Article
Biochemical Research Methods
Alberto Zenere, Olof Rundquist, Mika Gustafsson, Claudio Altafini
Summary: This article explores novel aspects of using paired RNA-seq and ATAC-seq data to investigate causal relationships between transcription factors, chromatin, and target genes. Results show a strong connection between selected regulatory motifs and structural balance in sample correlation graphs, suggesting that internal consistency is a necessary condition for satisfying causality rules in 3-node regulatory motifs.
Article
Biotechnology & Applied Microbiology
Aileen R. Ferraro, Abigail J. Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz, Zachary A. Lewis
Summary: Regulation of chromatin accessibility and transcription are coordinated processes. This study characterizes accessible chromatin regions in Neurospora crassa, revealing molecular features and histone modifications associated with accessibility and inaccessibility. H3K27 acetylation is the most predictive histone modification for open chromatin in N. crassa, while H3K36 methylation is a key marker of inaccessible chromatin.
Article
Biochemistry & Molecular Biology
Zhilong Zhang, Yongfeng Zhang, Qi Bao, Yarong Gu, Chunnian Liang, Min Chu, Xian Guo, Pengjia Bao, Ping Yan
Summary: This study investigated the dynamic changes in chromatin accessibility during yak adipocyte differentiation using ATAC-seq. The results revealed the unique characteristics of open chromatin and identified the involvement of key pathways and transcription factors in regulating adipogenesis. This study provides valuable insights into the transcriptional regulatory mechanisms of adipogenesis and the adaptation of plateau species to high-altitude environments through fat metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Polymer Science
Kuixia Xie, Jingrun Yang, Qianqian Yao, Yang Xu, Yonglin Peng, Xinhua Liu
Summary: This study investigated the dynamic changes of chromatin accessibility and the transcriptome in dermal fibroblasts (DFs) during keloid formation. The results showed extensive alterations in chromatin accessibility and transcriptome in keloid DFs compared to normal samples. In addition, the downregulation of BRCA1 in keloid DFs was found to be closely associated with changes in gene expression, which may contribute to the formation of keloids.
Article
Biochemistry & Molecular Biology
Yanis Zekri, Romain Guyot, Frederic Flamant
Summary: We have created a database that integrates RNA-seq and ChIP-seq data to better understand the target genes of thyroid hormone receptors in different cell types. This database serves as a resource for studying the mode of action of thyroid hormone and provides a user-friendly tool to access specific gene information and extract gene lists of interest.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Shicong Wang, Jieqiang He, Mengting Deng, Caixia Wang, Ruifeng Wang, Jinjiao Yan, Minrong Luo, Fengwang Ma, Qingmei Guan, Jidi Xu
Summary: Drought resistance in plants is influenced by multiple signaling pathways and epigenetic modifications, with changes in chromatin accessibility playing an important role in abiotic stress. Analysis in apples under drought conditions revealed 23,466 upregulated peaks and 2447 downregulated peaks in chromatin accessibility. Drought-induced chromatin accessibility changes genes enriched in metabolism, stimulus, and binding pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Nutrition & Dietetics
Zhong Xu, Junjing Wu, Jiawei Zhou, Yu Zhang, Mu Qiao, Hua Sun, Zipeng Li, Lianghua Li, Nanqi Chen, Favour Oluwapelumi Oyelami, Xianwen Peng, Shuqi Mei
Summary: This study used ATAC-seq and RNA-seq analysis to examine the accessible chromatin and gene expression in Xidu black pigs, identifying key genes and regulatory pathways associated with meat quality and fat deposition.
FRONTIERS IN NUTRITION
(2022)
Article
Zoology
Xiao-Ning Zhu, Yu-Zhe Wang, Chong Li, Han-Yu Wu, Ran Zhang, Xiao-Xiang Hu
Summary: This study systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) samples across 11 tissues. An average of 50,796 open chromatin regions were identified per sample, cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence.
ZOOLOGICAL RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Guan-Dong Shang, Zhou-Geng Xu, Mu-Chun Wan, Fu-Xiang Wang, Jia-Wei Wang
Summary: In this study, we introduce FindIT2, a software package that can process and analyze multi-omics data to infer influential transcription factors using ChIP-seq/ATAC-seq datasets. The package annotates ChIP-seq/ATAC-seq peaks, identifies transcription factor targets by combining ChIP-seq and RNA-seq data, and supports inference of influential transcription factors based on different types of data input. Moreover, FindIT2 is compatible with any species with genomic annotations, making it particularly useful for less well-studied non-model species.
