Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation

Xie, Zhongyu,Zhang, Di,Chung, Dongjun,Tang, Zhanyun,Huang, He,Dai, Lunzhi,Qi, Shankang,Li, Jingya,Colak, Gozde,Chen, Yue,Xia, Chunmei,Peng, Chao,Ruan, Haibin,Kirkey, Matt,Wang, Danli,Jensen, Lindy M. Elsevier 2016 Molecular cell Vol.62 No.2

<P><B>Summary</B></P> <P>Here we report the identification and verification of a β-hydroxybutyrate-derived protein modification, lysine β-hydroxybutyrylation (Kbhb), as a new type of histone mark. Histone Kbhb marks are dramatically induced in response to elevated β-hydroxybutyrate levels in cultured cells and in livers from mice subjected to prolonged fasting or streptozotocin-induced diabetic ketoacidosis. In total, we identified 44 histone Kbhb sites, a figure comparable to the known number of histone acetylation sites. By ChIP-seq and RNA-seq analysis, we demonstrate that histone Kbhb is a mark enriched in active gene promoters and that the increased H3K9bhb levels that occur during starvation are associated with genes upregulated in starvation-responsive metabolic pathways. Histone β-hydroxybutyrylation thus represents a new epigenetic regulatory mark that couples metabolism to gene expression, offering a new avenue to study chromatin regulation and diverse functions of β-hydroxybutyrate in the context of important human pathophysiological states, including diabetes, epilepsy, and neoplasia.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark </LI> <LI> 44 non-redundant histone Kbhb sites are identified in human and mouse cells </LI> <LI> Histone Kbhb increases under starvation and STZ-induced ketoacidosis </LI> <LI> Starvation-induced H3K9bhb is associated with active gene expression </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>

Regional Traffic Timing Plan Optimization Based on Improved Particle Swarm Algorithm

Zhongyu Li,Bing Li,Keli Chen,Tao Yang,Honge Li 보안공학연구지원센터 2016 International Journal of Hybrid Information Techno Vol.9 No.1

Elevated TRAF4 expression impaired LPS-induced autophagy in mesenchymal stem cells from ankylosing spondylitis patients

Jinteng Li,Peng Wang,Zhongyu Xie,Rui Yang,Yuxi Li,Xiaohua Wu,Hongjun Su,Wen Deng,Shan Wang,Zhenhua Liu,Shuizhong Cen,Yi Ouyang,Yanfeng Wu,Huiyong Shen 생화학분자생물학회 2017 Experimental and molecular medicine Vol.49 No.-

Ankylosing spondylitis (AS) is a type of autoimmune disease that predominantly affects the spine and sacroiliac joints. However, the pathogenesis of AS remains unclear. Some evidence indicates that infection with bacteria, especially Gram-negative bacteria, may have an important role in the onset and progression of AS. Recently, many studies have demonstrated that mesenchymal stem cells (MSCs) dysfunction may contribute to the pathogenesis of many rheumatic diseases. We previously demonstrated that MSCs from AS patients exhibited markedly enhanced osteogenic differentiation capacity in vitro under non-inflammatory conditions. However, the properties of MSCs from AS patients in an inflammatory environment have never been explored. Lipopolysaccharide (LPS), a proinflammatory substance derived from the outer membrane of Gram-negative bacteria, can alter the status and function of MSCs. However, whether MSCs from AS patients exhibit abnormal responses to LPS stimulation has not been reported. Autophagy is a lysosome-mediated catabolic process that participates in many physiological and pathological processes. The link between autophagy and AS remains largely unknown. The level of autophagy in ASMSCs after LPS stimulation remains to be addressed. In this study, we demonstrated that although the basal level of autophagy did not differ between MSCs from healthy donors (HDMSCs) and ASMSCs, LPS-induced autophagy was weaker in ASMSCs than in HDMSCs. Specifically, increased TRAF4 expression in ASMSCs impaired LPS-induced autophagy, potentially by inhibiting the phosphorylation of Beclin-1. These data may provide further insight into ASMSC dysfunction and the precise mechanism underlying the pathogenesis of AS.

