Article
Biochemistry & Molecular Biology
Fedor Bezrukov, Julien Prados, Adriana Renzoni, Olesya O. Panasenko
Summary: Antibiotic resistance may be caused by bacterial dormancy. This study found that the Staphylococcus aureus endoribonuclease toxin MazF can impact cell physiology in multiple ways, suggesting new targets for antibacterial drugs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Doyeon Kim, Sukjun Kim, Joori Park, Hee Ryung Chang, Jeeyoon Chang, Junhak Ahn, Heedo Park, Junehee Park, Narae Son, Gihyeon Kang, Jeonghun Kim, Kisoon Kim, Man-Seong Park, Yoon Ki Kim, Daehyun Baek
Summary: In this study, Kim et al. utilized various sequencing techniques to uncover the high-resolution translatome and transcriptome of SARS-CoV-2, identifying a novel translation initiation site TIS-L in the leader sequence. They found that TIS-L serves as a translation enhancer for ORF S and as translation suppressors for other ORFs, providing unique insights into the regulation of the SARS-CoV-2 translatome.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Zhuoning Zou, Chuanxin Zhang, Qiuyan Wang, Zhenzhen Hou, Zhuqing Xiong, Feng Kong, Qiujun Wang, Jinzhu Song, Boyang Liu, Bofeng Liu, Lijuan Wang, Fangnong Lai, Qiang Fan, Wenrong Tao, Shuai Zhao, Xiaonan Ma, Miao Li, Keliang Wu, Han Zhao, Zi-Jiang Chen, Wei Xie
Summary: This study utilized Ribo-lite and mRNA sequencing to analyze the transcriptome and translatome of human oocytes and early embryos. The results showed widespread differential translation during the oocyte-to-embryo transition (OET) and zygotic genome activation (ZGA), functioning in epigenetic reprogramming, transposon defense, and small RNA biogenesis. Additionally, TPRX1/2/L were identified as critical regulators of ZGA.
Article
Biotechnology & Applied Microbiology
Hongmei Zhang, Shuyan Ji, Ke Zhang, Yuling Chen, Jia Ming, Feng Kong, Lijuan Wang, Shun Wang, Zhuoning Zou, Zhuqing Xiong, Kai Xu, Zili Lin, Bo Huang, Ling Liu, Qiang Fan, Suoqin Jin, Haiteng Deng, Wei Xie
Summary: The proteome, transcriptome, and translatome show distinct dynamics during the oocyte-to-embryo transition in mice. The oocyte-originated proteome is remarkably stable and may serve to support the demanding needs of growing embryos. This study advances our understanding of the developmental process and gene expression regulation in mammalian embryos.
Article
Biochemistry & Molecular Biology
Hirotatsu Imai, Daisuke Utsumi, Hidetsugu Torihara, Kenzo Takahashi, Hidehito Kuroyanagi, Akio Yamashita
Summary: The coordinated regulation of dynamic RNA synthesis and translation is crucial for determining functional protein production. However, current reliable methods for simultaneously measuring nascent RNA synthesis and translation at the gene level are limited. In this study, a novel method combining 4-thiouridine (4sU) metabolic RNA labeling and translating ribosome affinity purification (TRAP) was developed to assess nascent RNA synthesis and translation simultaneously. This method may serve as a simple and powerful tool for analyzing the coordinated regulation of transcription and translation of individual genes in various eukaryotes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Yoseb Song, Jiyun Bae, Jongoh Shin, Sangrak Jin, Jung-Kul Lee, Sun Chang Kim, Suhyung Cho, Byung-Kwan Cho
Summary: Acetogens utilize gaseous feedstocks to synthesize biomass and metabolites efficiently through the Wood-Ljungdahl pathway, making them a potential platform for biochemical production. Understanding the transcriptional and translational regulation in acetogens during autotrophic growth can aid in designing strains for better productivity. Data on genome-scale transcriptional and translational responses of acetogens during CO2 fixation can help in discovering regulatory elements and engineering strains for desired biochemical production.
Article
Multidisciplinary Sciences
Tattym E. Shaiken, Sandra L. Grimm, Mohamad Siam, Amanda Williams, Abdol-Hossein Rezaeian, Daniel Kraushaar, Emily Ricco, Matthew J. Robertson, Cristian Coarfa, Antrix Jain, Anna Malovannaya, Fabio Stossi, Antone R. Opekun, Alyssa P. Price, Julien Dubrulle
Summary: Despite the unclear structural organization within the cytoplasm, recent models propose the existence of viscous fluid and solid elastic phases called cytosol and cytomatrix. The cytomatrix contains structural proteins, ribosomes, and metabolome enzymes, and it exhibits unique biosynthetic pathways. The cytosol and cytomatrix form an interconnected network that affects protein translation and promotes cellular flexibility, potentially contributing to the survival of malignant cells.
