Low-grade gliomas (LGGs) are the most common CNS tumors, and the main therapy for LGGs is complete surgical resection, due to its curative effect. However, LGG recurrence occurs frequently. Biomarkers play a crucial role in evaluating the recurrence and prognosis of LGGs. Numerous studies have focused on LGG prognosis. However, the multiomics research investigating the roles played by gene methylation and expression in LGG recurrence remains limited. In this study, we integrated the TCGA and GEO...
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DNA methylation is an epigenetic mechanism used by cells to control gene expression. DNA methylation is a commonly used epigenetic signaling tool that can hold genes in the “off” position. Chronic infection with hepatitis C virus (HCV) is considered a major risk for chronic liver impairment. It is the most common leading cause of HCC. The present work is aimed at studying whole genome 5-methylcytosine levels in cirrhotic HCV-infected Egyptian patients. In the present study, 120 Egyptian adults were...
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To explore heat response mechanisms of mircoRNAs (miRNAs) in rice post-meiosis panicle, microarray analysis was performed on RNA isolated from rice post-meiosis panicles which were treated at 40°C for 0 min, 10 min, 20 min, 60 min, and 2 h. By integrating paired differentially expressed (DE) miRNAs and mRNA expression profiles, we found that the expression levels of 29 DE-miRNA families were negatively correlated to their 178 DE-target genes. Further analysis showed that the majority of miRNAs in...
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Publication date: Available online 13 October 2020Source: GeneAuthor(s): Jackeline Santos Alves, Marcia da Silva Anjos, Marisa Silva Bastos, Louise Sarmento Martins de Oliveira, Ingrid Pereira Pinto Oliveira, Luis Fernando Batista Pinto, Chiara Albano de Araújo de Oliveira, Raphael Bermal Costa, Gregório Miguel Ferreira de Camargo
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Publication date: Available online 12 October 2020Source: GeneAuthor(s): Chengdong Wang, Feng Li, Linhua Deng, Mingzhou Li, Ming Wei, Bo Zeng, Kai Wu, Zhongxian Xu, Rongping Wei, Limin Wei, Weiping Liu, Siyuan Zhang, Lin Xu, Yan Huang, Desheng Li, Ying Li, Hemin Zhang
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Publication date: Available online 12 October 2020Source: GeneAuthor(s): Qianqian Sha, Wei Zheng, Xie Feng, Ruiying Yuan, Huiling Hu, Fei Gong, Liang Hu, Ge Lin, Xianghong Ou
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Publication date: Available online 12 October 2020Source: GeneAuthor(s): Stella C. Ogbu, Phillip R. Musich, Jinyu Zhang, Zhi Q. Yao, Philip H. Howe, Yong Jiang
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Publication date: Available online 12 October 2020Source: GeneAuthor(s): Amr A. Galal, Ahmed A. Abd Elmajeed, Rizk A. Elbaz, Alaa M. Wafa, Rami M. Elshazli
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Publication date: Available online 12 October 2020Source: GeneAuthor(s): Freda Lalrohlui, John Zohmingthanga, Vanlal hruaii, Andrew Vanlallawma, Nachimuthu Senthil Kumar
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Publication date: Available online 12 October 2020Source: GeneAuthor(s): Ekaterina Kondrateva, Anna Demchenko, Alexander Lavrov, Svetlana Smirnikhina
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Publication date: Available online 12 October 2020Source: GeneAuthor(s): Anita Alizadeh, Asiyeh Jebelli, Behzad Baradaran, Mohammad Amini, Fatemeh Oroojalian, Mahmoud Hashemzaei, Ahad Mokhtarzadeh, Michael R Hamblin
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Publication date: Available online 12 October 2020Source: GeneAuthor(s): Rui Zhang, Yi Wang, Shaohua Li, Long Yang, Zhenchang Liang
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Publication date: Available online 11 October 2020Source: GeneAuthor(s): Weiwei Zheng, Chuancheng Wu, Xiaoli Wu, Yuanhuan Cai, Baoying Liu, Chengdang Wang
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Publication date: Available online 11 October 2020Source: GeneAuthor(s): Yi-ying Jiang, Jian-li Li, Liu-yu Liu, Guo-qiu Zhou, Dong-can Mo, Dong-dong Jiang, Man Luo
