Editorial Material
Biochemistry & Molecular Biology
Susan E. Tsutakawa, Altaf H. Sarker
Summary: The canonical role of DNA glycosylase is in repairing global base damage, but it also plays a role in epigenetic gene regulation, immune response modulation, replication, and transcription. In this issue of Structure, Eckenroth et al. (2020) reveal the structure of NEIL2 glycosylase, showing that its catalytic domain flexibility sets it apart from other glycosylases and implies novel regulatory mechanisms.
Article
Multidisciplinary Sciences
Huawei Tong, Nana Liu, Yinghui Wei, Yingsi Zhou, Yun Li, Danni Wu, Ming Jin, Shuna Cui, Hengbin Li, Guoling Li, Jingxing Zhou, Yuan Yuan, Hainan Zhang, Linyu Shi, Xuan Yao, Hui Yang
Summary: Current base editors can only deaminate cytosine (C) or adenine (A), lacking the ability to edit guanine (G) or thymine (T). In this study, a deaminase-free glycosylase-based guanine base editor (gGBE) was developed by fusing Cas9 nickase with engineered N-methylpurine DNA glycosylase protein (MPG). Through mutagenesis of MPG and screening using an intron-split EGFP reporter, gGBE with engineered MPG showed over 1500-fold increase in G editing efficiency. Furthermore, this gGBE demonstrated high base editing efficiency and G-to-T or G-to-C conversion ratio in both cultured human cells and mouse embryos.
NATIONAL SCIENCE REVIEW
(2023)
Article
Biochemistry & Molecular Biology
Griffin Wright, Manoj Sonavane, Natalie R. Gassman
Summary: STAT3 is identified as a novel regulator of XRCC1, with its activation through the IL-6 signaling pathway increasing the expression level of XRCC1 and impacting its role in triple negative breast cancer. The upregulation of XRCC1 is associated with the aggressiveness and chemotherapeutic resistance in cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Filipe Rollo, Patricia T. Borges, Celia M. Silveira, Margarida T. G. Rosa, Smilja Todorovic, Elin Moe
Summary: This study investigated the structure and mechanism of the three EndoIII enzymes in Deinococcus radiodurans, revealing their different activities and specificities, which is important for addressing questions regarding their presence and characteristics in the organism.
Article
Chemistry, Multidisciplinary
Liudan Jiang, Jiayong Yin, Maoxiang Qian, Shaoqin Rong, Shengqi Zhang, Kejing Chen, Chengchen Zhao, Yuanqing Tan, Jiayin Guo, Hao Chen, Siyun Gao, Tingting Liu, Yi Liu, Bin Shen, Jian Yang, Yong Zhang, Fei-Long Meng, Jinchuan Hu, Honghui Ma, Yi-Han Chen
Summary: In this study, a Ucaps-seq method was developed to detect uracil in DNA at single-nucleotide resolution. The method was proven to be highly specific and effective on synthetic DNA and real genomes. Ucaps-seq not only detected the enrichment of uracil in cells but also had potential applications in evaluating base editing fidelity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Agronomy
Shiwen Liu, Shuhua Zhu, Guangqin Jing
Summary: Excessive reactive oxygen species (ROS) during storage can lead to oxidative damage to mitochondrial DNA (mtDNA) in peaches, exacerbating fruit damage. Nitric oxide (NO) has been found to help maintain the storage quality of peaches. This study investigates the effects of NO on mtDNA damage and repair, focusing on the base excision repair (BER) pathway. The results show that NO reduces ROS levels and oxidative damage markers in mitochondria, increases mtDNA copy number, and enhances the BER pathway, leading to improved repair efficiency and maintenance of mtDNA integrity.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Microbiology
Filipe Rollo, Guilherme D. Martins, Andre G. Gouveia, Solenne Ithurbide, Pascale Servant, Celia V. Romao, Elin Moe
Summary: This study demonstrates the importance of three Endonuclease III-like enzymes encoded by genes in Deinococcus radiodurans. While DrEndoIII2 is the main enzyme in this bacterium, DrEndoIII1 and 3 show unusual and undetectable activity, respectively. The knockout mutants of these genes were more resistant to oxidative stress induced by methyl viologen, indicating the crucial role of all three EndoIII homologs for cell survival. The upregulation of EndoIII homologs gene expression in response to oxidative stress may compensate for the loss of one gene.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Virology
Karen Salas-Briceno, Susan R. Ross
Summary: This study showed the critical role of UNG in removing uracils from APOBEC3-mediated MLV retroviral DNA, reducing G-to-A mutations in proviruses. The data suggest that UNG removes uracils at two stages of infection, preventing integration of viral DNA and leading to its repair or degradation.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mark L. Sowers, James W. Conrad, Bruce Chang-Gu, Ellie Cherryhomes, Linda C. Hackfeld, Lawrence C. Sowers
Summary: Although genomic DNA is predominantly duplex, specific sequence motifs can favor the formation of alternative structures such as G-quadruplex. The repair of DNA damage in non-duplex structures is less understood. Placing certain pyrimidine damage products and DNA repair intermediates can affect the stability and formation of quadruplex structures. These findings provide insights into the equilibrium between duplex and quadruplex and the impact of DNA damage and repair on this equilibrium.
