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Three-dimensional bioglass-collagen-phosphatidylserine scaffolds designed with functionally graded structure and mechanical features

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BIOMEdICAL ENGINEErING-BIOMEdIZINISCHE TECHNIK 2018年第3期63卷 255-259页

作者： Yang, Chunrong Wu, Huazhong Chen, Shou Kang, Guangyu Fujian Univ Technol Sch Mat Sci & Engn Fuzhou 350118 Fujian Peoples R China Fujian Prov Key Lab Adv Mat Proc & Applicat Fuzhou 350118 Fujian Peoples R China Univ Minjiang Dept Chem & Chem Engn Fuzhou 350118 Fujian Peoples R China Shenzhen 863 Program R&D Ctr Surface Technol Shenzhen 518100 Peoples R China

The development of scaffolds featuring spatiotemporal controlled release of drugs is highly desirable. The goal of this study is to construct an inhomogeneous scaffold with gradient pore structure from top layer to bottom layer. The scaffolds were prepared using bioglass (BG), phosphatidylserine (PS) and steroidal saponins (SS) loaded collagen (COL) microparticles as the main components. The resulting scaffold constructs were characterized in terms of their morphology, drug release kinetics and mechanisms, as well as macroscopic form stability and mechanical properties. Pore interconnectivity and graded distribution were demonstrated using scanning electron microscopy (SEM). Such constructs have been further shown to be advantageous for temporal and spatial control of drug release and deposition in the scaffolds, with a potential to repair bone defect more precisely and effectively. Changes in the BG content resulted in distinct macroscopic form stability and mechanical properties to scaffolds. An increase in the BG content in scaffolds led to less volume swell as well as higher ultimate strength and compressive modulus, which makes the scaffolds mechanically adjustable according to certain structures and properties of different bone defect sites. The developed scaffolds may show promise for promoting bone tissue regeneration.

关键词： bone controlled drug delivery scaffolds

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Prediction of dairy Product Quality risk Based on Extreme Learning Machine 2

Prediction of Dairy Product Quality Risk Based on Extreme Le...

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2nd International Conference on data Science and Business Analytics (ICdSBA)

作者： Zhang, ruifang Bi, Mingwen Zhou, Lin Jin, Qingyu Zuo, Min Xu, Zelong Zhang, Qingchuan Beijing Technol & Business Univ Sch Comp & Informat Engn Natl Engn Lab Agriprod Qual Traceabil Natl Key Technol R&D Program China Beijing Peoples R China Minist Environm Protect Nucl & Radiat Safety Ctr Beijing Peoples R China

ISBN: (纸本)9781538684313

The use of machine learning can study the objective laws of the data to find out the relationship between the data, but also can achieve data classification and prediction. This article is based on national food safety sampling platform for dairy products testing data for the study to predict the risk safety of dairy products. Firstly, the sampling data of dairy products was selected from the database and the data was preprocessed. Then, the characteristic data were selected and classified into these data. Finally, the key food safety risk early-warning model was constructed by using Extreme learning machine (ELM) and the kernel-based extreme learning machine (K-ELM) respectively. Commonly used BP neural network and Support Vector Machines(SVM) network contrast. After ELM and K-ELM again to compare the experimental results. From the experimental results, it can be seen that the neural network algorithm based on kernel extreme learning machine has a high accuracy in food safety prediction and the training time is short. Through the extreme learning machine effective prediction of food safety, to regulate the quality and safety of food, so as to protect the quality of food safety in China.

