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The evolution of cancer genomic medicine in Japan and the role of the National cancer center Japan

cancer Biology & Medicine 2024年第1期21卷 29-44页

作者： Teruhiko Yoshida Yasushi Yatabe Ken Kato Genichiro Ishii Akinobu Hamada Hiroyuki Mano Kuniko Sunami Noboru Yamamoto Takashi Kohno Department of Genetic Medicine and Services National Cancer Center HospitalTokyo 104-0045Japan Department of Diagnostic Pathology National Cancer Center HospitalTokyo 104-0045Japan Clinical Research Support Offce Clinical Research Coordinating SectionBiobank Translational Research Support SectionNational Cancer Center HospitalTokyo 104-0045Japan Department of Pathology and Clinical Laboratories National Cancer Center Hospital EastChiba 277-8577Japan Division of Molecular Pharmacology National Cancer Center Research InstituteTokyo 104-0045Japan National cancer center Research Institute Tokyo 104-0045Japan Department of Laboratory Medicine National Cancer Center HospitalTokyo 104-0045Japan Department of Experimental Therapeutics National Cancer Center HospitalTokyo 104-0045Japan Division of Genome Biology National Cancer Center Research InstituteTokyo 104-0045Japan

The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer *** the time,a variety of activating oncogenic alterations and their functional significance were unveiled in cancer cells,which led to the development of molecular targeted therapies in the 2000s and *** CGM is still a relatively new discipline and it is difficult to predict to what extent CGM will benefit the diverse pool of cancer patients,the National cancer center(NCC)of Japan has already contributed considerably to CGM advancement for the conquest of *** back at these past achievements of the NCC,we predict that the future of CGM will involve the following:1)A biobank of paired cancerous and non-cancerous tissues and cells from various cancer types and stages will be *** quantity and quality of these samples will be compatible with omics *** biobank samples will be linked to longitudinal clinical information.2)New technologies,such as whole-genome sequencing and artificial intelligence,will be introduced and new bioresources for functional and pharmacologic analyses(e.g.,a patient-derived xenograft library)will be systematically deployed.3)Fast and bidirectional translational research(bench-to-bedside and bedside-to-bench)performed by basic researchers and clinical investigators,preferably working alongside each other at the same institution,will be implemented;4)Close collaborations between academia,industry,regulatory bodies,and funding agencies will be established.5)There will be an investment in the other branch of CGM,personalized preventive medicine,based on the individual's genetic predisposition to cancer.

关键词： cancer genomic medicine biobank patient-derived xenograft multi-gene panel test whole genome sequencing

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Unveiling an ancient whole-genome duplication event in Stentor,the model unicellular eukaryotes

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Science China Life Sciences 2025年第03期 825-835页

作者： Weibo Zheng Chao Li Zhaorui Zhou Xiao Chen Michael Lynch Ying Yan School of Life Sciences Ludong University Key Laboratory of evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity Ocean University of China Biodesign center for Mechanisms of evolution Arizona State University Marine College Shandong University

Whole-genome duplication(WGD) events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms. In the present study, the newly sequenced genome of a giant ciliated protist, Stentor roeselii, provides an opportunity for the analysis of the collinearity and retention of reciprocal best-hit genes between two Stentor species. As a main result, we have unveiled a previously undetected ancient WGD event shaping the genome of its congener, Stentor coeruleus, a model protist used in cytological and evolutionary studies. Genomes of two congeners, S. coeruleus and S. roeselii, are compared and analyzed, revealing that:(i)the former exhibits a much higher retention rate of colinear-gene pairs(28%) than does S. roeselii, and in S. coeruleus, 75% of genes that have a RBH hit in S. roeselii, have paralogs with high amino-acid identity, consistent with a WGD event in the lineage leading to S. coeruleus;(ii) the S. roeselii genome possesses extremely short intergenic regions, implying that the lengths of intergenic regions are under strong selection;(iii) the unique characteristics of introns may have been shaped in the common ancestor of heterotrichs;(iv) gene families that play a role in activities of multiple protein kinases and voltage-gated ion channels expanded rapidly in the ancestor of both taxa, possibly relating to the remarkable regenerative ability in Stentor. This study offers new insights into the evolutionary dynamics of ciliate genomes,with implications for understanding of the processes underlying the evolution of genomic complexity.