Article
Biology
Divya Khattar, Sharlene Fernandes, John Snowball, Minzhe Guo, Matthew C. Gillen, Suchi Singh Jain, Debora Sinner, William Zacharias, Daniel T. Swarr, Edward E. Morrisey
Summary: The tips of developing respiratory buds are home to important progenitor cells marked by the expression of SOX9 and ID2. The transcription factors and PI3K signaling play a crucial role in controlling the proliferation and differentiation of these progenitor cells during lung organogenesis. This study demonstrates the importance of paired RNA and ATAC seq in defining regulatory networks in development.
Article
Biotechnology & Applied Microbiology
Trevor F. Freeman, Qiuxia Zhao, Agustian Surya, Reed Rothe, Elif Sarinay Cenik
Summary: This study investigates the impact of depleting the ribosome biogenesis components RPOA-2 and GRWD-1 on chromatin accessibility using ATAC-seq. The results show similar changes in chromatin accessibility for both perturbations, but a weak correlation with gene expression.
Article
Immunology
Chenshen Huang, Na Zhang, Hao Xiong, Ning Wang, Zhizhong Chen, Zhizhan Ni, Xiaohong Liu, Boxu Lin, Bujun Ge, Bing Du, Qi Huang
Summary: This study aims to explore a novel method for transcriptional regulation and proposes a new pipeline for analyzing the role of GPRC5B in COAD. By using RNA-seq, ATAC-seq, and ChIP-seq, researchers found the correlation between GPRC5B and macrophages and identified TF GATA4 as a key upstream factor.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Hao Zhang, Michael E. Rice, Joseph W. Alvin, Dominique Farrera-Gaffney, James J. Galligan, Michael D. L. Johnson, Darren A. Cusanovich
Summary: In this study, the effects of different protocol choices on ATAC-seq data quality were evaluated. Several different ATAC-seq components were tested, including reaction buffers, reaction temperatures, enzyme sources, and the use of native or fixed nuclei. The results showed that temperature and fixation had a major impact on data quality metrics. Additionally, the choice of protocol components could bias the functional class of profiled elements. The study recommends evaluating multiple metrics and formulations in new experiments.
Article
Biotechnology & Applied Microbiology
Chaowei Song, Wanbo Li, Zhiyong Wang
Summary: This study investigated the chromatin accessibility and conserved non-coding elements (CNEs) in the livers of three important economic fishes using ATAC-seq and comparative genomics approach. The results revealed the enrichment of specific transcription factor binding motifs in the chromatin accessibility landscape and the presence of active CNEs in gene promoter regions. These findings suggest the potential involvement of certain transcription factors in liver function and the regulatory role of CNEs in important genes. This study fills knowledge gaps in this field and provides valuable data for industrial application and theoretical research of these fish species.
MARINE BIOTECHNOLOGY
(2022)
Article
Oncology
Roshani Sinha, Mai Dvorak, Ananthakrishnan Ganesan, Larry Kalesinskas, Charlotte M. Niemeyer, Christian Flotho, Kathleen M. Sakamoto, Norman Lacayo, Rachana Vinay Patil, Rhonda Perriman, Alma-Martina Cepika, Yunying Lucy Liu, Alex Kuo, Paul J. Utz, Purvesh Khatri, Alice Bertaina
Summary: This study identifies potential druggable targets for the treatment of JMML through the analysis of DNA structures and histone modifications, providing a rich resource for improving the outcomes of JMML patients.
Article
Chemistry, Applied
Jinqiang Zhou, Bidong Wu, Miao Wang, Shujie Liu, Zhanxiong Xie, Chongwei An, Jingyu Wang
Summary: An effective method for preparing energetic microspheres by fluid-focusing microchannels is proposed, which combines the advantages of low reagent consumption, instrument miniaturization, accurate control, and efficient heat mass transfer. Compared with traditional water-suspension method, the microspheres prepared by the droplet microfluidic method show better morphology, particle size uniformity, and monodispersity. In addition, the fluidity and bulk density of the microspheres are significantly improved.
JOURNAL OF ENERGETIC MATERIALS
(2023)
Article
Chemistry, Applied
Wangjian Cheng, Kun Li, Lilong Gao, Chenhe Feng, Chongwei An, BaoYun Ye, Jingyu Wang
Summary: This study analyzed the distribution characteristics of the main explosive with different particle sizes and gradations using fractal theory and explored the effect of the gradation on the slurry. The results showed that particle size gradation can improve the fractal dimension of the explosive and reduce the thixotropic loop area of the slurry by increasing temperature and particle size distribution.