关键词： Machine learning Food safety Prediction Extreme learning machine

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design of a sustained-release nanosystem for ultra-efficient absorption of anthocyanins and regulating lung damage through the “lung-gut” axis

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Journal of Advanced research 2025年

作者： Tian, Jin-Long Wang, Nuo Zhao, Qin-Fu Zang, Zhi-Huan Li, Zhi-Ying Wang, Zhen-Yu Zhou, Ying Yang, Bao-ru Makarov, Sergey S. Chudetsky, Anton I. Wang, Liang He, Ying Li, Bin College of Food Science Shenyang Agricultural University National R&D Professional Center for Berry Processing National Engineering and Technology of Research Center for Small Berries Key Laboratory of Healthy Food Nutrition and Innovative Manufacturing Liaoning Province Shenyang 110866 China Department of Pharmaceutics School of Pharmacy Shenyang Pharmaceutical University 103 Wenhua Road Liaoning Province Shenyang 110016 China School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin China Food Sciences Department of Life Technologies University of Turku Turku Finland Moscow Timiryazev Agricultural Academy Russian State Agrarian University Moscow 127550 Russian Federation Zhejiang Lanmei Technology Co. Ltd. Zhejiang Zhuji 311800 China

Introduction: Anthocyanins have various health benefits but are limited by fast elimination and low bioavailability. Many studies have shown that nano delivery systems are effective in improving the intestinal absorption and bioavailability of anthocyanins. However, in the process of selecting anthocyanin nanomaterials, a dilemma is faced: numerous functional nanomaterials lack edible properties, it is difficult to meet the edible and functional requirements of nanomaterials simultaneously. Therefore, it is necessary and inevitable to select nano-anthocyanin carriers that are edible and have certain functional and morphological characteristics. Objectives: The study aim to provide an efficient, sustained-release and easy to industrialize nanosystem method to solve the problem of low bioavailability of anthocyanins. Methods: A succinylated casein-phospholipid-anthocyanin nanosystem (CLS) was designed via computational chemistry-guided one-step self-assembly. Morphological, in vitro/in vivo digestion, pharmacokinetic were conducted. Furthermore, the effects of CLS on intestinal microecology were verified by using enteritis model animals, and the lung-targeting effect of CLS on lung health was verified by using lung injury model animals. results: CLS exhibited 24-hour intestinal sustained release and lung-targeted enrichment. Pharmacokinetic studies showed 25.7-fold higher lung AUC(0-t) and 13.1-fold higher blood AUC(0-t) compared to free anthocyanins. CLS significantly alleviated lung injury and colitis in model rats via the gut-lung axis. Conclusion: This study significantly improved the bioavailability of anthocyanins and demonstrated the oral lung-targeting function of anthocyanins for the first time, paving the way for utilizing anthocyanins as dietary supplements and precision nutrition.

关键词： Anthocyanins Bioavailability Lung enrichment Nanodelivery Pharmacokinetics

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Shift in limiting nutrients in the late Ediacaran-early Cambrian marine systems of South China

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PALAEOGEOGrAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY 2019年 530卷 281-299页

作者： Nishizawa, Manabu Tsuchiya, Yuki du, Wei Sawaki, Yusuke Matsui, Yohei Wang, Yue Han, Jian Komiya, Tsuyoshi Japan Agcy Marine Earth Sci & Technol JAMSTEC Dept Subsurface Geobiol Anal & Res D SUGAR 2-15 Natsushima Cho Yokosuka Kanagawa 2370061 Japan JAMSTEC Inst Extra Cutting Edge Sci & Technol Avant Garde Super Cutting Edge Grand & Adv Res SUGAR Program 2-15 Natsushima Cho Yokosuka Kanagawa 2370061 Japan Univ Tokyo Dept Earth Sci & Astron 3-8-1 Komaba Tokyo 1538902 Japan JAMSTEC Res & Dev R&D Ctr Submarine Resources Yokosuka Kanagawa 2370061 Japan Univ Tokyo Atmosphere & Ocean Res Inst Marine Biogeochem Grp Kashiwa Chiba 2778564 Japan Guizhou Univ Sch Resources & Environm Guiyang 550025 Guizhou Peoples R China Northwest Univ Dept Geol State Key Lab Continental Dynam Shaanxi Key Lab Early Life & Environm 229 Taibai Rd Xian 710069 Shaanxi Peoples R China

