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4. The Ecology of Plague

Author

Stenseth, Nils Chr., Dong, Kaixing, Cui, Yujun, Slavin, Philip, Xu, Lei, Yang, Ruifu, Zhang, Chutian, Weber, Olaf, Series Editor, Atshabar, Bakyt B., editor, Stenseth, Nils Chr., editor, and Fair, Jeanne M., editor

Published
2024
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6. List of contributors

Author

Aizawa, Shin-Ichi, primary, Alberdi, Pilar, additional, Alexander, David C., additional, Alía, Alberto, additional, Allison, D.G., additional, Amyes, Sebastian G.B., additional, An, Haoran, additional, Andrade, María J., additional, Antelmann, Haike, additional, Arias, Cesar A., additional, Asensio, Miguel A., additional, Axell-House, Dierdre B., additional, Bae, Hee-Won, additional, Baena, Laura Muñoz, additional, Baig, Abdul Mannan, additional, Bailey, Spenser O., additional, Baize, Sylvain, additional, Baldi, Pablo C., additional, Barbosa, Angela Silva, additional, Barbuddhe, Sukhadeo B., additional, Bard, Emilie, additional, Barry, Eileen M., additional, Basarab, Gregory S., additional, Beloborodova, N.V, additional, Bermúdez, Elena, additional, Bidmos, Fadil A., additional, Bisgaard, Magne, additional, Blakely, Garry W., additional, Bloch, Evan, additional, Boesen, Thias Oberg, additional, Bose, Dipayan, additional, Botero, Javier Enrique, additional, Bouabe, Hicham, additional, Bouchard, Michael J., additional, Bozue, Joel A., additional, Bradbury, Richard S., additional, Brett Moreau, G., additional, Cabezas-Cruz, Alejandro, additional, Cai, Rong-Jun, additional, Calderón, Enrique J., additional, Cao, Boyang, additional, Carmena, David, additional, Carvalho, Eneas, additional, Caulfield, Amanda D., additional, Cen, Shan, additional, Chai, Jong-Yil, additional, Chamberland, Robin R., additional, Champredon, David, additional, Chan, Edward D., additional, Charbon, Godefroid, additional, Chato, Connor, additional, Chelomina, G.N., additional, Chen, Jingyu, additional, Chen, Min, additional, Chen, Shuyu, additional, Chen, Suilin, additional, Chen, Yanfei, additional, Chen, Zhaoyuan, additional, Cheng, Aimin, additional, Cheng, Keding, additional, Chiu, Charles Y., additional, Cho, You-Hee, additional, Christensen, Henrik, additional, Chrtdernevskaya, E.A., additional, Contreras, Adolfo, additional, Contreras, Marinela, additional, Córdoba, Juan J., additional, Córdoba, María G., additional, Costa, Rita, additional, Cote, Christopher K., additional, Cui, Xiangling, additional, Cui, Yujun, additional, Dacal, Elena, additional, Dammann, Allison N., additional, Das, Shubhagata, additional, Dashti, Alejandro, additional, de la Fuente, José, additional, de la Garza, Mireya, additional, Delgado, Josué, additional, Delgado-Cuesta, Juan, additional, Deng, Haiteng, additional, Deng, Li, additional, Dey, Debajit, additional, Dhama, Kuldeep, additional, Diego, Juan García-Bernalt, additional, Ding, Hao, additional, Doern, Christopher D., additional, Dorman, Charles J., additional, Du, Zongmin, additional, Dunbar, Sherry A., additional, Duthie, Malcolm, additional, Dybvig, Kevin F., additional, Eakin, Ann E., additional, Eallonardo, Samuel