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Publication date: Available online 9 October 2020Source: GeneAuthor(s): Bach Quang Le, Tuan Chun Tan, Seong-baek Lee, Ju Woong Jang, Young Sik Kim, Jung Soo Lee, Jae Won Choi, Padmapriya Sathiyanathan, Victor Nurcombe, Simon Cool
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Publication date: Available online 8 October 2020Source: GeneAuthor(s): Elina Bychkova, Olga Viktorovskaya, Elizaveta Filippova, Zhanna Eliseeva, Larisa Barabanova, Maria Sotskaya, Anton Markov
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Publication date: Available online 8 October 2020Source: GeneAuthor(s): Ajinkya Bharatraj Patil, Sagar Sharad Shinde, S. Raghavendra, B.N. Satish, C.G. Kushalappa, Nagarjun Vijay
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Publication date: Available online 7 October 2020Source: GeneAuthor(s): Hui Zhang, Ming Li Wang, Phat Dang, Tao Jiang, Shuzhen Zhao, Marshal Lamb, Charles Chen
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Publication date: Available online 7 October 2020Source: GeneAuthor(s): Rongjing Song, Xuecheng Zhao, Rong Cao, Yuerun Liang, Da-Qi Zhang, Rong Wang
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Publication date: Available online 7 October 2020Source: GeneAuthor(s): Koushik Ponnanna, Stafny M.D. Souza, C. Amruthavalli, Nallur B. Ramachandra
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Publication date: Available online 6 October 2020Source: GeneAuthor(s): Shijie Lyu, Peng Yang, Yanyong Liu, Tian Song, Zijing Zhang, Qiaoting Shi, Fuying Chen, Xian Liu, Zhiming Li, Baorui Ru, Cuicui Cai, Jianliang Xie, Chuzhao Lei, Hong Chen, Zhaoxue Xu, Eryao Wang, Yongzhen Huang
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Publication date: Available online 5 October 2020Source: GeneAuthor(s): Jian-Guo Gao
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Publication date: Available online 5 October 2020Source: GeneAuthor(s): Jacques Demongeot, Hervé Seligmann
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Publication date: Available online 5 October 2020Source: GeneAuthor(s): Vaishnavi Sundar, Sanjana Vimal, M.s. Sai Mithlesh, Anupam Dutta, Ramasamy Tamizhselvi, Venkatraman Manickam
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Publication date: Available online 5 October 2020Source: GeneAuthor(s): Ayyoob Khosravi, Seyyed Mehdi Jafari, Jahanbakhsh Asadi
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Publication date: Available online 5 October 2020Source: GeneAuthor(s): Laura Huning, Gary R. Kunkel
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Publication date: Available online 5 October 2020Source: GeneAuthor(s): Li Zhou, Shihong Xu, Fan Lin, Xueying Wang, Yunong Wang, Yanfeng Wang, Daode Yu, Qinghua Liu, Jun Li
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Publication date: Available online 30 September 2020Source: GeneAuthor(s): Kai Ma, Yuhan Chen, Lunni Zhou, Zhizhi Liu, Zhiwei Liu
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Publication date: Available online 30 September 2020Source: GeneAuthor(s): Juncheng Guo, Yijun Yang, Xiangling Jiang, Min Guo, Xiang Li, Ping Huang, Zhuo Liu
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Ze Li, Hui Gao, Yang Liu, Hongjiao Wu, Weiyuan Li, Yunce Xing, Zhi Zhang, Xuemei Zhang
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Publication date: Available online 30 September 2020Source: GeneAuthor(s): Tangwei Huang, Xinglu Luo, Zhupeng Fan, Yanni Yang, Wen Wan
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Publication date: Available online 30 September 2020Source: GeneAuthor(s): Zhixiu Wang, Lu Lu, Gu Tiantian, Hou Li'e, Du Lei, Zhang Yu, Zhang Yang, Xu Qi, Chen Guohong
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Itty Sethi, Gh. Rasool Bhat, Rakesh Kumar, Ekta Rai, Swarkar Sharma
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Osamah Batiha, Sherin T. Shaaban, Mohammad Al-Smadi, Yousef Jarun, Ahmad Maswadeh, Nour Alhoda Alahmad, Mohammad M Al-Talib
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Publication date: Available online 30 September 2020Source: GeneAuthor(s): Guangyu Liu, Mingfei Zeng, Xingxing Li, Yu Rong, Zhigang Hu, Huilin Zhang, Xiaolin Liu
