TY - JOUR A1 - Yang, Guang A1 - Ding, Hong-ming A1 - Kochovski, Zdravko A1 - Hu, Rongting A1 - Lu, Yan A1 - Ma, Yu-qiang A1 - Chen, Guosong A1 - Jiang, Ming T1 - Highly Ordered Self-Assembly of Native Proteins into 1D, 2D, and 3D Structures Modulated by the Tether Length of Assembly-Inducing Ligands JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition N2 - In nature, proteins self-assemble into various structures with different dimensions. To construct these nanostructures in laboratories, normally proteins with different symmetries are selected. However, most of these approaches are engineering-intensive and highly dependent on the accuracy of the protein design. Herein, we report that a simple native protein LecA assembles into one-dimensional nanoribbons and nanowires, two-dimensional nanosheets, and three-dimensional layered structures controlled mainly by small-molecule assembly-inducing ligands RnG (n = 1, 2, 3, 4, 5) with varying numbers of ethylene oxide repeating units. To understand the formation mechanism of the different morphologies controlled by the small-molecule structure, molecular simulations were performed from microscopic and mesoscopic view, which presented a clear relationship between the molecular structure of the ligands and the assembled patterns. These results introduce an easy strategy to control the assembly structure and dimension, which could shed light on controlled protein assembly. KW - carbohydrate-protein interactions KW - dual non-covalent interactions KW - molecular simulations KW - protein self-assembly Y1 - 2017 U6 - https://doi.org/10.1002/anie.201703052 SN - 1433-7851 SN - 1521-3773 VL - 56 SP - 10691 EP - 10695 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Yang, Guang A1 - Zheng, Wei A1 - Tao, Guoqing A1 - Wu, Libin A1 - Zhou, Qi-Feng A1 - Kochovski, Zdravko A1 - Ji, Tan A1 - Chen, Huaijun A1 - Li, Xiaopeng A1 - Lu, Yan A1 - Ding, Hong-ming A1 - Yang, Hai-Bo A1 - Chen, Guosong A1 - Jiang, Ming T1 - Diversiform and Transformable Glyco-Nanostructures Constructed from Amphiphilic Supramolecular Metallocarbohydrates through Hierarchical Self-Assembly: The Balance between Metallacycles and Saccharides JF - ACS nano N2 - During the past decade, self-assembly of saccharide-containing amphiphilic molecules toward bioinspired functional glycomaterials has attracted continuous attention due to their various applications in fundamental and practical areas. However, it still remains a great challenge to prepare hierarchical glycoassemblies with controllable and diversiform structures because of the complexity of saccharide structures and carbohydrate-carbohydrate interactions. Herein, through hierarchical self-assembly of modulated amphiphilic supramolecular metallocarbohydrates, we successfully prepared various well-defined glyco-nanostructures in aqueous solution, including vesicles, solid spheres, and opened vesicles depending on the molecular structures of metallocarbohydrates. More attractively, these glyco-nanostructures can further transform into other morphological structures in aqueous solutions such as worm-like micelles, tubules, and even tupanvirus-like vesicles (TVVs). It is worth mentioning that distinctive anisotropic structures including the opened vesicles (OVs) and TVVs were rarely reported in glycobased nano-objects. This intriguing diversity was mainly controlled by the subtle structural trade-off of the two major components of the amphiphiles, i.e., the saccharides and metallacycles. To further understand this precise structural control, molecular simulations provided deep physical insights on the morphology evolution and balancing of the contributions from saccharides and metallacycles. Moreover, the multivalency of glyco-nanostructures with different shapes and sizes was demonstrated by agglutination with a diversity of sugarbinding protein receptors such as the plant lectins Concanavalin A (ConA). This modular synthesis strategy provides access to systematic tuning of molecular structure and self-assembled architecture, which undoubtedly will broaden our horizons on the controllable fabrication of biomimetic glycomaterials such as biological membranes and supramolecular lectin inhibitors. KW - glycomaterials KW - diversiform structures KW - hierarchical self-assembly KW - metallocarbohydrates KW - anisotropic structures Y1 - 2019 U6 - https://doi.org/10.1021/acsnano.9b07134 SN - 1936-0851 SN - 1936-086X VL - 13 IS - 11 SP - 13474 EP - 13485 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Yang, Guang A1 - Hu, Rongting A1 - Ding, Hong-ming A1 - Kochovski, Zdravko A1 - Mei, Shilin A1 - Lu, Yan A1 - Ma, Yu-qiang A1 - Chen, Guosong A1 - Jiang, Ming T1 - CO2-switchable response of protein microtubules BT - behaviour and mechanism JF - Materials chemistry frontiers N2 - Recently, we proposed a small molecular inducing ligand strategy to assemble proteins into highly-ordered structures via dual non-covalent interactions, i.e. carbohydrate-protein interaction and dimerization of Rhodamine B. Using this approach, artificial protein microtubules were successfully constructed. In this study, we find that these microtubules exhibit a perfect CO2 responsiveness; assembly and disassembly of these microtubules were