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Disentangling microbial coupled fillers mechanisms for the permeable layer optimization process in multi-soil-layering systems

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Journal of Environmental Sciences 2025年第1期147卷 538-549页

作者： Daxin Sun Chuanping Feng Yongheng Zhan Bingbing Deng Duoduo Mei Nan Chen Weiwu Hu School of Water Resources and Environment MOE Key Laboratory of Groundwater Circulation and Environmental EvolutionChina University of Geosciences(Beijing)Beijing 100083China Journal center China University of Geosciences(Beijing)Beijing 100083China

Themulti-soil-layering(MSL)systems is an emerging solution for environmentally-friendly and cost-effective treatment of decentralized rural domestic ***,the role of the seemingly simple permeable layer has been overlooked,potentially holding the breakthroughs or directions to addressing suboptimal nitrogen removal performance in MSL *** this paper,the mechanism among diverse substrates(zeolite,green zeolite and biological ceramsite)coupled microorganisms in different systems(activated bacterial powder and activated sludge)for rural domestic wastewater purification was *** removal efficiencies performed by zeolite coupled with microorganisms within 3 days were 93.8%for COD,97.1%for TP,and 98.8%for NH_(4)^(+)-***,activated sludge showed better nitrification and comprehensive performance than specialized nitrifying bacteria *** attained an impressive 89.4%NH4+-N desorption efficiency,with a substantive fraction of NH_(4)^(+)-N manifesting as exchanged ***-throughput 16S rRNA gene sequencing revealed that aerobic and parthenogenetic anaerobic bacteria dominated the reactor,with anaerobic bacteria conspicuously *** the heterotrophic nitrificationaerobic denitrification(HN-AD)process was significant,with the presence of denitrifying phosphorus-accumulating organisms(DPAOs)for simultaneous nitrogen and phosphorus *** study not only raises awareness about the importance of the permeable layer and enhances comprehension of the HN-AD mechanism in MSL systems,but also provides valuable insights for optimizing MSL system construction,operation,and rural domestic wastewater treatment.

关键词： Rural domestic wastewater Multi-soil-layering(MSL)system Heterotrophic nitrification-aerobic denitrification(HN-AD) Nitrogen and phosphorus removal Microbial evolution

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Exploring the potential of extrachromosomal DNA as a novel oncogenic driver

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Science China(Life Sciences) 2025年第1期68卷 144-157页

作者： Huanbo Zhu Longtao Huangfu Junbing Chen Jiafu Ji Xiaofang Xing Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education/Beijing) Division of Gastrointestinal Cancer Translational Research LaboratoryPeking University Cancer Hospital&InstituteBeijing 100142China Department of Gastrointestinal cancer center Peking University Cancer Hospital&InstituteBeijing 100142China Department of Liver Surgery&Transplantation Liver Cancer InstituteZhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer InvasionMinistry of EducationShanghai200032China State Key Laboratory of Holistic Integrative Management of Gastrointestinal cancers Beijing Key Laboratory of Carcinogenesis and Translational ResearchDivision of Gastrointestinal Cancer Translational Research LaboratoryPeking University Cancer Hospital&InstituteBeijing 100142China

Extrachromosomal DNA(ecDNA)is a form of circular DNA mostly found in tumor *** the typical chromosomal DNA,ecDNA is circular,self-replicating,and carries complete or partial gene *** ecDNA occurrence remains a rare event in cancer,recent studies have shown that oncogene amplification on ecDNA is widespread throughout many types of cancer,implying that ecDNA plays a central role in accelerating tumor *** has also been associated with increased tumor mutation burden,chromosomal instability,and even tumor microenvironment *** may be crucial in influencing tumor heterogeneity,drug sensitivity,oncogenic senescence,and tumor immunogenicity,leading to a worsening prognosis for tumor *** this way,several clinical trials have been conducted to investigate the importance of ecDNA in clinical *** this review,we summarize the biogenesis,characteristics,and current research methods of ecDNA,discuss the vital role of ecDNA-caused tumor heterogeneity in cancers,and highlight the potential role of ecDNA in cancer therapy.

关键词： extrachromosomal DNA cancer therapy tumor heterogeneity drug resistance tumor evolution

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Characterization and genomic analysis of Pseudoalteromonas phage v B_Pal P_Y7,representing a novel viral genus,Miuvirus

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Journal of Oceanology and Limnology 2025年第1期43卷 299-312页