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Yang Yan, Lanlan Fang, Yuxi Li, Yiping Yu, Yiran Li, Jung-Chien Cheng, Ying-Pu Sun
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): R.D. Acemel, J.J. Tena, J.L. Gomez-Skarmeta, J. Fibla, J.L. Royo
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Publication date: Available online 28 September 2020Source: GeneAuthor(s): Wenjun Chen, Xinlin Chen, Minting Zhang, Zunnan Huang
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Francesca Ricci, Pierangelo Luporini, Claudio Alimenti, Adriana Vallesi
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Seokhyun Lee, Joon Ha Lee, Ra Ham Lee, Yong Pyo Shin, In-Woo Kim, Minchul Seo, Mi-Ae Kim, Jae Sam Hwang, Donghyun Shin, Hak-Kyo Lee
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Zhengmin Tang, Yijie Fan, Li Zhang, Congcong Zheng, Aiyun Chen, Yuxiao Sun, Haixia Guo, Jianfei Wu, Tongtong Li, Yupeng Fan, Xin Lian, Huihui Guo, Xiongfeng Ma, Haifeng Chen, Fanchang Zeng
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Jing Zhu, Jingtao Li, Yi Wei, Jianchu Wang, Xiao-Yu Zhang
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Damir Dittrich, Marija Maskalan, Zeljko Kastelan, Hrvoje Palenkic, Zorana Grubic
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Haixia Li, Hongwei Xu, Zhanerke Akhatayeva, Hongfei Liu, Chunjian Lin, Xufei Han, Xiaofang Lu, Xianyong Lan, Qingfeng Zhang, Chuanying Pan
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Publication date: Available online 28 September 2020Source: GeneAuthor(s): Li Liu, Zhenglong Zhai, Danyang Wang, Yun Ding, Xiaoqing Chen, Qiqi Wang, Zheyue Shu, Minglan Wu, Lei Chen, Xuelin He, Dazhi Fan, Faming Pan, Meiyuan Xing
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Xingguo Wang, Yongfeng Li, Liang Qu, Jun Guo, Taocun Dou, Yuping Hu, Meng Ma, Kehua Wang
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Yi-Zhi Cao, Jin-Yu Sun, Yan-Xiang Chen, Cheng-Cai Wen, Liqing Wei
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Alexandra N. Nail, Brett T. Spear, Martha L. Peterson
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Xinxin Zhang, Mengqi Zhu, Hui Wang, Zaozhi Song, Danka Zhan, Wenjing Cao, Yajuan Han, Jianguang Jia
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Ying Lv, Han Cao, Liangzhao Chu, Han Peng, Xiangchun Shen, Hua Yang
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Chunming Xu, Qingjia Chi, Li Yang, K.L. Paul Sung, Chunli Wang
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Shabnam Ashouri, Reza Farshbaf Pourabad
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Archana Mishra, Neetu Singh, Hari Shyam, Mayank Jain, Dinesh Kumar Sahu, Pratap Shankar, Nawazish Alam, Anil Kumar, Riddhi Jaiswal, Shailendra Kumar
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Sajad Jeddi, Nasibeh Yousefzadeh, Hamideh Afzali, Asghar Ghasemi
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Chun-Li Yang, Wen-Kai Yang, Zhao-Hui He, Jing-Hua Guo, Xiao-Gang Yang, Hong-Bo Li
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Publication date: Available online 17 September 2020Source: GeneAuthor(s): Shao'e Sun, Zhongli Sha, Yanrong Wang
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Jie Li, Chenglong Shen, Kaijuan Zhang, Zhihan Niu, Zhengqing Liu, Shaoli Zhang, Yongsheng Wang, Xianyong Lan
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Ping Chen, Xinyan Zhao, Geng G. Tian, Xiaoyan Yuan, Xinyue Li, Zezhong Li, Xiaoli Yu, Rong Hu, Yanrong Wang, Xiuying Pei, Huchen Zhou, Ji Wu
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Shu-hua Huang, Yu-xiu Liu, Rui Deng, Tian-tian Lei, Ai-juan Tian, Hai-hua Ren, Shu-fen Wang, Xiao-feng Wang
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Yongjun Zhang, Bin Chen
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Wangjun Wu, Zengkai Zhang, Zhe Chao, Bojiang Li, Rongyang Li, Aiwen Jiang, Kee-Hong Kim, Honglin Liu
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Publication date: 30 January 2021Source: Gene, Volume 767Author(s): Wu Zhang, Yuqin Wu, Hong Chen, Dan Yu, Jinfeng Zhao, Jing Chen
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Lirong Yang, Yang Yang, Mingyao Meng, Wenju Wang, Shan He, Yiyi Zhao, Hui Gao, Weiwei Tang, Shijie Liu, Zhuying Lin, Lin Li, Zongliu Hou
