1,621 Works

Data from: Structure of the epiphyte community in a tropical montane forest in SW China

Mingxu Zhao, Nalaka Geekiyanage, Jianchu Xu, Myo Myo Khin, Dian Ridwan Nurdiana, Ekananda Paudel & Rhett Daniel Harrison
Vascular epiphytes are an understudied and particularly important component of tropical forest ecosystems. However, owing to the difficulties of access, little is known about the properties of epiphyte-host tree communities and the factors structuring them, especially in Asia. We investigated factors structuring the vascular epiphyte-host community and its network properties in a tropical montane forest in Xishuangbanna, SW China. Vascular epiphytes were surveyed in six plots located in mature forests. Six host and four micro-site...

Data from: Population genetic structure of Oryza rufipogon and O. nivara: implications for the origin of O. nivara

Rong Liu, Xiao-Ming Zheng, Lian Zhou, Hai-Fei Zhou & Song Ge
Ecological speciation plays a primary role in driving species divergence and adaptation. Oryza rufipogon and Oryza nivara are two incipient species at the early stage of speciation with distinct differences in morphology, life history traits and habitat preference, and therefore provide a unique model for the study of ecological speciation. However, the population genetic structure of the ancestral O. rufipogon has been controversial despite substantial study, and the origin of the derivative O. nivara remains...

Data from: Testing the scaling effects and mechanisms of N-induced biodiversity loss: evidence from a decade-long grassland experiment

Zhichun Lan, G. Darrel Jenerette, Shuxia Zhan, Wenhuai Li, Shuxia Zheng & Yongfei Bai
Although extensive studies demonstrate that nitrogen (N) enrichment frequently reduces plant diversity within small quadrats (0.5 –4 m2), only a few studies have evaluated N effects on biodiversity across different spatial scales. We conducted the first experimental test of the scale dependence of N effects on species richness from a 10-year N treatment (1.75- 28 g N m−2 yr−1) in a typical steppe. We used species area relationship (SAR) to analyze the scale dependence of...

The use of TLR2 modified BMSCs for enhanced bone regeneration in the inflammatory micro-environment

Qin Zhou, Xiaoyu Gu, Jiachen Dong, Chao Zhu, Zhen Cai, Dongmei He, Chi Yang, Ling Xu & Jiawei Zheng
The repair of periodontal bone tissue defects in patients with periodontitis is one of the major challenges for dentists. Stem cell-based bone regeneration has been considered as a promising strategy to restore the lost periodontal bone tissue. However, the local inflammatory environment of periodontal tissue affects stem cell-based periodontal bone regeneration. Toll-like receptor 2 (TLR2), a member of the TLR family, plays an important role in regulating immunoreaction. Previous studies have shown that the activation...

The use of TLR2 modified BMSCs for enhanced bone regeneration in the inflammatory micro-environment

Qin Zhou, Xiaoyu Gu, Jiachen Dong, Chao Zhu, Zhen Cai, Dongmei He, Chi Yang, Ling Xu & Jiawei Zheng
The repair of periodontal bone tissue defects in patients with periodontitis is one of the major challenges for dentists. Stem cell-based bone regeneration has been considered as a promising strategy to restore the lost periodontal bone tissue. However, the local inflammatory environment of periodontal tissue affects stem cell-based periodontal bone regeneration. Toll-like receptor 2 (TLR2), a member of the TLR family, plays an important role in regulating immunoreaction. Previous studies have shown that the activation...

Data from: Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific

Zi-Min Hu, Jing-Jing Li, Zhong-Min Sun, Jung-Hyun Oak, Jie Zhang, Pablo Fresia, W. Stewart Grant & De-Lin Duan
A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from...

Data from: A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features

Hui Wu, Zhen Ma, Ming-Ming Wang, Ai-Li Qin, Jin-Hua Ran & Xiao-Quan Wang
The origin and evolution of polyploids have been studied extensively in angiosperms and ferns but very rarely in gymnosperms. With the exception of three species of conifers, all natural polyploid species of gymnosperms belong to Ephedra, in which more than half of the species show polyploid cytotypes. Here we investigate the origin and evolution of polyploids of Ephedra distributed in the Qinghai-Tibetan Plateau (QTP) and neighboring areas. Flow cytometry (FCM) was used to measure the...