nicely controlled by the alternative passage of CO2 and N-2. Upon the injection of CO2, a negative net-charged SBA turns into a neutral or positive net-charged SBA, which elongated, to some extent, the effective distance between SBA and Rhodamine B, resulting in the disassociation of the Rhodamine B dimer. Further experimental and simulation results reveal that the CO2-responsive mechanism differs from that of solubility change of the previously reported CO2-responsive synthetic materials. Y1 - 2018 U6 - https://doi.org/10.1039/c8qm00245b SN - 2052-1537 VL - 2 IS - 9 SP - 1642 EP - 1646 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Luo, Yingyi A1 - Yan, Ming A1 - Yan, Shaorong A1 - Zhou, Xiaolin A1 - Inhoff, Albrecht W. T1 - Syllabic tone articulation influences the identification and use of words during Chinese sentence reading: Evidence from ERP and eye movement recordings JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - In two experiments, we examined the contribution of articulation-specific features to visual word recognition during the reading of Chinese. In spoken Standard Chinese, a syllable with a full tone can be tone-neutralized through sound weakening and pitch contour change, and there are two types of two-character compound words with respect to their articulation variation. One type requires articulation of a full tone for each constituent character, and the other requires a full- and a neutral-tone articulation for the first and second characters, respectively. Words of these two types with identical first characters were selected and embedded in sentences. Native speakers of Standard Chinese were recruited to read the sentences. In Experiment 1, the individual words of a sentence were presented serially at a fixed pace while event-related potentials were recorded. This resulted in less-negative N100 and anterior N250 amplitudes and in more-negative N400 amplitudes when targets contained a neutral tone. Complete sentences were visible in Experiment 2, and eye movements were recorded while participants read. Analyses of oculomotor activity revealed shorter viewing durations and fewer refixations on-and fewer regressive saccades to-target words when their second syllable was articulated with a neutral rather than a full tone. Together, the results indicate that readers represent articulation-specific word properties, that these representations are routinely activated early during the silent reading of Chinese sentences, and that the representations are also used during later stages of word processing. KW - Lexical tone KW - Neutral tone KW - Articulation duration KW - Syllabic tone KW - Sentence reading KW - Chinese Y1 - 2016 U6 - https://doi.org/10.3758/s13415-015-0368-1 SN - 1530-7026 SN - 1531-135X VL - 16 SP - 72 EP - 92 PB - Springer CY - New York ER - TY - JOUR A1 - Zhou, Wei A1 - Shu, Hua A1 - Miller, Kevin A1 - Yan, Ming T1 - Reliance on orthography and phonology in reading of Chinese BT - a developmental study JF - Journal of research in reading : a journal of the United Kingdom Reading Association N2 - BackgroundDisruptions of reading processes due to text substitutions can measure how readers use lexical information. MethodsWith eye-movement recording, children and adults viewed sentences with either identical, orthographically similar, homophonic or unrelated substitutions of the first characters in target words. To the extent that readers rely on orthographic or phonological cues, substitutions that contain such cues should cause less disruption reading than do unrelated substitutions. ResultsOn pretarget words, there was a reliable reduction in gaze duration due to homophonic substitution only for children. On target words, we observed reliable recovery effects due to orthographic similarity for adults. On post-target words, adults had better orthographic-based and phonological-based recovery abilities than children. ConclusionsThe combination of eye movement recording and the error detection paradigm offers a novel implicit paradigm for studying reading development: during sentence reading, beginning readers of Chinese may rely on phonological mediation, while skilled readers have more direct access to semantics from orthography. Y1 - 2017 U6 - https://doi.org/10.1111/1467-9817.12111 SN - 0141-0423 SN - 1467-9817 VL - 41 IS - 2 SP - 370 EP - 391 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Pan, Jinger A1 - Yan, Ming A1 - Laubrock, Jochen T1 - Perceptual span in oral reading BT - the case of Chinese JF - Scientific Studies of Reading N2 - The present study explores the perceptual span, that is, the physical extent of the area from which useful visual information is obtained during a single fixation, during oral reading of Chinese sentences. Characters outside a window of legible text were replaced by visually similar characters. Results show that the influence of window size on the perceptual span was consistent across different fixation and oculomotor measures. To maintain normal reading behavior when reading aloud, it was necessary to have information provided from three characters to the right of the fixation. Together with findings from previous research, our findings suggest that the physical size of the perceptual