The Ediacaran to Cambrian periods are characterized by the diversification and extinction of metazoans, carbon cycle perturbation, and ocean oxygenation. Ocean nutrient cycles play a major role in the primary production and productivity-driven shallow water anoxia that was responsible for mass extinction in some Phanerozoic intervals. However, the relationships between these cycles and primary production and biological events during the Ediacaran to Cambrian periods have not previously been well-explored. This study presents stratigraphic profiles of nitrogen and organic carbon isotopes for sections belonging to the shelf and deep basin regions of the Yangtze Platform, South China. The nitrogen isotope profiles for these two regions share a similar trend, showing 1) relatively stable delta N-15 values of 5-6 parts per thousand in the early middle Ediacaran (635 Ma-ca. 560 Ma) and 2) a shift towards lower delta N-15 values (3-4 parts per thousand) since the Shuram delta C-13(carb) Excursion. The delta N-15 values in the shelf section experienced a two-stage decrease from the late Ediacaran to Cambrian Stage 2 of the Terreneuvian series (down to -1 parts per thousand) and then an increase from -1 parts per thousand to +4 parts per thousand across the Cambrian Stage 2/3 boundary (Le., the Terreneuvian/Cambrian Series 2 boundary at 521 Ma). These data, in combination with previously reported nutrient profiles (delta N-15, P, and Mo), allow the following new conclusions to be drawn. 1) The early middle Ediacaran ocean was characterized by N-Mo colimitation of primary production on a geological timescale that is different from the P limitation on long-term primary production in the modern ocean. 2) A shift in the ultimate limiting nutrient from N and Mo to P likely occurred in late Ediacaran-early Cambrian marine systems. This shift may have been a prerequisite for the extinction of small shelly fossils in response to the development of photic zone anoxia for several mill

关键词： Nitrogen Phosphorous Molybdenum Photic zone anoxia

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CHArMM at 45: Enhancements in Accessibility, Functionality, and Speed

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JOUrNAL OF PHYSICAL CHEMISTrY B 2024年第41期128卷 9976-10042页