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Liang-xing Guo, Fu-rong Nie, An-qun Huang, Rui-ning Wang, Meng-yun Li, Hong-yu Deng, Yan-zhou Zhou, Xian-min Zhou, Yan-kun Huang, Jia Zhou, Yu-dan Ji
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Masaya Sugiyama, Noriko Kinoshita, Satoshi Ide, Hidetoshi Nomoto, Takato Nakamoto, Sho Saito, Masahiro Ishikane, Satoshi Kutsuna, Kayoko Hayakawa, Masao Hashimoto, Manabu Suzuki, Shinyu Izumi, Masayuki Hojo, Kiyoto Tsuchiya, Hiroyuki Gatanaga, Jin Takasaki, Masahide Usami, Toshikazu Kano, Hidekatsu Yanai, Nao Nishida
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Eglė Jakubauskienė, Laurynas Vilys, Inga Pečiulienė, Arvydas Kanopka
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Publication date: 15 January 2021Source: Gene, Volume 766Author(s): Dhuha M.B. AlDehaini, Suzanne A. Al-Bustan, Zainab Hasan Abdulla Malalla, Muhalab E. Ali, Mai Sater, Hayder A. Giha
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Abstract With rapid advancements of sequencing technologies and accumulations of electronic health records, a large number of genetic variants and multiple correlated human complex traits have become available in many genetic association studies. Thus, it becomes necessary and important to develop new methods that can jointly analyze the association between multiple genetic variants and multiple traits. Compared with methods that only use a single marker or trait, the joint analysis of multiple...
16h
Abstract Multiple methods have been proposed to aggregate genetic variants in a gene or a region and jointly test their association with a trait of interest. However, these joint tests do not provide estimates of the individual effect of each variant. Moreover, few methods have evaluated the joint association of multiple variants with DNA methylation. We propose a method based on linear mixed models to estimate the joint and individual effect of multiple genetic variants on DNA methylation leveraging...
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Abstract Germline mutations in many genes have been shown to increase the risk of developing cancer. This risk can vary across families who carry mutations in the same gene due to differences in the specific variants, gene–gene interactions, other susceptibility mutations, environmental factors, and behavioral factors. We develop an analytic tool to explore this heterogeneity using family history data. We propose to evaluate the ratio between the number of observed cancer cases in a family and the...
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Abstract The intensities from genotyping array data can be used to detect copy number variants (CNVs) but a high level of noise in the data and overlap between different copy‐number intensity distributions produces unreliable calls, particularly when only a few probes are covered by the CNV. We present a novel pipeline (CamCNV) with a series of steps to reduce noise and detect more reliably CNVs covering as few as three probes. The pipeline aims to detect rare CNVs (below 1% frequency) for association...
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Abstract Estimating the prevalence of rare germline genetic mutations in the general population is of interest as it can inform genetic counseling and risk management. Most studies that estimate the prevalence of mutations are performed in high‐risk populations, and each study is designed with differing inclusion criteria, resulting in ascertained populations. Quantifying the effects of ascertainment is necessary to estimate the prevalence in the general population. This quantification is difficult...
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Abstract Genes, including those with transgenerational effects, work in concert with behavioral, environmental, and social factors via complex biological networks to determine human health. Understanding complex relationships between causal factors underlying human health is an essential step towards deciphering biological mechanisms. We propose a new analytical framework to investigate the interactions between maternal and offspring genetic variants or their surrogate single nucleotide polymorphisms...
