49 Works

Data from: Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model

Gang He, Kang Huang, SongTao Guo, WeiHong Ji, Yi Ren, XueLin Jin & BaoGuo Li
Molecular studies using trace DNA, such as from museum specimens, ancient or forensic samples and samples obtained noninvasively, often have a common problem of low quality of DNA templates. Amplification errors, such as allelic dropout and false allele, may arise during polymerase chain reaction (PCR) using such samples. A mathematical model which treats homozygotes and heterozygotes discriminately has been developed to measure sample quality and compute the confidence level of using multiple-tube approaches. We use...

Drivers of intraspecific differentiation of the alpine cold tolerant herb Notopterygium oviforme: the roles of isolation by distance and ecological factors

Mili Liu
Determining the driver mechanisms of phenotypic and genetic divergence of species have long been the central topic in evolutionary biology. However, the relative roles of isolation by distance (IBD) and environment factors in contributing to species divergence is largely undetermined in perennial herbs in East Asia. In this study, we collected population genetic samples of a cold-tolerant perennial herb Notopterygium oviforme in central China. We integrated the population transcriptomes, whole chloroplast genomes, genotyping-by-sequencing, microsatellite markers...

NLRC5 restricts dengue virus infection by promoting the autophagic degradation of viral NS3 through E3 ligase CUL2 (cullin 2)

Jiawei Hao, Jinqian Li, Zhenzhen Zhang, Yang Yang, Qing Zhou, Tiantian Wu, Tongling Chen, Zhongdao Wu, Ping Zhang, Jun Cui & Yi-Ping Li
NLRC5 has been reported to be involved in antiviral immunity; however, the underlying mechanism remains poorly understood. Here, we investigated the functional role of NLRC5 in the infection of a flavivirus, dengue virus (DENV). We found that the expression of NLRC5 was strongly induced by virus infection and IFNB or IFNG stimulation in different cell lines. Overexpression of NLRC5 remarkably suppressed DENV infection, whereas knockout of NLRC5 led to a significant increase in DENV infection....

Additional file 9 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 9: Table S4. The 21 prognositc DE-MRGs based on the TCGA GBM cohort.

Additional file 6 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 6: Table S1. The mitochondria-related genes extracted from the uniprot database.

Additional file 4 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 4: Table S3.qPCR results of gDNA after DNase treatment. (recording data values of Additional file 1: Fig. S6B).

Additional file 5 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 5: Table S4.Normalized abundance of marker genes in each GC cell type. (recording data values of Additional file 1: Fig. S7D).

Additional file 10 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 10: Table S5. GO enrichment analysis by using DAVID.

Additional file 2 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 2: Table S2. Some summary statistics from two-way analysis of variance of 12 traits of rice hybrid QYSM, derived RIL and BCF1 hybrid (RIL × Q9311) populations evaluated in three environments (Hefei, Nanning and Deyang).

Additional file 12 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 12: Table S7. The function of 45 cloned yield related genes identified as the candidate genes for determining the performance of hybrid rice variety QYSM.

Additional file 8 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 8: Table S5. Classification of 2,736 epistatic QTL pairs into 13 types according to their gene actions identified in the Q9311/WSSM combined population.

Comment on \"Ultrastructure reveals ancestral vertebrate pharyngeal skeleton in yunnanozoans\"

Kaiyue He, Jianni Liu, Jian Han, Qiang Ou, Ailin Chen, Zhifei Zhang, Dongjing Fu, Hong Hua, Xingliang Zhang & Degan Shu
Yunnanozoans (Yunnanozoon and Haikouella) from the early Cambrian Chengjiang fauna, which have been controversial in affinity, was claimed recently to strengthen the hypothesis of stem-group vertebrates based on so-called cellular cartilage, fibrillin microfibers, and subchordal at branchial arches of yunnanozoans. We contend that these interpretations are incredible based on the morphology of more than 8000 specimens. As the absence of conclusive evidence for the preservation of cellular cartilage and microfibrils on yunnanozoans. It is necessary...

Additional file 10 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 10: Table S5. GO enrichment analysis by using DAVID.

Additional file 9 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 9: Table S4. The 21 prognositc DE-MRGs based on the TCGA GBM cohort.

Additional file 6 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 6: Table S3. Summary of 639 main-effect QTL affecting 12 traits identified in the combined population across three environments by inclusive composite interval mapping.

Additional file 6 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 6: Table S3. Summary of 639 main-effect QTL affecting 12 traits identified in the combined population across three environments by inclusive composite interval mapping.

Additional file 8 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 8: Table S5. Classification of 2,736 epistatic QTL pairs into 13 types according to their gene actions identified in the Q9311/WSSM combined population.

