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Journal of Genetics and Genomics, Yi Chuan Xue Bao

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https://www.readbyqxmd.com/read/30391410/gene-diagnosis-and-targeted-breeding-for-blast-resistant-kongyu-131-without-changing-regional-adaptability
#1
Xiangchun Zhou, Gonghao Jiang, Longwei Yang, Lei Qiu, Ping He, Chunxiao Nong, Yunyue Wang, Yuqing He, Yongzhong Xing
The fungus Magnaporthe oryzae threatens the rice production of Kongyu 131 (KY131), a leading japonica variety in Northeast China. In this study, two rice lines, KP1 and KP2-Hd1, were obtained by introgressing the blast resistance genes Pi1 and Pi2 into KY131, respectively. However, both lines headed later than KY131. RICE60K SNP array analysis showed that Hd1 closely linked to Pi2 was introgressed into KP2-Hd1, and the linkage drag of Hd1 was broken by recombination. On the other hand, no known flowering genes were introgressed into KP1...
October 22, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30391409/the-present-and-future-of-whole-exome-sequencing-in-studying-and-treating-human-reproductive-disorders
#2
REVIEW
Wei Guo, Xiaohui Zhu, Liying Yan, Jie Qiao
The causes of recurrent spontaneous abortion (RSA) and fetal malformations are multifactorial and unclear in most cases. Environmental, maternal, and genetic factors have been shown to contribute to these defects. Whole-exome sequencing (WES) is widely used to detect genetic variations associated with human diseases and has recently been successfully applied to unveil genetic causes of unexplained recurrent spontaneous abortion (URSA) and fetal malformations. Here, we review the current discovery and diagnosis strategies to identify the underlying pathogenic mutations of URSA and fetal malformations using WES technology and propose to further develop WES, both to advance our understanding of these diseases and to eventually lead to targeted therapies for reproductive disorders...
October 22, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30392784/genomic-landscapes-of-chinese-sporadic-autism-spectrum-disorders-revealed-by-whole-genome-sequencing
#3
Jinyu Wu, Ping Yu, Xin Jin, Xiu Xu, Jinchen Li, Zhongshan Li, Mingbang Wang, Tao Wang, Xueli Wu, Yi Jiang, Wanshi Cai, Junpu Mei, Qingjie Min, Qiong Xu, Bingrui Zhou, Hui Guo, Ping Wang, Wenhao Zhou, Zhengmao Hu, Yingrui Li, Tao Cai, Yi Wang, Kun Xia, Yong-Hui Jiang, Zhong Sheng Sun
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with considerable clinical and genetic heterogeneity. In this study, we identified all classes of genomic variants from whole-genome sequencing (WGS) dataset of 32 Chinese trios with ASD, including de novo mutations, inherited variants, copy number variants (CNVs) and genomic structural variants. A higher mutation rate (Poisson test, P < 2.2 × 10-16 ) in exonic (1.37 × 10-8 ) and 3'-UTR regions (1.42 × 10-8 ) was revealed in comparison with that of whole genome (1...
October 21, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30352733/instability-of-microsatellites-linked-to-targeted-genes-in-crispr-cas9-edited-and-traditional-gene-knockout-mouse-strains
#4
LETTER
Xueyun Huo, Xiulin Zhang, Yihan Liu, Yizhu Sun, Yu Ren, Changlong Li, Xiaoyan Du, Zhenwen Chen
No abstract text is available yet for this article.
October 10, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30297192/developing-a-one-step-triplet-repeat-primed-pcr-assay-for-diagnosing-myotonic-dystrophy
#5
LETTER
Xiaoping Lan, Na Li, Hongling Wan, Lintong Luo, Yiming Wu, Sanxiang Li, Yu An, Bai-Lin Wu
No abstract text is available yet for this article.
September 8, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30174135/mid1ip1b-modulates-apical-reorientation-of-non-centrosomal-microtubule-organizing-center-in-epithelial-cells
#6
Xin Zhou, Chun Xiao, Yu Li, Yanna Shang, Dongqin Yin, Siying Li, Bo Xiang, Ran Lu, Yi Ji, Yang Wu, Wentong Meng, Hongyan Zhu, Jin Liu, Huozhen Hu, Xianming Mo, Hong Xu
In most kinds of animal cells, the centrosome serves as the main microtubule organizing center (MTOC) that nucleates microtubule arrays throughout the cytoplasm to maintain cell structure, cell division and intracellular transport. Whereas in epithelial cells, non-centrosomal MTOCs are established in the apical domain for generating asymmetric microtubule fibers and cilia in epithelial cells for the organ morphogenesis during embryonic development. However, the mechanism by which MTOCs localize to the apical domain in epithelial cells remains largely unknown...