Article
Chemistry, Analytical
Bocheng Tu, Zishan Feng, Haitao Wang, Wei Zhang, Weicong Ye, Hongbo Wang, Xianjin Xiao, Wenbo Zhao, Tongbo Wu
Summary: This new method utilizes lambda exonuclease and a background signal suppression probe, which successfully suppresses the background signal through probe structure design to achieve highly sensitive OGG detection. The detection limit is 5.0 x 10(-4) U mL(-1), and its potential clinical application value was demonstrated in biological samples.
ANALYTICA CHIMICA ACTA
(2021)
Review
Cell Biology
Yeldar Baiken, Damira Kanayeva, Sabira Taipakova, Regina Groisman, Alexander A. Ishchenko, Dinara Begimbetova, Bakhyt Matkarimov, Murat Saparbaev
Summary: Complex DNA damage (CDD) is challenging to repair due to its complex structure compared to singular lesions, and if left unrepaired, can lead to serious consequences such as chromosomal rearrangements and genome instability. Repair of CDD requires the concurrent involvement of multiple DNA repair pathways to ensure effective repair.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Michal Hammel, Ishtiaque Rashid, Aleksandr Sverzhinsky, Yasin Pourfarjam, Miaw-Sheue Tsai, Tom Ellenberger, John M. Pascal, In-Kwon Kim, John A. Tainer, Alan E. Tomkinson
Summary: In this study, biophysical methods were used to reveal the shape and conformational flexibility of the XRCC1-DNA ligase III alpha complex (XL), showing that XL is more compact and identifying the components of its molecular interface. The findings suggest a potential new strategy for treating cancer cells deficient in homologous recombination by targeting the XRCC1-DNA ligase III alpha complex.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sunbok Jang, Matthew A. Schaich, Cindy Khuu, Brittani L. Schnable, Chandrima Majumdar, Simon C. Watkins, Sheila S. David, Bennett Van Houten
Summary: The study reveals that UV-DDB can stimulate MUTYH turnover rate, increase complex formation between MUTYH and UV-DDB, and enhance MUTYH mobility and dissociation rate during 8-oxoG:A repair, suggesting a facilitative role of UV-DDB in MUTYH activity at abasic sites.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Mansour Akbari, Hilde Loge Nilsen, Nicola Pietro Montaldo
Summary: Mitochondria are essential for cellular energy production and play a crucial role in organismal development and normal function. Understanding the mechanisms of mtDNA maintenance and transcription can provide insights into the pathogenesis of various diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Qing-Nan Li, Dong-Xia Wang, Gui-Mei Han, Bo Liu, An-Na Tang, De-Ming Kong
Summary: The background issue in CRISPR/Cas12a-based biosensors has been efficiently solved by designing the activator strand (AS) using the RESET effect. The low background allows for sensitive detection and accurate imaging analysis of different targets in live cells, and the high-performance biosensors have potential for point-of-care testing. Several biosensing systems have been developed for the detection of nucleic acid, small molecules, and enzymes.
ANALYTICAL CHEMISTRY
(2023)
Article
Computer Science, Software Engineering
Xiaohua Wang, Ming Xu, Min Hu, Fuji Ren
Summary: The clinical assessment of bone age is critical, but traditional methods are time-consuming and prone to errors. This study proposes a fully automated bone age assessment system that requires no additional annotation or extraction of regions of interest. By using a puzzle generator and a new label processing method, the system achieves excellent performance in experiments.
