392 Works

Data from: Ancestral whole genome duplication in the marine chelicerate horseshoe crabs

Nathan J. Kenny, Ka Wo Chan, Wenyan Nong, Zhe Qu, Ignacio Maeso, Ho Yin Yip, Ting Fung Chan, Hoi Shan Kwan, Peter W. H. Holland, Ka Hou Chu & Jerome H. L. Hui
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs—Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence...

Data from: Improvement in nitrogen fixation capacity could be part of the domestication process in soybean

Nacira Muñoz, Xinpeng Qi, Man-Wah Li, Min Xie, Yishu Gao, Ming-Yan Cheung, Fuk-Ling Wong & Hon-Ming Lam
Biological nitrogen fixation (BNF) in soybeans is a complex process involving the interplay between the plant host and the symbiotic rhizobia. As nitrogen supply has a crucial role in growth and development, higher nitrogen fixation capacity would be important to achieve bigger plants and larger seeds, which were important selection criteria during plant domestication by humans. To test this hypothesis, we monitored the nitrogen fixation-related performance in 31 cultivated and 17 wild soybeans after inoculation...

Additional file 10 of Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings

Jia Li, Wei Xin, Weiping Wang, Shijiao Zhao, Lu Xu, Xingdong Jiang, Yuxuan Duan, Hongliang Zheng, Luomiao Yang, Hualong Liu, Yan Jia, Detang Zou & Jingguo Wang
Additional file 10: Table S9. Sequences of primers used in this study.

Additional file 3 of Genetic diversity in the transmission-blocking vaccine candidate Plasmodium vivax gametocyte protein Pvs230 from the China–Myanmar border area and central Myanmar

Xin Zhao, Yubing Hu, Yan Zhao, Lin Wang, Zifang Wu, Myat Thu Soe, Myat Phone Kyaw, Liwang Cui, Xiaotong Zhu & Yaming Cao
Additional file 3: Table S3. Codon-based tests for selection on Pvs230 in China–Myanmar border and Myanmar isolates.

Additional file 2 of A simplified multiplex methylated DNA testing for early detection of colorectal cancer in stool DNA

Yanmiao Dai, Guodong Zhao, Jun Yang, Xilang Zhou, Shangmin Xiong, Xirong Lu, Liming Gao, Jianfang Wu, Zouhua Xu, Sujuan Fei, Minxue Zheng & Hongwei Xu
Additional file 2: Supplemental Tables.

Additional file 2 of Proteomic alterations associated with residual disease in neoadjuvant chemotherapy treated ovarian cancer tissues

Emily R. Penick, Nicholas W. Bateman, Christine Rojas, Cuauhtemoc Magana, Kelly Conrads, Ming Zhou, Brian L. Hood, Guisong Wang, Niyati Parikh, Ying Huang, Kathleen M. Darcy, Yovanni Casablanca, Paulette Mhawech-Fauceglia, Thomas P. Conrads & G. Larry Maxwell
Additional file 2: Table S1. Proteins significantly altered between post versus pre-NACT tissues (LIMMA p-value<0.01). Table S2. Proteins significantly altered between R1 versus R0 patients in pre-NACT tissues (LIMMA p-value<0.05). Table S3. Significantly (LIMMA p<0.05) co-altered proteins between pre-NACT tumors from patients with any level of residual disease vs R0 patients from an independent ovarian cancer cohort (CPTAC 2016) that exhibit highly correlated abundance trends with the present ovarian cancer cohort. Table S4. Diseases and...

Additional file 5 of Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings

Jia Li, Wei Xin, Weiping Wang, Shijiao Zhao, Lu Xu, Xingdong Jiang, Yuxuan Duan, Hongliang Zheng, Luomiao Yang, Hualong Liu, Yan Jia, Detang Zou & Jingguo Wang
Additional file 5: Table S4. Annotation and haplotype analysis of associated genes.

