Chinese Journal of Nature

Defects in solids: From the dislocation to topological vortex

ZHOU Xinjia, MA Lin, WU Zhenwei, WANG Weihua

2024, 46(2): 83-87. doi:10.3969/j.issn.0253-9608.2024.02.001

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In solid state physics and materials science, the subject of how solids flow and deform has historically been of great interest. The essence of the proverb “The mountains flowed before the Lord” lies in the recognition that solid materials are inherently imperfect, in which of the defects dominating their rheological behaviors at the long-time scales. In a recent work, researchers combined theoretical topological analysis with cutting-edge simulation methods and finally confirmed the existence of topological defects in glasses and their crucial role for plasticity. This is the first time for the study of glass physics, people showing how the classical eigenmode geometry shapes the plastic behavior of amorphous materials.

T2T human reference genomes mark the new starting point of the precision medicine era

KANG Yu

2024, 46(2): 88-94. doi:10.3969/j.issn.0253-9608.2024.02.002

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Driven by the rapid advancement of DNA sequencing technology, human genome research entered the era of “telomere to telomere (T2T)”. The central hallmark of this era is achieving high-quality and high-continuity linear assembly of every human chromosome molecule, from telomere to telomere, which could be served as the gold standard for quality control in precision medicine. This enables accurate and stable identification of individual variation information. The complete assembly of an increasing number of individual genomes has revealed significantly higher levels of human genome variations than initially anticipated. It has also provided a crucial theoretical foundation for each population to utilize its own reference genome for variation analysis. By employing a closely matched reference genome, it would be more precise in identification and locating individual variations. Dataset of accurate variation information forms the fundamental basis for studying the association between variations and phenotypes in precision medicine. This novel paradigm based on population-based genome analysis and research will undoubtedly have a significant impact on the future development of precision medicine.

Recent advances of transcription-translation coupling in bacteria

ZHANG Jing, WANG Chengyuan

2024, 46(2): 95-104. doi:10.3969/j.issn.0253-9608.2024.02.003

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The central dogma elucidates the process by which genetic information is transferred from DNA to RNA and ultimately to protein. During transcription, messenger RNA (mRNA) is synthesized by RNA polymerase using DNA as a template. Subsequently, ribosomes utilize the newly synthesized mRNA during translation to generate proteins. In contrast to eukaryotes, bacteria and archaea exhibit simultaneous transcription and translation within the same cellular compartment. This co-occurrence of processes is facilitated through transcription-translation coupling, wherein the leading ribosome follows transcribing RNA polymerase. Physical interactions among these macromolecular machines are important for both transcription and translation processes. Extensive research on bacterial transcription-translation coupling has progressively unveiled its pivotal role in gene regulation for last decades while identifying various regulatory factors involved in this process. Recent structural studies investigating different states of the transcriptiontranslation coupling complex have systematically demonstrated dynamic changes occurring under varying mRNA spacing conditions, thereby providing a theoretical foundation for further investigations into the gene regulation mechanisms governed by transcriptiontranslation
coupling.

Research progress on the types, structures and regulation mechanisms of cofactor riboswitches#br#

XU Xiaochen, REN Aiming

2024, 46(2): 105-116. doi:10.3969/j.issn.0253-9608.2024.02.004

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Riboswitches are highly conserved RNA elements capable of recognizing small molecule ligands and modulating downstream gene expression. To date, nearly 60 types of riboswitches have been identified, each recognizing different metabolites and small molecules. With the increasing discovery of riboswitches, their sequence features, tertiary structures, and regulatory mechanisms become focal points of research. Tertiary structure-based studies provide invaluable insights into understanding the ligand recognition and downstream gene expression mechanisms of riboswitches. In this review, we provide an overview of the diversity and primary functions of known riboswitches, with a specific focus on the tertiary structures and ligand recognition mechanisms of cofactor riboswitches. Additionally, we discuss the applications and future prospects of riboswitches.

