) and decreased expression of COX2, IL-1β, coagulation intermediates and nuclear receptors needed for stress signaling. All vaccinated monkeys showed ML29-specific antibody responses and ML29-specific cell-mediated immunity. Conclusion SIV-infected and uninfected rhesus macaques responded similarly to ML29 vaccination, and none developed chronic arenavirus infection. Importantly, none of the macaques developed signs, classical or non-classical, of arenavirus disease.
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    Body Weight Selection Affects Quantitative Genetic Correlated Responses in Gut Microbiota
    Meng, He; Zhang, Yan; Zhao, Lele; Zhao, Wenjing; He, Chuan; Honaker, Christa F.; Zhai, Zhengxiao; Sun, Zikui; Siegel, Paul B. (PLOS, 2014-03-07)
    The abundance of gut microbiota can be viewed as a quantitative trait, which is affected by the genetics and environment of the host. To quantify the effects of host genetics, we calculated the heritability of abundance of specific microorganisms and genetic correlations among them in the gut microbiota of two lines of chickens maintained under the same husbandry and dietary regimes. The lines, which originated from a common founder population, had undergone >50 generations of selection for high (HW) or low (LW) 56-day body weight and now differ by more than 10-fold in body weight at selection age. We identified families of Paenibacillaceae, Streptococcaceae, Helicobacteraceae, and Burkholderiaceae that had moderate heritabilities. Although there were no obvious phenotypic correlations among gut microbiota, significant genetic correlations were observed. Moreover, the effects were modified by genetic selection for body weight, which altered the quantitative genetic background of the host. Heritabilities for Bacillaceae, Flavobacteriaceae, Helicobacteraceae, Comamonadaceae, Enterococcaceae, and Streptococcaceae were moderate in LW line and little to zero in the HW line. These results suggest that loci associated with these microbiota families, while exhibiting genetic variation in LW, have been fixed in HW line. Also, long term selection for body weight has altered the genetic correlations among gut microbiota. No microbiota families had significant heritabilities in both the LW and HW lines suggesting that the presence and/or absence of a particular microbiota family either has a strong growth promoting or inhibiting effect, but not both. These results demonstrate that the quantitative genetics of the host have considerable influence on the gut microbiota.
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    Charge distribution guided by grain crystallographic orientations in polycrystalline battery materials
    Xu, Zhengrui; Jiang, Zhisen; Kuai, Chunguang; Xu, Rong; Qin, Changdong; Zhang, Yan; Rahman, Muhammad Mominur; Wei, Chenxi; Nordlund, Dennis; Sun, Cheng-Jun; Xiao, Xianghui; Du, Xi-Wen; Zhao, Kejie; Yan, Pengfei; Liu, Yijin; Lin, Feng (2020-01-08)
    Architecting grain crystallographic orientation can modulate charge distribution and chemomechanical properties for enhancing the performance of polycrystalline battery materials. However, probing the interplay between charge distribution, grain crystallographic orientation, and performance remains a daunting challenge. Herein, we elucidate the spatially resolved charge distribution in lithium layered oxides with different grain crystallographic arrangements and establish a model to quantify their charge distributions. While the holistic "surface-to-bulk" charge distribution prevails in polycrystalline particles, the crystallographic orientation-guided redox reaction governs the charge distribution in the local charged nanodomains. Compared to the randomly oriented grains, the radially aligned grains exhibit a lower cell polarization and higher capacity retention upon battery cycling. The radially aligned grains create less tortuous lithium ion pathways, thus improving the charge homogeneity as statistically quantified from over 20 million nanodomains in polycrystalline particles. This study provides an improved understanding of the charge distribution and chemomechanical properties of polycrystalline battery materials.
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    Dynamics of Small Non-coding RNA Profiles and the Intestinal Microbiome of High and Low Weight Chickens
    Zhou, Hao; Yang, Lingyu; Ding, Jinmei; Xu, Ke; Liu, Jiajia; Zhu, Wenqi; Zhu, Jianshen; He, Chuan; Han, Chengxiao; Qin, Chao; Luo, Huaixi; Chen, Kangchun; Zheng, Yuming; Honaker, Christa F.; Zhang, Yan; Siegel, Paul B.; Meng, He (Frontiers, 2022-06-30)
    The host and its symbiotic bacteria form a biological entity, holobiont, in which they share a dynamic connection characterized by symbiosis, co-metabolism, and coevolution. However, how these collaborative relationships were maintained over evolutionary time remains unclear. In this research, the small non-coding RNA (sncRNA) profiles of cecum and their bacteria contents were measured from lines of chickens that have undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. The results from these lines that originated from a common founder population and maintained under the same husbandry showed an association between host intestinal sncRNA expression profile (miRNA, lncRNA fragment, mRNA fragment, snoRNA, and snRNA) and intestinal microbiota. Correlation analyses suggested that some central miRNAs and mRNA fragments had interactions with the abundance of intestinal microbial species and microbiota functions. miR-6622-3p, a significantly differentially expressed (DE) miRNA was correlated with a body weight gain related bacterium, Alistipes putredinis. Our results showed that host sncRNAs may be mediators of interaction between the host and its intestinal microbiome. This provides additional clue for holobiont concepts.
