136 Works

Can polyploidy confer invasive plants with a wider climatic tolerance? a test using Solidago canadensis

Junmin Li, Jizhong Wan, Ayub Oduor, Robin Pouteau, Beilei Wang, Luxi Chen, Beifen Yang & Feihai Yu
Polyploidy can cause variation in plant functional traits and thereby generate individuals that can adapt to fluctuating environments and exploit new environments. However, few empirical studies have tested for an association between ploidy level and climatic tolerance of invasive cytotypes relative to conspecific native-range cytotypes. Here, we used an invasive plant Solidago canadensis to test whether invasive populations had a higher proportion of polyploids, greater height and stem-base diameter, and occupied a wider range of...

Data from: Contrasting effects of specialist and generalist herbivores on resistance evolution in invasive plants

Zhijie Zhang, Xiaoyun Pan, Dana Blumenthal, Mark Van Kleunen, Mu Liu & Bo Li
Invasive alien plants are likely to be released from specialist herbivores and at the same time encounter biotic resistance from resident generalist herbivores in their new ranges. The Shifting Defense Hypothesis predicts that this will result in evolution of decreased defense against specialist herbivores and increased defense against generalist herbivores. To test this, we performed a comprehensive meta-analysis of 61 common garden studies that provide data on resistance and/or tolerance for both introduced and native...

Risks and features of secondary infections in severe and critical ill COVID-19 patients

Haocheng Zhang, Yi Zhang, Jing Wu, Yang Li, Xian Zhou, Xin Li, Haili Chen, Mingquan Guo, Shu Chen, Feng Sun, Richeng Mao, Chao Qiu, Zhaoqin Zhu, Jingwen Ai & Wenhong Zhang
Objectives Severe or critical COVID-19 is associated with intensive care unit admission, increased secondary infection rate, and would lead to significant worsened prognosis. Risks and characteristics relating to secondary infections in severe COVID-19 have not been described. Methods Severe and critical COVID-19 patients from Shanghai were included. We collected lower respiratory, urine, catheters, and blood samples according to clinical necessity and culture and mNGS were performed. Clinical and laboratory data were archived. Results We found...

Data from: Nitrogen acquisition of Central European herbaceous plants that differ in their global naturalization success

Yanjie Liu, Mark Van Kleunen & Mark Kleunen
It is frequently assumed that species capable of fast nitrogen (N) acquisition under different N-availability conditions should have a higher establishment success after their introduction into new regions. However, few experimental studies have explicitly tested this. Our multispecies experiment tested whether global naturalization success of plant species native to Central Europe is related to a high N-acquisition ability. We selected 41 common herbaceous species native to Germany that have all become naturalized, and thus been...

A matter of time: Recovery of plant species diversity in wild plant communities at declining nitrogen deposition

Frank Berendse, Rob Geerts, Wim Elberse, Martijn Bezemer, Paul Goedhart, Wei Xue, Erik Noordijk, Cajo Ter Braak & Hein Korevaar
Aim: High levels of nitrogen deposition have been responsible for important losses of plant species diversity. It is often assumed that reduction of ammonia and nitrogen oxide emissions will result in the recovery of the former biodiversity. In Western Europe N deposition peaked between 1980 and 1988 and declined thereafter. In a 60-year experiment in hay meadows we tested the hypothesis that increasing and declining nitrogen deposition had negative, respectively, positive effects on plant species...

Eukaryotic translation initiation factor 3 subunit B could serve as a potential prognostic predictor for breast cancer

Shaoran Song, Jie Liu, Miao Zhang, Xiaoqian Gao, Wei Sun, Peijun Liu, Yaochun Wang & Juan Li
The EIF3 gene family is essential in controlling translation initiation during the cell cycle. The significance of the EIF3 subunits as prognostic markers and therapeutic targets in breast cancer is not yet clear. We analyzed the expression of EIF3 subunits in breast cancer on the GEPIA and Oncomine databases and compared their expression in breast cancer and normal tissues using BRCA data downloaded from TCGA. Then we performed clinical survival analysis on the Kaplan–Meier Plotter...