Analytical Solution of Loosening Pressure Model for Shallow Tunnel Based on Pile-beam-arch Method

Tao Li,Zhongyu Zhang,Muchi Luo,Bo Liu,Yanlong Wang,Lingfeng Li 대한토목학회 2022 KSCE JOURNAL OF CIVIL ENGINEERING Vol.26 No.8

Loosening of earth pressure by tunnels is an important parameter for the structural design of subway stations, this study analyzes the difference between the loosening pressures of each span of a shallow multi-span tunnel station using the pile-beam-arch (PBA) method. By conducting a similarity model test of the PBA method, we simulate the complete excavation process. We study the sliding failure mode of the overlying soil of the shallow-buried station and the law of change of the loosening pressure of each span. A simplified calculation model for the loosening pressure of shallow buried multi-span tunnels by the cavity pile method was developed, and the applicability of the formulae and sensitivity analysis of the parameters were carried out. The results reveal that the loosening pressure of the mid-span is transferred to the stress of the side-span during tunnel excavation. This finding contradicts Terzaghi’s and Bierbaumer’s methods, which do not consider the influence of tunnel structure on the loosening pressure of the overlying soil. The side span relaxation pressure is only related to the soil capacity and the depth of burial of the tunnel This research can provide an important theoretical reference for the design of the overburden load and lateral confining pressure of the PBA structure design.

A novel preparation and formation mechanism of carbon nanotubes aerogel

Li Shaolong,He Yan,Jing Chengwei,Gong Xiubin,Cui Lianlei,Cheng Zhongyue,Zhang Chuanqi,Nan Fei 한국탄소학회 2018 Carbon Letters Vol.28 No.-

A novel, unique, and effective method for carbon nanotube (CNT) dispersion by the free arc stimulation is proposed. CNTs are introduced as an aerogel into the air space via the dispersion method and can be utilized as a solution by adding it to solvents. The volume of the original generated CNT aerogel with a high-volume expansion ratio displays a performance two orders of magnitudes better than that of raw CNTs, which is considered a powerful characterization of the dispersion effect. The CNT aerogel, which was observed by scanning electron microscopy also showed a satisfactory dispersion morphology. Its structure and properties were tested before and after dispersion by Raman spectroscopy and great consistency was observed, which proved that the CNTs were undamaged. This approach may greatly promote the large-scale application of CNTs.

Symplectic Elasticity Analysis of Stress in Surrounding Rock of Elliptical Tunnel

Zhongyu Jiang,Guoqing Zhou,Li Jiang 대한토목학회 2020 KSCE Journal of Civil Engineering Vol.24 No.10

A large number of non-circular tunnels are widely used in engineering practice. The application of these geometric structures not only makes the boundary conditions of mechanical problems more complex, but also makes the theoretical solution more difficult. The introduction of curvilinear coordinate system can easily transform the elliptical region into a circular region, and the physical relationship can also be adjusted accordingly. In the state space, the transformed problem can be solved by using the dual variables of Hamiltonian mechanics, and the special solution equation can be obtained. With regard to the non-homogeneous boundary conditions of general engineering problems, Fourier expansion is used to transform them into algebraic sums. According to the special solution equation, the relationship between the direction eigenvalues and the angle coefficients of each order of the expansion term is found. Then the analytical solution of the non-homogeneous problem is obtained by superposing the special solutions of the expansion terms of each order. By comparing the calculation results of the boundary stress around the elliptical tunnel, it can be seen that the results are completely consistent with the finite element calculation results, which verifies the correctness and reliability of the method in this paper. This paper analyzes the influence of internal pressure, lateral pressure coefficient and elliptical shape coefficient on the circumferential stress around the elliptical hole, and obtains the following conclusions: increasing the internal pressure of the elliptical hole can effectively reduce the circumferential compressive stress at the hole edge; when the lateral pressure coefficient approaches 1, the circumferential stress distribution around the elliptical hole tends to be uniform; the minimum value of the circumferential stress around the elliptical hole is independent of the shape coefficient, while the maximum value is closely related to the shape coefficient. The research results can not only provide specific theoretical guidance for the construction and construction of elliptical tunnel, but also expand the application scope of the symplectic elasticity method.

Study on the influence of building materials processing technology on diversified artistic expression of Architecture

Zhongyu Liang,Zhang Yina,Li Taofeng 한양대학교 청정에너지연구소 2023 Journal of Ceramic Processing Research Vol.24 No.6

Building materials stand as a crucial cornerstone in the realm of architecture in China. Enhancing the processing technologyof diverse building materials to effectively elevate the level of architectural art has emerged as a prominent research focus. Inlight of this, the paper develops an analysis model centered on the influence of architectural art, utilizing the Taurus searchalgorithm. The study delves into the impact of distinct processing technologies on the diversified artistic expression of buildings. It commences with an analysis of the current state of building materials processing technologies and their connection toarchitectural art. Following this, the paper constructs an analysis model elucidating the influence of architectural art, examiningits effects on diversified artistic expression through experiments. Finally, by amalgamating established building materialsprocessing technology with experimental verification, the paper scrutinizes the actual efficacy of the analysis model forthe influence of architectural art based on the Taurus search algorithm. The experimental outcomes underscore the variedinfluence of different processing technologies on the diversity of artistic expression in buildings, showcasing the quantitativeevaluation capabilities of the impact analysis model.