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    A feminizing switch in a hemimetabolous insect
    Zhuo, Ji-Chong; Zhang, Hou-Hong; Hu, Qing-Ling; Zhang, Jin-Li; Lu, Jia-Bao; Li, Han-Jing; Xie, Yu-Cheng; Wang, Wei-Wei; Zhang, Yan; Wang, Hai-Qiang; Huang, Hai-Jian; Lu, Gang; Chen, Jian-Ping; Li, Jun-Min; Tu, Zhijian Jake; Zhang, Chuan-Xi (AAAS, 2021-11-01)
    The mechanism of sex determination remains poorly understood in hemimetabolous insects. Here, in the brown planthopper (BPH), Nilaparvata lugens, a hemipteran rice pest, we identified a feminizing switch or a female determiner (Nlfmd) that encodes a serine/arginine-rich protein. Knockdown of Nlfmd in female nymphs resulted in masculinization of both the somatic morphology and doublesex splicing. The female-specific isoform of Nlfmd, Nlfmd-F, is maternally deposited and zygotically transcribed. Depletion of Nlfmd by maternal RNAi or CRISPR-Cas9 resulted in female-specific embryonic lethality. Knockdown of an hnRNP40 family gene named female determiner 2 (Nlfmd2) also conferred masculinization. In vitro experiments showed that an Nlfmd2 isoform, NlFMD2340, bound the RAAGAA repeat motif in the Nldsx pre-mRNA and formed a protein complex with NlFMD-F to modulate Nldsx splicing, suggesting that NlFMD2 may function as an RNA binding partner of the feminizing switch NlFMD. Our results provide novel insights into the diverse mechanisms of insect sex determination.
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    Genome sequences of wild and domestic bactrian camels
    Jirimutu; Wang, Zhen; Ding, Guohui; Chen, Gangliang; Sun, Yamin; Sun, Zhihong; Zhang, Heping; Wang, Lei; Hasi, Surong; Zhang, Yan; Li, Jianmei; Shi, Yixiang; Xu, Ze; He, Chuan; Yu, Siriguleng; Li, Shengdi; Zhang, Wenbin; Batmunkh, Mijiddorj; Ts, Batsukh; Narenbatu; Unierhu; Bat-Ireedui, Shirzana; Gao, Hongwei; Baysgalan, Banzragch; Li, Qing; Jia, Zhiling; Turigenbayila; Subudenggerile; Narenmanduhu; Wang, Zhaoxia; Wang, Juan; Pan, Lei; Chen, Yongcan; Ganerdene, Yaichil; Dabxilt; Erdemt; Altansha; Altansukh; Liu, Tuya; Cao, Minhui; Aruuntsever; Bayart; Hosblig; He, Fei; Zha-ti, A.; Zheng, Guangyong; Qiu, Feng; Sun, Zikui; Zhao, Lele; Zhao, Wenjing; Liu, Baohong; Li, Chao; Chen, Yunqin; Tang, Xiaoyan; Guo, Chunyan; Liu, Wei; Ming, Liang; Temuulen; Cui, Aiying; Li, Yi; Gao, Junhui; Li, Jing; Wurentaodi; Niu, Shen; Sun, Tao; Zhai, Zhengxiao; Zhang, Min; Chen, Chen; Baldan, Tunteg; Bayaer, Tuman; Li, Yixue; Meng, He (Springer Nature, 2012-11)
    Bactrian camels serve as an important means of transportation in the cold desert regions of China and Mongolia. Here we present a 2.01 Gb draft genome sequence from both a wild and a domestic bactrian camel. We estimate the camel genome to be 2.38 Gb, containing 20,821 protein-coding genes. Our phylogenomics analysis reveals that camels shared common ancestors with other even-toed ungulates about 55-60 million years ago. Rapidly evolving genes in the camel lineage are significantly enriched in metabolic pathways, and these changes may underlie the insulin resistance typically observed in these animals. We estimate the genome-wide heterozygosity rates in both wild and domestic camels to be 1.0 x 10(-3). However, genomic regions with significantly lower heterozygosity are found in the domestic camel, and olfactory receptors are enriched in these regions. Our comparative genomics analyses may also shed light on the genetic basis of the camel's remarkable salt tolerance and unusual immune system.