JOURNAL OF ENERGETIC MATERIALS
(2023)
Article
Agriculture, Dairy & Animal Science
Xian Liu, Peng Yang, Haoming Sun, Zijing Zhang, Cuicui Cai, Jiawei Xu, Xiaoting Ding, Xianwei Wang, Shijie Lyu, Zhiming Li, Zejun Xu, Qiaoting Shi, Eryao Wang, Chuzhao Lei, Hong Chen, Baorui Ru, Yongzhen Huang
Summary: This study found an association between copy number variation of the VAMP7 gene and growth traits in cattle. In Yunling cattle, the Duplication type of the gene was significantly related to height at the hip cross, with individuals having this type showing poorer growth and development. Individuals with other CNV types may be considered for breeding purposes.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Lixian Zou, Yuan Zheng, Jialing Chen, Yu Ding, Hui Liu, Yubao Liu, Jian Xu, Hairong Zheng, Xin Liu
Summary: Autocalibrated MB + CS-FPP improves the anatomical coverage of myocardial perfusion imaging while maintaining comparable image quality to conventional FPP. This is of great significance for the diagnosis of coronary artery disease.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Automation & Control Systems
Jianlin Wang, Xinquan Zhang
Summary: This article studies the problem of overcoming controller vulnerability in nonlinear continuous-time switched systems with saturating actuators. The sufficient condition for non-fragile stabilization of the system is derived using multiple Lyapunov functions. Then, a switching law and non-fragile state feedback controllers are designed to achieve asymptotic stabilization of the closed-loop system at the origin. Finally, the design issue of the controllers and switching law is transformed into a convex optimization problem with linear matrix inequalities (LMI) constraints, and a numerical example is provided to verify the effectiveness of the proposed method.
JOURNAL OF CONTROL AND DECISION
(2023)
Article
Clinical Neurology
Weilong Guo, Jin Liu, Bangshan Liu, Mi Wang, Qiangli Dong, Xiaowen Lu, Jinrong Sun, Liang Zhang, Hua Guo, Futao Zhao, Weihui Li, Zexuan Li, Mei Liao, Li Zhang, Yan Zhang, Yumeng Ju, Lingjiang Li
Summary: This study examines the impact of childhood maltreatment and major depressive disorder (MDD) on cognitive function in unmedicated patients. MDD significantly impairs cognitive function in all domains, while childhood maltreatment only affects memory. No interactive effect was found between MDD and childhood maltreatment.
EUROPEAN ARCHIVES OF PSYCHIATRY AND CLINICAL NEUROSCIENCE
(2023)
Article
Computer Science, Artificial Intelligence
Tingting Chai, Jiahui Li, Yanhong Wang, Guoying Sun, Changyong Guo, Zhaoxin Zhang
Summary: Finger-vein has been widely used in automatic personal recognition systems. This study investigates lightweight CNN models and the effect of image enhancement on finger-vein biometrics. Transfer learning plays an important role in extracting informative features. The experimental results show that the proposed lightweight model outperforms existing competition winners and image enhancement is not essential for CNN-based finger-vein biometrics.
NEURAL PROCESSING LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Jia-yun Ni, Xin Wang, Hong-yan Xie, Ning-hao Yang, Jing-yao Li, Xi-ang Sun, Heng-jiang Guo, Li Zhou, Wei Zhang, Jun Liu, Li-min Lu
Summary: Transforming growth factor-beta 1 (TGF-beta 1) plays a key role in promoting renal fibrosis during chronic kidney disease (CKD). Cellular senescence is associated with CKD progression, and accelerated tubular cell senescence contributes to renal fibrosis. The elevation of Usp11 under pathological condition is implicated in promoting renal fibrosis by deubiquitinating Tgfbr2, reducing its degradation, and facilitating downstream senescent signaling pathway activation.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Engineering, Environmental
Jiaqin He, Xunxun Li, Yaru Wang, Jun Xiao, Yunchong Liu, Hua Li, Najun Li, Qingfeng Xu, Jinghui He, Dongyun Chen, Jianmei Lu
Summary: A facile and eco-friendly strategy was developed to synthesize a series of Au-modified hollow Ni-Mn spinel nanospheres decorated on graphene aerogels (termed Auy-hNixMn3_x/GAz) composite catalysts for deep catalytic oxidation of Volatile organic compounds (VOCs). The introduction of hollow structure led to a larger specific surface area and more accessible active sites. The subsequent cooperation of Au further strengthened the low-temperature reducibility along with more active surface oxygen species.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Cardiac & Cardiovascular Systems
Jing Li, Juan Zhang, Yu Shi, Horst Sievert, Cynthia C. Taub, Stefan Bertog, Shengjun Ta, Lei Changhui, Ethan Senser, Jing Wang, Rui Hu, Junzhe Huang, Fangqi Ruan, Yupeng Han, Xiaojuan Li, Bo Wang, Xueli Zhao, Jiao Liu, David H. Hsi, Liwen Liu
Summary: PIMSRA is an effective treatment option for hypertrophic obstructive cardiomyopathy (HOCM), leading to improved exercise capacity, reduced left ventricular outflow tract gradients, and increased myocardial contractile function.