Additional file 6 of Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification

Changchuan Ye, Yuting Yang, Xi Chen, Lijie Yang, Xia Hua, Mengjie Yang, Xiangfang Zeng & Shiyan Qiao
Additional file 6: Fig S6. Standard Plot for ALA measurement. x: the absorbance at 554 nm; y: ALA concentration of sample after diluted (mg/L).

Additional file 3 of RBCK1 is an endogenous inhibitor for triple negative breast cancer via hippo/YAP axis

Zhongbo Li, Peng Su, Yinlu Ding, Honglei Gao, Huijie Yang, Xin Li, Xiao Yang, Yan Xia, Chenmiao Zhang, Mingxi Fu, Dehai Wang, Ye Zhang, Shu Zhuo, Jian Zhu & Ting Zhuang
Additional file 2. Clinicopathological Data for 40 TNBC.

Additional file 4 of RBCK1 is an endogenous inhibitor for triple negative breast cancer via hippo/YAP axis

Zhongbo Li, Peng Su, Yinlu Ding, Honglei Gao, Huijie Yang, Xin Li, Xiao Yang, Yan Xia, Chenmiao Zhang, Mingxi Fu, Dehai Wang, Ye Zhang, Shu Zhuo, Jian Zhu & Ting Zhuang
Additional file 3. Digital raw data.

Additional file 3 of Exogenous ABA and IAA modulate physiological and hormonal adaptation strategies in Cleistocalyx operculatus and Syzygium jambos under long-term waterlogging conditions

El-Hadji Malick Cisse, Juan Zhang, Da-Dong Li, Ling-Feng Miao, Li-Yan Yin & Fan Yang
Additional file 3.

Additional file 5 of Exogenous ABA and IAA modulate physiological and hormonal adaptation strategies in Cleistocalyx operculatus and Syzygium jambos under long-term waterlogging conditions

El-Hadji Malick Cisse, Juan Zhang, Da-Dong Li, Ling-Feng Miao, Li-Yan Yin & Fan Yang
Additional file 5.

Delocalization State-Induced Selective Bond Breaking for Efficient Methanol Electrosynthesis from CO2

Shuyi Kong, Ximeng Lv, Xin Wang, Zhengzheng Liu, Zichuang Li, Bingquan Jia, Du Sun, Chao Yang, Lijia Liu, Anxiang Guan, Jiacheng Wang, Gengfeng Zheng & Fuqiang Huang
Source data of XRD, .hkl file from 3D electron diffraction, and electrolysis data.

Additional file 1 of Chronic constriction injury-induced changes in circular RNA expression profiling of the dorsal root ganglion in a rat model of neuropathic pain

Wanxia Xiong, Min Wei, Li Zhang, Jie Wang, Fan Liu & Zhiyao Wang
Additional file 1: Table S1. List of DNA primer sequences designed for qPCR.

Protective effect of brain-derived neurotrophic factor and neurotrophin-3 overexpression by adipose-derived stem cells combined with silk fibroin/chitosan scaffold in spinal cord injury

Wen-Chen Ji, Meng Li, Wan-Ting Jiang, Xing Ma & Jia Li
Objectives: Spinal cord injury (SCI) is a most debilitating traumatic injury, and cytotherapy is a promising alternative treatment strategy. Here we investigated the effect and mechanism of adipose-derived stem/stromal cells (ASCs) with overexpressing brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT3) (BDNF-NT3) in combination with silk fibroin/chitosan scaffold (SFCS) in SCI. Methods: Female Sprague-Dawley rats were used as an SCI model. SFCS,SFCS and ASCs, or ASCs overexpressing NT3, BDNF, and BDNF-NT3 were implanted into SCI rats....

Epidemiology, evolution, and biological characteristics of H6 avian influenza viruses in China

Xiaohao Xu, Qi Chen, Min Tan, Jia Liu, Xiyan Li, Lei Yang, Yuelong Shu, Dayan Wang & Wenfei Zhu
H6 avian influenza virus (AIV) is one of the most prevalent AIV subtypes in birds globally. To investigate the current situation and characteristics of H6 AIVs circulating in China, we analysed the epidemiology, genetic evolution and pathogenic features of this subtype. During 2000-2021, H6 subtype AIVs spread widely through Southern China and presented high host diversity. On analysing 171 H6 viruses isolated during 2009-2021, dynamic reassortments were observed among H6 and other co-circulating AIV subtypes,...