J., additional, Eberly, Allison R., additional, Echeverry, Adriana Jaramillo, additional, Egland, Paul G., additional, El Zowalaty, Mohamed E., additional, Endsley, Janice Jones, additional, Eom, Keeseon S., additional, Evans, Benjamin A., additional, Falkinham, Joseph O., additional, Feng, Siwei, additional, Feng, Yaoyu, additional, Feng, Zongdi, additional, Fernández-Soto, Pedro, additional, Ferreira, Roux-Cil, additional, Flores-Huerta, Nadia, additional, Foster, Timothy J., additional, Fox-Moon, Sandra M., additional, Fraga, Tatiana Rodrigues, additional, Fredricks, David N., additional, Freitag, Nancy E., additional, Frimodt-Møller, Jakob, additional, Fuller, Risa, additional, Ganesh, Balasubramanian, additional, Gao, Ning, additional, García-Carnero, Laura C., additional, Garzetti, Debora, additional, Geoghegan, Joan A., additional, Ghenim, Raed, additional, Giambartolomei, Guillermo H., additional, Gilbert, Nicole M., additional, Gillis, Thomas Phillip, additional, Gladstone, Camilla A., additional, Gómez-Gaviria, Manuela, additional, Gómez-Marín, Jorge E., additional, Gong, Tengfang, additional, González, Ramón A., additional, Gray-Owen, Scott D., additional, Gu, Bing, additional, Guzmán-Téllez, Paula, additional, Hajal, Caroline, additional, Han, Yanping, additional, Hao, Yi, additional, Harrington, Amanda T., additional, Harris, Jason B., additional, Harvill, Eric T., additional, Hasan, S. Saif, additional, He, Guang-Jun, additional, He, Yongqun, additional, Heffron, Jared D., additional, Hidalgo, Paloma, additional, Hindiyeh, Musa Y., additional, Hreha, Teri N., additional, Hu, Xiaoyu, additional, Huang, Guanghua, additional, Huang, Jiangqing, additional, Huang, Liang, additional, Huang, Shifeng, additional, Huang, Xingxu, additional, Huang, Xueting, additional, Huang, Yilun, additional, Huffman, Anthony, additional, Humphreys, Tricia L., additional, Hunstad, David A., additional, Inglis, Timothy J.J., additional, Isaac, Lourdes, additional, Jacobs, Samantha E., additional, Janowicz, Diane M., additional, Jeon, Hyeong-Kyu, additional, Ji, Quanjiang, additional, Jia, Qi, additional, Jia, Wei, additional, Jin, Shouguang, additional, Jneidi, Lama, additional, Jose, Shinsmon, additional, Jung, Bong-Kwang, additional, Kattan, Randa, additional, Kaushik, Rahul, additional, Khare, Reeti, additional, Kim, Eun Sook, additional, Kirn, Thomas J., additional, Koo, Hyun, additional, Köster, Pamela C., additional, Krause, Peter J., additional, Kumar, Sanjai, additional, Kupz, Andreas, additional, Lambert, P.A., additional, Lamont, Richard J., additional, Langford, Paul R., additional, Lebeaux, David, additional, Legname, Giuseppe, additional, Li, Bin, additional, Li, Chunhao, additional, Li, Fen, additional, Li, Jun, additional, Li, Lanjuan, additional, Li, Ruofan, additional, Li, Ruoyu, additional, Li, Ting, additional, Li, Yang-Yang, additional, Li, Yanhua, additional, Li, Zhuorong, additional, Liang, Xiaomeng, additional, Liao, Guojian, additional, Lin, Ping, additional, Ling, Yun, additional, Liu, Bo, additional, Liu, Dongyou, additional, Liu, Guohua, additional, Liu, Huidi, additional, Liu, Jiafeng, additional, Liu, Jintao, additional, Liu, Qi, additional, Liu, Shu-Lin, additional, Liu, Taiping, additional, Liu, Tongbao, additional, Liu, Wei, additional, Liu, Yan, additional, Liu, Yanni, additional, Liu, Yisong, additional, Liu, Yuan, additional, Løbner-Olesen, Anders, additional, Loeffelholz, Michael, additional, Lu, Hongzhou, additional, Luna, Brian, additional, Ma, Bingting, additional, Ma, Chengying, additional, Ma, Shuang, additional, Ma, TianLi, additional, Madan, Rajat, additional, Mahle, Rachael E., additional, Mahlen, Steven D., additional, Malik, Satya Veer Singh, additional, Malik, Yashpal Singh, additional, Malvy, Denis, additional, Mann, Barbara J., additional, Marasini, Daya, additional, Maris, Alexander S., additional, Marjomäki, Varpu, additional, Marjuki, Henju, additional, Martín, Alberto, additional, Martín, Irene, additional, Martínez-Castillo, Moisés, additional, Martínez-Pabón, María Cecilia, additional, Mathison, Blaine A., additional, Ma’ayeh, Showgy, additional, McDowell, Andrew, additional, McLaughlin, Stephanie E., additional, McSheffrey, Gordon G., additional, Medrano, Francisco J., additional, Meehan, Conor J., additional, Mehta, Dhwani, additional, Mejía-Oquendo, Manuela, additional, Melo-Cristino, José, additional, Mendoza-Barberá, Elena, additional, Meng, Xinan, additional, Merino, Susana, additional, Merritt, Adam J., additional, Miller, Steve, additional, Miller, William R., additional, Minamino, Tohru, additional, Mirzaei, Mohammadali Khan, additional, Mora-Montes, Héctor M., additional, Mortensen, Joel, additional, Mostafa, Heba H., additional, Muhsen, Khitam, additional, Mujahed, Ahlam, additional, Muro, Antonio, additional, Murphy, Olwen C., additional, Newton, Hayley J., additional, Nguyen, April H., additional, Nichols, Wright W., additional, Niu, Siqiang, additional, Núñez, Félix, additional, Obregon, Dasiel, additional, Okamoto, Akira, additional, Okutani, Akiko, additional, Olabode, Abayomi, additional, Omar, Muna, additional, Ong, Edison, additional, Ouyang, Zhiming, additional, Pacak, Christina A., additional, Pacheco-Yépez, Judith, additional, Palmer, John, additional, Pang, Xiaoli, additional, Paredes-Sabja, Daniel, additional, Peng, Zhong, additional, Peng, Zonggen, additional, Pérez-Nevado, Francisco, additional, Poon, Art, additional, Pospíšilová, Petra, additional, Potts, Caelin C., additional, Pu, Qinqin, additional, Pujic, Petar, additional, Qi, Rui, additional, Qian, Chenyun, additional, Qian, Liu, additional, Qin, Aiping, additional, Qu, Fen, additional, Rakin, Alexander, additional, Ramesh, Ashwin, additional, Ramirez, Mario, additional, Rao, Yu, additional, Ratner, Adam J., additional, Rawool, Deepak B., additional, Rehman, Asma, additional, Ren, Jie, additional, Ren, Ping, additional, Retchless, Adam C., additional, Robertson, Erle S., additional, Rodríguez, Alicia, additional, Rodriguez, Azucena, additional, Rodríguez-Medina, Carolina, additional, Rodriguez-Nava, Veronica, additional, Rohde, Manfred, additional, Romero-Rodríguez, Alba, additional, Rosales-Morgan, Gabriela, additional, Rosenkranz, Andrea