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    Gut Microbiota Co-microevolution with Selection for Host Humoral Immunity
    Yang, Lingyu; Liu, Shuyun; Ding, Jinmei; Dai, Ronghua; He, Chuan; Xu, Ke; Honaker, Christa F.; Zhang, Yan; Siegel, Paul B.; Meng, He (Frontiers, 2017-07-04)
    To explore coevolution between the gut microbiota and the humoral immune system of the host, we used chickens as the model organism. The host populations were two lines (HAS and LAS) developed from a common founder that had undergone 40 generations of divergent selection for antibody titers to sheep red blood cells (SRBC) and two relaxed sublines (HAR and LAR). Analysis revealed that microevolution of host humoral immunity contributed to the composition of gut microbiota at the taxa level. Relaxing selection enriched some microorganisms whose functions were opposite to host immunity. Particularly, Ruminococcaceae and Oscillospira enriched in high antibody relaxed (HAR) and contributed to reduction in antibody response, while Lactobacillus increased in low antibody relaxed (LAR) and elevated the antibody response. Microbial functional analysis showed that alterations were involved in pathways relating to the immune system and infectious diseases. Our findings demonstrated co-microevolution relationships of host-microbiota and that gut microorganisms influenced host immunity.
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    Identification of a Common Lupus Disease-Associated microRNA Expression Pattern in Three Different Murine Models of Lupus
    Dai, Rujuan; Zhang, Yan; Khan, Deena; Heid, Bettina; Caudell, David L.; Crasta, Oswald R.; Ahmed, Sattar Ansar (PLOS, 2010-12-10)
    Background Recent reports have shown that microRNAs (miRNAs) regulate vital immunological processes and have emerged as key regulators of immune system development and function. Therefore, it is important to determine miRNA dysregulation and its pathogenic contribution in autoimmune diseases, an aspect not adequately addressed thus far. Methodology/Principal Findings In this study, we profiled miRNA expressions in splenic lymphocytes from three murine lupus models (MRL-lpr, B6-lpr and NZB/WF1) with different genetic background by miRNA microarray assays and Real-time RT-PCR. Despite the genetic differences among these three lupus stains, a common set of dysregulated miRNAs (miR-182-96-183 cluster, miR-31, and miR-155) was identified in splenocytes when compared with age-matched control mice. The association of these miRNAs with the disease was highlighted by our observation that this miRNA expression pattern was evident in NZB/W mice only at an age when lupus disease is manifested. Further, we have shown that the miRNA dysregulation in MRL-lpr mice was not simply due to the activation of splenocytes. By Real-time RT-PCR, we confirmed that these miRNAs were upregulated in both purified splenic B and T cells from MRL-lpr mice. miR-127 and miR-379, which were greatly upregulated in splenocytes from lpr mice, were moderately increased in diseased NZB/W mice. In addition, Real-time RT-PCR revealed that miR-146a, miR-101a, and miR-17-92 were also markedly upregulated in splenic T, but not B cells from MRL-lpr mice. Conclusions/Significance The identification of common lupus disease-associated miRNAs now forms the basis for the further investigation of the pathogenic contribution of these miRNAs in autoimmune lupus, which will advance our knowledge of the role of miRNAs in autoimmunity. Given that miRNAs are conserved, with regard to both evolution and function, our observation of a common lupus disease-associated miRNA expression pattern in murine lupus models is likely to have significant pathogenic, diagnostic, and/or therapeutic implications in human lupus.