Article
Plant Sciences
Lan Zhang, Zheng Zhang, Golam Jalal Ahammed, Xiaorong Wang, Huihan Fang, Peng Yan, Li-Ping Zhang, Shibei Ge, Jianyu Fu, Wen-Yan Han, Xin Li
Summary: 24-epibrassinolide (EBR) can improve tea resistance against the fungal pathogen Colletotrichum fructicola by inducing lignin synthesis in tea leaves.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Green & Sustainable Science & Technology
Lifang Peng, Jiawei Wang, Yinghua Huang, Xiaorong Wang
Summary: Drawing on moral disengagement theory and liquid consumption theory, this study investigated and tested a conceptual model of guests' unethical behavior in peer-to-peer (P2P) accommodation. The study found that self-construal has both positive and negative effects on guests' unethical behavior, and this relationship is mediated by moral disengagement and moderated by perceived consumption liquidity.
JOURNAL OF SUSTAINABLE TOURISM
(2023)
Article
Engineering, Industrial
Zhaoqin Wang, Yu Shi, Xiaorong Wang
Summary: This paper investigates the additive manufacturing approach of a spatial complex curve feature on a complex surface using plasma built-up welding with a serial robot. The study combines the NURBS theory with the serial robotic kinematics to lay a foundation for plasma additive manufacturing of SCCFs on complex surfaces.
INDUSTRIAL ROBOT-THE INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH AND APPLICATION
(2023)
Article
Automation & Control Systems
Weijia Zheng, YangQuan Chen, Xiaohong Wang, Meijin Lin, Jing Guo
Summary: Fractional order PID (FOPID) controller offers more flexibility in design options compared to integer order PID (IOPID) controller. However, in practical implementation, it is necessary to select achievable design specifications and controller parameters. This study collects and analyzes the complete achievable regions of design specifications and models the selectable integral and derivative orders of the FOPID controller. A synthesis method is proposed to achieve the desired flat-phase characteristic.
MEASUREMENT & CONTROL
(2023)
Article
Automation & Control Systems
Xiaojing Wang, Guangqiang Shi, Meizhen Liu, Yarning Feng
Summary: A robust control strategy based on Adaboost prediction was proposed to improve the robustness and low-speed performance of an electro-hydraulic servo system. By using RBF neural network and H-infinity control theory, the system's feedback mechanism and robust controller were designed to effectively enhance the system's low-speed performance and anti-interference ability.
MEASUREMENT & CONTROL
(2023)
Article
Food Science & Technology
Ying Liang, Jiayang Song, Zilu Chen, Mei Liu, Shihua Chen, Hao Liu, Xia Zhang, Xingquan Wu, Baoshan He, Jinshui Wang
Summary: This study investigates the use of sanxan to improve the quality of salt-free frozen-cooked wheat noodles (FCNs) and explores the underlying mechanism. The results demonstrate that adding sanxan can minimize the decrease in quality parameters and improve the chrominance and thermal stability of salt-free FCNs during freeze-thaw treatments (FTs).
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Clinical Neurology
Jiacheng Liu, Liying Yang, Yue Zheng, Chuanyi Kang, Xiaohong Wang, Jingjing Shi, Siyu Qiu, Ying Zhao, Jiahong Yu, Na Zhao
Summary: This study examined the differences in prevalence and associated factors of suicidal ideation (SI) among adolescents with depression between urban and rural areas. The results showed that urban patients had a higher prevalence of SI compared to rural patients, and there were also differences in parental rearing behavior. The study emphasizes the importance of focusing on parenting styles in adolescent patients for early identification and intervention of SI.
JOURNAL OF AFFECTIVE DISORDERS
(2023)
Article
Ecology
Haoyang Zhu, Hongyu Li, Xiaolei Wang, Ting Jiang, Lin Sun, Yi Luo
Summary: The broad leaf, deciduous black locust and needle leaf, evergreen Chinese pine are the major afforestation species on the Loess Plateau of China. However, concerns have been raised about the decay of black locust and drying of the forest land soil in this region. A study using a model and incomplete observations found that Chinese pine is more tolerant to soil water drought than black locust.