Eukaryotic translation initiation factor 3 subunit B could serve as a potential prognostic predictor for breast cancer

Shaoran Song, Jie Liu, Miao Zhang, Xiaoqian Gao, Wei Sun, Peijun Liu, Yaochun Wang & Juan Li
The EIF3 gene family is essential in controlling translation initiation during the cell cycle. The significance of the EIF3 subunits as prognostic markers and therapeutic targets in breast cancer is not yet clear. We analyzed the expression of EIF3 subunits in breast cancer on the GEPIA and Oncomine databases and compared their expression in breast cancer and normal tissues using BRCA data downloaded from TCGA. Then we performed clinical survival analysis on the Kaplan–Meier Plotter...

Integrative analyses of hub genes and their association with immune infiltration in adipose tissue, liver tissue and skeletal muscle of obese patients after bariatric surgery

Kemin Yan, Pengyuan Zhang, Jiewen Jin, Xin Chen, Hongyu Guan, Yanbing Li & Hai Li
Bariatric surgery (BS) is an effective treatment for obesity. Adipose tissue, liver tissue and skeletal muscle are important metabolic tissues. This study investigated hub genes and their association with immune infiltration in these metabolic tissues of obese patients after BS by bioinformatic analysis with Gene Expression Omnibus datasets. Differentially expressed genes (DEGs) were identified, and a protein–protein interaction network was constructed to identify hub genes. As a result, 121 common DEGs were identified and mainly...

Data from: Plant diversity improves resistance of plant biomass and soil microbial communities to drought

Yan Li, Jiang Wang, Congcong Shen, Jichen Wang, Brajesh K. Singh & Yuan Ge
1. Biodiversity is known to affect ecosystem resistance and have implications for the maintenance of ecosystem functions and services under climate change. Compared to numbers of studies focusing on aboveground vegetation, the response of belowground communities to abiotic stresses along plant diversity gradients is often ignored and is considered an important knowledge gap in ecosystem ecology. Here we conducted an integrative research to evaluate the resistance of plant biomass, and soil microbial communities and associated...

MERS-CoV nsp1 impairs the cellular metabolic processes by selectively downregulating mRNAs in a novel granules

Zhaoyi Pan, Yujie Feng, Zhihui Wang, Zhengyang Lei, Qiuju Han & Jian Zhang
MERS-CoV infection can damage the cellular metabolic processes, but the underlying mechanisms are largely unknown. Through screening, we found non-structural protein 1 (nsp1) of MERS-CoV could inhibit cell viability, cell cycle, and cell migration through its endonuclease activity. Transcriptome sequencing revealed that MERS-CoV nsp1 specifically downregulated the mRNAs of ribosomal protein genes, oxidative phosphorylation protein genes, and antigen presentation genes, but upregulated the mRNAs of transcriptional regulatory genes. Further analysis shown nsp1 existed in a...

Interactions between soil microbes and native species drive a diversity-invasibility relationship

Xiao-Yan Wang, Song Gao, Tong Chen, Jiang Wang & Fei-Hai Yu
Soil microbes can affect both the invasiveness of exotic plants and the invasibility of native plant communities, but it still remains unclear whether soil microbes can influence the relationship between native plant species diversity and community invasibility. We constructed native plant communities with three levels of species richness (one, three, or six species) in un-sterilized or sterilized soil (i.e., with or without soil microbes) and let them not be invaded by exotic plant species or...

Clonal functional traits favor the invasive success of alien plants into native communities

Yong-Jian Wang, Yuan-Yuan Liu, Duo Chen, Dao-Lin Du, Heinz Müller-Schärer & Fei-Hai Yu
Functional traits are frequently proposed to determine the invasiveness of alien species. However, few empirical studies have directly manipulated functional traits and tested their importance in the invasion success of alien species into native plant communities, particularly under global change. We manipulated clonal integration (a key clonal functional trait) of four alien clonal plants by severing inter-ramet connections or keeping them intact, and simulated their invasion into native plant communities with two levels of species...