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Abstract Bronchodilator (BD) drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of BD medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken before BD medication have been extensively studied, and the genetics of the BD response itself have received some attention. However, few studies have focused on the genetics...
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Abstract In this paper, we develop TWO‐SIGMA, a TWO‐component SInGle cell Model‐based Association method for differential expression (DE) analyses in single‐cell RNA‐seq (scRNA‐seq) data. The first component models the probability of “drop‐out” with a mixed‐effects logistic regression model and the second component models the (conditional) mean expression with a mixed‐effects negative binomial regression model. TWO‐SIGMA is extremely flexible in that it: (i) does not require a log‐transformation...
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Abstract Carotid artery atherosclerotic disease (CAAD) is a risk factor for stroke. We used a genome‐wide association (GWAS) approach to discover genetic variants associated with CAAD in participants in the electronic Medical Records and Genomics (eMERGE) Network. We identified adult CAAD cases with unilateral or bilateral carotid artery stenosis and controls without evidence of stenosis from electronic health records at eight eMERGE sites. We performed GWAS with a model adjusting for age, sex,...
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Front Cover Caption: The cover image is based on the Original Article SNP‐HLA Reference Consortium (SHLARC): HLA and SNP data sharing for promoting MHC‐centric analyses in genomics by Nicolas Vince et al., https://doi.org/10.1002/gepi.22334.
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Abstract Clinical trial results have recently demonstrated that inhibiting inflammation by targeting the interleukin‐1β pathway can offer a significant reduction in lung cancer incidence and mortality, highlighting a pressing and unmet need to understand the benefits of inflammation‐focused lung cancer therapies at the genetic level. While numerous genome‐wide association studies (GWAS) have explored the genetic etiology of lung cancer, there remains a large gap between the type of information that...
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Abstract locStra is an ‐package for the analysis of regional and global population stratification in whole‐genome sequencing (WGS) studies, where regional stratification refers to the substructure defined by the loci in a particular region on the genome. Population substructure can be assessed based on the genetic covariance matrix, the genomic relationship matrix, and the unweighted/weighted genetic Jaccard similarity matrix. Using a sliding window approach, the regional similarity matrices are...
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AbstractThe ‘discovery’ stage of genome-wide association studies required amassing large, homogeneous cohorts. In order to attain clinically useful insights, we must now consider the presentation of disease within our clinics and, by extension, within our medical records. Large-scale use of electronic health record (EHR) data can help to understand phenotypes in a scalable manner, incorporating lifelong and whole-phenome context.However, extending analyses to incorporate EHR and biobank-based analyses...
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Background X-linked ichthyosis (XLI) is an uncommon dermatological condition resulting from a deficiency of the enzyme steroid sulfatase (STS), often caused by X-linked deletions spanning STS. Some medical comorbidities have been identified in XLI cases, but small samples of relatively young patients has limited this. STS is highly expressed in subcortical brain structures, and males with XLI and female deletion carriers appear at increased risk of developmental/mood disorders and associated traits;...
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Primary lymphatic anomalies may present in a myriad of ways and are highly heterogenous. Careful consideration of the presentation can lead to an accurate clinical and/or molecular diagnosis which will assist with management. The most common presentation is lymphoedema, swelling resulting from failure of the peripheral lymphatic system. However, there may be internal lymphatic dysfunction, for example, chylous reflux, or lymphatic malformations, including the thorax or abdomen. A number of causal...
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Background The of zone of polarizing activity regulatory sequence (ZRS) is a regulatory element residing in intron 5 of LMBR1 and regulates Sonic Hedgehog expression in the limb bud. Variants in the ZRS are generally fully penetrant and can cause triphalangeal thumb (TPT) and polydactyly in affected families. Objective In this report, we describe two families with mild phenotypical presentation. Methods We performed a field study for clinical evaluation and sequenced the ZRS for variantsusing...
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Background Multiple morphological abnormalities of the flagella (MMAF) consistently lead to male infertility due to a reduced or absent sperm motility defined as asthenozoospermia. Despite numerous genes recently described to be recurrently associated with MMAF, more than half of the cases analysed remain unresolved, suggesting that many yet uncharacterised gene defects account for this phenotype Methods Exome sequencing was performed on 167 infertile men with an MMAF phenotype. Immunostaining...