作者： Hwang, Wonmuk Austin, Steven L. Blondel, Arnaud Boittier, Eric d. Boresch, Stefan Buck, Matthias Buckner, Joshua Caflisch, Amedeo Chang, Hao-Ting Cheng, Xi Choi, Yeol Kyo Chu, Jhih-Wei Crowley, Michael F. Cui, Qiang damjanovic, Ana deng, Yuqing devereux, Mike ding, Xinqiang Feig, Michael F. Gao, Jiali Glowacki, david r. Gonzales, James E. Hamaneh, Mehdi Bagerhi Harder, Edward d. Hayes, ryan L. Huang, Jing Huang, Yandong Hudson, Phillip S. Im, Wonpil Islam, Shahidul M. Jiang, Wei Jones, Michael r. Kaser, Silvan Kearns, Fiona L. Kern, Nathan r. Klauda, Jeffery B. Lazaridis, Themis Lee, Jinhyuk Lemkul, Justin A. Liu, Xiaorong Luo, Yun MacKerell Jr, Alexander d. Major, dan T. Meuwly, Markus Nam, Kwangho Nilsson, Lennart Ovchinnikov, Victor Paci, Emanuele Park, Soohyung Pastor, richard W. Pittman, Amanda r. Post, Carol Beth Prasad, Samarjeet Pu, Jingzhi Qi, Yifei rathinavelan, Thenmalarchelvi roe, daniel r. roux, Benoit rowley, Christopher N. Shen, Jana Simmonett, Andrew C. Sodt, Alexander J. Topfer, Kai Upadhyay, Meenu van der Vaart, Arjan Vazquez-Salazar, Luis Itza Venable, richard M. Warrensford, Luke C. Woodcock, H. Lee Wu, Yujin Brooks, Charles L. Brooks III, Bernard r. Karplus, Martin Texas A&M Univ Dept Biomed Engn College Stn TX 77843 USA Texas A&M Univ Dept Mat Sci & Engn College Stn TX 77843 USA Texas A&M Univ Dept Phys & Astron College Stn TX 77843 USA Korea Inst Adv Study Ctr AI & Nat Sci Seoul 02455 South Korea Univ S Florida Dept Chem Tampa FL 33620 USA Univ Paris Cite Inst Pasteur Struct Bioinformat Unit CNRS UMR3825 F-75015 Paris France Univ Basel Dept Chem CH-4056 Basel Switzerland Univ Vienna Fac Chem Dept Computat Biol Chem A-1090 Vienna Austria Case Western Reserve Univ Sch Med Dept Physiol & Biophys Cleveland OH 44106 USA Univ Michigan Dept Chem Ann Arbor MI 48109 USA Univ Zurich Dept Biochem CH-8057 Zurich Switzerland Natl Yang Ming Chiao Tung Univ Inst Bioinformat & Syst Biol Hsinchu 30010 Taiwan Chinese Acad Sci Shanghai Inst Mat Med Shanghai 201203 Peoples R China Lehigh Univ Dept Biol Sci Bethlehem PA 18015 USA Natl Yang Ming Chiao Tung Univ Inst Bioinformat & Syst Biol Dept Biol Sci & Technol Inst Mol Med & Bioengn Hsinchu 30010 Taiwan Natl Yang Ming Chiao Tung Univ Ctr Intelligent Drug Syst & Smart Biodevices IDS2B Hsinchu 30010 Taiwan Natl Renewable Energy Lab Renewable Resources & Enabling Sci Ctr Golden CO 80401 USA Boston Univ Dept Chem Boston MA 02215 USA Boston Univ Dept Phys Boston MA 02215 USA Boston Univ Dept Biomed Engn Boston MA 02215 USA Johns Hopkins Univ Dept Biophys Baltimore MD 21218 USA Johns Hopkins Univ Dept Phys & Astron Baltimore MD 21218 USA NHLBI Lab Computat Biol NIH Bethesda MD 20892 USA DP Technol Ltd Shanghai R&D Ctr Shanghai 201210 Peoples R China Tufts Univ Dept Chem Medford MA 02155 USA Michigan State Univ Dept Biochem & Mol Biol E Lansing MI 48824 USA Peking Univ Shenzhen Grad Sch Sch Chem Biol & Biotechnol Shenzhen 518055 Guangdong Peoples R China Shenzhen Bay Lab Inst Syst & Phys Biol Shenzhen 518055 Guangdong Peoples R China Univ Minnesota Dept Chem Minneapolis MN 55455 USA Univ Minnesota Supercomp Inst Minneapolis MN 55455 USA USC CiTIUS

Since its inception nearly a half century ago, CHArMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHArMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHArMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHArMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHArMM is freely available for academic and nonprofit research at https://***/program.

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Attribute Attention for Semantic disambiguation in Zero-Shot Learning

Attribute Attention for Semantic Disambiguation in Zero-Shot...

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International Conference on Computer Vision (ICCV)

作者： Yang Liu Jishun Guo deng Cai Xiaofei He State Key Lab of CAD&CG College of Computer Science Zhejiang University Hangzhou China Fabu Inc. Hangzhou China Alibaba-Zhejiang University Joint Institute of Frontier Technologies GAC R&D Center Guangzhou China

ISBN: (数字)9781728148038

ISBN: (纸本)9781728148045

Zero-shot learning (ZSL) aims to accurately recognize unseen objects by learning mapping matrices that bridge the gap between visual information and semantic attributes. Previous works implicitly treat attributes equally in compatibility score while ignoring that they have different importance for discrimination, which leads to severe semantic ambiguity. Considering both low-level visual information and global class-level features that relate to this ambiguity, we propose a practical Latent Feature Guided Attribute Attention (LFGAA) framework to perform object-based attribute attention for semantic disambiguation. By distracting semantic activation in dimensions that cause ambiguity, our method outperforms existing state-of-the-art methods on AwA2, CUB and SUN datasets in both inductive and transductive settings.