Article
Chemistry, Organic
Lixia Ding, Zhifei Zhu, Xinyue Zhou, Gongming Zhu, Jian-Hua Wang, Shu-Tong Zhu, Bing Hu, Xiao-Na Wang, Junbiao Chang
Summary: We present two efficient intermolecular self-cycloadditions of N-aryl-substituted ynamides via metal-free approaches, resulting in the synthesis of valuable aminocyclobutenes and 4-aminoquinoline derivatives with good yields and wide substrate scope. Our modified method allowed for the effective preparation of terminal N-aryl ynamides, which then underwent thermally driven and solvent-free [2 + 2] cycloaddition to form functionalized aminocyclobutenes, or TMSOTf/TfOH-catalyzed [4 + 2] cycloaddition to produce 4-aminoquinoline derivatives. Furthermore, evaluation of their in vitro activity revealed that some of the cycloaddition products and their derivatives exhibited highly potent activities against SARS-CoV-2, DENV-2, and tumor cell lines.
ORGANIC CHEMISTRY FRONTIERS
(2023)
Article
Computer Science, Artificial Intelligence
Guangming Wang, Xinrui Wu, Shuyang Jiang, Zhe Liu, Hesheng Wang
Summary: This paper proposes an efficient 3D point cloud learning architecture called EfficientLO-Net for LiDAR odometry. It introduces the projection-aware representation of the 3D point cloud to achieve efficiency. The Pyramid, Warping, and Cost volume (PWC) structure is built to estimate and refine the pose. The architecture incorporates a projection-aware attentive cost volume, a trainable embedding mask, and a trainable pose warp-refinement module to improve the pose estimation and filter outlier points.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2023)
Article
Chemistry, Physical
Shuaishuai Shang, Shuhao An, He Li, Jianping Li, Shenping Zhang, Changjun Peng, Honglai Liu, Jun Hu
Summary: We developed a sulfonate-based covalent organic framework (sCOF) for the fast and sensitive detection of tetracycline hydrochloride (TCH). By incorporating disulfonic acid into COF, we achieved self-exfoliation of the framework and obtained fluorescent covalent organic nanosheets (f-sCON). These f-sCON nanosheets showed excellent sensitivity towards TCH residuals and could be used to create a naked-eye fluorescent device. Furthermore, by combining sulfonate-COF adsorbent and f-sCON-gel in a mixed column, we successfully achieved simultaneous TCH removal and detection.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
Article
Hematology
Lili Song, Peifeng Li, Huiying Sun, Lixia Ding, Jing Wang, Benshang Li, Bin-Bing S. Zhou, Haizhong Feng, Yanxin Li
Summary: This study found that mutations in phosphoribosyl pyrophosphate synthetase 2 (PRPS2) drive relapse of childhood acute lymphoblastic leukemia (ALL) by influencing the stability of PRPS1/2 hexamers. Mutations in PRPS2 decrease the effectiveness of thiopurine therapy in relapsed childhood ALL. This discovery provides important clues for finding biomarkers for relapsed ALL.
Article
Chemistry, Physical
Yanlin Feng, Jianlin Wang, Xin Ning, Aiyun Li, Qing You, Wanzhen Su, Deping Wang, Jianyun Shi, Lan Zhou, Fangfang Cao, Xiaoyuan Chen, Jimin Cao
Summary: We developed a stable pyroelectric BaTiO3@Au core-shell nanostructure that can selectively block energy generation of tumor cells, providing a promising therapeutic approach for triple-negative breast cancer.