August 24, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30292791/cgps-a-machine-learning-based-approach-integrating-multiple-gene-set-analysis-tools-for-better-prioritization-of-biologically-relevant-pathways
#7
Chen Ai, Lei Kong
Gene set enrichment (GSE) analyses play an important role in the interpretation of large-scale transcriptome datasets. Multiple GSE tools can be integrated into a single method as obtaining optimal results is challenging due to the plethora of GSE tools and their discrepant performances. Several existing ensemble methods lead to different scores in sorting pathways as integrated results; furthermore, it is difficult for users to choose a single ensemble score to obtain optimal final results. Here, we develop an ensemble method using a machine learning approach called Combined Gene set analysis incorporating Prioritization and Sensitivity (CGPS) that integrates the results provided by nine prominent GSE tools into a single ensemble score (R score) to sort pathways as integrated results...
September 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30287172/identifying-normal-embryos-from-reciprocal-translocation-carriers-by-whole-chromosome-haplotyping
#8
LETTER
Zhiqiang Yan, Yuqian Wang, Yanli Nie, Xu Zhi, Xiaohui Zhu, Meng Qin, Shuo Guan, Yixin Ren, Ying Kuo, Di Chang, Wei Chen, Peng Yuan, Liying Yan, Jie Qiao
No abstract text is available yet for this article.
September 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30279094/characterization-of-a-novel-regulatory-pathway-for-mannitol-metabolism-and-its-coordination-with-biofilm-formation-in-mycobacterium-smegmatis
#9
Jialing Hu, Hua Zhang, Si Zhou, Weihui Li, Zheng-Guo He
Biofilm formation has been implicated to be tightly regulated in bacteria. Mycobacterial species possess a unique cell-wall structure; however, the underlying regulation mechanism for their biofilm formation remains largely unclear. In this study, we characterized a hypothetical mannitol metabolism and transportation gene cluster (Ms5571-Ms5576), designated as mmt operon, whose expression significantly contributes to the biofilm formation in Mycobacterium smegmatis. We showed that in the operon the Ms5575 gene encodes a GntR-like transcriptional repressor and the Ms5576 gene encodes a mannitol 2-dehydrogenase which can produce D-mannitol from D-mannose...
September 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30279093/tel1-and-rif2-oppositely-regulate-telomere-protection-at-uncapped-telomeres-in-saccharomyces-cerevisiae
#10
Ling-Li Zhang, Zhenfang Wu, Jin-Qiu Zhou
It has been well documented that Tel1 positively regulates telomere-end resection by promoting Mre11-Rad50-Xrs2 (MRX) activity, while Rif2 negatively regulates telomere-end resection by inhibiting MRX activity. At uncapped telomeres, whether Tel1 or Rif2 plays any role remains largely unknown. In this work, we examined the roles of Tel1 and Rif2 at uncapped telomeres in yku70Δ and/or cdc13-1 mutant cells cultured at non-permissive temperature. We found that deletion of TEL1 exacerbates the temperature sensitivity of both yku70Δ and cdc13-1 cells...
September 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30270014/highly-efficient-genome-editing-using-oocyte-specific-zcas9-transgenic-zebrafish
#11
LETTER
Yuanyuan Liu, Chong Zhang, Yanjun Zhang, Siyao Lin, De-Li Shi, Ming Shao
No abstract text is available yet for this article.
September 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30268359/generation-of-two-transgenic-amphioxus-lines-using-the-tol2-transposon-system
#12
LETTER
Chenggang Shi, Jing Huang, Shixi Chen, Guang Li, Yiquan Wang
No abstract text is available yet for this article.
September 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30172581/overexpression-of-the-nuclear-protein-gene-atduf4-increases-organ-size-in-arabidopsis-thaliana-and-brassica-napus
#13
LETTER
Guangxia Chen, Xi Cao, Zhaoxia Ma, Yu Tang, Yuejuan Zeng, Liqun Chen, De Ye, Xue-Qin Zhang
No abstract text is available yet for this article.
