1,228 research outputs found
A Review of Zhan Wang\u27s New Works
No full textJiang Jiantao wrote this essay about Zhan Wang in Chinese, published in Art Research, issue 1, 1995, and an English translation as included in the document. The author discusses Zhan Wang\u27s Kong Ling· Kong (literally mean ethereal: void ) exhibition, held from May 19th to May 23rd, 1994, at the Central Academy of Fine Arts Museum. The author begins to illustrate the structure of the show. The artists created eighteen pieces of floating clothes, which appear being worn but the bodies are absent. The author emphasized the exhibition\u27s significance in terms of modern human life. Then it was discussed how the artist is inspired by different artists, from a variety of time periods and cultures, and how the artist injects his own artistic language and aspiration into his works. (Zhuocheng Jiang \u2726)https://digital.kenyon.edu/zhoudocs/1426/thumbnail.jp
Effective model of loop extrusion predicts chromosomal domains
No full textAn active loop-extrusion mechanism is regarded as the main out-of-equilibrium mechanism responsible forthe structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics ofthe chromosome fiber by solving the kinetic equations associated with the motion of the extruder. By averagingout the position of the extruder along the chain, we build an effective equilibrium model capable of reproducingexperimental contact maps based solely on the positions of extrusion-blocking proteins. We assessed the qualityof the effective model using numerical simulations of chromosomal segments and comparing the results withexplicit-extruder models and experimental data
Polymer Folding Simulations from Hi-C Data
No full textIn the absence of a clear molecular understanding of the mechanism that stabilizes specific contacts in interphasic chromatin, we resort to the principle of maximum entropy to build a polymeric model based on the Hi-C data of the specific system one wants to study. The interactions are set by an iterative Monte Carlo algorithm to reproduce the average contacts summarized by the Hi-C map. The study of the ensemble of conformations generated by the algorithm can report a much richer set of information than the experimental map alone, including colocalization of multiple sites, fluctuations of the contacts, and kinetical properties
Bifractal nature of chromosome contact maps
No full textModern biological techniques such as Hi-C permit one to measure probabilities that different chromosomal regions are close in space. These probabilities can be visualized as matrices called contact maps. In this paper, we introduce a multifractal analysis of chromosomal contact maps. Our analysis reveals that Hi-C maps are bifractal, i.e., complex geometrical objects characterized by two distinct fractal dimensions. To rationalize this observation, we introduce a model that describes chromosomes as a hierarchical set of nested domains and we solve it exactly. The predicted multifractal spectrum is in excellent quantitative agreement with experimental data. Moreover, we show that our theory yields a more robust estimation of the scaling exponent of the contact probability than existing methods. By applying this method to experimental data, we detect subtle conformational changes among chromosomes during differentiation of human stem cells.journal articl
The Unity of Destruction and Construction
No full textLiu Xiaochun\u27s critique, published on Art Currents, issue 1, 1995, of the group show Sculpture 1994 featured five sculptors. Zhan Wang was one of them. The authors discussed Zhan Wang\u27s work Temptation, made of clothes, linen and glue, and examined the aesthetics and philosophical thought contained within. The author considers this show as the result of the destruction and reconstruction of classical sculpture, which is then combined with Avant-Garde sculpture. In Zhan Wang’s case, the contorted garments embodies his classical sculpture education but the language he used, the message to convey, is reconstructed into Avant-Garde sculpture. (Zhuocheng Jiang \u2726)https://digital.kenyon.edu/zhoudocs/1437/thumbnail.jp
A Significant Turn- on Sculpture 1994 Show 重要的转折- 关于雕塑家1994系列个人作品展
No full textThis review by Yin Shuangxi covered the show Sculpture 1994 , which is a group show with five sculptors. Zhan Wang was one of them. The authors discussed Zhan Wang\u27s piece, Kong Ling· Kong (literally means ethereal: void ) and analyzed the aesthetics and philosophical thinking embodied within. Then, the author went from discussion of specific pieces to general conditions of Chinese sculpture conditions and the problems that sculptors were facing. (Zhuocheng Jiang \u2726)https://digital.kenyon.edu/zhoudocs/1431/thumbnail.jp
Cohesin and CTCF control the dynamics of chromosome folding
No full textThe dataset contains all the tracking data from Mach et al 2022 paper.