Data from: Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

Li-Na Zhang, Xian-Zhi Zhang, Yu-Xiao Zhang, Chun-Xia Zeng, Peng-Fei Ma, Lei Zhao, Zhen-Hua Guo & De-Zhu Li
The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared to...

Data from: Factors determining forest diversity and biomass on a tropical volcano, Mt. Rinjani, Lombok, Indonesia

Gbadamassi G. O. Dossa, Ekananda Paudel, Junichi Fujinuma, Haiying Yu, Wanlop Chutipong, Yuan Zhang, Sherryl Paz, Rhett D. Harrison & Nathan G. Swenson
Tropical volcanoes are an important but understudied ecosystem, and the relationships between plant species diversity and compositional change and elevation may differ from mountains created by uplift, because of their younger and more homogeneous soils. We sampled vegetation over an altitudinal gradient on Mt. Rinjani, Lombok, Indonesia. We modeled alpha- (plot) and beta- (among plot) diversity (Fisher’s alpha), compositional change, and biomass against elevation and selected covariates. We also examined community phylogenetic structure across the...

Data from: Comparative transcriptome resources of eleven Primulina species, a group of “stone plants” from a biodiversity hotspot

Bin Ai, Yong Gao, Xiaolong Zhang, Junjie Tao, Ming Kang & Hongwen Huang
The genus Primulina is an emerging model system in studying the drivers and mechanisms of species diversification, for its high species richness and endemism, together with high degree of habitat specialization. In this study, we sequenced transcriptomes for eleven Primulina species across the phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of 336 million clean reads were processed into 355 573 unigenes with a mean length of 1336 bp and an...

Data from: Spatial variation of soil respiration in a cropland under winter wheat and summer maize rotation in the North China Plain

Ni H. Huang, Li Wang, Yongsen Hu, Haifeng Tian & Zheng Niu
Spatial variation of soil respiration (Rs) in cropland ecosystems must be assessed to evaluate the global terrestrial carbon budget. This study aims to explore the spatial characteristics and controlling factors of Rs in a cropland under winter wheat and summer maize rotation in the North China Plain. We collected Rs data from 23 sample plots in the cropland. At the late jointing stage, the daily mean Rs of summer maize (4.74 μmol CO2 m-2 s-1)...

Data from: Home-field advantages of litter decomposition increase with increasing N deposition rates: a litter and soil perspective

Ying-Bin Li, Qi Li, Jun-Jie Yang, Xiao-Tao Lv, Wen-Ju Liang, Xing-Guo Han & T. Martijn Bezemer
1. Differences in litter quality and in soil microbial community composition can influence the litter decomposition and “home-field advantage” (HFA). However, our knowledge about the relative role of litter and soil characteristics on litter decomposition and HFA effects is still limited, especially under long-term N deposition. 2. We collected soil and two types of litter (monospecific and mixed species litter) from five replicate plots from a long-term N-deposition field experiment with seven N-addition treatments (0,...

Data from: DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

Lemian Liu, Min Liu, David M. Wilkinson, Huihuang Chen, Xiaoqing Yu & Yang Jun
Microeukaryotic plankton (0.2–200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore-size sieve –by using...

Data from: Divergence in strategies for coping with winter embolism among co-occurring temperate tree species: the role of positive xylem pressure, wood type and tree stature

Cun-Yang Niu, Frederick C. Meinzer & Guang-You Hao
1. In temperate ecosystems, freeze-thaw events are an important environmental stress that can induce severe xylem embolism (i.e. clogging of conduits by air bubbles) in overwintering organs of trees. However, no comparative studies of different adaptive strategies among sympatric tree species for coping with winter embolism have examined the potential role of the presence or absence of embolism refilling by positive xylem pressure. 2. We evaluated the degree of winter embolism and hydraulic architecture traits...

