Browsing by Author "Wang, Hong"

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    Chinese Tallow Trees (Triadica sebifera) from the Invasive Range Outperform Those from the Native Range with an Active Soil Community or Phosphorus Fertilization
    (Public Library of Science, 2013) Zhang, Ling; Zhang, Yaojun; Wang, Hong; Zou, Jianwen; Siemann, Evan
    Two mechanisms that have been proposed to explain success of invasive plants are unusual biotic interactions, such as enemy release or enhanced mutualisms, and increased resource availability. However, while these mechanisms are usually considered separately, both may be involved in successful invasions. Biotic interactions may be positive or negative and may interact with nutritional resources in determining invasion success. In addition, the effects of different nutrients on invasions may vary. Finally, genetic variation in traits between populations located in introduced versus native ranges may be important for biotic interactions and/or resource use. Here, we investigated the roles of soil biota, resource availability, and plant genetic variation using seedlings of Triadica sebifera in an experiment in the native range (China). We manipulated nitrogen (control or 4 g/m2), phosphorus (control or 0.5 g/m2), soil biota (untreated or sterilized field soil), and plant origin (4 populations from the invasive range, 4 populations from the native range) in a full factorial experiment. Phosphorus addition increased root, stem, and leaf masses. Leaf mass and height growth depended on population origin and soil sterilization. Invasive populations had higher leaf mass and growth rates than native populations did in fresh soil but they had lower, comparable leaf mass and growth rates in sterilized soil. Invasive populations had higher growth rates with phosphorus addition but native ones did not. Soil sterilization decreased specific leaf area in both native and exotic populations. Negative effects of soil sterilization suggest that soil pathogens may not be as important as soil mutualists for T. sebifera performance. Moreover, interactive effects of sterilization and origin suggest that invasive T. sebifera may have evolved more beneficial relationships with the soil biota. Overall, seedlings from the invasive range outperformed those from the native range, however, an absence of soil biota or low phosphorus removed this advantage.
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    Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA–DNA pairing
    (Oxford University Press, 2016) Lin, Jiangguo; Countryman, Preston; Chen, Haijiang; Pan, Hai; Fan, Yanlin; Jiang, Yunyun; Kaur, Parminder; Miao, Wang; Gurgel, Gisele; You, Changjiang; Piehler, Jacob; Kad, Neil M.; Riehn, Robert; Opresko, Patricia L.; Smith, Susan; Tao, Yizhi Jane; Wang, Hong
    Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids. Cohesion is thought to occur through the entrapment of DNA within the tripartite ring (Smc1, Smc3 and Rad21) with enforcement from a fourth subunit (SA1/SA2). Surprisingly, cohesin rings do not play a major role in sister telomere cohesion. Instead, this role is replaced by SA1 and telomere binding proteins (TRF1 and TIN2). Neither the DNA binding property of SA1 nor this unique telomere cohesion mechanism is understood. Here, using single-molecule fluorescence imaging, we discover that SA1 displays two-state binding on DNA: searching by one-dimensional (1D) free diffusion versus recognition through subdiffusive sliding at telomeric regions. The AT-hook motif in SA1 plays dual roles in modulating non-specific DNA binding and subdiffusive dynamics over telomeric regions. TRF1 tethers SA1 within telomeric regions that SA1 transiently interacts with. SA1 and TRF1 together form longer DNA–DNA pairing tracts than with TRF1 alone, as revealed by atomic force microscopy imaging. These results suggest that at telomeres cohesion relies on the molecular interplay between TRF1 and SA1 to promote DNA–DNA pairing, while along chromosomal arms the core cohesin assembly might also depend on SA1 1D diffusion on DNA and sequence-specific DNA binding.
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    High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL
    (Elsevier, 2023) Kaur, Parminder; Lu, Xiaotong; Xu, Qi; Irvin, Elizabeth Marie; Pappas, Colette; Zhang, Hongshan; Finkelstein, Ilya J.; Shi, Zhubing; Tao, Yizhi Jane; Yu, Hongtao; Wang, Hong
    3D chromatin organization plays a critical role in regulating gene expression, DNA replication, recombination, and repair. While initially discovered for its role in sister chromatid cohesion, emerging evidence suggests that the cohesin complex (SMC1, SMC3, RAD21, and SA1/SA2), facilitated by NIPBL, mediates topologically associating domains and chromatin loops through DNA loop extrusion. However, information on how conformational changes of cohesin-NIPBL drive its loading onto DNA, initiation, and growth of DNA loops is still lacking. In this study, high-speed atomic force microscopy imaging reveals that cohesin-NIPBL captures DNA through arm extension, assisted by feet (shorter protrusions), and followed by transfer of DNA to its lower compartment (SMC heads, RAD21, SA1, and NIPBL). While binding at the lower compartment, arm extension leads to the capture of a second DNA segment and the initiation of a DNA loop that is independent of ATP hydrolysis. The feet are likely contributed by the C-terminal domains of SA1 and NIPBL and can transiently bind to DNA to facilitate the loading of the cohesin complex onto DNA. Furthermore, high-speed atomic force microscopy imaging reveals distinct forward and reverse DNA loop extrusion steps by cohesin-NIPBL. These results advance our understanding of cohesin by establishing direct experimental evidence for a multistep DNA-binding mechanism mediated by dynamic protein conformational changes.
