Ping Xie

Ping Xie
Chinese Academy of Sciences | CAS · Laboratory of Soft Matter Physics

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600
Publications
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Publications

Publications (600)
Article
Kinesin is a molecular motor that can step processively on microtubules via the hydrolysis of ATP molecules. An important factor characterizing the processivity of the kinesin motor is its dissociation from the microtubule. Here, using all-atom molecular dynamics simulations, we studied the dissociation process of the kinesin head in weak-microtubu...
Article
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Rivers and their lakes are among the world’s most important ecosystems ‒ supporting high biodiversity and providing various services through connections with vast landscapes. Reconciling exploitation with sustainability remains one of the world’s greatest challenges to maintain and/or recover the health of river ecosystems and hence their biodivers...
Article
In shallow eutrophic lakes, submersed macrophytes are essential for maintaining a clear water state, and they are affected markedly by fishes directly through herbivory and indirectly by fish-invertebrate-periphyton complexity, a pathway that presently is not well understood in subtropical lakes but probably vital to lake managements. We conducted...
Article
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DNA polymerases are an essential class of enzymes or molecular motors that catalyze processive DNA syntheses during DNA replications. A critical issue for DNA polymerases is their molecular mechanism of processive DNA replication. We have proposed a model for chemomechanical coupling of DNA polymerases before, based on which the predicted results h...
Preprint
Full-text available
DNA polymerases are an essential class of enzymes or molecular motors that catalyze processive DNA syntheses during DNA replications. A critical issue for DNA polymerases is their molecular mechanism of processive DNA replication. We have previously proposed a model for chemomechanical coupling of DNA polymerases, based on which the predicted resul...
Article
Significant differences in the morphological and physiological characteristics of submerged macrophytes have been studied following nutrient addition, but little research has investigated the changes in plant trait network topology structures and trait interactions at the whole-plant perspective along nutrient gradients. Plant trait interactions an...
Article
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The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin he...
Article
Eutrophication strongly influences plant stoichiometric characteristics and physiological status by altering nutrient and light availability in the water column. However, the mechanisms linking plant functional traits with ecosystem structure and functioning to clarify the decline of submerged macrophytes have not been fully elucidated to date. The...
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Global climate change likely alters the structure and function of vegetation and the stability of terrestrial ecosystems. It is therefore important to assess the factors controlling ecosystem resilience from local to global scales. Here we assess terrestrial vegetation resilience over the past 35 years using early warning indicators calculated from...
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Black bloom is a worldwide environmental problem. Sediment microbes play important roles in the process of black bloom. The dynamic change of sedimental microbial community and their potential link between taste and odor compounds during black bloom was investigated in an in situ black bloom enclosure simulation experiment. Through high-throughput...
Article
The allocation of limiting elements among plant organs is an important aspect of the adaptation of plants to their ambient environment. Although eutrophication can extremely alter light and nutrient availability, little is known about nutrient partitioning among organs of submerged macrophytes in response to eutrophication. Here, we analyzed the st...
Article
Orphan and conventional kinesin dimers represent two families of the kinesin superfamily molecular motors. Conventional kinesin, having a 14-residue neck linker (NL) in each head, can step processively on microtubule (MT), with an ATP hydrolysis being coupled with a mechanical stepping under no load. Orphan kinesin phragmoplast-associated kinesin-r...
Article
The decline in submersed macrophytes induced by low-light stress is ubiquitous in mid-lower Yangtze lakes in China. However, the trade-offs among the adaptation mechanisms used by submersed macrophytes to low-light stress remain unclear. Moreover, the experimental period used in most previous studies was relatively short, and plant traits were not...
Article
Zooplankton could efficiently graze algae and thus improve water quality. However, as thermal stratification commonly occurs in deep lakes, the effect of warming on the trophic interactions of plankton in depth profiles is still not clear. To explore the pressure of crustacean grazing on phytoplanktonic responses to enhanced thermal stratification...
Article
Benthivorous fish disturbance and snail herbivory are two important factors that determine the community structure of submersed macrophytes. We conducted an outdoor mesocosm experiment to examine the separate and combined effects of these two factors on water quality and the growth of two mixed-cultivation submersed macrophytes, Vallisneria natans...
Article
Worldwide, increasing attention is being paid to the issue of microplastic pollution in marine ecosystems, yet there is a relative lack of knowledge concerning the pollution of microplastic in inland water systems, although these microplastics are major sources of ocean pollution. In aquatic environments, previous efforts have mainly been devoted t...
Article
Kinesin is a typical molecular motor that can step processively on microtubules powered by hydrolysis of adenosine triphosphate (ATP) molecules, playing a critical role in intracellular transports. Its dynamical properties such as its velocity, stepping ratio, run length, dissociation rate, etc. as well as the load dependencies of these quantities...