Population genetics and forensic efficiency of 30 InDel markers in four Chinese ethnic groups residing in Sichuan

Fei Wang, Guanglin He, Zheng Wang, Mengge Wang, Jing Liu, Xing Zou, Shouyu Wang, Mengyuan Song, Ziwei Ye, Mingkun Xie & Yiping Hou
Sichuan Province is located at the transitional junction regions of the Qinghai-Tibet Plateau and the low-altitude plains. It also serves as the corridor of Sino-Tibetan-speaking population migration and expansion since neolithic expansion of Proto-Tibeto-Burman populations from Middle/Upper Yellow River during Majiayao period (3300–2000 BC). However, the population structure and the corresponding genetic diversity of forensic-related markers in this region remain unclear. Thus, we genotyped 30 insertion-deletion (InDel) markers in 444 samples from four ethnic groups...

Mapping the global potential transmission hotspots for severe fever with thrombocytopenia syndrome by machine learning methods

Dong Miao, Ke Dai, Guo-Ping Zhao, Xin-Lou Li, Wen-Qiang Shi, Jiu Song Zhang, Yang Yang, Wei Liu & Li-Qun Fang
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease with increasing spread. Currently SFTS transmission has expanded beyond Asian countries, however, with definitive global extents and risk patterns remained obscure. Here we established an exhaustive database that included globally reported locations of human SFTS cases and the competent vector, Haemaphysalis longicornis (H. longicornis), as well as the explanatory environmental variables, based on which, the potential geographic range of H. longicornis and risk areas...

Data from: Long-term antagonistic effect of increased precipitation and nitrogen addition on soil respiration in a semiarid steppe

Hongyan Han, Yue Du, Dafeng Hui, Lin Jiang, Mingxing Zhong & Shiqiang Wan
Changes in water and nitrogen (N) availability due to climate change and atmospheric N deposition could have significant effects on soil respiration, a major pathway of carbon (C) loss from terrestrial ecosystems. A manipulative experiment simulating increased precipitation and atmospheric N deposition has been conducted for 9 years (2005–2013) in a semiarid grassland in Mongolian Plateau, China. Increased precipitation and N addition interactively affect soil respiration through the 9 years. The interactions demonstrated that N...

Long non-coding RNA PCAT1 drives clear cell renal cell carcinoma by upregulating YAP via sponging miR-656 and miR-539

Rui Wang, Bin Zheng, Hongyan Liu & Xiuxian Wan
Clear cell renal cell carcinoma (ccRCC) is the most common RCC subtype with high metastasis, poor prognosis and conventional chemotherapy resistance. Prostate cancer associated transcript 1 (PCAT1) is an important lncRNA that was reported to be involved in cell proliferation, migration and invasion of several types of cancer cells. However, its role in ccRCC is still undetermined. This study found that PCAT1 levels were elevated in ccRCC tumors as well as several ccRCC cells, and...

Data from: Control of proline accumulation under drought via a novel pathway comprising the histone methylase CAU1 and the transcription factor ANAC055

Yanlei Fu, Hailing Ma, Siying Chen, Tianyu Gu & Jiming Gong
Proline plays a crucial role in the drought stress response in plants. However, there are still gaps in our knowledge about the molecular mechanisms that regulate proline metabolism under drought stress. Here, we report that the histone methylase encoded by CAU1, which is genetically upstream of P5CS1 (encoding the proline biosynthetic enzyme Δ1-pyrroline-5-carboxylate synthetase 1), plays a crucial role in proline-mediated drought tolerance. We determined that the transcript level of CAU1 decreased while that of...

Preventing Candida albicans from subverting host plasminogen for invasive infection treatment

Si-Min Chen, Zui Zou, Shi-Yu Guo, Wei-Tong Hou, Xi-Ran Qiu, Yu Zhang, Li-Jun Song, Xin-Yu Hu, Yuan-Ying Jiang, Hui Shen & Mao-Mao An
Candida albicans is a common fungal pathogen in humans that colonizes the skin and mucosal surfaces of the majority healthy individuals. How C. albicans disseminates into the bloodstream and causes life-threatening systemic infections in immunocompromised patients remains unclear. Plasminogen system activation can degrade a variety of structural proteins in vivo and is involved in several homeostatic processes. Here, for the first time, we characterized that C. albicans could capture and “subvert” host plasminogen to invade...