L., additional, Ruiz-Moyano, Santiago, additional, Ruokolainen, Visa, additional, Sabateen, Ali, additional, Sahu, Radhakrishna, additional, Sails, Andrew, additional, Sang, Yu, additional, Santana, Clarissa H., additional, Santos, Jesus A., additional, Santos, Renato L., additional, Schmitz, Jonathan E., additional, Serrano-Luna, Jesús, additional, Shen, Jianzhong, additional, Shen, Zhangqi, additional, Shibayama, Mineko, additional, Shirtliff, Mark E., additional, Silva-Costa, Catarina, additional, Silva-Olivares, Angélica, additional, Singh, Niraj Kumar, additional, Šmajs, David, additional, Smith, Robert P., additional, Smith, Sophie, additional, Snyder, Lori A.S., additional, Song, Yinggai, additional, Soro, Aurea Simon, additional, Spearman, Paul, additional, Spellberg, Brad, additional, Sprague, Lisa D., additional, Stratton, Charles W., additional, Strenk, Susan M., additional, Strugnell, Richard A., additional, Sun, Keer, additional, Suo, Xun, additional, Suzuki-Hatano, Silveli, additional, Svärd, Staffan, additional, Talbot, Elizabeth A., additional, Tamez-Castrellón, Alma K., additional, Tan, Nie, additional, Tang, Cynthia Y., additional, Tang, Yi-Wei, additional, Tao, Jia, additional, Tao, Lili, additional, Terrero-Salcedo, David, additional, Tharmalingam, Jayaraman, additional, Thwe, Phyu M., additional, Tiamani, Kawtar, additional, Tomás, Juan M., additional, Topaz, Nadav, additional, Tsai, Ang-Chen, additional, Tsalik, Ephraim L., additional, Tuomanen, Elaine I., additional, Turenne, Christine Y., additional, Tyagi, Anuj, additional, Uprety, Priyanka, additional, Valour, Florent, additional, van Hensbergen, Vincent P., additional, Venkatesan, Arun, additional, Vergis, Jess, additional, Villar, Margarita, additional, Vollmer, Waldemar, additional, Waites, Ken B., additional, Wan, Xiu-Feng, additional, Wang, Guiqing, additional, Wang, Lijun, additional, Wang, Lin, additional, Wang, Linqi, additional, Wang, Xiangru, additional, Wang, Xin, additional, Wang, Xinjie, additional, Wang, Ya-Ting, additional, Wang, Yang, additional, Wang, Yating, additional, Weil, Ana A., additional, Welkos, Susan L., additional, Wengenack, Nancy L., additional, Westblade, Lars F., additional, Whitfield, Chris, additional, Wu, Hui, additional, Wu, Lijuan, additional, Wu, Min, additional, Wu, Yarong, additional, Wu, Zhaowei, additional, Xiang, Ye, additional, Xiao, Di, additional, Xiao, Li, additional, Xiao, Lihua, additional, Xu, Tao, additional, Xu, Wenyue, additional, Xu, Xinping, additional, Xue, Jinling, additional, Yadav, Jay Prakash, additional, Yan, Junxiang, additional, Yan, Yixin, additional, Yang, Changmei, additional, Yang, Ruifu, additional, Yang, Ying, additional, Yao, Kaihu, additional, Yao, Yu-Feng, additional, Yeakle, Kyle C., additional, Yu, Demin, additional, Yu, Hao, additional, Yu, Xue-Jie, additional, Yuan, Zhenghong, additional, Zai, Wenjing, additional, Zhang, Jianzhong, additional, Zhang, Jing-Ren, additional, Zhang, Lanyue, additional, Zhang, Lijie, additional, Zhang, Qiwei, additional, Zhang, Wenbao, additional, Zhang, Wenhong, additional, Zhang, Xinxin, additional, Zhao, Youbao, additional, Zhou, Chuanmin, additional, Zhu, Feng, additional, Zhu, Jingting, additional, and Zhu, Yongqun, additional