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Background The shelterin complex is composed of six proteins that protect and regulate telomere length, including protection of telomeres 1 (POT1). Germline POT1 mutations are associated with an autosomal dominant familial cancer syndrome presenting with diverse malignancies, including glioma, angiosarcoma, colorectal cancer and melanoma. Although somatic POT1 mutations promote telomere elongation and genome instability in chronic lymphocytic leukaemia, the contribution of POT1 mutations to development...
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Background Silver-Russell syndrome is an imprinting disorder that restricts growth, resulting in short adult stature that may be ameliorated by treatment. Approximately 50% of patients have loss of methylation of the imprinting control region (H19/IGF2:IG-DMR) on 11p15.5 and 5%–10% have maternal uniparental disomy of chromosome 7. Most published research focuses on the childhood phenotype. Our aim was to describe the phenotypic characteristics of older patients with SRS. Methods A retrospective...
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Background Little is known about knowledge of, and attitudes towards, genome sequencing (GS) among individuals with a personal history of cancer who decide to undergo GS. This qualitative study aimed to investigate baseline knowledge and attitudes among individuals previously diagnosed with a cancer of likely genetic origin who have consented to GS. Methods Semistructured interviews were conducted with purposively selected participants (n=20) from the longitudinal Psychosocial Issues in...
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Background Loeys-Dietz syndrome (LDS), an autosomal dominant rare connective tissue disorder, has multisystemic manifestations, characterised by vascular tortuosity, aneurysms and craniofacial manifestations. Based on the associated gene mutations along the transforming growth factor-beta (TGF-β) pathway, LDS is presently classified into six subtypes. Methods We present the oro-dental features of a cohort of 40 patients with LDS from five subtypes. Results The most common oro-dental manifestations...
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Background Serrated polyposis syndrome (SPS) is a clinical entity characterised by large and/ormultiple serrated polyps throughout the colon and increased risk for colorectal cancer (CRC). The basis for SPS genetic predisposition is largely unknown. Common, low-penetrance genetic variants have been consistently associated with CRC susceptibility, however, their role in SPS genetic predisposition has not been yet explored. Objective The aim of this study was to evaluate if common, low-penetrance...
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Background Rare variants in hundreds of genes have been implicated in developmental delay (DD), intellectual disability (ID) and neurobehavioural phenotypes. TNRC6B encodes a protein important for RNA silencing. Heterozygous truncating variants have been reported in three patients from large cohorts with autism, but no full phenotypic characterisation was described. Methods Clinical and molecular characterisation was performed on 17 patients with TNRC6B variants. Clinical data were obtained...
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Evolutionary conservation of opsin gene expression patterns in the compound eyes of darkling beetles
Abstract Recent large-scale studies of opsin gene contents in representatives of the largest order of insects, the Coleoptera (beetles), revealed that the blue wavelength-sensitive (B) opsin subfamily is absent in this clade, while the ultraviolet- (UV) and long wavelength-sensitive (LW) opsin subfamilies are broadly conserved with gene duplications possibly reintroducing blue sensitivity in select subclades. Little is known yet, however, how opsin genes are expressed in the compound...
21h
Abstract Vertebrate mitochondrial genomes (mitogenomes) are valuable for studying phylogeny, evolutionary genetics and genomics. To date, however, compared to other vertebrate groups, our knowledge about the mitogenomes of skinks (the family Scincidae), even of reptile, has been relatively limited. In the present study, we determined the complete mitogenome of a blue-tailed skink Plestiodon capito for the first time, and compared it with other skinks available in GenBank. The circular...
19h
Abstract Availability of genome sequence of different legume species has provided an opportunity to characterize the abundance, distribution, and divergence of canonical intact long terminal retrotransposons (In-LTR-RT) superfamilies. Among seven legume species, Arachis ipaensis (Aip) showed the highest number of full-length canonical In-LTR-RTs (3325), followed by Glycine max (Gma, 2328), Vigna angularis (Van, 1625), Arachis durensis (Adu, 1348), Lotus japonicus (Lja, 1294), Medicago...
19h
Abstract In the present work, two complete genome sequences of SARS-CoV-2 were obtained from nasal swab samples of Tunisian SARS-CoV-2 PCR-positive patients using nanopore sequencing. The virus genomes of two of the patients examined, a Tunisian soldier returning from a mission in Morocco and a member of another Tunisian family, showed significant differences in analyses of the total genome and single nucleotide polymorphisms (SNPs). Phylogenetic relationships with known SARS-CoV-2...