Article
Biomolecular motors make use of free energy released from chemical reaction (typically ATP hydrolysis) to perform mechanical motion or work. An important issue is whether a molecular motor exhibits tight or non-tight chemomechanical (CM) coupling. The tight CM coupling refers to that each ATPase activity is coupled with a mechanical step, while the...
Article
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Kinesin-3 and kinesin-1 molecular motors are two families of the kinesin superfamily. It has been experimentally revealed that in monomeric state kinesin-3 is inactive in motility and cargo-mediated dimerization results in superprocessive motion, with an average run length being more than 10-fold longer than that of kinesin-1. In contrast to kinesi...
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Phytoplankton species composition has long been recognized to be structured by environmental filtering, but our knowledge of patterns of spatial dissimilarity congruence between the phytoplankton community and environmental divers is rather limited. Specifically, a study on whether there are specific temporal properties that could be more related t...
Article
Low underwater light availability and benthivorous fish-mediated disturbance are two important factors that influence the growth of submersed macrophytes. However, the combined effects of these factors remain unclear. To determine the combined effects of low light and fish-mediated disturbance on the growth of two submersed macrophytes with contras...
Article
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Bacterial communities are an important part of biological diversity and biogeochemical cycling in aquatic ecosystems. In this study, the relationship amongst the phytoplankton species composition and abiotic environmental factors on seasonal changes in the community composition of free-living and attached bacteria in Lake Erhai were studied. Using...
Article
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Kinesin dimer walks processively along a microtubule (MT) protofilament in a hand‐over‐hand manner, transiting alternately between one‐head‐bound (1HB) and two‐heads‐bound (2HB) states. In 1HB state, one head bound by ADP is detached from MT and the other head is bound to MT. Here, using all‐atom molecular dynamics simulations we determined the pos...
Article
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The influence of seasonality of the aquatic environment on food web has been notoriously understudied in empirical ecology. In this study, we focus on seasonal changes in one key attribute of a food web, the trophic level. We determine whether seasonal variations of fish trophic levels could be indicated by the change in food resources. Silver carp...
Article
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Leaf soluble carbohydrates (SC), free amino acids (FAA), starch, total phenolics (TOPH), carbon (C), and nitrogen (N) stoichiometry of 24 aquatic macrophyte species were studied at 52 selected sites in eastern, 31 sites in southwestern and 6 sites in western China, including 12 submerged, 6 floating-leaved, 4 emergent and 2 free-floating macrophyte...
Article
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Kinesin-1, kinesin-2 and kinesin-5 are three families of a superfamily of motor proteins; which can walk processively on microtubule filaments by hydrolyzing ATP. It was experimentally shown that while the three kinesin dimers show similar feature on the force dependence of velocity, they show rather different features on the force dependence of ru...
Article
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Herein, a model for the chemomechanical coupling of dimeric myosin-V motors is presented. Based on this model and the proposal that the rate constants of the ATPase activity of the two heads are independent of an external force in a range smaller than the stall force, we analytically studied the dynamics of the motor, such as the stepping ratio, dw...
Article
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Adaptive transgenerational plasticity is an important evolutionary strategy in plants. We investigated the resource allocation strategy in sexual reproduction and performed an in situ seed germination experiment of Potamogeton maackianus to reveal their responses to different water depths. Later, we discussed the biased adaptability to the maternal...
Article
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As we know, the survival of young ramets and stolons is essential for the clonal growth of many aquatic plants. However, few NH4⁺ enrichment experiments on clonal growth of submerged macrophytes have been conducted to provide possible evidences for their declines in eutrophic lakes. Here, the growth and physiological responses of V. natans to the e...
Article
Catastrophic regime shifts in shallow lakes are hard to predict due to a lack of clear understanding of the associate mechanisms. Theory of alternative stable states suggests that eutrophication has profound negative effects on the structure, function and stability of freshwater ecosystems. However, it is still unclear how eutrophication destabiliz...
Article
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Changes of affinity of kinesin head to microtubule regulated by changes in the nucleotide state are essential to processive movement of kinesin on microtubule. Here, using all‐atom molecular dynamics simulations we show that besides the nucleotide state, large conformational changes of microtubule‐tubulin heterodimers induced by strong interaction...
Article
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Kinesin‐1 is a homodimeric motor protein that can move along microtubule filaments by hydrolyzing ATP with a high processivity. How the two motor domains are coordinated to achieve such high processivity is not clear. To address this issue, we computationally studied the run length of the dimer with our proposed model. The computational data quanti...
Article
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The occurrence of algal blooms in drinking water sources and recreational water bodies have been increasing and causing severe environmental problems worldwide, particularly when blooms dominated by Microcystis spp. Bloom prediction and early warning mechanisms are becoming increasingly important for preventing harmful algal blooms in freshwater ec...
Article
Repeated flocculations of 0.3 g/L CMK soil greatly improved water quality. • Phytoplankton biomass decreased by 90%, and community shift was observed. • Number of copepods increased, but zooplankton biomass wasn't altered significantly. • Physiological stresses of V. natans were observed but still can be restored synchronously. The geo-engineering...