Published
2024
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12. Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2.

Author

Sun, Shihui, Gu, Hongjing, Cao, Lei, Chen, Qi, Ye, Qing, Yang, Guan, Li, Rui-Ting, Fan, Hang, Deng, Yong-Qiang, Song, Xiaopeng, Qi, Yini, Li, Min, Lan, Jun, Feng, Rui, Guo, Yan, Zhu, Na, Qin, Si, Wang, Lei, Zhang, Yi-Fei, Zhou, Chao, Zhao, Lingna, Chen, Yuehong, Shen, Meng, Cui, Yujun, Yang, Xiao, Wang, Xinquan, Tan, Wenjie, Wang, Hui, Wang, Xiangxi, and Qin, Cheng-Feng

Subjects
Amino Acid Substitution, Angiotensin-Converting Enzyme 2, Animals, Binding Sites, COVID-19, Disease Models, Animal, Female, Humans, Male, Mice, Protein Binding, Protein Domains, SARS-CoV-2, Severity of Illness Index, Spike Glycoprotein, Coronavirus
Abstract

There is an urgent need for animal models to study SARS-CoV-2 pathogenicity. Here, we generate and characterize a novel mouse-adapted SARS-CoV-2 strain, MASCp36, that causes severe respiratory symptoms, and mortality. Our model exhibits age- and gender-related mortality akin to severe COVID-19. Deep sequencing identified three amino acid substitutions, N501Y, Q493H, and K417N, at the receptor binding domain (RBD) of MASCp36, during in vivo passaging. All three RBD mutations significantly enhance binding affinity to its endogenous receptor, ACE2. Cryo-electron microscopy analysis of human ACE2 (hACE2), or mouse ACE2 (mACE2), in complex with the RBD of MASCp36, at 3.1 to 3.7 Å resolution, reveals the molecular basis for the receptor-binding switch. N501Y and Q493H enhance the binding affinity to hACE2, whereas triple mutations at N501Y/Q493H/K417N decrease affinity and reduce infectivity of MASCp36. Our study provides a platform for studying SARS-CoV-2 pathogenesis, and unveils the molecular mechanism for its rapid adaptation and evolution.

Published
2021

14. Impact of fines on the accumulated strain of unsaturated road base aggregate under cyclic loadings

Author

Cao, Zhigang, Zhang, Qi, Cai, Yuanqiang, Cui, Yujun, Gu, Chuan, and Wang, Jun

Subjects
Aggregates (Building materials) -- Mechanical properties, Streets -- Mechanical properties -- Testing -- China, Dynamic testing -- Methods, Roads -- Mechanical properties -- Testing -- China, Soil structure -- Analysis, Earth sciences
Abstract

The property of a road base depends on its fine content (FC) and water content/suction. In this study, a cyclic loading test was carried out on road base aggregate with different FCs under controlled suction. The different effects of fines on the accumulated strain of road base aggregate at different FCs and suctions were identified. Under the saturated condition, the accumulated strain increased with FC due to the reduction of soil interparticle friction caused by the inclusion of fines. Under unsaturated conditions, the effect of fines on the accumulated strain depended on the inner structure of the soil. For the 'coarse-graincontrolled soil' (FC in the range of 0%-4%), the accumulated strain increased with the increase of FC due to the reduction of interparticle friction, while for the 'transition soil' (FC in the range of 4%-8%), the accumulated strain decreased with the increase of FC as the major impact of the fines shifted to the enhancement of suction, and the inclusion of fines is beneficial for this case; for the 'fine-grain-controlled soil' (FC in the range of 8%-16%), the accumulated strain increased rapidly with FC as the effect of interparticle friction reduction dominated again. Key words: road base aggregate, fine content, cyclic loading, accumulated strain, unsaturated soil La propriete de la base de la route depend de sa teneur en fines (FC) et de sa teneur en eau/suction. Dans cette etude, l'essai de chargement cyclique a ete effectue sur un agregat de base de route avec differentes teneurs en fines sous des succions controlees. Les differents effets des fines sur la deformation accumulee du granulat de la base de la route a differentes teneurs en fines et suctions ont ete identifies. Dans des conditions de saturation, la deformation accumulee augmente avec la teneur en fines en raison de la reduction de la friction interparticulaire du sol causee par l'inclusion de fines. Dans des conditions non saturees, l'effet des fines sur la deformation accumulee depend de la structure interne du sol. Pour le << sol a gros grains controles (FC dans la gamme de 0-4 %)>>, la deformation accumulee augmente avec l'augmentation de la teneur en fines en raison de la reduction de la friction interparticulaire; tandis que pour le << sol de transition (FC dans la gamme de 4-8%)>>, la deformation accumulee diminue avec l'augmentation de la teneur en fines comme l'impact majeur des fines se deplace vers l'amelioration de la succion, et l'inclusion de fines sera benefique pour ce cas; pour le << sol a grains fins controles (FC dans la gamme de 8-16%)>>, la deformation accumulee augmente rapidement avec la teneur en fines, car l'effet de la reduction de la friction interparticulaire domine a nouveau. [Traduit par la Redaction] Mots-cles : agregat de base de route, teneur en fines, chargement cyclique, deformation accumulee, sol non sature, Introduction Road base aggregates mainly consist of unbound granular materials such as gravel and sand. During a road's service, the road base aggregate can be invaded by fines from particle [...]

