Article
Chemistry, Applied
Delphine Winstel, Delphine Bahammou, Warren Albertin, Pierre Waffo-Teguo, Axel Marchal
Summary: Taste plays a crucial role in the acceptability of food and beverages, especially natural products with complex tastes. A comprehensive methodology applied to spirits led to the discovery of new taste-active compounds, showcasing the relevance and effectiveness of the approach.
Article
Cell Biology
Saisai Wei, Wenhao Guo, Yu Qian, Jie Xiang, Kangli Liu, Xiang-Jing Gao, Xiangwei Gao, Yicheng Chen
Summary: Our study reveals that zinc oxide nanoparticles (ZnO NPs) affect the transcription of 78 genes and translation of 1,448 genes in A549 human lung cancer cells within one hour of exposure. The mitogen-activated protein kinase (MAPK) pathway is up-regulated upon ZnO NP treatment, and upstream open reading frame (uORF) plays a crucial role in the induction of up-regulated genes such as TLNRD1 and CCNB1IP1, which in turn reduces ZnO NP-induced cytotoxicity. This study characterizes the landscape of translational alteration under ZnO NPs treatment and identifies potential targets to enhance the anticancer effect of ZnO NPs.
Article
Physics, Particles & Fields
Simone Amoroso, Deepak Kar, Matthias Schott
Summary: The concept of Instantons in the Standard Model has not been experimentally observed yet. New calculations suggest possible observation of QCD Instanton processes at the LHC. Researchers propose analysis strategies and derive a first limit on Instanton production cross section using published data.
EUROPEAN PHYSICAL JOURNAL C
(2021)
Article
Biochemistry & Molecular Biology
Alla D. Fedorova, Jack A. S. Tierney, Audrey M. Michel, Pavel V. Baranov
Summary: Ribo-Seq is a technology that captures the locations of ribosomes in the entire transcriptome, providing insights into gene expression and discovering novel translated regions. RiboGalaxy is a Galaxy-based platform for processing Ribo-Seq data, with links to Riboseq.Org resources and other tools to improve data analysis interoperability.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
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.
Review
Pharmacology & Pharmacy
Dermot Cox
Summary: Despite the immense potential integrins hold in medicine, the investment in anti-integrin drug discovery programs has yielded little results so far. The main reasons for this are the toxicity and limited efficacy of these drugs, as well as the complex pathophysiology of integrins making drug development challenging.
EXPERT OPINION ON DRUG DISCOVERY
(2021)
Article
Neurosciences
Judit Pallos, Sophia Jeng, Shannon McWeeney, Ian Martin
Summary: LRRK2 mutations are the most common genetic cause of late-onset Parkinson's disease, enhancing kinase activity and causing neurodegeneration. Using TRAP and RNA-seq, researchers profiled gene expression changes specifically in dopamine neurons induced by LRRK2 G2019S in Drosophila, uncovering a range of differentially expressed genes.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Biology
Susanne Bauer, Lars Dittrich, Lech Kaczmarczyk, Melvin Schleif, Rui Benfeitas, Walker S. Jackson
Summary: Selective neuronal vulnerability is a common phenomenon in neurodegenerative diseases but not well understood. This study found that in mice modeling genetic prion diseases, specific cells types showed abnormal changes in gene expression, with a high overlap between fatal familial insomnia and Creutzfeldt-Jakob disease. Neurodegenerative disease pathways were up-regulated and synaptic function and signaling pathways were down-regulated in fatal familial insomnia mice. These findings suggest that finding common therapeutic approaches may be beneficial for multiple genetic prion diseases.
LIFE SCIENCE ALLIANCE
(2022)
Review
Multidisciplinary Sciences
Pedro Pessoa, Steve Presse
Summary: It is common for scientific publishing to ask authors for reviewer suggestions. However, it is difficult to find friendly reviewers. To investigate this, we conducted a simulation and used Bayesian framework to classify suggested reviewers. We found that even with optimistic conditions, it would require hundreds of submissions to classify a small subset of reviewers. This highlights the robustness of the peer review system in allowing authors to suggest their own reviewers.