Conservation and specificity of chromatin-remodeling complexes in plants

GUO Jing, HE Xinjian

2024, 46(2): 117-129. doi:10.3969/j.issn.0253-9608.2024.01.011

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In eukaryotes, nucleosomes which are formed by the genomic DNA and the histone octamer wrapped around, are the basic units of chromatin. The formation of nucleosomes contributes to package genomic DNA into the limited-space nucleus. It also has a significant impact on gene expression. Chromatin-remodeling factors utilize the energy generated by ATP hydrolysis to regulate nucleosomes assembly and removal, nucleosomes sliding, and histone variant exchange, thus controlling gene expression and various biological processes. The chromatin-remodeling factors mainly include SWI/SNF, ISWI, CHD, and INO80, which primarily exists in the form of multi-subunit complexes. Recent studies have systematically identified the subunit composition and functions of plant chromatin-remodeling complexes, revealing the conservation and specificity of these complexes relative to yeast’s and animal’s. The molecular mechanisms of these complexes regulating gene transcription are also revealed. These findings establish the foundation for further research on the role of chromatin remodeling in plant growth, development, and stress responses.

Progress in the structures of class I histone deacetylase complexes

WANG Yannan, WANG Xiao, ZHANG Heqiao

2024, 46(2): 130-138. doi:10.3969/j.issn.0253-9608.2024.01.010

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Type I histone deacetylase complex (type I HDAC complex), conserved from yeast to human, is a zinc-dependent histone modifying enzyme. Both Saccharomyces cerevisiae Rpd3S and Schizosaccharomyces pombe Clr6S, two homologous multiplesubunit complexes, are recruited by histone H3 methylation K36 (H3K36me) to open reading frame and remove the acetyl groups from specific lysine residues at histones H3 and H4, thereby suppressing cryptic transcription. In this review, the recent cryo-EM work on type I HDAC complexes is summarized, and the mechanisms of nucleosome recognition and subsequent deacetylation by type I HDAC complex are discussed.

The role of protein post-translational modification in bacterial pathogenesis

ZHOU Tao, YAO Yufeng , WANG Danni

2024, 46(2): 139-149. doi:10.3969/j.issn.0253-9608.2023.03.009

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Post-translation modifications (PTMs) are considered to have the effect of changing the stability and activity of proteins, which is one of the important steps to regulate the biological function of proteins, and widely exists in eukaryotes and prokaryotes. PTMs plays a crucial role in regulating bacterial life activities, such as metabolism, signal transduction, pathogenic process, and so on. In this review, we summarized the main types and functions of PTMs in bacteria, the regulation mechanism of PTMs in bacterial virulence and adaptability, the way that bacterial effectors regulates host proteins through PTMs, and the new progress of PTMs detection technology. The study of PTMs are of great significance to understand the bacterial pathogenesis and the bacteria-host interactions. Meanwhile, this study can also provide a new target for the development of specific therapeutic drugs.

Emotion analysis for machine intelligence

PENG Junjie

2024, 46(2): 150-156. doi:10.3969/j.issn.0253-9608.2024.01.013

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The rise of large language models, especially the development and application of artificial intelligence technology based on large language models, has attracted widespread attentions from the whole society to artificial intelligence technology, as it can reach or even surpass humans in many aspects, and accomplish tasks with high skill requirements that can only be done by humans before. However, there are still many challenges that need to be overcome and solved on the path of artificial intelligence towards human intelligence. One of the important issues is emotional analysis and understanding, that is, how to accurately understand human emotions with artificial intelligence technology. In response to this issue, the paper presents the definition and classification of emotions, and discusses the problems to be solved, research directions, current research status, challenges, applications, and prospects of the study on emotion analysis.

Mathematical philosophy and life wisdom

ZHU Hongwei

2024, 46(2): 157-160. doi:10.3969/j.issn.0253-9608.2024.02.009

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Mathematical concepts profoundly influence our worldview and decision-making processes. This article delves into how the Bayesian theorem, Poisson distribution, and Fourier transform find applications in everyday life, thereby revealing the deep life philosophies behind them. These theories not only explain scientific phenomena but also provide frameworks for personal decisionmaking, guiding us on how to update beliefs, seize opportunities, and understand complex issues from different perspectives.

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