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    Measurement of the B0 lifetime and flavor-oscillation frequency using hadronic decays reconstructed in 2019-2021 Belle II data
    Ablikim, M.; Achasov, M. N.; Adlarson, P.; Ahmed, S.; Albrecht, M.; Amoroso, A.; An, Q.; Bai, X. H.; Bai, Y.; Bakina, O.; Ferroli, R. Baldini; Balossino, I.; Ban, Y.; Begzsuren, K.; Bennett, J.; Berger, N.; Bertani, M.; Bettoni, D.; Bianchi, F.; Biernat, J.; Bloms, J.; Bortone, A.; Boyko, I.; Briere, R. A.; Cai, H.; Cai, X.; Calcaterra, A.; Cao, G. F.; Cao, N.; Cetin, S. A.; Chang, J. F.; Chang, W. L.; Chelkov, G.; Chen, D. Y.; Chen, G.; Chen, H. S.; Chen, M. L.; Chen, S. J.; Chen, X. R.; Chen, Y. B.; Cheng, W.; Cibinetto, G.; Cossio, F.; Cui, X. F.; Dai, H. L.; Dai, J. P.; Dai, X. C.; Dbeyssi, A.; de Boer, R. B.; Dedovich, D.; Deng, Z. Y.; Denig, A.; Denysenko, I.; Destefanis, M.; De Mori, F.; Ding, Y.; Dong, C.; Dong, J.; Dong, L. Y.; Dong, M. Y.; Du, S. X.; Fang, J.; Fang, S. S.; Fang, Y.; Farinelli, R.; Fava, L.; Feldbauer, F.; Felici, G.; Feng, C. Q.; Fritsch, M.; Fu, C. D.; Fu, Y.; Gao, X. L.; Gao, Y.; Gao, Y.; Gao, Y. G.; Garzia, I.; Gersabeck, E. M.; Gilman, A.; Goetzen, K.; Gong, L.; Gong, W. X.; Gradl, W.; Greco, M.; Gu, L. M.; Gu, M. H.; Gu, S.; Gu, Y. T.; Guan, C. Y.; Guo, A. Q.; Guo, L. B.; Guo, R. P.; Guo, Y. P.; Guskov, A.; Han, S.; Han, T. T.; Han, T. Z.; Hao, X. Q.; Harris, F. A.; He, K. L.; Heinsius, F. H.; Held, T.; Heng, Y. K.; Himmelreich, M.; Holtmann, T.; Hou, Y. R.; Hou, Z. L.; Hu, H. M.; Hu, J. F.; Hu, T.; Hu, Y.; Huang, G. S.; Huang, L. Q.; Huang, X. T.; Huesken, N.; Hussain, T.; Andersson, W. Ikegami; Imoehl, W.; Irshad, M.; Jaeger, S.; Ji, Q.; Ji, Q. P.; Ji, X. B.; Ji, X. L.; Jiang, H. B.; Jiang, X. S.; Jiang, X. Y.; Jiao, J. B.; Jiao, Z.; Jin, S.; Jin, Y.; Johansson, T.; Kalantar-Nayestanaki, N.; Kang, X. S.; Kappert, R.; Kavatsyuk, M.; Ke, B. C.; Keshk, I. K.; Khoukaz, A.; Kiese, P.; Kiuchi, R.; Kliemt, R.; Koch, L.; Kolcu, O. B.; Kopf, B.; Kuemmel, M.; Kuessner, M.; Kupsc, A.; Kurth, M. G.; Kuehn, W.; Lane, J. J.; Lange, J. S.; Larin, P.; Lavezzi, L.; Leithoff, H.; Lellmann, M.; Lenz, T.; Li, C.; Li, C. H.; Li, Cheng; Li, D. M.; Li, F.; Li, G.; Li, H. B.; Li, H. J.; Li, J. L.; Li, J. Q.; Li, Ke; Li, L. K.; Li, Lei; Li, P. L.; Li, P. R.; Li, W. D.; Li, W. G.; Li, X. H.; Li, X. L.; Li, Z. B.; Li, Z. Y.; Liang, H.; Liang, H.; Liang, Y. F.; Liang, Y. T.; Liao, L. Z.; Libby, J.; Lin, C. X.; Liu, B.; Liu, B. J.; Liu, C. X.; Liu, D.; Liu, D. Y.; Liu, F. H.; Liu, Fang; Liu, Feng; Liu, H. B.; Liu, H. M.; Liu, Huanhuan; Liu, Huihui; Liu, J. B.; Liu, J. Y.; Liu, K.; Liu, K. Y.; Liu, Ke; Liu, L.; Liu, L. Y.; Liu, Q.; Liu, S. B.; Liu, T.; Liu, X.; Liu, Y. B.; Liu, Z. A.; Liu, Zhiqing; Long, Y. F.; Lou, X. C.; Lu, H. J.; Lu, J. D.; Lu, J. G.; Lu, X. L.; Lu, Y.; Lu, Y. P.; Luo, C. L.; Luo, M. X.; Luo, P. W.; Luo, T.; Luo, X. L.; Lusso, S.; Lyu, X. R.; Ma, F. C.; Ma, H. L.; Ma, L. L.; Ma, M. M.; Ma, Q. M.; Ma, R. Q.; Ma, R. T.