92 Works

Data from: Upregulation of NLRP3 inflammasome in the tears and ocular surface of dry eye patients

Liangliang Niu, Shujie Zhang, Jihong Wu, Ling Chen & Yan Wang
Purpose: To evaluate the mRNA and protein expressions of NLRP3 inflammasome and its downstream inflammatory factors in human dry eye. Methods: We recruited 54 patients with Sjögren’s syndrome dry eye (SSDE), 50 patients with non-Sjögren’s syndrome dry eye (NSSDE), and 46 healthy controls. Tear film breakup time (TBUT), Schirmer I test, and fluorescein staining (FL) were performed on all subjects. Tear samples were obtained to analyze the inflammatory cytokine levels of IL-1β and IL-18 via...

Regional assemblages shaped by historical and contemporary factors: evidence from a species-rich insect group

Mengdi Hao, Qian Jin, Guanliang Meng, Caiqing Yang, Shenzhou Yang, Zhiyong Shi, Min Tang, Shanlin Liu, Yinan Li, Dan Zhang, Xu Su, Chungkun Shih, Yiran Sun, Xin Zhou & Ai-Bing Zhang
Understanding the complex diversity patterns is one of the main aims of community ecology. It is important to take both historical and contemporary factors into account in investigating the potential roles in assembling diversity patterns. Here, We compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State-Speciation and Extinction model to track the origins of these patterns. We subsequently estimate diversification...

Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study

Mengdi Hao, Qian Jin, Guanliang Meng, Caiqing Yang, Shenzhou Yang, Zhiyong Shi, Min Tang, Shanlin Liu, Yinan Li, Jing Li, Dan Zhang, Xu Su, Chungkun Shih, Yiran Sun, John James Wilson, Xin Zhou & Aibing Zhang
How insect communities are assembled in nature remains largely unknown. In particular, whether habitat filtering or competition serves as the main mechanism in forming insect communities is rarely subject to an in-depth investigation. One bottleneck lies in the difficulty of species identification when dealing with a large number of diverse insects. However, High-Throughput Sequencing (HTS) technology coupled with classic DNA barcoding offers a great opportunity to infer community assembly for this speciose group. In this...

Data from: Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution

Dong-Yuan Song, Zhe Wang, Zhuo-Jun Song, Cheng-Chuan Zhou, Peng-Hao Xu, Jie Yang, Ji Yang & Bao-Rong Lu
Substantial genetic variation is found in weedy rice (Oryza sativa f. spontanea Roshev.) populations from different rice-planting regions with the change of farming styles. To determine the association of such genetic variation with rice farming changes is critical for understanding the adaptive evolution of weedy rice. We studied weedy-rice specific novel SNPs by genome-wide comparison between DNA sequences of weedy and cultivated rice, in addition to PCR fingerprinting at 22 selected novel SNP loci in...

Clinical characteristics of patients hospitalized for ocular chemical injuries in Shanghai from 2012 to 2017

Tao Li, Bo Jiang & Xiaodong Zhou
Objective: To summarize the clinical characteristics of patients with ocular chemical injuries and evaluate their potential relationship with the visual outcome by analyzing the medical records of these patients from January 1, 2012, to December 31, 2017. Design: A retrospective case series study. Setting: Jinshan Hospital of Fudan University in Shanghai. Methods: Patient data included age, gender, occupational classification, location of ocular chemical injury, initial and final best-corrected distance visual acuity (BCDVA), intraocular pressure (IOP),...

Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae

Hao Li, Qian Shi, Zaibao Zhang, Liping Zeng, Ji Qi, Hong Ma, Zai-Bao Zhang & Li-Ping Zeng
Gene duplication allows for functional divergence and innovation that provide selective advantages. However, in flowering plants genetic studies have revealed that single-gene mutations affecting one of two or more closely related paralogs often fail to cause detectable morphological defects, suggesting functional redundancy. Flowering plants have hundreds of genes encoding leucine-rich repeat receptor-like protein kinases (LRR-RLKs), several of which play important roles in anther development but little is known about their evolutionary history and possible functional...

Data from: The association of outdoor activity and age-related cataract in a rural population of Taizhou Eye Study: phase 1 report

Yating Tang, Yinghong Ji, Xiaofang Ye, Xiaofeng Wang, Lei Cai, Jianming Xu & Yi Lu
Purpose: To study the relationship between outdoor activity and risk of age-related cataract (ARC) in a rural population of Taizhou Eye Study (phrase 1 report). Method: A population-based, cross-sectional study of 2006 eligible rural adults (≥45 years old) from Taizhou Eye Study was conducted from Jul. to Sep. 2012. Participants underwent detailed ophthalmologic examinations including uncorrected visual acuity (UCVA), best corrected visual acuity (BCVA), intraocular pressure (IOP), slit lamp and fundus examinations as well as...

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...