关键词： Semantics Visualization Prototypes Training Search problems Feature extraction Aggregates

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Progress and prospects of next-generation redox flow batteries

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ENErGY STOrAGE MATErIALS 2018年 15卷 324-350页

作者： Zhang, Changkun Zhang, Leyuan ding, Yu Peng, Sangshan Guo, Xuelin Zhao, Yu He, Gaohong Yu, Guihua Univ Texas Austin Mat Sci & Engn Program Austin TX 78712 USA Univ Texas Austin Dept Mech Engn Austin TX 78712 USA Dalian Univ Technol Sch Chem Engn R&D Ctr Membrane Sci & Technol State Key Lab Fine Chem Dalian 116023 Peoples R China Soochow Univ Inst Funct Nano & Soft Mat FUNSOM 199 Renai RdInd Pk Suzhou 215123 Jiangsu Peoples R China

As one of the most promising electrochemical energy storage systems, redox flow batteries (rFBs) have received increasing attention due to their attractive features for large-scale storage applications. However, their practical deployment in commerce and industry is still impeded by their relatively high cost and low energy density. Therefore, developments of the next-generation rFBs should address these challenges by exploring new redoxactive electrolytes and novel membranes with higher ionic selectivity and conductivity, which help to achieve lower cost, longer life and higher energy and power density. In this review, we present a critical overview of the latest progress on the key components of rFBs, including redox species and membranes. Current progress on optimization strategies of the performance of rFB systems, computational modeling, prospects and opportunities in exploration of the advanced rFB systems are also summarized.

关键词： Flow batteries

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MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

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NUCLEIC ACIdS rESEArCH 2025年第D1期53卷 D678-D690页