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Understanding trophic interactions in food webs is crucial to revealing the transfer of substances and energy from primary food sources to consumers in aquatic ecosystems. We hypothesize that the trophic structure of consumers can be significantly affected by primary food sources (pelagic, benthic, and littoral sources) through complex trophic inte...
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The elasticity of polypeptide chains is usually characterized by the worm-like chain model that was proposed first to describe the elasticity of double-stranded DNA. However, the molecular dynamics simulation data on the elasticity of the polypeptide chains are deviated significantly away from the theoretical data obtained based on the worm-like ch...
Article
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Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate (NTP) selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an in...
Article
Carbon (C) and nitrogen (N) metabolism are essential for the growth and maintenance of submersed macrophytes. They are affected by nutrient and light availability and seasonal changes. In this study, we investigated the changes of C/N metabolism and growth of three natural submersed macrophyte populations (i.e., each in a different site), Potamoget...
Article
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The present study was carried out to determine the efficacy of root foraging and the physiological response of Vallisnaria natans grown in heterogeneous sediments. V. natans was cultivated in two homogeneous and two heterogeneous sediments. The results suggested that V. natans grown in heterogeneous sediments presented a significantly higher root p...
Article
To explore the changes of the zooplankton community in response to excessive interferences of anthropogenic eutrophication and aquaculture on aquatic ecosystem, we performed a survey to determine the variations in these communities in 100 eastern plain lakes of China in summer. Our results showed that when filter-feeding planktivorous fishes were i...
Article
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Microcystin-LR (MCLR), a cyanotoxin widely present in freshwater, has been shown to have potent acute hepatotoxicity. However, the chronic toxicity of low-dose MCLR remains confusing by traditional measurements of toxicity. This has impeded understanding of the chronic liver damage of low-dose MCLR and corresponding safety risks of the human exposu...
Data
Appendix S1. Details of model selection of path analysis.
Article
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To assess whether and how zooplankton communities respond to variations in temperature and how these assemblages change with eutrophication, we performed a large-scale, monthly survey from August 2011 to July 2012 to determine the seasonal and spatial variations in these communities in a high-altitude lake. A detrended correspondence analysis and a...
Article
There is mounting evidence indicating that microcystins (MCs) are heptapeptide toxins. Recent studies have also shown that MCLR can transfer from mother to offspring, but it is unclear whether maternal MCLR can influence the liver of offspring or not. In this study, pregnant SD rats were injected intraperitoneally with a saline solution (control) o...
Article
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Microcystin-LR (MCLR) is one of the most toxic cyanotoxins produced in algal blooms. The toxic effects of MCLR on the expression of some organelles genes (mitochondrion, endoplasmic reticulum, and cytoskeleton etc) have been widely investigated, but little is known how it impacts on the expression of ribosomal genes. In this study we identified sev...
Article
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An in situ soil experimental system was designed to determine how urbanization impacts soil nitrogen and phosphorus dynamics. Variables including the road density, normalized difference vegetation index, distance to the nearest highway and industrial area from the soil experimental site, land use impact index, population density, population change...
Article
Black bloom has an offensive odor (caused by, e.g., dimethyl sulfide, DMS; dimethyl disulfide, DMDS; and dimethyl trisulfide, DMTS) and disastrous consequences for natural limnic ecosystems worldwide. However, research on black bloom and its taste and odor (T&O) compounds has been limited by the difficulty of predicting the time and location of bla...
Data
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Bacterial chromosomal DNA is a highly compact nucleoid. The organization of this nucleoid is poorly understood due to limitations in the methods used to monitor the complexities of DNA organization in live bacteria. Here, we report that circular plasmid DNA is auto-packaged into a uniform dualtoroidal-spool conformation in response to mechanical st...
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Idiopathic pulmonary fibrosis (IPF) is a rare, progressive, and lethal interstitial lung disease with unknown etiology. Divergent observations have suggested that genetic factors contribute to IPF susceptibility. This study investigated the relationship between human leukocyte antigen (HLA), cytokine gene polymorphisms, and IPF in a Chinese Han pop...
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Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we stu...
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As external nutrients inputs above a critical level may drive shallow lakes to shift from clear water to a turbid state, it is important to detect ecological changes of the lake at an early stage of the eutrophication process. In this way, it is possible to assess the stress tolerance of the system and thereby improve the possibilities for proper m...
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Microcystis, a genus of cyanobacteria that is dominant in eutrophic lakes, occurs mainly as colonial morphs under natural conditions but as single cells in laboratory cultures. Recent studies have suggested that Microcystis–bacteria interactions significantly influence Microcystis morphology, but the underlying mechanism remains unclear. In this st...
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The ribosomal translocation involves both intersubunit rotations between the small 30S and large 50S subunits and the intrasubunit rotations of the 30S head relative to the 30S body. However, the detailed molecular mechanism on how the intersubunit and intrasubunit rotations are related to the translocation remains unclear. Here, based on available...