; Ma, X. N.; Ma, X. X.; Ma, X. Y.; Ma, Y. M.; Maas, F. E.; Maggiora, M.; Maldaner, S.; Malde, S.; Malik, Q. A.; Mangoni, A.; Mao, Y. J.; Mao, Z. P.; Marcello, S.; Meng, Z. X.; Messchendorp, J. G.; Mezzadri, G.; Min, T. J.; Mitchell, R. E.; Mo, X. H.; Mo, Y. J.; Muchnoi, N. Yu; Muramatsu, H.; Nakhoul, S.; Nefedov, Y.; Nerling, F.; Nikolaev, I. B.; Ning, Z.; Nisar, S.; Olsen, S. L.; Ouyang, Q.; Pacetti, S.; Pan, Y.; Pan, Y.; Papenbrock, M.; Pathak, A.; Patteri, P.; Pelizaeus, M.; Peng, H. P.; Peters, K.; Pettersson, J.; Ping, J. L.; Ping, R. G.; Pitka, A.; Poling, R.; Prasad, V.; Qi, H.; Qi, M.; Qi, T. Y.; Qian, S.; Qiao, C. F.; Qin, L. Q.; Qin, X. P.; Qin, X. S.; Qin, Z. H.; Qiu, J. F.; Qu, S. Q.; Rashid, K. H.; Ravindran, K.; Redmer, C. F.; Rivetti, A.; Rodin, V.; Rolo, M.; Rong, G.; Rosner, Ch; Rump, M.; Sarantsev, A.; Savrie, M.; Schelhaas, Y.; Schnier, C.; Schoenning, K.; Shan, W.; Shan, X. Y.; Shao, M.; Shen, C. P.; Shen, P. X.; Shen, X. Y.; Shi, H. C.; Shi, R. S.; Shi, X.; Shi, X. D.; Song, J. J.; Song, Q. Q.; Song, Y. X.; Sosio, S.; Spataro, S.; Sui, F. F.; Sun, G. X.; Sun, J. F.; Sun, L.; Sun, S. S.; Sun, T.; Sun, W. Y.; Sun, Y. J.; Sun, Y. K.; Sun, Y. Z.; Sun, Z. T.; Tan, Y. X.; Tang, C. J.; Tang, G. Y.; Thoren, V.; Tsednee, B.; Uman, I.; Wang, B.; Wang, B. L.; Wang, C. W.; Wang, D. Y.; Wang, H. P.; Wang, K.; Wang, L. L.; Wang, M.; Wang, M. Z.; Wang, Meng; Wang, W. P.; Wang, X.; Wang, X. F.; Wang, X. L.; Wang, Y.; Wang, Y.; Wang, Y. D.; Wang, Y. F.; Wang, Y. Q.; Wang, Z.; Wang, Z. Y.; Wang, Ziyi; Wang, Zongyuan; Weber, T.; Wei, D. H.; Weidenkaff, P.; Weidner, F.; Wen, H. W.; Wen, S. P.; White, D. J.; Wiedner, U.; Wilkinson, G.; Wolke, M.; Wollenberg, L.; Wu, J. F.; Wu, L. H.; Wu, L. J.; Wu, Z.; Xia, L.; Xiao, S. Y.; Xiao, Y. J.; Xiao, Z. J.; Xie, Y. G.; Xie, Y. H.; Xing, T. Y.; Xiong, X. A.; Xu, G. F.; Xu, J. J.; Xu, Q. J.; Xu, W.; Xu, X. P.; Yan, L.; Yan, W. B.; Yan, W. C.; Yang, H. J.; Yang, H. X.; Yang, L.; Yang, R. X.; Yang, S. L.; Yang, Y. H.; Yang, Y. X.; Yang, Yifan; Yang, Zhi; Ye, M.; Ye, M. H.; Yin, J. H.; You, Z. Y.; Yu, B. X.; Yu, C. X.; Yu, G.; Yu, J. S.; Yu, T.; Yuan, C. Z.; Yuan, W.; Yuan, X. Q.; Yuan, Y.; Yue, C. X.; Yuncu, A.; Zafar, A. A.; Zeng, Y.; Zhang, B. X.; Zhang, Guangyi; Zhang, H. H.; Zhang, H. Y.; Zhang, J. L.; Zhang, J. Q.; Zhang, J. W.; Zhang, J. Y.; Zhang, J. Z.; Zhang, Jianyu; Zhang, Jiawei; Zhang, L.; Zhang, Lei; Zhang, S.; Zhang, S. F.; Zhang, T. J.; Zhang, X. Y.; Zhang, Y.; Zhang, Y. H.; Zhang, Y. T.; Zhang, Yan; Zhang, Yao; Zhang, Yi; Zhang, Z. H.; Zhang, Z. Y.; Zhao, G.; Zhao, J.; Zhao, J. Y.; Zhao, J. Z.; Zhao, Lei; Zhao, Ling; Zhao, M. G.; Zhao, Q.; Zhao, S. J.; Zhao, Y. B.; Zhao, Z. G.; Zhemchugov, A.; Zheng, B.; Zheng, J. P.; Zheng, Y.; Zheng, Y. H.; Zhong, B.; Zhong, C.; Zhou, L. P.; Zhou, Q.; Zhou, X.; Zhou, X. K.; Zhou, X. R.; Zhu, A. N.; Zhu, J.; Zhu, K.; Zhu, K. J.; Zhu, S. H.; Zhu, W. J.; Zhu, X. L.; Zhu, Y. C.; Zhu, Z. A.; Zou, B. S.; Zou, J. H. (American Physical Society, 2023-05-15)