Additional file 1 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 1: Table S1. Phenotypic performance and heterosis of traits in Q9311B/WSSM RILs and backcross F1s (Q9311A × RIL).

Additional file 4 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 4: Table S3.qPCR results of gDNA after DNase treatment. (recording data values of Additional file 1: Fig. S6B).

Additional file 5 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 5: Table S4.Normalized abundance of marker genes in each GC cell type. (recording data values of Additional file 1: Fig. S7D).

Data from: Nutrient-specific compensation for seasonal cold stress in a free-ranging temperate colobine monkey

Songtao Guo, Rong Hou, Paul A. Garber, David Raubenheimer, Nicoletta Righini, Weihong Ji, Ollie Jay, Shujun He, Fan Wu, Fangfang Li, Baoguo Li, Song-Tao Guo, Shu-Jun He, Fang-Fang Li, Bao-Guo Li & Wei-Hong Ji
1. Homeostatic responses of animals to environmentally-induced changes in nutrient requirements provide a powerful basis for predictive ecological models, and yet such responses are virtually unstudied in the wild. 2. We tested for macronutrient-specific compensatory feeding responses by free-ranging golden snub-nosed monkeys (Rhinopithecus roxellana) inhabiting high altitude temperate forests where they experience a substantial difference in ambient temperature in cold winters vs. warmer springs. The monkeys had free access to natural foods throughout the year,...

Data from: Phylogeographic patterns of the desert poplar in northwest China shaped by both geology and climatic oscillations

Yan-Fei Zeng, Jian-Guo Zhang, Bawerjan Abuduhamiti, Wen-Ting Wang & Zhi-Qing Jia
Background: The effects of historical geology and climatic events on the evolution of plants around the Qinghai-Tibetan Plateau region have been at the center of debate for years. To identify the influence of the uplift of the Tianshan Mountains and/or climatic oscillations on the evolution of plants in arid northwest China, we investigated the phylogeography of the Euphrates poplar (Populus euphratica) using chloroplast DNA (cpDNA) sequences and nuclear microsatellites, and estimated its historical distribution using...

Data from: Changes in the chlorophyll content of grape leaves could provide a physiological index for responses and adaptation to UV-C radiation

Yangyang Luo, Ruixiang Li, Qiushi Jiang, Ru Bai & Dong Duan
Stilbenes are a group of phytoalexins that play an important role in grapevine (Vitis) basal immunity and can be induced by biotic and abiotic stresses. The levels of chlorophylls, the main pigments in plant cells, can also indicate the tolerance of plants to various stresses. Here, the response of different grapevine genotypes to UV-C radiation treatment was tested and the abundance of chlorophyll in the Hoe29 and Ke53 genotypes was observed to increase significantly within...

Data from: Cambrian rhynchonelliform nisusioid brachiopods: phylogeny and distribution

Lars E. Holmer, Mohammad-Reza Kebria-Ee Zadeh, Leonid E. Popov, Mansoureh Ghobadi Pour, Javier J. Álvaro, Vachik Hairapetian & Zhifei Zhang
A comprehensive review and phylogenetic analysis of genera and species presently assigned to the rhynchonelliform superfamily Nisusioidea and family Nisusiidae suggests that this short-lived but important group of brachiopods first appeared in peri-Gondwana during the second half of the Cambrian Series 2, before going extinct by the end of Drumian time. Nisusiides achieved their maximum morphological disparity and geographical distribution during Wuliuan age, and most likely Laurentia was the major center of dispersal. The new...

Southwest China, the last refuge of continental primates in East Asia

He Zhang, Jiqi Lu, Shiyi Tang, Zhipang Huang, Liangwei Cui, Daoying Lan, Rong Hou, Wen Xiao, Haitao Wang, Songtao Guo Guo, Gang He, Kang Huang, Pei Zhang, Hao Pan, Charles Oxnard, Ruliang Pan & Baoguo Li
Knowledge of primate evolutionary history from the Late Miocene to the present in East Asia is necessary to develop a tangible conservation strategy for their today and future. This background is especially evident from the distributions of fossil-bearing sites in the Pleistocene and historical records over the past 800 years. They illustrate catarrhines’ early dispersal and radiation routes, paths, and later shrinking trajectories, based on which their future distribution areas can be predicted, providing robust...

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Affiliations

  • Northwest University
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  • Sun Yat-sen University
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  • Central South University
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  • Shanghai Jiao Tong University
    29
  • Chinese Academy of Medical Sciences & Peking Union Medical College
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  • Chinese Academy of Agricultural Sciences
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  • Fudan University
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  • Agricultural Genomics Institute at Shenzhen
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  • Peking University First Hospital
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  • Sun Yat-sen University Cancer Center
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