Additional file 2 of Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0

Jieyu Zhao, Eugene Yui-Ching Chow, Pui Yan Yeung, Qiangfeng Cliff Zhang, Ting-Fung Chan & Chun Kit Kwok
Additional file 2. Details of identified rG4 in each rG4-seq library.

Additional file 4 of Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0

Jieyu Zhao, Eugene Yui-Ching Chow, Pui Yan Yeung, Qiangfeng Cliff Zhang, Ting-Fung Chan & Chun Kit Kwok
Additional file 4. The list of consensus rG4s across rG4-seq 2.0 libraries.

Additional file 8 of Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0

Jieyu Zhao, Eugene Yui-Ching Chow, Pui Yan Yeung, Qiangfeng Cliff Zhang, Ting-Fung Chan & Chun Kit Kwok
Additional file 8. Raw data of Figures.

Biological mechanisms of growth performance and meat quality in porcine muscle tissue

Chen Fang, Fei Guo, Xiaoqi Zhao, Zining Zhang, Junlan Lu, Hongbin Pan, Taojie Xu, Weizhen Li, Minghua Yang, Ying Huang, Yanguang Zhao & Sumei Zhao
Growth performance and meat quality are important traits for pig production. The aim of the present study was to investigate the molecular mechanisms underlying growth performance and meat quality, and to identify novel target molecules for predicting the growth performance and meat quality. The differentially expressed genes (DEGs) in Diannan small ears pigs (DSP) and Landrace pigs (LP) were assessed by RNA-sequencing analyzing technology. A total of 339 DEGs were obtained between DSP and LP....

Ocean warming reduces gastropod survival despite maintenance of feeding and oxygen consumption rates

Kathryn Anderson, Laura Falkenberg & Dina-Leigh Simons
Short-term, sub-lethal response variables are increasingly used to provide rapid indications of whole organism responses to future climate conditions. Accumulating evidence suggests, however, that these response variables may not consistently reflect whole organism responses which manifest over longer time scales. Here, we consider the effect of moderate warming on longer-term whole organism fitness, as reflected by survival, as well as two shorter-term response variables, feeding rate and oxygen consumption, for two tropical gastropod species. We...

YhjC is a novel transcriptional regulator required for Shigella flexneri virulence

Wanwu Li, Lingyan Jiang, Xiaoqian Liu, Rui Guo, Shuai Ma, Jingting Wang, Shuangshuang Ma, Shujie Li & Huiying Li
Shigella is an intracellular pathogen that primarily infects the human colon and causes shigellosis. Shigella virulence relies largely on the type III secretion system (T3SS) and secreted effectors. VirF, the master Shigella virulence regulator, is essential for the expression of T3SS-related genes. In this study, we found that YhjC, a LysR-type transcriptional regulator, is required for Shigella virulence through activating the transcription of virF. Pathogenicity of the yhjC mutant, including colonization in the colons of...

Data from: PPARγ promotes diabetes-associated centrosome amplification via increasing the expression of SKA1 directly at the transcriptional level

Qin Qin Liu, Pu Wang, Qin Ju He, Ronald Ma & Shao Chin Lee
We have published recently that type 2 diabetes can induce cell centrosome amplification, due to the action of high glucose, palmitic acid and insulin, and ROCK1 and 14-3-3σ are signal mediators. In this study, we further investigated the molecular mechanisms of the centrosome amplification in colon cancer HCT116 cells. Treatment of the cells with high glucose, palmitic acid and insulin increased the expression of peroxisome proliferator-activated receptor γ (PPARγ) as well as the spindle- and...

Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

Beomseok Seo, Lin Lin & Jia Li
Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with...

Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

Beomseok Seo, Lin Lin & Jia Li
Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with...

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