作者： Miaolan WU Hongmin WANG Ye MI Yantao LIANG Kaiyang ZHENG Yundan LIU Yue DONG Linyi REN Yue SU Hongbing SHAO Yeong Yik SUNG Wen Jye MOK Li Lian WONG Min WANG College of Marine Life Sciences Institute of Evolution and Marine BiodiversityMoE Laboratory of Evolution and Marine BiodiversityFrontiers Science Center for Deep Ocean Multispheres and Earth SystemCenter for Ocean Carbon NeutralityOcean University of ChinaQingdao 266100China Qingdao City center for Disease Control and Prevention Qingdao Institute of Prevention MedicineQingdao 266033China UMT-OUC Joint Centre for Marine Studies Qingdao 266100China Institute of Marine Biotechnology Universiti Malaysia TerengganuKuala Terengganu 21030Malaysia Haide College Ocean University of ChinaQingdao 266100China The Affiliated Hospital of Qingdao University Qingdao 266000China

Pseudoalteromonas is a group of marine bacteria widespread in diverse marine sediments,producing a wide range of bioactive ***,only a limited number of Pseudoalteromonas phages have been isolated and *** this study,a novel lytic Pseudoalteromonas phage,denoted as vB_PalP_Y7,was isolated from sewage samples collected at the Seafood Market in Qingdao,***_PalP_Y7 remained stable across a wide range of temperatures(-20–50℃)and a wide pH range(3–12).The vB_PalP_Y7 phage harbors a linear double-stranded DNA molecule of 57699 base pairs(bp)with a G+C content of 45.90%.Furthermore,it is predicted to contain 58 open reading frames(ORFs).Phylogenetic analysis and protein network relationship analysis revealed low similarity between vB_PalP_Y7 and viruses in the ICTV and IMG/VR4 database,suggesting that vB_PalP_Y7 may be a potential new genus,*** study contributed valuable insights to comprehend the relationship between Pseudoalteromonas phages and their host organisms.

关键词： Pseudoalteromonas phage genomic analysis phylogenetic analysis viral cluster

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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China(Life Sciences) 2025年第1期68卷 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao Key Laboratory of evolution&Marine Biodiversity(Ministry of Education)and Institute of evolution&Marine Biodiversity Ocean University of ChinaQingdao 266003China Marine College Shandong UniversityWeihai 264209China Zoology Department College of ScienceKing Saud UniversityRiyadh 11451Saudi Arabia Department of Biology Bradley UniversityPeoria 61625USA Laboratory for Marine Biology and Biotechnology Qingdao Marine Science and Technology CenterQingdao 266237China

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

关键词： sexual reproduction transcriptomic proteomic genome rearrangement PIWI NHEJ

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Cortical hem signaling center: functions, development, and potential implications for evolution and brain disorders

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Neural Regeneration Research 2025年第4期20卷 1079-1080页

作者： Victor V.Chizhikov Igor Y.Iskusnykh Department of Anatomy and Neurobiology University of Tennessee Health Science CenterMemphisTNUSA

Development of the telencephalon relies upon several signaling centers-localized cellular populations that supply secreted factors to pattern the cortical *** such signaling center is the cortical hem,which arises during embryonic development at the telencephalic dorsal midline,adjacent to the choroid plexus and hippocampal primordium(Figure 1A).While the cortical hem has also been described in reptiles and birds,most of our knowledge about the developmental roles of the cortical hem is derived from the analysis in *** cortical hem produces several types of secreted molecules,including wingless-related integration site(Wnt)and bone morphogenetic(Bmp)*** cortical hem is particularly important for the development of the hippocampus,which is involved in learning and memory,and the neocortex,which is the most complex brain region that mediates multiple types of behavior and higher cognitive functions(Mangale et al.,2008;Dal-Valle-Anton and Borrell,2022).

关键词： epithelium Figure center

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First documentation of early Silurian conodonts from western Thailand and its geological implications

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Journal of Palaeogeography 2025年第1期14卷 157-171页

作者： Zhong-Yang Chen Hathaithip Thassanapak Wen-Jie Li Xue-Jin Wu Mongkol Udchachon Xiang Fang Clive Burrett State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and PalaeontologyChinese Academy of Sciences University of Chinese Academy of Sciences Excellence center in evolution of Life Basin Studies and Applied Palaeontology Palaeontological Research and Education Center Mahasarakham University Department of Biology Faculty of Science Mahasarakham University

The early Silurian conodonts are firstly described and illustrated from western Thailand. Samples were collected from the Kroeng Kravia Forest Park area for conodont and lithofacies analyses. An upper Telychian Lower Pterospathodus amorphognathoides amorphognathoides Subzone is recognized for the studied succession. Three lithofacies were identified from the carbonate succession, including stromatolite-thrombolite limestone, nodular limestone, and red limestone. Both analyses on lithofacies and conodont assemblages indicate a deeper marine depositional environment. The conodont fauna in the study area is similar to that from Baoshan of Yunnan Province and Langao of Shaanxi Province in West China and resembles that from similar depositional environments in Australia, Laurentia, and peri-Gondwana, suggesting good connections among these regions by ocean currents.