    We measure the B0 lifetime and flavor-oscillation frequency using B0→D(∗)-π+ decays collected by the Belle II experiment in asymmetric-energy e+e- collisions produced by the SuperKEKB collider operating at the ϒ(4S) resonance. We fit the decay-time distribution of signal decays, where the initial flavor is determined by identifying the flavor of the other B meson in the event. The results, based on 33000 signal decays reconstructed in a data sample corresponding to 190 fb-1, are τB0=(1.499±0.013±0.008) ps, Δmd=(0.516±0.008±0.005) ps-1, where the first uncertainties are statistical and the second are systematic. These results are consistent with the world-average values.
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    Miniature fiber-optic multicavity Fabry-Perot interferometric biosensor
    Zhang, Yan (Virginia Tech, 2005-12-06)
    Fiber-optic Fabry-Perot interferometric (FFPI) sensors have been widely used due to their high sensitivity, ease of fabrication, miniature size, and capability for multiplexing. However, direct measurement of self-assembled thin films, receptor immobilization process or biological reaction is limited in the FFPI technique due to the difficulty of forming Fabry-Perot cavities by the thin film itself. Novel methods are needed to provide an accurate and reliable measurement for monitoring the thin-film growth in the nanometer range and under various conditions. In this work, two types of fiber-optic multicavity Fabry-Perot interferometric (MFPI) sensors with built-in temperature compensation were designed and fabricated for thin-film measurement, with applications in chemical and biological sensing. Both the tubing-based MFPI sensor and microgap MFPI sensor provide simple, yet high performance solutions for thin-film sensing. The temperature dependence of the sensing cavity is compensated by extracting the temperature information from a second multiplexed cavity. This provides the opportunity to examine the thin-film characteristics under different environment temperatures. To demonstrate the potential of this structure for practical applications, immunosensors were fabricated and tested using these structures. Self-assembled polyelectrolytes served as a precursor film for immobilization of antibodies to ensure they retain their biological activity. This not only provides a convenient method for protein immobilization but also presents the possibility of increasing the binding capacity and sensitivity by incorporating multilayers of antibodies into polyelectrolyte layers. The steady-state measurement demonstrated the surface concentration and binding ratio of the immunoreaction. Analysis of the kinetic binding profile provided a fast and effective way to measure antigen concentration. Monitoring the immunoreaction between commercially available immunoglobulin G (IgG) and anti-IgG demonstrated the feasibility of using the MFPI sensing system for immunosensing applications.