Published
2022
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15. Temporal and Spatial Distribution of SARS-CoV-2 Aerosols in a Large-Scale Fangcang Shelter Hospital in Shanghai, China

Author

Jiang, Jiafu, Yin, Zhe, Li, Jing, Jia, Leili, He, Rulin, Yang, Wenhui, Yang, Jihu, Fan, Hang, Zhang, Sen, Wang, Yunfei, Zhao, Zengming, Peng, Haoran, Li, Lizhong, Yang, Yi, Fan, Shi-Yong, Xiang, Rong, Guo, Jianshu, Wang, Jinjin, Wei, Juanning, Zhou, Fengling, Liu, Ding, Zhao, Ping, Cui, Yujun, Liu, Yunxi, Zhou, Dongsheng, and Dong, Gang

Published
2023
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33. On Higher-Order Nonlinear Fractional Elastic Equations with Dependence on Lower Order Derivatives in Nonlinearity.

Author

Cui, Yujun, Liang, Chunyu, and Zou, Yumei

Subjects
*EQUATIONS
Abstract

The paper studied high-order nonlinear fractional elastic equations that depend on low-order derivatives in nonlinearity and established the existence and uniqueness results by using the Leray–Schauder alternative theorem and Perov's fixed point theorem on an appropriate space under mild assumptions. Examples are given to illustrate the key results. [ABSTRACT FROM AUTHOR]

Published
2024
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34. Quantitative and dynamic profiling of human gut core microbiota by real-time PCR.

Author

Yan, Ziheng, Hao, Tongyu, Yan, Yanfeng, Zhao, Yanting, Wu, Yarong, Tan, Yafang, Bi, Yujing, Cui, Yujun, Yang, Ruifu, and Zhao, Yong

Subjects
GUT microbiome, DNA primers, HUMAN microbiota, POLYMERASE chain reaction, GENOMICS, GENETIC markers, WATER sampling
Abstract

The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson's r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease. Key points: • A panel of original qPCR assays was developed to quantify human gut core microbes. • The qPCR assays were evaluated and compared with mNGS using real fecal samples. • This method was used to dynamically profile the gut core microbiota in individuals. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Effects of microorganism within organic matter on the mechanical behaviour of solidified municipal dredged mud

Author

Deng, Yongfeng, Wu, Jun, Tan, Yunzhi, Cui, Yujun, Tang, Chao-sheng, and Zhou, Annan

Subjects
Microorganisms -- Influence, Solidification -- Analysis, Dredging spoil -- Management, Mud -- Mechanical properties -- Contamination, Company business management, Earth sciences
Abstract