Additional file 2 of Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)

Fei Li, Ye Liu, Xiaohua Zhang, Lingzhi Liu, Yun Yan, Xin Ji, Fanshu Kong, Yafan Zhao, Junzhou Li, Ting Peng, Hongzheng Sun, Yanxiu Du & Quanzhi Zhao
Additional file 2. Table S2. Gene names and numbers for differential pathways.

Additional file 3 of Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)

Fei Li, Ye Liu, Xiaohua Zhang, Lingzhi Liu, Yun Yan, Xin Ji, Fanshu Kong, Yafan Zhao, Junzhou Li, Ting Peng, Hongzheng Sun, Yanxiu Du & Quanzhi Zhao
Additional file 3. Table S3. The name and number of metabolites.

Additional file 1 of Nasopharyngeal aspirates in children with severe community-acquired pneumonia collected within 3 days before bronchoscopy can partially reflect the pathogens in bronchoalveolar lavage fluids

Qiguo Zhu, Junli Zhou, Fei Li, Peng Shi, Yi Lu, Xiaoliang Lin, Lin Yuan, Zhiqiang Zhuo & Jun Shen
Supplementary Material 1: Original clinical data of 204 cases.

Integrative analyses of hub genes and their association with immune infiltration in adipose tissue, liver tissue and skeletal muscle of obese patients after bariatric surgery

Kemin Yan, Pengyuan Zhang, Jiewen Jin, Xin Chen, Hongyu Guan, Yanbing Li & Hai Li
Bariatric surgery (BS) is an effective treatment for obesity. Adipose tissue, liver tissue and skeletal muscle are important metabolic tissues. This study investigated hub genes and their association with immune infiltration in these metabolic tissues of obese patients after BS by bioinformatic analysis with Gene Expression Omnibus datasets. Differentially expressed genes (DEGs) were identified, and a protein–protein interaction network was constructed to identify hub genes. As a result, 121 common DEGs were identified and mainly...

Additional file 3 of Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships

Chenqian Tang, Xin Chen, Yunfei Deng, Liyang Geng, Jianhui Ma & Xueyan Wei
Additional file 3: Table S3. Codon usage and relative synonymous codon usage (RSCU) values of protain-coding genes of the 16 Sorbus s.s. chloroplast genomes

Additional file 7 of Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships

Chenqian Tang, Xin Chen, Yunfei Deng, Liyang Geng, Jianhui Ma & Xueyan Wei
Additional file 7: Table S7. Information of species included in phylogenetic analyses

Transcriptomic reprogramming of diatom Minutocellus polymorphus grown on urea

Mei Zhang, Ying Li, Tiezhu Mi, Feng Chen & Yu Zhen
Minutocellus polymorphus MMDL5290, a minute diatom, can efficiently utilize organic nitrogen (N) urea as the sole N source and achieve equivalent growth rate and photosynthesis capacity as it does with nitrate. Interestingly, M. polymorphus MMDL5290 growing on urea-replete (400 µM) medium yields a similar growth rate to that on nitrate-replete (882 µM). So far, very few reports are available on the molecular regulation mechanisms of microalgae with similar growth potential under different N sources. To...

Additional file 2 of Prenatal diagnosis and mRNA profiles of fetal tetralogy of Fallot

Zhongshan Gou, Yan Zhou, Hongjing Jia, Zhong Yang, Qian Zhang & Xinxin Yan
Additional file 2: Table S1. Differential lncRNAs between TOF and control groupincluding 21 up- and 73 down-regulated lncRNAs. Table S2. Differential mRNAs between TOF and control groupincluding 41 up- and 42 down-regulated genes. Table S3. lncRNA correlations to mRNA showed difference betweenTOF and control group.