Article
Biochemistry & Molecular Biology
Chun Wu, Xiaolong Lu, Shaohua Lu, Hongwei Wang, Dehua Li, Jing Zhao, Jingjie Jin, Zhenghua Sun, Qing-Yu He, Yang Chen, Gong Zhang
Summary: In this study, a full-length RNC-seq strategy was demonstrated to construct a protein database containing all AS isoforms, and it showed higher efficiency and accuracy in identifying protein isoforms.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Wenqi Hu, Haitao Zeng, Yanan Shi, Chuanchuan Zhou, Jiana Huang, Lei Jia, Siqi Xu, Xiaoyu Feng, Yanyan Zeng, Tuanlin Xiong, Wenze Huang, Peng Sun, Yajie Chang, Tingting Li, Cong Fang, Keliang Wu, Lingbo Cai, Wuhua Ni, Yan Li, Zhiyong Yang, Qiangfeng Cliff Zhang, RiCheng Chian, Zijiang Chen, Xiaoyan Liang, Kehkooi Kee
Summary: This study developed a dual-omics methodology for analyzing the transcriptome and translatome of single-cell oocyte samples. The analysis revealed differences in translational expression patterns between mouse and human oocytes, and identified OOSP2 as an induction factor during human oocyte maturation.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Guillermo Eastman, Elizabeth R. Sharlow, John S. Lazo, George S. Bloom, Jose R. Sotelo-Silveira
Summary: This study analyzed gene expression in the brain of AD model mice and identified differences in translational regulation between AD model mice and wild type mice. A microglial signature associated with early stages of A beta accumulation was upregulated in both the transcriptome and translatome. Although there were not many shared regulated genes between the two mouse strains, they showed common regulated pathways related to A beta PP metabolism.
JOURNAL OF ALZHEIMERS DISEASE
(2022)
Article
Multidisciplinary Sciences
Caspar Glock, Anne Biever, Georgi Tushev, Belquis Nassim-Assir, Allison Kao, Ina Bartnik, Susanne Tom Dieck, Erin M. Schuman
Summary: Neurons continuously remodel their proteomes to maintain synaptic proteins, with local translation playing a significant role in this process. Differences in RNA abundance explain most translational changes between cell body and synaptic regions, suggesting the importance of on-site translational control in regulating synaptic strength.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Olena Zhulyn, Hannah D. D. Rosenblatt, Leila Shokat, Shizhong Dai, Duygu Kuzuoglu-Ozturk, Zijian Zhang, Davide Ruggero, Kevan M. M. Shokat, Maria Barna
Summary: An outstanding mystery in biology is why some species can regenerate tissues whereas mammals cannot. This study found that rapid activation of protein synthesis is a unique feature of limb regeneration in the axolotl. The mTORC1 pathway was identified as a key signal that mediates tissue regeneration and translational control in the axolotl.
Article
Microbiology
Mengfan Xu, Shanhu Hu, Yiwen Wang, Tao Wang, Piotr Dziugan, Bolin Zhang, Hongfei Zhao
Summary: The study found that Lactobacillus helveticus utilizes protein by extracellular hydrolysis and upregulation of various factors to prepare for proteolysis. Changes in key factors associated with glycolysis, trehalose phosphotransferase system (PTS), and aerobic respiration were observed during casein utilization in these bacteria.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Laetitia Poidevin, Javier Forment, Dilek Unal, Alejandro Ferrando
Summary: The study identified that heat stress significantly down-regulates key membrane transporters required for pollen growth, uncovering specific heat-sensitive targets. Additionally, specific regulations at the translational level and the presence of ribosomes on non-coding RNAs highlight novel regulatory mechanisms in plant fertilization.
PLANT CELL AND ENVIRONMENT
(2021)
Correction
Multidisciplinary Sciences
Woori Kim, Soonkyu Hwang, Namil Lee, Yongjae Lee, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
Summary: The paper has been corrected and the details can be found at the provided link.