Single-cell RNA sequencing analysis of human bone-marrow-derived mesenchymal stem cells and functional subpopulation identification

Xie Zhongyu,Yu Wenhui,Ye Guiwen,Li Jinteng,Zheng Guan,Liu Wenjie,Lin Jiajie,Su Zepeng,Che Yunshu,Ye Feng,Zhang Zhaoqiang,Wang Peng,Wu Yanfeng,Shen Huiyong 생화학분자생물학회 2022 Experimental and molecular medicine Vol.54 No.-

Mesenchymal stem cells (MSCs) are a common kind of multipotent cell in vivo, but their heterogeneity limits their further applications. To identify MSC subpopulations and clarify their relationships, we performed cell mapping of bone-marrow-derived MSCs through single-cell RNA (scRNA) sequencing. In our study, three main subpopulations, namely, the stemness subpopulation, functional subpopulation, and proliferative subpopulation, were identified using marker genes and further bioinformatic analyses. Developmental trajectory analysis showed that the stemness subpopulation was the root and then became either the functional subpopulation or the proliferative subpopulation. The functional subpopulation showed stronger immunoregulatory and osteogenic differentiation abilities but lower proliferation and adipogenic differentiation. MSCs at different passages or isolated from different donors exhibited distinct cell mapping profiles, which accounted for their corresponding different functions. This study provides new insight into the biological features and clinical use of MSCs at the single-cell level, which may contribute to expanding their application in the clinic.

Assessment and comparison of three different air quality indices in China

Youping Li,Ya Tang,Zhongyu Fan,Hong Zhou,Zhengzheng Yang 대한환경공학회 2018 Environmental Engineering Research Vol.23 No.1

Air pollution index (API) is used in Mainland China and includes only SO₂, NO₂ and PM10. In 2016, air quality index (AQI) replaced API. AQI contains three more air pollutants (CO, O₃ and PM2.5). Both the indices emphasize on the effect of a single pollutant, whereas the contributions of all other pollutants are ignored. Therefore, in the present work, a novel air quality index (NAQI), which emphasizes on all air pollutants, has been introduced for the first time. The results showed that there were 19 d (5.2%) in API, 28 d (7.7%) in AQI and 183 d (50.1%) in NAQI when the indices were more than 100. In API, PM10 and SO₂ were regarded as the primary pollutants, whereas all five air pollutants in AQI were regarded as primary. Furthermore, four air pollutants (other than the CO) in NAQI were regarded as primary pollutants. PM10, as being the primary pollutant, contributed greatly in these air quality indices, and accounted for 51.2% (API), 37.0% (AQI) and 52.6% (NAQI). The results also showed that particulate matter pollution was significantly high in Luzhou, where stricter pollution control measures should be implemented.

ALKBH5 facilitates CYP1B1 mRNA degradation via m6A demethylation to alleviate MSC senescence and osteoarthritis progression

Ye Guiwen,Li Jinteng,Yu Wenhui,Xie Zhongyu,Zheng Guan,Liu Wenjie,Wang Shan,Cao Qian,Lin Jiajie,Su Zepeng,Li Dateng,Che Yunshu,Fan Shuai,Wang Peng,Wu Yanfeng,Shen Huiyong 생화학분자생물학회 2023 Experimental and molecular medicine Vol.55 No.-

Improving health and delaying aging is the focus of medical research. Previous studies have shown that mesenchymal stem cell (MSC) senescence is closely related to organic aging and the development of aging-related diseases such as osteoarthritis (OA). m6A is a common RNA modification that plays an important role in regulating cell biological functions, and ALKBH5 is one of the key m6A demethylases. However, the role of m6A and ALKBH5 in MSC senescence is still unclear. Here, we found that the m6A level was enhanced and ALKBH5 expression was decreased in aging MSCs induced by multiple replications, H2O2 stimulation or UV irradiation. Downregulation of ALKBH5 expression facilitated MSC senescence by enhancing the stability of CYP1B1 mRNA and inducing mitochondrial dysfunction. In addition, IGF2BP1 was identified as the m6A reader restraining the degradation of m6A-modified CYP1B1 mRNA. Furthermore, Alkbh5 knockout in MSCs aggravated spontaneous OA in mice, and overexpression of Alkbh5 improved the efficacy of MSCs in OA. Overall, this study revealed a novel mechanism of m6A in MSC senescence and identified promising targets to protect against aging and OA.