Article
Immunology
Parul Mehra, Andrew D. Wells
Summary: The breakdown of immunological tolerance can lead to autoimmune diseases, and the mechanisms that maintain self-tolerance are not fully understood. Genome-wide association studies have identified many human genetic loci statistically linked to autoimmune disease risk, but identifying causal variants and their functional consequences has been challenging due to their distant locations from genes. Recent advances in understanding the spatial organization of the genome in the nucleus offer insights into gene regulation and potential solutions to questions raised by GWAS findings.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Endocrinology & Metabolism
Sofia Thomaidou, Roderick C. Slieker, Arno R. van der Slik, Jasper Boom, Flip Mulder, Amadeo Munoz-Garcia, Leen M. 't Hart, Bobby Koeleman, Francoise Carlotti, Rob C. Hoeben, Bart O. Roep, Hailiang Mei, Arnaud Zaldumbide
Summary: Type 1 diabetes is an autoimmune disease where insulin-producing pancreatic beta-cells are destroyed by autoimmunity. Recent research suggests that beta-cells may contribute to their own destruction by generating new antigens. Stress-induced ribosomal infidelity could lead to the generation of new antigens, and studying the transcriptome of beta-cells can reveal new functional biomarkers.
Editorial Material
Medicine, Research & Experimental
Wenjie Liang, Julien Diana
Summary: The study identified a novel antimicrobial peptide from human oral actinomyces, actinomycesin, which showed efficacy and safety against various bacterial strains. This discovery highlights the potential of human oral bacteria as a source of antimicrobial agents in the fight against multidrug-resistant bacteria.
EMBO MOLECULAR MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Luigi Donato, Domenico Morda, Concetta Scimone, Simona Alibrandi, Rosalia D'Angelo, Antonina Sidoti
Summary: Alzheimer's disease (AD) is the most widespread dementia globally, posing a major public health concern. Our understanding of this disease has significantly progressed, from a clinical and histopathologic description to a molecular comprehension. Unfortunately, there are no disease-modifying therapies currently available.
Review
Biology
Addy Pross
Summary: The central thesis of the modern scientific revolution is that nature is objective, yet projective systems emerged from that objective reality. Chemical systems emerged and evolved to take advantage of nature's objective laws, which were uncovered by nature twice. The challenging question remains: how did nature become self-aware and discover its own laws?
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
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.
Article
Infectious Diseases
Dan Lei, Linlin Cao, Tairan Zhong, Qing-Yu He, Xuesong Sun
Summary: In this study, the researchers found that the mutation of the key residue Lys219 leads to a conformational change in CpxR, resulting in loss of its regulatory ability in antibiotic resistance.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Instruments & Instrumentation
Lihui Zhou, Qingyu He, Xinglu Que, Andreas W. W. Rost, Hide Takagi
Summary: Cryogenic scanning tunneling microscopy and spectroscopy with a high vector magnetic field is used to image surface magnetic structures, study anisotropic superconductivity, and explore spin physics in quantum materials. This paper describes the design, construction, and performance of a low-temperature, ultra-high-vacuum spectroscopic imaging STM with a vector magnet capable of applying a field of up to 3 T in any direction. The STM can operate at variable temperatures and is suitable for studying layered compounds and thin films.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
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.
Article
Engineering, Electrical & Electronic
Xu Zhang, Honglin Ji, Ming Luo, Qingyu He, Chao Yang, Jie Li, Wu Liu, Chao Li, Qibing Wang, Zichen Liu, Chuyu Peng, Hao Guo, Huang Yu, Zhiwen Fan, Zhixue He, Xi Xiao, Shaohua Yu
Summary: We experimentally demonstrate a 3.61 Pbit/s estimated throughput of generalized mutual information (GMI) achieved through combined space division multiplexing (SDM) and wavelength division multiplexing (WDM) over a 19-core single-mode fiber. The transmission utilizes 680 wavelength channels covering a 17 THz bandwidth in the S, C, and L bands, delivering probabilistically constellation-shaped (PCS) 256 quadrature amplitude modulation (QAM) and PCS-64QAM signals at a data rate of 24.5 GBaud. The measured data rate shows significant potential for enhancing the achievable data rate in multi-core fibers.
IEEE PHOTONICS TECHNOLOGY LETTERS
(2023)
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
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)