Article
Thermodynamics
Yuxuan Zhang, Xiaoqiang Zhai, Fengyuan Zhang, Zhongbin Zhang, Kamel Hooman, Hai Zhang, Xiaolin Wang
Summary: This article proposes a novel carbon capture capsule inspired by red blood cells (RBC) to enhance CO2 hydrate formation kinetics. Compared to spherical capsules, the RBC-shaped capsule shows a 143% higher gas uptake efficiency. The study also investigates the effects of initial pressure and capsule size on CO2 hydrate formation kinetics.
Article
Environmental Sciences
Yuqin Wang, Wenfu Zhu, Guangyi Zhao, Guangzheng Ye, Yujun Jiao, Xiaohong Wang, Fan Yao, Weixiao Peng, Haomin Huang, Daiqi Ye
Summary: The influence of lignocellulose contents on the pore structure and distribution characteristics of porous carbon has been investigated. It was found that the microvolumes of ultra-micropores decreased with a decrease in cellulose contents, while mesopores followed the reverse trend. Carbon materials with abundant micropores and narrow mesopores exhibited better adsorption performance, while porous carbon with a hierarchical pore structure showed better regeneration abilities.
ENVIRONMENTAL POLLUTION
(2023)
Retraction
Oncology
Dan Jin, Jiwei Guo, Yan Wu, Jing Du, Lijuan Yang, Xiaohong Wang, Weihua Di, Baoguang Hu, Jiajia An, Lingqun Kong, Lei Pan, Guoming Su
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2023)
Article
Instruments & Instrumentation
Hao Chen, Chaoyang Zhao, Zhonghai Wang, Lingli Li, Yanhan Zhou, Jie Zhang, Hongbing Xu, Shikui Cheng, Yuxuan Zhu, Yipo Zhang
Summary: A new hard X-ray (HXR) camera is being designed for the HL-2M tokamak to measure the fast electrons in the energy range of 20-200 keV during RF drive or heating experiments. The camera integrates 63 channels of independent detectors and a composite collimator to reduce background rays. The optimal geometric parameters of the collimator were determined using Geant4 simulation.
JOURNAL OF INSTRUMENTATION
(2023)
Article
Multidisciplinary Sciences
Georgios D. Kitsios, Vi D. Nguyen, Khaled Sayed, Nameer Al-Yousif, Caitlin Schaefer, Faraaz A. Shah, William Bain, Haopu Yang, Adam Fitch, Kelvin Li, Xiaohong Wang, Shulin Qin, Heather Gentry, Yingze Zhang, Jack Varon, Antonio Arciniegas Rubio, Joshua A. Englert, Rebecca M. Baron, Janet S. Lee, Barbara Methe, Panayiotis Benos, Alison Morris, Bryan J. McVerry
Summary: The importance of anaerobic bacteria as pathogens in aspiration pneumonia remains uncertain. A study conducted on mechanically ventilated patients classified as macro-aspiration pneumonia (MAsP), non-macro-aspiration pneumonia (NonMAsP), and uninfected controls, found that MAsP and NonMAsP patients had similar microbiota profiles and host-response profiles, with comparable 60-day survival rates. However, distinct bacterial clusters in the upper and lower respiratory tracts, enriched with facultative anaerobes and typical pathogens, were associated with higher plasma levels of SPD and sCD14 and worse 60-day survival.
Article
Environmental Sciences
Yaojun Fan, Quan Su, Xiaohong Wang, Min Fan
Summary: With the acceleration of digital technology construction process, digitization has driven the transformation and upgrading of China's economy and micro businesses. This study aims to investigate whether digitization affects corporate green innovation. The findings reveal that digitization genuinely drives green innovation by easing corporate financing constraints and enhancing corporate awareness of fulfilling social responsibility. The study enriches the related theories of digitization and sustainability and provides empirical evidence for the positive externalities of digitization.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Genetics & Heredity
Marit A. E. van Bueren, Aniek Janssen
Summary: Eukaryotic nuclei rely on multiple repair pathways to accurately repair DNA damage, particularly in chromatin domains enriched for repetitive DNA sequences. Tailored repair mechanisms are necessary to maintain genome stability in these domains.