Data from: Species decline under nitrogen fertilization increases community-level competence of fungal diseases

Xiang Liu, Shengman Lyu, Dexin Sun, Corey J. A. Bradshaw & Shurong Zhou
The artificial fertilization of soils can alter the structure of natural plant communities and exacerbate pathogen emergence and transmission. Although the direct effects of fertilization on disease resistance in plants have received some research attention, its indirect effects of altered community structure on the severity of fungal disease infection remain largely uninvestigated. We designed manipulation experiments in natural assemblages of Tibetan alpine meadow vegetation along a nitrogen-fertilization gradient over 5 years to compare the relative...

Data from: Functional dissimilarity, not phylogenetic relatedness, determines interspecific interactions among plants in the Tibetan alpine meadows

Shengman Lyu, Xiang Liu, Patrick Venail & Shurong Zhou
The hypotheses suggesting that the nature and strength of species interactions should be determined by phylogenetic relatedness have important implications for the understanding of community structure. However, to date, there is limited empirical evidence to support them. At least two basic conditions need to be met in order to expect species interactions to be determined by evolutionary relatedness: a phylogenetic signal in the traits involved in the interactions and changes in the interactions as species...

Data from: Changes in corneal biomechanical properties after long-term topical prostaglandin therapy

Na Wu, Yuhong Chen, Xiaobo Yu, Mengwei Li, Wen Wen & Xinghuai Sun
Objective: To compare corneal biomechanical properties, measured by a newly developed tonometer (Corneal Visualization Scheimpflug Technology?Corvis ST), in untreated primary open angle glaucoma (POAG) patients?POAG patients with long-term topical prostaglandin analog (PGA) therapy and in normal controls. Further is to investigate the potential effects of PGA on corneal biomechanics. Methods: In this case-control study, 35 consecutive medication naïve eyes with POAG, 34 POAG eyes with at least 2 years treatment by PGA and 19 normal...

Data from: Trophic dynamics of filter feeding bivalves in the Yangtze Estuarine Intertidal Marsh: stable isotope and fatty acid analyses

Sikai Wang, Binsong Jin, Haiming Qin, Qiang Sheng & Jihua Wu
Benthic bivalves are important links between primary production and consumers, and are essential intermediates in the flow of energy through estuarine systems. However, information on the diet of filter feeding bivalves in estuarine ecosystems is uncertain, as estuarine waters contain particulate matter from a range of sources and as bivalves are opportunistic feeders. We surveyed bivalves at different distances from the creek mouth at the Yangtze estuarine marsh in winter and summer, and analyzed trophic...

Consistent pattern of higher lability of leaves from high latitudes for both native Phragmites australis and exotic Spartina alterniflora

Youzheng Zhang, Steven Pennings, Zixia Liu, Bo Li & Jihua Wu
1. Global variation in litter decomposition rates is driven by climate, decomposer taxa and litter quality. Most large-scale studies of litter quality have made comparisons across species, rather than within a species sourced from different latitudes. Here, we aim to explore latitudinal variation in leaf litter decomposition rate and litter quality within a species. 2. We investigated whether the typical interspecific pattern of increased litter lability at higher latitudes also holds within plant species, by...

Data from: Shifts in plant community composition weaken the negative effect of nitrogen addition on community-level arbuscular mycorrhizal fungi colonization

Shurong Zhou
Nitrogen addition affects plant-arbuscular mycorrhizal fungi (AMF) association greatly. However, although the direct effect of nitrogen addition on AMF colonization has received investigation, its indirect effect through shifts in plant community composition has never been quantified. Based on a 7-year nitrogen addition experiment in an alpine meadow of Qinghai-Tibetan Plateau, we investigated the effects of nitrogen addition on both plant community, AMF diversity and colonization, and disentangled the direct and indirect effects of nitrogen addition...

United we stand: evolution of increased competitive response and defense in response to crowding in an invasive plant

Liru Chen, Xiaoyun Pan, Mu Liu & Bo Li
1. The evolution of increased competitive ability (EICA) hypothesis predicts that invasive plant could evolve to be more competitive but be less defended as a result of releasing from their natural enemies, yet this hypothesis has rarely been addressed in density-dependence. 2. Here, we grew five native (Argentina) and five introduced (USA) genotypes of perennial herb invasive plant Alternanthera philoxeroides, using an experimental setup that simulated different levels of neighbours heights and densities. 3. Our...

Daphnia sinensis genome

Xiuping Zhang
The genomic mechanism by which aquatic organisms adapt to high-altitude environments remains unknown. In this study, we provide a high-quality chromosome-level genome assembly (~133 Mb, scaffold N50 11.3 Mb) of a water flea (Daphnia sinensis). This enabled us to discover that there have been chromosomal rearrangements between two subgenera of Daphnia. We further show that the D. sinensis population living on the Tibetan Plateau exhibits several key genomic adaptive features (e.g., enhanced expression of genes...