Each file has the following header:
x,y,z: spot coordinate. For dual color imaging, the distance along x,y and z across channels
track: track id
frame: time frame
cell: cell i
Two Essays on Corporate Social Responsibility
No full textZhan, Xintong.Thesis Ph.D. Chinese University of Hong Kong 2016.Includes bibliographical references (leaves ).Abstracts also in Chinese.Title from PDF title page (viewed on …)
CaTCHing the functional and structural properties of chromosome folding
No full textProper development requires that genes are expressed at the right time, in the right tissue, and at the right transcriptional level. In metazoans, this involves long-range cis-regulatory elements such as enhancers, which can be located up to hundreds of kilobases away from their target promoters. How enhancers find their target genes and avoid aberrant interactions with non-target genes is currently under intense investigations. The predominant model for enhancer function involves its direct physical looping between the enhancer and target promoter. The three-dimensional organization of chromatin, which accommodates promoter- enhancer interactions, therefore might play an important role in the specificity of these interactions. In the last decade, the development of a class of techniques called chromosome conformation capture (3C) and its derivatives have revolutionized the field of chromatin folding. In particular, the genome-wide version of 3C, Hi-C, revealed that mammalian chromosomes possess a rich hierarchy of folding layers, from multi-megabase compartments corresponding to mutually exclusive associations of active and inactive chromatin to topologically associating domains (TADs), which reflect regions with preferential internal interactions. Although the mechanisms that give rise to this hierarchy are still poorly understood, there is increasing evidence to suggest that TADs represent fundamental functional units for establishing the correct pattern of enhancer-promoter interactions. This is thought to occur through two complementary mechanisms: on the one hand, TADs are thought to increase the chances that regulatory elements meet each other by confining them within the same domain; on the other hand, by segregation of physical interactions across the boundary to avoid unwanted events to occur frequently.
It is however unclear whether the properties that have been attributed to TADs are specific to TADs, or rather common features among the whole hierarchy. To address this question, I have implemented an algorithm named Caller of Topological Chromosomal Hierarchies (CaTCH). CaTCH is able to detect nested hierarchies of domains, allowing a comprehensive analysis of structural and functional properties across the folding hierarchy. By applying CaTCH to published Hi-C data in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs), I showed that TADs emerge as a functionally privileged scale. In particular, TADs appear to be the scale where accumulation of CTCF at domain boundaries and transcriptional co-regulation during differentiation is maximal. Moreover, TADs appear to be the folding scale where the partitioning of interactions within transcriptionally active domains (and notably between active enhancers and promoters) is optimized.
3C-based methods have enabled fundamental discoveries such as the existence of TADs and CTCF-mediated chromatin loops. 3C methods detect chromatin interactions as ligation products after crosslinking the DNA. Crosslinking and ligation have been often criticized as potential sources of experimental biases, raising the question of whether TADs and CTCF- mediated chromatin loops actually exist in living cells. To address this, in collaboration with Josef Redolfi, we developed a new method termed ‘DamC’ which combines DNA methylation with physical modeling to detect chromosomal interactions in living cells, at the molecular scale, without relying on crosslinking and ligation. By applying DamC to mouse ESCs, we provide the first in vivo and crosslinking- and ligation-free validation of chromosomal structures detected by 3C-methods, namely TADs and CTCF-mediated chromatin loops.
DamC, together with 3C-based methods, thus have shown that mammalian chromosomes possess a rich hierarchy of folding layers. An important challenge in the field is to understand the mechanisms that drive the establishment these folding layers. In this sense, polymer physics represent a powerful tool to gain mechanistic insights into the hierarchical folding of mammalian chromosomes. In polymer models, the scaling of contact probability, i.e. the contact probability as a function of genomic distance, has been often used to benchmark polymer simulations and test alternative models. However, the scaling of contact probability is only one of the many properties that characterize polymer models raising the question of whether it would be enough to discriminate alternative polymer models. To address this, I have built finite-size heteropolymer models characterized by random interactions. I showed that finite-size effects, together with the heterogeneity of the interactions, are sufficient to reproduce the observed range of scaling of contact probability. This suggests that one should be careful in discriminating polymer models of chromatin folding based solely on the scaling.
In conclusion, my findings have contributed to achieve a better understanding of chromatin folding, which is essential to really understand how enhancers act on promoters. The comprehensive analyses using CaTCH have provided conceptually new insights into how the architectural functionality of TADs may be established. My work on heteropolymer models has highlighted the fact that one should be careful in using solely scaling to discriminate physical models for chromatin folding. Finally, the ability to detect TADs and chromatin loops using DamC represents a fundamental result since it provides the first orthogonal in vivo validation of chromosomal structures that had essentially relied on a single technology
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