August 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30174134/genome-wide-variants-of-eurasian-facial-shape-differentiation-and-a-prospective-model-of-dna-based-face-prediction
#14
Lu Qiao, Yajun Yang, Pengcheng Fu, Sile Hu, Hang Zhou, Shouneng Peng, Jingze Tan, Yan Lu, Haiyi Lou, Dongsheng Lu, Sijie Wu, Jing Guo, Li Jin, Yaqun Guan, Sijia Wang, Shuhua Xu, Kun Tang
It is a long-standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Europeans and Han Chinese look different. Facial traits were analyzed based on high-dense 3D facial images; numerous biometric spaces were examined for divergent facial features between European and Han Chinese, ranging from inter-landmark distances to dense shape geometrics. Genome-wide association studies (GWAS) were conducted on a discovery panel of Uyghurs...
August 16, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30172582/efficient-and-fast-identification-of-differentially-methylated-regions-using-whole-genome-bisulfite-sequencing-data
#15
LETTER
Dinh Diep, Kun Zhang
No abstract text is available yet for this article.
August 9, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30174136/prpf4-is-essential-for-cell-survival-and-posterior-lateral-line-primordium-migration-in-zebrafish
#16
Yixia Wang, Yanchao Han, Pengfei Xu, Shihui Ding, Guangyuan Li, Hongbin Jin, Yaping Meng, Anming Meng, Shunji Jia
Prpf4 (pre-mRNA processing factor 4), a key component of spliceosome, plays critical roles in pre-mRNA splicing and its mutations result in retinitis pigmentosa due to photoreceptor defects. In this study, we characterized a zebrafish prpf4t243 mutant harboring a Tol2 transposon-based gene trap cassette in the third intron of the prpf4 gene. Cells in the brain and spinal cord gradually undergo p53-dependent apoptosis after 28 hpf in prpf4t243 mutants, suggesting that a widespread function of prpf4 in neural cell survival...
August 7, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30055875/a-comparison-of-next-generation-sequencing-analysis-methods-for-cancer-xenograft-samples
#17
REVIEW
Wentao Dai, Jixiang Liu, Quanxue Li, Wei Liu, Yi-Xue Li, Yuan-Yuan Li
The application of next-generation sequencing (NGS) technology in cancer is influenced by the quality and purity of tissue samples. This issue is especially critical for patient-derived xenograft (PDX) models, which have proven to be by far the best preclinical tool for investigating human tumor biology, because the sensitivity and specificity of NGS analysis in xenograft samples would be compromised by the contamination of mouse DNA and RNA. This definitely affects downstream analyses by causing inaccurate mutation calling and gene expression estimates...
July 25, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30054214/the-drugpattern-tool-for-drug-set-enrichment-analysis-and-its-prediction-for-beneficial-effects-of-oxldl-on-type-2-diabetes
#18
Chuanbo Huang, Weili Yang, Junpei Wang, Yuan Zhou, Bin Geng, Georgios Kararigas, Jichun Yang, Qinghua Cui
Enrichment analysis methods, e.g., gene set enrichment analysis, represent one class of important bioinformatical resources for mining patterns in biomedical datasets. However, tools for inferring patterns and rules of a list of drugs are limited. In this study, we developed a web-based tool, DrugPattern, for drug set enrichment analysis. We first collected and curated 7019 drug sets, including indications, adverse reactions, targets, pathways, etc. from public databases. For a list of interested drugs, DrugPattern then evaluates the significance of the enrichment of these drugs in each of the 7019 drug sets...
July 24, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30115328/omics-tools-for-the-needle-out-of-haystack
#19
EDITORIAL
Zhiwei Cao, Xiu-Jie Wang, Shihua Zhang
No abstract text is available yet for this article.
July 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30057342/characterizing-functional-consequences-of-dna-copy-number-alterations-in-breast-and-ovarian-tumors-by-spacemap
#20
Christopher J Conley, Umut Ozbek, Pei Wang, Jie Peng
We propose a novel conditional graphical model - spaceMap - to construct gene regulatory networks from multiple types of high dimensional omic profiles. A motivating application is to characterize the perturbation of DNA copy number alterations (CNAs) on downstream protein levels in tumors. Through a penalized multivariate regression framework, spaceMap jointly models high dimensional protein levels as responses and high dimensional CNAs as predictors. In this setup, spaceMap infers an undirected network among proteins together with a directed network encoding how CNAs perturb the protein network...
July 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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