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    Nitrification in premise plumbing and its effect on corrosion and water quality degradation
    Zhang, Yan (Virginia Tech, 2008-12-03)
    Nitrification is increasingly of concern in US potable water systems, due to changes from chlorine to chloramine as a secondary disinfectant in order to comply with new regulations for disinfectant by-products. The ammonia that is released from the chloramine decay supports nitrification. A comprehensive literature review systematically examined the complex inter-relationships between nitrification, materials corrosion and metals release. That analysis suggested that nitrification could accelerate decay of chloramine, enhance corrosion of water distribution system materials, and increase leaching of lead and copper to potable water under at least some circumstances. Moreover, that certain plumbing materials would inhibit nitrification, but that in other situations the plumbing materials would enhance nitrification. Experiments verified that nitrification could affect the relative efficacy of chlorine versus chloramine in controlling heterotrophic bacteria in premise plumbing. Without nitrification, chloramine was always more persistent and effective than chlorine in controlling biofilms. But with nitrification and in pipe materials that are relatively non-reactive with chlorine, chloramine was much less persistent and less effective than chlorine. In materials that are reactive with chlorine such as iron pipes, the relative efficacy of chloramine versus chlorine depends on the relative rate of corrosion and rate of nitrification. High rates of corrosion and low rates of nitrification favor the use of chloramine versus free chlorine in controlling bacteria. Plumbing materials had profound impacts on the incidence of nitrification in homes. Effects were due to toxicity (i.e., release of Cu⁺²), recycling of nitrate back to ammonia substrate by reaction (zero-valent iron, lead or zinc materials), or release of nutrients that are essential to nitrification by leaching from concrete or other materials. As a general rule it was determined that concrete and iron materials encouraged growth of nitrifiers in certain oligotrophic waters, materials such as lead, PVC/plastic pipe, glass and surfaces of other materials were readily colonized by nitrifiers, and materials such as copper and brass were very toxic and relatively resistant to nitrifier colonization. Dependent on circumstance, nitrification had no effect, increased or decreased aspects of materials corrosion. Nitrification markedly increased lead contamination of low alkalinity potable water by reducing the pH. In some cases nitrification dramatically decreased leaching of zinc to potable water from galvanized iron, because of lowered dissolved oxygen and reduced pH. Nitrification did not affect copper solubility in low alkalinity water, but is expected to increase copper solubility in higher alkalinity waters. Finally, nitrification in homes plumbed with PVC or plastics can drop the pH and increase leaching of lead from downstream brass materials in faucets. This can explain why some modern homes plumbed with PVC can have more lead in water when compared to homes plumbed with copper pipe. Phosphate had profound impacts on the incidence of nitrification and resulting effects on water quality. While phosphate levels below about 5 ppb could strongly inhibit nitrification due to a nutrient limitation, nitrifiers can obtain sufficient phosphate from plastic, concrete, copper and iron pipe materials to meet nutritional needs. High levels of phosphate inhibitor can reduce the concentration of Cu⁺² ions and make nitrification more likely, but phosphate can also sometimes lower the corrosion rate and increase the stability of disinfectant and its efficacy in controlling nitrifiers. Phosphate plays a key role in determining where, when and if problems with nitrification will occur in a given water distribution system. This work provides some new fundamental and practical insights to nitrification issues through a comprehensive literature review, lab experiments, solubility modeling and field studies. The results and practical tools developed can be used by utilities and consumers to predict nitrification events and resulting water quality problems, and to make rational decisions about practices such as inhibitor dosing, plumbing material selection and use of whole house filters.
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    An olive-derived elenolic acid stimulates hormone release from L-cells and exerts potent beneficial metabolic effects in obese diabetic mice
    Wang, Yao; Wu, Yajun; Wang, Aiping; Wang, Aihua; Alkhalidy, Hana; Helm, Richard; Zhang, Shijun; Ma, Hongguang; Zhang, Yan; Gilbert, Elizabeth R.; Xu, Bin; Liu, Dongmin (Frontiers, 2022-11-01)
    Insulin resistance and progressive decline in functional β-cell mass are two key factors for developing type 2 diabetes (T2D), which is largely driven by overweight and obesity, a significant obstacle for effective metabolic control in many patients with T2D. Thus, agents that simultaneously ameliorate obesity and act on multiple pathophysiological components could be more effective for treating T2D. Here, we report that elenolic acid (EA), a phytochemical, is such a dual-action agent. we show that EA dose-dependently stimulates GLP-1 secretion in mouse clonal L-cells and isolated mouse ileum crypts. In addition, EA induces L-cells to secrete peptide YY (PYY). EA induces a rapid increase in intracellular [Ca2+]i and the production of inositol trisphosphate in L-cells, indicating that EA activates phospholipase C (PLC)-mediated signaling. Consistently, inhibition of (PLC) or Gαq ablates EA-stimulated increase of [Ca2+]i and GLP-1 secretion. In vivo, a single dose of EA acutely stimulates GLP-1 and PYY secretion in mice, accompanied with an improved glucose tolerance and insulin levels. Oral administration of EA at a dose of 50 mg/kg/day for 2 weeks normalized the fasting blood glucose and restored glucose tolerance in high-fat diet-induced obese (DIO) mice to levels that were comparable to chow-fed mice. In addition, EA suppresses appetite, reduces food intake, promotes weight loss, and reverses perturbated metabolic variables in obese mice. These results suggest that EA could be a dual-action agent as an alternative or adjuvant treatment for both T2D and obesity.
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    PATRIC, the bacterial bioinformatics database and analysis resource
    Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Timothy; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew S.; Will, Rebecca; Wilson, Meredith J. C.; Yoo, Hyunseung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno (2014-01)
    The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e. g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.