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Transcriptional programs of infectious spleen and kidney necrosis virus (ISKNV) in vitro and in vivo
Abstract Infectious spleen and kidney necrosis virus (ISKNV), causing serious infectious diseases to marine and freshwater fishes, is the type species of the genus Megalocytivirus, family Iridoviridae. In this study, the transcriptional programs of ISKNV in vitro (MFF-1 cells) and in vivo (spleens from mandarin fish) were investigated using real-time PCR. Transcription of all the putative open reading frames (ORFs) of ISKNV was verified. The temporal expression patterns of ISKNV...
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Abstract MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate gene expression by complementary binding to target mRNAs. Virus-encoded miRNAs play important roles in virus life cycle and virus-host interactions. Viruses from the Megalocytivirus genus, family Iridoviridae, infect a wide range of fishes, bringing great challenges to aquaculture. Infectious spleen and kidney necrosis virus (ISKNV) is the type species of the Megalocytivirus genus. In this...
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Abstract In this work, a novel ssRNA (+) viral genomic sequence with gene organization typical of members of the subfamily Quinvirinae (family Betaflexiviridae) was identified using high- throughput sequencing data of date palm obtained from the Sequence Read Archive database. The viral genome sequence consists of 7860 nucleotides and contains five ORFs encoding for the replication protein (Rep), triple gene block proteins 1, 2, 3 (TGB 1, 2, and 3), and coat protein (CP). Phylogenetic...
6d
Abstract Fowlpox virus (FPV) is used as a vaccine vector to prevent diseases in poultry and mammals. The insertion site is considered as one of the main factors influencing foreign gene expression. Therefore, the identification of insertion sites that can stably and efficiently express foreign genes is crucial for the construction of recombinant vaccines. In this study, we found that the insertion of foreign genes into ORF054 and the ORF161/ORF162 intergenic region of the FPV...
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Abstract To date, avian influenza viruses (AIVs) have persisted in domestic poultry in wet markets in East Asian countries. We have performed ongoing virus surveillance in poultry populations in Vietnam since 2011, with the goal of controlling avian influenza. Throughout this study, 110 H3 AIVs were isolated from 2760 swab samples of poultry in markets and duck farms. H3 hemagglutinin (HA) genes of the isolates were phylogenetically classified into eight groups (I–VIII). Genetic...
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Abstract Recently, multiple spillover events between domesticated poultry and wild birds have been reported for several avian viruses. This phenomenon highlights the importance of the livestock-wildlife interface in the possible emergence of novel viruses. The aim of the current study was to investigate the potential spillover and epidemiological links of infectious bursal disease virus (IBDV) between wild birds and domestic poultry. To this end, twenty-eight cloacal swabs were...
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Abstract Porcine circovirus-like agents comprise two types of viruses: porcine circovirus-like viruses (P1, P2, P3, and P4) and porcine circovirus-like mini agents (PCVL258, PCVL264, PCVL201, and PCVL347). Of these, P1 has been identified in pigs, cattle, goats, and rabbits in China; P2, P3, P4, PCVL258, and PCVL264 have been identified in pigs; and PCVL201 and PCVL347 have been identified in cattle. The purpose of this study was to determine whether dogs and cats have been exposed...
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Abstract The dynamics of interactions of viral proteins with their host are pivotal in establishing a successful infection and ensuring systemic spread. To uncover these, an in silico analysis of the interactions between the coat protein (CP) of Sesbania mosaic virus (SeMV), a group IV virus with single-stranded positive-sense RNA genome was carried out with the known crystal structures of proteins belonging to the Fabaceae family, which is its natural host. SeMV is an isometric...
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Abstract Porcine deltacoronavirus (PDCoV) has been recently identified as an emerging enteropathogenic coronavirus that mainly infects newborn piglets and causes enteritis, diarrhea and high mortality. Although coronavirus N proteins have multifarious activities, the subcellular localization of the PDCoV N protein is still unknown. Here, we produced mouse monoclonal antibodies against the PDCoV N protein. Experiments using anti-haemagglutinin antibodies and these monoclonal antibodies...
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