span is smaller when reading aloud than in silent reading. This is in agreement with previous studies in English, suggesting that the mechanisms causing the reduced span in oral reading have a common base that generalizes across languages and writing systems. Y1 - 2017 U6 - https://doi.org/10.1080/10888438.2017.1283694 SN - 1088-8438 SN - 1532-799X VL - 21 SP - 254 EP - 263 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Yan, Wenhao A1 - Chen, Dijun A1 - Schumacher, Julia A1 - Durantini, Diego A1 - Engelhorn, Julia A1 - Chen, Ming A1 - Carles, Cristel C. A1 - Kaufmann, Kerstin T1 - Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis JF - Nature Communications N2 - Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase. hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-09513-2 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Hyona, Jukka A1 - Yan, Ming A1 - Vainio, Seppo T1 - Morphological structure influences the initial landing position in words during reading Finnish JF - The quarterly journal of experimental psychology N2 - The preferred viewing location in words [Rayner, K. (1979). Eye guidance in reading: Fixation locations within words. Perception, 8, 21–30] during reading is near the word centre. Parafoveal word length information is utilized to guide the eyes toward it. A recent study by Yan and colleagues [Yan, M., Zhou, W., Shu, H., Yusupu, R., Miao, D., Krügel, A., & Kliegl, R. (2014). Eye movements guided by morphological structure: Evidence from the Uighur language. Cognition, 132, 181–215] demonstrated that the word’s morphological structure may also be used in saccadic targeting. The study was conducted in a morphologically rich language, Uighur. The present study aimed at replicating their main findings in another morphologically rich language, Finnish. Similarly to Yan et al., it was found that the initial fixation landed closer to the word beginning for morphologically complex than for monomorphemic words. Word frequency, saccade launch site, and word length were also found to influence the initial landing position. It is concluded that in addition to low-level factors (word length and saccade launch site), also higher level factors related to the word’s morphological structure and frequency may be utilized in saccade programming during reading. KW - Eye movements KW - Morphological structure KW - Reading KW - Saccades KW - Word frequency Y1 - 2018 U6 - https://doi.org/10.1080/17470218.2016.1267233 SN - 1747-0218 SN - 1747-0226 VL - 71 IS - 1 SP - 122 EP - 130 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Pan, Jinger A1 - Yan, Ming A1 - Laubrock, Jochen A1 - Shu, Hua T1 - Lexical and Sublexical Phonological Effects in Chinese Silent and Oral Reading JF - Scientific studies of reading N2 - What is the time course of activation of phonological information in logographic writing systems like Chinese, in which meaning is prioritized over sound? We used a manipulation of phonological regularity to examine foveal and parafoveal phonological processing of Chinese phonograms at lexical and sublexical levels during Chinese sentence reading in 2 eye-tracking experiments. In Experiment 1, using an error disruption task during silent reading, we observed foveal lexical phonological activation in second-pass reading. In Experiment 2, using the boundary paradigm, both parafoveal lexical and sublexical phonological preview benefits were found in first-fixation duration in oral reading, whereas only lexical phonological benefits were found in gaze duration during silent reading. Thus, phonological information had earlier and more pronounced parafoveal effects in oral reading, and these extended to sublexical processing. These results are compatible with the view that oral reading prioritizes parafoveal phonological processing in Chinese. Y1 - 2019 U6 - https://doi.org/10.1080/10888438.2019.1583232 SN - 1088-8438 SN - 1532-799X VL - 23 IS - 5 SP - 403 EP - 418 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Pan, Jinger A1 - Laubrock, Jochen A1 - Yan, Ming T1 - Phonological consistency effects in Chinese sentence reading JF - Scientific studies of reading N2 - In two eye-tracking experiments, we investigated the processing of information about phonological consistency of Chinese phonograms during sentence reading. In Experiment 1, we adopted the error disruption paradigm in silent reading and found significant effects of phonological consistency and homophony in the foveal vision, but only in a late processing stage. Adding oral reading to Experiment 2, we found both effects shifted to earlier indices of parafoveal processing. Specifically, low-consistency characters led to a better homophonic foveal recovery effect in Experiment 1 and stronger homophonic preview benefits in Experiment 2. These findings suggest that phonological consistency information can be obtained during sentence reading, and compared to the low-consistency previews the high-consistency previews are processed faster, which leads to greater interference to the recognition of target characters. Y1 - 2020 U6 - https://doi.org/10.1080/10888438.2020.1789146 SN - 1088-8438 SN - 1532-799X VL - 25 IS - 4 SP - 335 EP - 350 PB - Routledge, Taylor & Francis Group CY - Abingdon ER -