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    Quantitative Genetic Background of the Host Influences Gut Microbiomes in Chickens
    Zhao, Lele; Wang, Gang; Siegel, Paul B.; He, Chuan; Wang, Hezhong; Zhao, Wenjing; Zhai, Zhengxiao; Tian, Fengwei; Zhao, Jianxin; Zhang, Hao; Sun, Zikui; Chen, Wei; Zhang, Yan; Meng, He (Nature Publishing Group, 2013-01)
    Host genotype and gender are among the factors that influence the composition of gut microbiota. We studied the population structure of gut microbiota in two lines of chickens maintained under the same husbandry and dietary regimes. The lines, which originated from a common founder population, had undergone 54 generations of selection for high (HW) or low (LW) 56-day body weight, and now differ by more than 10-fold in body weight at selection age. Of 190 microbiome species, 68 were affected by genotype (line), gender, and genotype by gender interactions. Fifteen of the 68 species belong to Lactobacillus. Species affected by genotype, gender, and the genotype by gender interaction, were 29, 48, and 12, respectively. Species affected by gender were 30 and 17 in the HW and LW lines, respectively. Thus, under a common diet and husbandry host quantitative genotype and gender influenced gut microbiota composite.
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    Relative Effects of Water Chemistry on Aspects of Iron Corrosion
    Zhang, Yan (Virginia Tech, 2005-09-13)
    The net present replacement value of all publicly and privately owned potable water pipes in the U.S. is on the order of $2.4 trillion dollars, and costs associated with deteriorating iron pipes is billions of dollars per year. Problems arising from iron corrosion include reduced lifetime of the material, scale buildup and energy loss, nonuniform corrosion and leaks, catastrophic failure, "red water," disinfectant loss and bacterial re-growth. Iron corrosion is a very complicated process and is affected by many factors. This research focused on the effect of disinfectant type, sulfate/chloride ratios, nitrate concentration, and magnesium hardness on iron corrosion. For the waters tested, chlorine better controlled red water and microbial activity in the bulk solution than chloramine. Changes in the sulfate/chloride ratio did not have a large effect on iron corrosion. High levels of nitrate increased the rate of chlorine decay as a result of free ammonia formation, and also increased the release of iron. Increased magnesium and zinc decreased the red water caused by high silicate. Microbiological activity is important in iron corrosion, and control of re-growth in water distribution systems is a major challenge for water utilities. A separate study examined the inter-relationship between iron corrosion and bacterial re-growth, with a special focus on the potential of iron pipe to serve as a source of phosphorus. Under some circumstances corroding iron and steel may serve as a source for all macronutrients necessary for bacterial re-growth including fixed carbon, fixed nitrogen and phosphorus. Conceptual models and experimental data illustrate that levels of phosphorus released from corroding iron are significant relative to that necessary to sustain high levels of biofilm bacteria. Consequently, it may be more difficult to limit re-growth on iron surfaces by limiting phosphorus in the bulk water.
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    Transcriptome Analysis of Human Peripheral Blood Mononuclear Cells Exposed to Lassa Virus and to the Attenuated Mopeia/Lassa Reassortant 29 (ML29), a Vaccine Candidate.
    Zapata, Juan Carlos; Carrion, Ricardo Jr.; Patterson, Jean L.; Crasta, Oswald; Zhang, Yan; Mani, Sachin; Jett, Marti; Poonia, Bhawna; Djavani, Mahmoud; White, David M.; Lukashevich, Igor S.; Salvato, Maria S. (PLoS Negl Troop Dis, 2013-09-12)
    Lassa virus (LASV) is the causative agent of Lassa Fever and is responsible for several hundred thousand infections and thousands of deaths annually in West Africa. LASV and the non-pathogenic Mopeia virus (MOPV) are both rodent-borne African arenaviruses. A live attenuated reassortant of MOPV and LASV, designated ML29, protects rodents and primates from LASV challenge and appears to be more attenuated than MOPV. To gain better insight into LASV-induced pathology and mechanism of attenuation we performed gene expression profiling in human peripheral blood mononuclear cells (PBMC) exposed to LASV and the vaccine candidate ML29. PBMC from healthy human subjects were exposed to either LASV or ML29. Although most PBMC are non-permissive for virus replication, they remain susceptible to signal transduction by virus particles. Total RNA was extracted and global gene expression was evaluated during the first 24 hours using highdensity microarrays. Results were validated using RT-PCR, flow cytometry and ELISA. LASV and ML29 elicited differential expression of interferon-stimulated genes (ISG), as well as genes involved in apoptosis, NF-kB signaling and the coagulation pathways. These genes could eventually serve as biomarkers to predict disease outcomes. The remarkable differential expression of thrombomodulin, a key regulator of inflammation and coagulation, suggests its involvement with vascular abnormalities and mortality in Lassa fever disease.