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Chunpeng Yu,Jian Li,Qun Li,Shuai Chang,Yufeng Cao,Hui Jiang,Lingling Xie,Gang Fan,Song Wang 한국미생물학회 2022 The journal of microbiology Vol.60 No.11
Due to the evolutionary arms race between hosts and viruses, viruses must adapt to host translation systems to rapidly synthesize viral proteins. Highly expressed genes in hosts have a codon bias related to tRNA abundance, the primary RNA translation rate determinant. We calculated the relative synonymous codon usage (RSCU) of three hepatitis viruses (HAV, HBV, and HCV), SARS-CoV-2, 30 human tissues, and hepatocellular carcinoma (HCC). After comparing RSCU between viruses and human tissues, we calculated the codon adaptation index (CAI) of viral and human genes. HBV and HCV showed the highest correlations with HCC and the normal liver, while SARS-CoV-2 had the strongest association with lungs. In addition, based on HCC RSCU, the CAI of HBV and HCV genes was the highest. HBV and HCV preferentially adapt to the tRNA pool in HCC, facilitating viral RNA translation. After an initial trigger, rapid HBV/HCV translation and replication may change normal liver cells into HCC cells. Our findings reveal a novel perspective on virus-mediated oncogenesis.
Thermal Oxidation of WSe<sub>2</sub> Nanosheets Adhered on SiO<sub>2</sub>/Si Substrates
Liu, Yingnan,Tan, Cheng,Chou, Harry,Nayak, Avinash,Wu, Di,Ghosh, Rudresh,Chang, Hsiao-Yu,Hao, Yufeng,Wang, Xiaohan,Kim, Joon-Seok,Piner, Richard,Ruoff, Rodney S.,Akinwande, Deji,Lai, Keji American Chemical Society 2015 NANO LETTERS Vol.15 No.8
<P>Because of the drastically different intralayer versus interlayer bonding strengths, the mechanical, thermal, and electrical properties of two-dimensional (2D) materials are highly anisotropic between the in-plane and out-of-plane directions. The structural anisotropy may also play a role in chemical reactions, such as oxidation, reduction, and etching. Here, the composition, structure, and electrical properties of mechanically exfoliated WSe<SUB>2</SUB> nanosheets on SiO<SUB>2</SUB>/Si substrates were studied as a function of the extent of thermal oxidation. A major component of the oxidation, as indicated from optical and Raman data, starts from the nanosheet edges and propagates laterally toward the center. Partial oxidation also occurs in certain areas at the surface of the flakes, which are shown to be highly conductive by microwave impedance microscopy. Using secondary ion mass spectroscopy, we also observed extensive oxidation at the WSe<SUB>2</SUB>–SiO<SUB>2</SUB> interface. The combination of multiple microcopy methods can thus provide vital information on the spatial evolution of chemical reactions on 2D materials and the nanoscale electrical properties of the reaction products.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/nalefd/2015/nalefd.2015.15.issue-8/acs.nanolett.5b02069/production/images/medium/nl-2015-02069p_0005.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/nl5b02069'>ACS Electronic Supporting Info</A></P>
Yu Feng,Yutao Liu,Mingming Yuan,Guilan Dong,Hongxia Zhang,Tongmei Zhang,Lianpeng Chang,Xuefeng Xia,Lifeng Li,Haohua Zhu,Puyuan Xing,Hongyu Wang,Yuankai Shi,Zhijie Wang,Xingsheng Hu 대한암학회 2022 Cancer Research and Treatment Vol.54 No.3
Purpose To investigate the feasibility of biomarkers based on dynamic circulating tumor DNA (ctDNA) to classify small cell lung cancer (SCLC) into different subtypes. Materials and Methods Tumor and longitudinal plasma ctDNA samples were analyzed by next-generation sequencing of 1,021 genes. PyClone was used to infer the molecular tumor burden index (mTBI). Pre-treatment tumor tissues [T1] and serial plasma samples were collected (pre-treatment [B1], after two [B2], six [B3] cycles of chemotherapy and at progression [B4]). Results Overall concordance between T1 and B1 sequencing (n=30) was 66.5%, and 89.5% in the gene of <i>RB1</i>. A classification method was designed according to the changes of <i>RB1</i> mutation, named as subtype Ⅰ (both positive at B1 and B2), subtype Ⅱ (positive at B1 but negative at B2), and subtype Ⅲ (both negative at B1 and B2). The median progressive-free survival for subtype Ⅰ patients (4.5 months [95%CI: 2.6-5.8]) was inferior to subtype Ⅱ (not reached, p<0.0001) and subtype Ⅲ (10.8 months [95%CI: 6.0-14.4], p=0.002). The median overall survival for subtype Ⅰ patients (16.3 months [95%CI: 5.3-22.9]) was inferior to subtype Ⅱ (not reached, p=0.01) and subtype Ⅲ (not reached, p=0.02). Patients with a mTBI dropped to zero at B2 had longer median overall survival (not reached vs. 19.5 months, p=0.01). The changes of mTBI from B4 to B1 were sensitive to predict new metastases, with a sensitivity of 100% and a specificity of 85.7%. Conclusion Monitoring ctDNA based <i>RB1</i> mutation and mTBI provided a feasible tool to predict the prognosis of SCLC.