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    Non-Native Plant Litter Enhances Soil Carbon Dioxide Emissions in an Invaded Annual Grassland
    (Public Library of Science, 2014) Zhang, Ling; Wang, Hong; Zou, Jianwen; Rogers, William E.; Siemann, Evan
    Litter decomposition is a fundamental ecosystem process in which breakdown and decay of plant detritus releases carbon and nutrients. Invasive exotic plants may produce litter that differs from native plant litter in quality and quantity. Such differences may impact litter decomposition and soil respiration in ways that depend on whether exotic and native plant litters decompose in mixtures. However, few field experiments have examined how exotic plants affect soil respiration via litter decomposition. Here, we conducted an in situ study of litter decomposition of an annual native grass (Eragrostis pilosa), a perennial exotic forb (Alternanthera philoxeroides), and their mixtures in an annual grassland in China to examine potential invasion effects on soil respiration. Alternanthera litter decomposed faster than Eragrostis litter when each was incubated separately. Mass loss in litter mixes was more rapid than predicted from rates in single species bags (only 35% of predicted mass remained at 8 months) showing synergistic effects. Notably, exotic plant litter decomposition rate was unchanged but native plant litter decomposition rate was accelerated in mixtures (decay constant k = 0.20 month-1) compared to in isolation (k = 0.10 month-1). On average, every litter type increased soil respiration compared to bare soil from which litter was removed. However, the increases were larger for mixed litter (1.82 times) than for Alternanthera litter (1.58 times) or Eragrostis litter (1.30 times). Carbon released as CO2 relative to litter carbon input was also higher for mixed litter (3.34) than for Alternathera litter (2.29) or Eragrostis litter (1.19). Our results indicated that exotic Alternanthera produces rapidly decomposing litter which also accelerates the decomposition of native plant litter in litter mixtures and enhances soil respiration rates. Thus, this exotic invasive plant species will likely accelerate carbon cycling and increase soil respiration even at intermediate stages of invasion in these annual grasslands.
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    Room-temperature ferroelectricity in CuInP2S6 ultrathin flakes
    (Springer Nature, 2016) Liu, Fucai; You, Lu; Seyler, Kyle L.; Li, Xiaobao; Yu, Peng; Lin, Junhao; Wang, Xuewen; Zhou, Jiadong; Wang, Hong; He, Haiyong; Pantelides, Sokrates T.; Zhou, Wu; Sharma, Pradeep; Xu, Xiaodong; Ajayan, Pulickel M.; Wang, Junling; Liu, Zheng
    Two-dimensional (2D) materials have emerged as promising candidates for various optoelectronic applications based on their diverse electronic properties, ranging from insulating to superconducting. However, cooperative phenomena such as ferroelectricity in the 2D limit have not been well explored. Here, we report room-temperature ferroelectricity in 2D CuInP2S6 (CIPS) with a transition temperature of ~320 K. Switchable polarization is observed in thin CIPS of ~4 nm. To demonstrate the potential of this 2D ferroelectric material, we prepare a van der Waals (vdW) ferroelectric diode formed by CIPS/Si heterostructure, which shows good memory behaviour with on/off ratio of ~100. The addition of ferroelectricity to the 2D family opens up possibilities for numerous novel applications, including sensors, actuators, non-volatile memory devices, and various vdW heterostructures based on 2D ferroelectricity.
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    Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase
    (Oxford University Press, 2022) Li, Zhuo; Kaur, Parminder; Lo, Chen-Yu; Chopra, Neil; Smith, Jamie; Wang, Hong; Gao, Yang
    Twinkle is a mitochondrial replicative helicase which can self-load onto and unwind mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human mitochondrial diseases. Using cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM), we obtained the atomic-resolution structure of a vertebrate Twinkle homolog with DNA and captured in real-time how Twinkle is self-loaded onto DNA. Our data highlight the important role of the non-catalytic N-terminal domain of Twinkle. The N-terminal domain directly contacts the C-terminal helicase domain, and the contact interface is a hotspot for disease-related mutations. Mutations at the interface destabilize Twinkle hexamer and reduce helicase activity. With HS-AFM, we observed that a highly dynamic Twinkle domain, which is likely to be the N-terminal domain, can protrude ∼5 nm to transiently capture nearby DNA and initialize Twinkle loading onto DNA. Moreover, structural analysis and subunit doping experiments suggest that Twinkle hydrolyzes ATP stochastically, which is distinct from related helicases from bacteriophages.