Identification of novel tetracycline resistance gene tet(X14) and its co-occurrence with tet(X2) in a tigecycline-resistant and colistin-resistant Empedobacter stercoris

Yingying Cheng, Yong Chen, Yang Liu, Yuqi Guo, Yanzi Zhou, Tingting Xiao, Shuntian Zhang, Hao Xu, Yunbo Chen, Tongling Shan, Yonghong Xiao & Kai Zhou
Tigecycline is one of the last-resort antibiotics to treat severe infections. Recently, tigecycline resistance has sporadically emerged with an increasing trend, and Tet(X) family represents a new resistance mechanism of tigecycline. In this study, a novel chromosome-encoded tigecycline resistance gene, tet(X14), was identified in a tigecycline-resistant and colistin-resistant Empedobacter stercoris strain ES183 recovered from a pig fecal sample in China. Tet(X14) shows 67.14-96.39% sequence identity to the other variants [Tet(X) to Tet(X13)]. Overexpression of Tet(X14)...

Mice deficient in UXT exhibit retinitis pigmentosa-like features via aberrant autophagy activation

Mingyu Pan, Yue Yin, Xinxia Wang, Quanyi Wang, Lele Zhang, Haiyang Hu & Chen Wang
UXT (ubiquitously expressed prefoldin like chaperone), a small chaperone-like protein, is widely expressed in diverse human and mouse tissues and is more abundant in retina and kidney. However, the functional characterization of UXT at tissue level was largely unknown. Here, we reported that mice deficient in UXT exhibited salient features of retinal degenerative disease, similar to retinitis pigmentosa. Conditional knockout (CKO) of Uxt led to retinal degeneration and pigmentation in mice retina along with significant...

Data from: Responses of growing‐season soil respiration to water and nitrogen addition as affected by grazing intensity

Jianjun Li, Yin Huang, Fengwei Xu, Liji Wu, Dima Chen & Yongfei Bai
1. Most grasslands in the world, including the semi-arid steppe in China, are threatened by nitrogen deposition, precipitation change, and livestock grazing, which greatly affect soil carbon processes (e. g., soil respiration). Although the individual effects of nitrogen deposition and precipitation change on soil respiration are well understood, how their effects on soil respiration are altered by different grazing intensities is unclear. 2. To determine how the effects of nitrogen deposition and precipitation change on...

The lipoprotein NlpD in Cronobacter sakazakii responds to acid stress and regulates macrophage resistance and virulence by maintaining membrane integrity

Xuemeng Ji, Ping Lu, Juan Xue, Ning Zhao, Yan Zhang, Lu Dong, Xuejiao Zhang, Ping Li, Yaozhong Hu, Jin Wang, Bowei Zhang, Jingmin Liu, Huan lv & Shuo Wang
Cronobacter sakazakii, an emerging opportunistic pathogen, is implicated in severe foodborne outbreak infections in premature and full-term infants. Generally, acid tolerance is vital for the pathogenesis of foodborne pathogens; however, its role in C. sakazakii virulence remains largely unknown. To screen out acid-tolerance determinants from transposon mutants, anovel counterselection method using gentamicin and acid was developed. Using the counterselection method and growth assay, we screened several acid-sensitive mutants and found that nlpD encodes an acid-resistance...

Data from: Congruent species delimitation of two controversial gold-thread nanmu tree species based on morphological and restriction site-associated DNA sequencing data

Xin Ding, Jianhua Xiao, Lang Li, John G Canran, Jie Li, John G. Conran & Jian Hua Xiao
Species delimitation is fundamental to conservation and sustainable use of economically important forest tree species. However, the delimitation of two highly valued gold-thread nanmu species (Phoebe bournei and P. zhennan) has been confusing and debated. To address this problem, we integrated morphology and restriction site-associated DNA sequencing (RADseq) to define their species boundaries. We obtained highly consistent results from both data sets, supporting two distinct lineages corresponding to P. bournei and P. zhennan. In Phoebe...

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