Municipal mud consists of organic matter naturally deposited in a microbial-rich environment, and its common pre-treatment in the laboratory is normally different from that in situ. In this study, an improved pre-loading method and the common pre-treatment method (by air or oven drying) were first applied to investigate the effect of microorganisms within organic matter on performance of the solidified soils. Results reveal that (i) Atterberg limits in the pre-loading method were higher than those in the drying method; (ii) the time-dependent strength became stable for the solidified soils pre- treated by the drying method, while strength decreased for the soils pre-treated by the pre- loading method; (iii) pH value of solidified soils by the pre-loading method decreased more significantly. After excluding the possible porosity influence on solidified soils, the effects of microorganisms within organic matter were investigated by microbial identification tests, including fluorescence detection and high-throughput sequencing. The pre-treatment procedure changed the vitality and diversity of microorganisms, leading to a rebalance between acid erosion and cement hydration during long- term curing. At the end, the long-term strength of the solidified municipal mud by the traditional pre-treatment method (by air or oven drying) could be overevaluated. Key words: pre-treatment procedure, dredged mud, microorganism, solidification, strength performance, durability. La boue municipale est constituee de matieres organiques deposees naturellement dans un environnement riche en microbes, et son pretraitement courant en laboratoire est normalement different de celui in situ. Dans cette etude, une methode de prechargement amelioree et la methode de pretraitement courante (par sechage a l'air ou au four) ont d'abord ete appliquees pour etudier l'effet du microorganisme dans la matiere organique sur la performance des sols solidifies. Les resultats revelent que : (i) les limites d'Atterberg dans la methode de precharge etaient plus elevees que celles de la methode de sechage; (ii) la resistance en fonction du temps est devenue stable pour les sols solidifies pretraites par la methode de sechage, tandis qu'elle a diminue pour les sols pretraites par la methode de precharge; (iii) la valeur du pH des sols solidifies par la methode de precharge a diminue de maniere plus significative. Apres avoir exclu l'influence possible de la porosite sur les sols solidifies, les effets des microorganismes dans les matieres organiques ont ete etudies par des tests d'identification microbienne, y compris la detection de la fluorescence et le sequencage a haut debit. La procedure de pretraitement a modifie la vitalite et la diversite des microorganismes, entrainant un reequilibrage entre l'erosion acide et l'hydratation du ciment apres un durcissement pendant long terme. Au final, la resistance a long terme de la boue municipale solidifiee par la methode traditionnelle de pretraitement (par sechage a l'air ou au four) pourrait etre surevaluee. Mots-cles : procedure de pretraitement, boue de dragage, micro-organisme, solidification, performance de resistance, durabilite., 1. Introduction Urban river and lake sediments are regularly dredged to prevent flooding or to reclaim the ecosystem of water environments (Tang et al. 2001; Dubois et al. 2009; Samara [...]

Published
2020
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41. The ypT may better predict the efficacy of neoadjuvant chemoradiotherapy than tumor regression grade in locally advanced rectal cancer patients diagnosed ypT1-4N0

Author

Cui, Yujun, primary, Liu, Xinzhi, additional, Li, Shuai, additional, Wang, Hongzhi, additional, Xiang, Yirong, additional, Zhang, Yangzi, additional, Song, Maxiaowei, additional, Geng, Jianhao, additional, Liu, Zhiyan, additional, Teng, Huajing, additional, Zhu, Xianggao, additional, Cai, Yong, additional, Li, Yongheng, additional, and Wang, Weihu, additional

Published
2023
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42. Characterization of an aspartate aminotransferase encoded by YPO0623 with frequent nonsense mutations in Yersinia pestis

Author

Jin, Junyan, primary, Xiao, Liting, additional, Wu, Yarong, additional, Sun, Zhulin, additional, Xiong, Ziyao, additional, Li, Yanbing, additional, Zhao, Yanting, additional, Yao, Wenwu, additional, Shen, Leiming, additional, Cui, Yiming, additional, Tan, Yafang, additional, Han, Yanping, additional, Du, Zongmin, additional, Cui, Yujun, additional, Yang, Ruifu, additional, Song, Kai, additional, and Song, Yajun, additional

Published
2023
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44. Epidemic clones, oceanic gene pools and eco-LD in the free living marine pathogen Vibrio parahaemolyticus

Author

Cui, Yujun, Yang, Xianwei, Didelot, Xavier, Guo, Chenyi, Li, Dongfang, Yan, Yanfeng, Zhang, Yiquan, Yuan, Yanting, Yang, Huanming, Wang, Jian, Wang, Jun, Song, Yajun, Zhou, Dongsheng, Falush, Daniel, and Yang, Ruifu