关键词： Silurian Conodonts Deep marine environment Western Thailand Sibumasu

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Gradient maturation experiment on hairs implies taphonomic changes in fossil hairs

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Science China Earth Sciences 2025年第1期68卷 62-73页

作者： Xin LI Yibo ZHOU Tao ZHAO Xingjian HE Yanhong PAN State Key Laboratory for Mineral Deposits Research Center for Critical Earth Material CyclingCentre for Research and Education on Biological Evolution and Environment and Frontiers ScienceSchool of Earth Sciences and EngineeringNanjing UniversityNanjing210023China Institute of Palaeontology Yunnan Key Laboratory of Earth System ScienceYunnan Key Laboratory for PalaeobiologyYunnan UniversityKunming650500China

Mammalian hair,as a key feature related to endothermy,physical protection,and camouflage,has a long geohistorical record that dates back even to the ***,the limited information on the taphonomy of hair hinders the understanding of its evolutionary significance in deep *** address this,we conducted taphonomic experiments to simulate the transformation process of black *** changes in the morphological structure,microscopic characteristics,and chemical composition of hair during the simulated fossilization process were documented by scanning electron microscopy,Fourier transform infrared(FTIR)spectroscopy,and Raman *** results revealed that damage to the morphology of hair began at a mild temperature(150–175℃),and hair transformed into a fluid-like mass at a relatively high temperature(200℃).In addition,the morphological structure of melanosomes had relatively greater preservation potential than keratins did,and the microscopic features of melanosomes were persistently *** Raman and FTIR spectra indicated that the characteristic melanin and keratin peaks changed as the temperature *** the chemical signals were not lost completely,the variations in the characteristic amide bands in the FTIR spectra indicate that the keratins severely degraded at high temperatures(>200℃),whereas the characteristic melanin bands in the Raman spectra suggested that melanin signals were still recognizable,even at high temperatures(>200℃).These results were confirmed by principal component analysis(PCA)and principal component analysis linear discriminant analysis(PCA–LDA).In addition,the Raman signals of all the samples in the simulated experiments were distinguished from the signals of common geological carbonaceous materials(humic acid),which suggested that Raman spectroscopy can be used to detect melanin in fossils.

关键词： Mammalian hair Melanin Keratin Fossilization Experimental taphonomy

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Robust interface and excellent as-built mechanical properties of Ti–6Al–4V fabricated through laser-aided additive manufacturing with powder and wire

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International Journal of Minerals,Metallurgy and Materials 2025年第1期32卷 154-168页

作者： Fei Weng Guijun Bi Youxiang Chew Shang Sui Chaolin Tan Zhenglin Du Jinlong Su Fern Lan Ng Key Laboratory for Liquid-Solid Structural evolution and Processing of Materials Ministry of EducationShandong Engineering&Technology Research Center for Superhard MaterialSchool of Materials Science and EngineeringShandong UniversityJinan 250061China Institute of Intelligent Manufacturing Guangdong Academy of SciencesGuangzhou 510095China Singapore Institute of Manufacturing Technology 5 Cleantech Loop636732Singapore

The feasibility of manufacturing Ti-6Al-4V samples through a combination of laser-aided additive manufacturing with powder(LAAM_(p))and wire(LAAM_(w))was explored.A process study was first conducted to successfully circumvent defects in Ti-6Al-4V deposits for LAAM_(p) and LAAM_(w),*** the optimized process parameters,robust interfaces were achieved between powder/wire deposits and the forged substrate,as well as between powder and wire *** characterization results revealed the epitaxial prior β grains in the deposited Ti-6Al-4V,wherein the powder deposit was dominated by a finerα′microstructure and the wire deposit was characterized by lamellar α *** mechanisms of microstructure formation and correlation with mechanical behavior were analyzed and *** mechanical properties of the interfacial samples can meet the requirements of the relevant Aerospace Material Specifications(AMS 6932)even without post heat *** fracture occurred within the interfacial area,further suggesting the robust *** findings of this study highlighted the feasibility of combining LAAM_(p) and LAAM_(w) in the direct manufacturing of Ti-6Al-4V parts in accordance with the required dimensional resolution and deposition rate,together with sound strength and ductility balance in the as-built condition.

关键词： laser-aided additive manufacturing powder deposition wire deposition interfacial characteristic mechanical behavior

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