Additional file 8 of Genome-wide identification and analysis of bZIP gene family reveal their roles during development and drought stress in Wheel Wingnut (Cyclocarya paliurus)

Yu-Tian Tao, Lu-Xi Chen, Jie Jin, Zhao-Kui Du & Jun-Min Li
Additional file 8: Table S1. Information on duplicated bZIP gene pairs in C. paliurus. Table S2. Orthologous relationships between CpbZIP genes and bZIP genes in Oryza sativa, Arabidopsis thaliana, Fragaria vesca, and Juglans regia. Table S3. Domain organization of CpbZIP genes predicted using pfam. Table S4. Cis-regulatory elements in CpbZIP promoter regions. Table S5. Gene annotation using eggnog-mapper. Table S6. Gene Ontology analysis of CpbZIP genes. Table S7. Potential genes involved in drought stress responses...

Genome-wide identification of genes critical for in vivo fitness of multi-drug resistant porcine extraintestinal pathogenic Escherichia coli by transposon-directed insertion site sequencing using a mouse infection model

Fan Yin, Yan Hu, Zixuan Bu, Yuying Liu, Hui Zhang, Yawen Hu, Ying Xue, Shaowen Li, Chen Tan, Xiabing Chen, Lu Li, Rui Zhou & Qi Huang
Extraintestinal pathogenic Escherichia coli (ExPEC) is an important zoonotic pathogen. Recently, ExPEC has been reported to be an emerging problem in pig farming. However, the mechanism of pathogenicity of porcine ExPEC remains to be revealed. In this study, we constructed a transposon (Tn) mutagenesis library covering Tn insertion in over 72% of the chromosome-encoded genes of a virulent and multi-drug resistant porcine ExPEC strain PCN033. By using a mouse infection model, a transposon-directed insertion site...

Supplementary Materials for Genotypic and phenotypic spectrum and pathogenesis of WNT1 variants in a large cohort of patients with OI / osteoporosis

Jing Hu, Xiaoyun Lin, Peng Gao, Qian Zhang, Bingnan Zhou, Ou Wang, Yan Jiang, Weibo Xia, Xiaoping Xing & Mei Li
Mutations in WNT1 can cause rare inherited disorders such as osteogenesis imperfecta (OI) and early-onset osteoporosis (EOOP). Due to its rarity, the clinical characteristics and pathogenic mechanism of WNT1 mutations remain unclear. We aimed to explore the phenotypic and genotypic spectrum and treatment responses of a large cohort of patients with WNT1-related OI/OP and the molecular mechanisms of WNT1 variants. The phenotypes and genotypes of patients and their responses to bisphosphonates or denosumab were evaluated....

Does land use age influence carbon cycling in the Tibetan Plateau?

Meta Francis Justine, Pan Kaiwen, Nambajimana Jean De Dieu, Fidele Karamage, Zebene Tadesse, Bikram Pandey, Yang Wanqin, Wu Fuzhong, Olusanya Abioudun Olatunji, Nirdesh Nepal, Friday Uchege, Akash Tariq, Lin Zhang & Xiaoming Sun
Although substantial information had been generated on the effects of land use change on soil organic carbon (SOC) and total nitrogen (TN) storage, studies are absent on multifactorial effects of land use types, land use age, and elevation on SOC and TN storage. SOC and TN were therefore investigated in 30 field sites comprising natural forests, planted forests, shrub, and grasslands. SOC and TN stocks differed and correlated significantly with land use age; the C...

Risks and features of secondary infections in severe and critical ill COVID-19 patients

Haocheng Zhang, Yi Zhang, Jing Wu, Yang Li, Xian Zhou, Xin Li, Haili Chen, Mingquan Guo, Shu Chen, Feng Sun, Richeng Mao, Chao Qiu, Zhaoqin Zhu, Jingwen Ai & Wenhong Zhang
Objectives Severe or critical COVID-19 is associated with intensive care unit admission, increased secondary infection rate, and would lead to significant worsened prognosis. Risks and characteristics relating to secondary infections in severe COVID-19 have not been described. Methods Severe and critical COVID-19 patients from Shanghai were included. We collected lower respiratory, urine, catheters, and blood samples according to clinical necessity and culture and mNGS were performed. Clinical and laboratory data were archived. Results We found...

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