Reconstruction of reticulate evolution and divergence timing based on RNA-seq: Hippophae as a case

Wenju Zhang
Phylotranscriptomic analysis has successfully been used to reconstruct phylogenies of higher taxa. However, depicting the patterns of phylogenies in more details and, especially, estimating time of introgression for lower taxa remain challenging. Here, we selected Hippophae (Elaeagnaceae), a small genus restricted to the Qinghai-Tibet Plateau (QTP) and adjacent areas, as an example to optimize approaches to investigate reticulate evolution in lower taxa with RNA-seq. Plastid genes and low copy nuclear genes were extracted from RNA-seq...

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

Diego F. Morales-Briones, Berit Gehrke, Chien-Hsun Huang, Aaron Liston, Hong Ma, Hannah Marx, David Tank & Ya Yang
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone...

Data from: Functional roles of Mg2+ binding sites in ion-dependent gating of a Mg2+ channel, MgtE, revealed by solution NMR

Tatsuro Maruyama, Shunsuke Imai, Tsukasa Kusakizako, Motoyuki Hattori, Ryuichiro Ishitani, Osamu Nureki, Koichi Ito, Andrès D. Maturana, Ichio Shimada & Masanori Osawa
Magnesium ions (Mg2+) are divalent cations essential for various cellular functions. Mg2+ homeostasis is maintained through Mg2+ channels such as MgtE, a prokaryotic Mg2+ channel whose gating is regulated by intracellular Mg2+ levels. Our previous crystal structure of MgtE in the Mg2+-bound, closed state revealed the existence of seven crystallographically-independent Mg2+-binding sites, Mg1–Mg7. The role of Mg2+-binding to each site in channel closure remains unknown. Here, we investigated Mg2+-dependent changes in the structure and dynamics...

Data from: Order-level fern plastome phylogenomics: new insights from Hymenophyllales

Li-Yaung Kuo, Xinping Qi, Hong Ma & Fay-Wei Li
PREMISE OF THE STUDY: Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To better understand the evolutionary history of filmy ferns, we sequenced the first complete plastome for this order. METHODS: We compiled a plastome phylogenomic dataset encompassing all eleven...

Data from: Are habitat fragmentation, local adaptation and isolation by distance driving population divergence in wild rice Oryza rufipogon?

Yao Zhao, Klaas Vrieling, Hui Liao, Manqiu Xiao, Yongqing Zhu, Jun Rong, Wenju Zhang, Yuguo Wang, Ji Yang, Jiakuan Chen & Zhiping Song
Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and...

Data from: Axial myopia is associated with visual field prognosis of primary open-angle glaucoma

Chen Qiu, Shaohong Qian, Xinghuai Sun, Chuandi Zhou & Fanrong Meng
Purpose: To identify whether myopia was associated with the visual field (VF) progression of primary open-angle glaucoma (POAG). Methods: A total of 270 eyes of 270 POAG followed up for more than 3 years with ≥9 reliable VFs by Octopus perimetry were retrospectively reviewed. Myopia was divided into: mild myopia (-2.99 diopter [D], 0), moderate myopia (-5.99, 3.00 D), marked myopia (-9.00, -6.00 D) and non-myopia (0 D or more). An annual change in the...

Data from: Evolution of increased intraspecific competitive ability following introduction: the importance of relatedness among genotypes.

Zhijie Zhang, Fang Zhou, Xiaoyun Pan, Mark Van Kleunen, Mu Liu, Bo Li & Mark Kleunen
1.A long‐standing explanation for invasion success is that invasive plants could evolve to be more competitive following introduction. This evolution of increased competitive ability (EICA) hypothesis, however, has seldom been tested with regard to intraspecific competition. Given that plants can display different responses to related and unrelated conspecifics, the evolution of intraspecific competitive ability might be specific to genotypes of different relatedness. 2.Here, we grew five native (South American) and five introduced (North American) genotypes...

Data from: Simultaneous declines in summer survival of three shorebird species signals a flyway at risk

Theunis Piersma, Tamar Lok, Ying Chen, Chris J. Hassell, Hong-Yan Yang, Adrian Boyle, Matt Slaymaker, Ying-Chi Chan, David S. Melville, Zheng-Wang Zhang & Zhijun Ma
There is increasing concern about the world's animal migrations. With many land-use and climatological changes occurring simultaneously, pinning down the causes of large-scale conservation problems requires sophisticated and data-intensive approaches. Declining shorebird numbers along the East Asian–Australasian Flyway, in combination with data on habitat loss along the Yellow Sea (where these birds refuel during long-distance migrations), indicate a flyway under threat. If habitat loss at staging areas indeed leads to flyway-wide bird losses, we would...

Data from: Genetic structure of Daphnia galeata populations in Eastern China

Wenzhi Wei, Sabine Gießler, Justyna Wolinska, Xiaolin Ma, Zhong Yang, Wei Hu & Mingbo Yin
This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that...

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