Article
Computer Science, Artificial Intelligence
Qingyu He, Ruigen Pan
Summary: This study analyzed the application value of dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) based on computer semi-automatic segmentation (CSS) algorithm in the histological grading of breast cancer patients. Results showed that CSS had lower false positive rate (FPR) and higher true positive rate (TPR) compared to fuzzy-c-means (FCM) and wavelet transform (WT) algorithms. The CSS algorithm was found to be superior to FCM and WT in evaluating breast tumor histological grading. Furthermore, the obtained tumor diameter, fractional anisotropy (FA) value, apparent diffusion coefficient (ADC) value, and number of lymph node metastasis based on DCE-MRI were significantly different among patients with grade I, II, and III, and could be used to predict the histological grading of breast cancer patients.
Article
Biochemical Research Methods
Xuejuan Gao, Qionghua Lian, Baiye Guan, Qiu-Yu Liu, Meng Meng, Yang Chen, Jingjie Jin, Huihua Li, Xiaohui Liu, Zhenghua Sun, Langxia Liu, Qing-Yu He, Gong Zhang
Summary: This study investigated the function and mechanism of ZSWIM1 in lung adenocarcinoma. ZSWIM1 was found to be upregulated in lung adenocarcinoma and correlated with poor prognosis. It promoted cancer cell proliferation, migration, invasion, and epithelial-to-mesenchymal transition. The protein interactome of ZSWIM1 was identified, and its interaction with STK38 was verified. ZSWIM1 antagonized the function of STK38 and activated the MEKK2/ERK1/2 pathway. Overall, ZSWIM1 acts as an oncogene in lung adenocarcinoma and its effects are mediated through the STK38/MEKK2/ERK1/2 axis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Hui-Fang Hu, Gui-Bin Gao, Xuan He, Yu-Ying Li, Yang-Jia Li, Bin Li, Yunlong Pan, Yang Wang, Qing-Yu He
Summary: This study identifies the ARF1-IQGAP1 interaction-mediated reactivation of ERK signaling as critical for vemurafenib resistance and cancer metastasis. LY2835219 is shown to be a promising therapeutic agent for CRC, both alone and in combination with vemurafenib, with significant inhibitory effects on ARF1-mediated cancer.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Oncology
Kun Meng, Yuyu Hu, Dingkang Wang, Yuying Li, Fujin Shi, Jiangli Lu, Yang Wang, Yun Cao, Chris Zhiyi Zhang, Qing-Yu He
Summary: A seven-mitochondrial-gene signature was generated to predict prognosis of ccRCC patients, with EFHD1 being less studied but found to be correlated with unfavorable outcome. Overexpression of EFHD1 reduced mitochondrial Ca2+ and inhibited cell migration and tumor metastasis by binding to mitochondrial calcium uniporter (MCU) and deactivating the Hippo/YAP pathway. Upregulation of STARD13 induced by EFHD1 enhanced the phosphorylation of YAP at Ser-127. The EFHD1-MCU-STARD13 axis serves as a novel regulator in ccRCC progression.
Review
Geosciences, Multidisciplinary
Min Li, Song Huang, Tianyao Hao, Miao Dong, Ya Xu, Jian Zhang, Qingyu He, Gui Fang
Summary: This paper reviews the initiation models of Neogene subduction in the western Pacific, including polarity-reversal, induced subduction re-initiation, and non-inherited subduction initiation. It also collates the parameters of different subduction zones to form five categories: basic features, subducting plate features, upper plate features, kinematic features, and subsequent activity. The regularity of the subduction processes, the specificity of different subduction cases, and the possible constraints between subduction initiation types and subduction zone parameters are discussed and analyzed. The compiled dataset of subduction zone parameters can provide data support for related studies.
SCIENCE CHINA-EARTH SCIENCES
(2023)
Article
Medicine, General & Internal
Wen Wen, Long Liao, Wei Dai, Can-Can Zheng, Xiang-Peng Tan, Yan He, Qi-Hua Zhang, Zhi-Hao Huang, Wen-You Chen, Yan-Ru Qin, Kui-Sheng Chen, Ming-Liang He, Simon Law, Maria Li Lung, Qing-Yu He, Bin Li
Summary: Through genome-wide CRISPR/Cas9 screening and gene profiling, the MEST-PURA-SRCIN1/RASAL1-ERK-snail signaling cascade was identified as an important mechanism underlying cancer metastasis in esophageal squamous cell carcinoma. Blocking the interaction between MEST and PURA could be a potential therapeutic approach for managing tumor metastasis.
Article
Biochemistry & Molecular Biology
Qianqian Yang, Lulu Wang, Yuehong Liang, Qingyu He, Qi Sun, Jing Luo, Hongdi Cao, Yi Fang, Yang Zhou, Junwei Yang, Ping Wen, Lei Jiang
Summary: Mitochondrial dysfunction, regulated by UCP2, plays a crucial role in the development of podocyte injury and proteinuria.