Subjects
Quantitative Biology - Populations and Evolution
Abstract

We investigated global patterns of variation in 157 whole genome sequences of Vibrio parahaemolyticus, a free-living and seafood associated marine bacterium. Pandemic clones, responsible for recent outbreaks of gastroenteritis in humans have spread globally. However, there are oceanic gene pools, one located in the oceans surrounding Asia and another in the Mexican Gulf. Frequent recombination means that most isolates have acquired the genetic profile of their current location. We investigated the genetic structure in the Asian gene pool by calculating the effective population size in two different ways. Under standard neutral models, the two estimates should give similar answers but we found a thirty fold difference. We propose that this discrepancy is caused by the subdivision of the species into a hundred or more ecotypes which are maintained stably in the population. To investigate the genetic factors involved, we used 51 unrelated isolates to conduct a genome-wide scan for epistatically interacting loci. We found a single example of strong epistasis between distant genome regions. A majority of strains had a type VI secretion system associated with bacterial killing. The remaining strains had genes associated with biofilm formation and regulated by c-di-GMP signaling. All strains had one or other of the two systems and none of isolate had complete complements of both systems, although several strains had remnants. Further top-down analysis of patterns of linkage disequilibrium within frequently recombining species will allow a detailed understanding of how selection acts to structure the pattern of variation within natural bacterial populations.

Published
2014

46. Isolation and complete genome analysis of Staphylococcus aureus bacteriophage vB_SauH_IME522

Author

GAO Mingming, LIU Huiying, LI Puyuan, ZHANG Zhihua, QIN Yanhong, HUANG Yong, CUI Yujun, PEI Guangqian, TONG Yigang, and BAI Changqing

Subjects
staphylococcus aureus, bacteriophage, biological characteristics, genomic analysis, Medicine (General), R5-920
Abstract

Objective To isolate, sequence, and identify biological characterization and complete genome sequencing of a virulent Staphylococcus aureus (S. aureus) bacteriophage vB_SauH_IME522. Methods A phage was isolated from sewage of PLA Chinese General Hospital using a clinically isolated S. aureus strain as host bacteria. The double-layer agar plate was used to determine the optimal multiplicity of infection (optimal MOI) and one-step growth curve. Phage morphology was observed by transmission electron microscopy after purification using sucrose gradient separation. Phage DNA was sequenced using the Illumina Miseq sequencing platform. The complete genome sequence was annotated, then comparative genomics and evolutionary analyses were performed. Results A lytic phage of S. aureus was isolated from hospital sewage and named as vB_SauH_IME522. The optimal MOI of the phage was 0.01. One step growth curve showed that its latent period and burst period were 20 and 200 min, respectively. The burst size was about 89 PFU/cell. Electron microscopy displayed the phage having an icosahedral head (70±1) nm and a long contractile tail (135±2) nm. Genome sequencing results showed that the total length of the phage genome was 140 246 bp and the G+C content accounted for 30.2%. The genomic annotation revealed that the phage contained 223 genes coding proteins, 164 putative promoters, 66 terminators, 4 tRNAs, and 7 resistance-related regions. Phylogenetic analysis suggested that the phage was a member of the genus Kayvirus within the subfamily Twortvirinae. Conclusion A lytic phage of S. aureus vB_SauH_IME522 is identified as a new member of the Twortvirinae subfamily, with strong lytic ability and short latent period.

Published
2020
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49. Whole-Genome Analysis of Salmonella enterica Serovar Enteritidis Isolates in Outbreak Linked to Online Food Delivery, Shenzhen, China, 2018

Author

Jiang, Min, Zhu, Feng, Yang, Chao, Deng, Yinhua, Kwan, Patrick S.L., Li, Yinghui, Lin, Yiman, Qiu, Yaqun, Shi, Xiaolu, Chen, Hui, Cui, Yujun, and Hu, Qinghua

Subjects
United States. Centers for Disease Control and Prevention, Salmonella food poisoning -- Health aspects, Delivery services -- Health aspects, Salmonella -- Health aspects, Disease transmission -- Health aspects, Bacterial genetics -- Health aspects, Genomes -- Health aspects, Genomics -- Health aspects, Wireless telephone software, Gastroenteritis, Online food ordering and delivery, Accounting, Diseases, DNA sequencing, Mobile applications, Smart phones, Backup software, Infection, Salmonellosis, Health
Abstract

Salmonella spp. are a leading bacterial cause of acute gastroenteritis globally, resulting in <40% of human cases worldwide and >30% in China (2,3). This serovar frequently has been isolated in [...]

Published
2020
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