Letter
Infectious Diseases
Bianchuan Cao, Mei Liu, Rui Zhu, Tianru Yuan, A'shamu E'er, Shaofang Song, Tong Wang, Li Zhong
SEXUALLY TRANSMITTED INFECTIONS
(2023)
Article
Multidisciplinary Sciences
Shaohua Lu, Hong Lu, Tingkai Zheng, Huiming Yuan, Hongli Du, Youhe Gao, Yongtao Liu, Xuanzhen Pan, Wenlu Zhang, Shuying Fu, Zhenghua Sun, Jingjie Jin, Qing-Yu He, Yang Chen, Gong Zhang
Summary: The development of high-throughput omics technology has greatly promoted the development of biomedicine, but its poor reproducibility limits its application. The use of standard reference materials is necessary to test and calibrate the accuracy and reproducibility of omics workflows. In this study, we demonstrated that the human hepatocellular cell line MHCC97H has a very stable transcriptome and proteome after 9 subculturing generations, providing a steady standard sample for industrial-scale production in the long term. Furthermore, this stability was consistent across labs and platforms.
Review
Chemistry, Physical
Yisha Huang, Xuejuan Gao, Qing-Yu He, Wanting Liu
Summary: This article investigates the role of TRIM21 in intracellular immunity and proposes a model for how TRIM21 interacts with proteins. The model suggests that TRIM21 participates in inflammatory responses through ubiquitination and facilitates antibody destruction of target proteins by detecting antibody complexes. This systematic understanding of TRIM21's interactions provides insights into the pathogenesis of related diseases and potential applications.
Article
Public, Environmental & Occupational Health
Jing Wang, Patrick Kwan, Gong Zhang, Mingwang Shen, Loretta Piccenna, Terence J. O'Brien, Lei Zhang
Summary: China is faced with a growing aging population and understanding the health status of older adults is crucial for resource allocation and healthcare provision. This study aimed to comprehensively assess the disability level and identify risk factors associated with disability among older adults in China. A multidimensional ability assessment survey was used to evaluate daily living activities, mental status, sensory and communication abilities, and social participation. Demographic risk factors were analyzed using logistic regression and the correlations between the four dimensions of ability were assessed.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2023)
Article
Biochemistry & Molecular Biology
Zimei Chen, Ke Yang, Jiayi Zhang, Shufan Ren, Hui Chen, Jiahui Guo, Yizhi Cui, Tong Wang, Min Wang
Summary: In this study, the proteome of HIV-1 associated colorectal cancer (HA-CRC) and paired remote tissues (HA-RT) were analyzed, revealing differential protein expression. It was found that HA-CRC exhibited crosstalk between antiviral response and cancerous pathways. Moreover, it was demonstrated that HIV-1 reservoir cells could activate the interferon pathway in macrophages through the horizontal transfer of cell-associated HIV-1 RNA carried by extracellular vesicles.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Kun Meng, Yu-Ying Li, Dan-Ya Liu, Li-Ling Hu, Yun-Long Pan, Chris Zhiyi Zhang, Qing-Yu He
Summary: By analyzing the datasets of TCGA and CPTAC, we established a five-protein prognostic signature for ccRCC. This signature was closely correlated with advanced stage, higher pathological grade, and unfavorable survivals in ccRCC patients. Further studies revealed that GBP2 plays an oncogenic role by modulating JAK-STAT signaling and tumor immune infiltration.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Xiaolong Lu, Yang Chen, Gong Zhang
Summary: We analyzed SARS-CoV-2 sequence data from the end of 2019 to January 2023 and found that most genes are undergoing negative purifying selection, while the spike protein gene (S-gene) is undergoing rapid positive selection. The Ka/Ks of the S-gene increases from the original strain to different variants, but decreases within one variant over time. Additionally, only S-gene mutations show a trend of accumulating more positive charges, indicating a functional evolution that facilitates infection.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Analytical
Min Ma, Miyang Li, Yinlong Zhu, Yingyi Zhao, Feixuan Wu, Zicong Wang, Yu Feng, Hung-Yu Chiang, Manish S. Patankar, Cheng Chang, Lingjun Li
Summary: This study introduces a new method, called MAGNI, for multiplexed, quantitative, and targeted glycan analysis. By using isobaric-labeling and ultrahigh-resolution mass spectrometers, low-abundance glycans can be recognized and provide rich information on glycan structures. Using this method, a large number of unique N-glycans were identified in two ovarian cancer cell lines, revealing differences in glycosylation patterns between cell lines.
ANALYTICAL CHEMISTRY
(2023)