作者： Zdouc, Mitja M. Blin, Kai Louwen, Nico L. L. Navarro, Jorge Loureiro, Catarina Bader, Chantal d. Bailey, Constance B. Barra, Lena Booth, Thomas J. Bozhueyuek, Kenan A. J. Cediel-Becerra, Jose d. d. Charlop-Powers, Zachary Chevrette, Marc G. Chooi, Yit Heng d'Agostino, Paul M. de rond, Tristan del Pup, Elena duncan, Katherine r. Gu, Wenjia Hanif, Novriyandi Helfrich, Eric J. N. Jenner, Matthew Katsuyama, Yohei Korenskaia, Aleksandra Krug, daniel Libis, Vincent Lund, George A. Mantri, Shrikant Morgan, Kalindi d. Owen, Charlotte Phan, Chin-Soon Philmus, Benjamin reitz, Zachary L. robinson, Serina L. Singh, Kumar Saurabh Teufel, robin Tong, Yaojun Tugizimana, Fidele Ulanova, dana Winter, Jaclyn M. Aguilar, Cesar Akiyama, daniel Y. Al-Salihi, Suhad A. A. Alanjary, Mohammad Alberti, Fabrizio Aleti, Gajender Alharthi, Shumukh A. Arias rojo, Mariela Y. Arishi, Amr A. Augustijn, Hannah E. Avalon, Nicole E. Avelar-rivas, J. Abraham Axt, Kyle K. Barbieri, Hellen B. Barbosa, Julio Cesar J. Barboza Segato, Lucas Gabriel Barrett, Susanna E. Baunach, Martin Beemelmanns, Christine Beqaj, dardan Berger, Tim Bernaldo-Agueero, Jordan Bettenbuehl, Sandra M. Bielinski, Vincent A. Biermann, Friederike Borges, ricardo M. Borriss, rainer Breitenbach, Milena Bretscher, Kevin M. Brigham, Michael W. Buedenbender, Larissa Bulcock, Brodie W. Cano-Prieto, Carolina Capela, Joao Carrion, Victor J. Carter, riley S. Castelo-Branco, raquel Castro-Falcon, Gabriel Chagas, Fernanda O. Charria-Giron, Esteban Chaudhri, Ayesha Ahmed Chaudhry, Vasvi Choi, Hyukjae Choi, Yukyung Choupannejad, roya Chromy, Jakub donahey, Melinda S. Chue Collemare, Jerome Connolly, Jack A. Creamer, Kaitlin E. Cruesemann, Max Arredondo Cruz, Andres Cumsille, Andres dallery, Jean-Felix damas-ramos, Luis Caleb damiani, Tito de Kruijff, Martinus delgado Martin, Belen della Sala, Gerardo dillen, Jelle doering, drew T. dommaraju, Shravan r. durusu, Suhan Egbert, Susan Ellerhorst, Mark Faussurier, Baptiste Fetter, Artem Feuermann, Marc Fewer, david P. Foldi, Jonathan Frediansyah, A Wageningen Univ & Res Bioinformat Grp Droevendaalsesteeg 1 NL-6708 PB Wageningen Netherlands Tech Univ Denmark Novo Nordisk Fdn Ctr Biosustainabil Bldg 220 DK-2800 Lyngby Denmark Helmholtz Inst Pharmaceut Res Saarland HIPS Helmholtz Ctr Infect Res HZI Campus E8-1 D-66123 Saarbrucken Germany Univ Sydney Sch Chem Chem BldgEastern Ave Sydney NSW 2050 Australia Univ Konstanz Dept Chem Univ Str 10 D-78464 Constance Germany Myria Biosci AG Tech Pk BaselHochbergstr 60C CH-4057 Basel Switzerland Univ Florida Dept Microbiol & Cell Sci 1355 Museum Dr Gainesville FL 32611 USA Ginkgo Bioworks 27 Drydock Ave8th Floor Boston MA 02210 USA Univ Florida Genet Inst 2033 Mowry Rd Gainesville FL 32611 USA Univ Western Australia Sch Mol Sci 35 Stirling Highway Perth WA 6009 Australia Tech Univ Dresden Chair Tech Biochem Bergstr 66 D-01069 Dresden Germany Univ Auckland Sch Chem Sci 23 Symonds St Auckland 1010 New Zealand Newcastle Univ Biosci Inst Catherine Cookson Bldg Newcastle Upon Tyne NE2 4HH Tyne & Wear England Sutro Biopharma 111 Oyster Point Blvd San Francisco CA 94080 USA IPB Univ Fac Math & Nat Sci Dept Chem Gedung Kimia Wing 1 Lantai 3Jalan Tanjung Bogor 16680 Jawa Barat Indonesia Goethe Univ Frankfurt Inst Mol Bio Sci Max von Laue Str 9 D-60438 Frankfurt Germany LOEWE Ctr Translat Biodivers Genom TBG Senckenberganlage 25 D-60325 Frankfurt Germany Senckenberg Soc Nat Res Senckenberganlage 25 D-60325 Frankfurt Germany Univ Warwick Dept Chem Gibbet Hill Rd Coventry CV4 7AL W Midlands England Univ Warwick Warwick Integrat Synthet Biol Ctr WISB Gibbet Hill Rd Coventry CV4 7AL W Midlands England Univ Tokyo Grad Sch Agr & Life Sci Dept Biotechnol 1-1-1 YayoiBunkyo Ku Tokyo 1138657 Japan Univ Tokyo Collaborat Res Inst Innovat Microbiol 1-1-1 YayoiBunkyo Ku Tokyo 1138657 Japan Univ Tubingen Interfac Inst Microbiol & Infect Med Tubingen IMI Interfac Inst Biomed Informat IBMI Translat Genome Min Nat Prod Sand 14 D-72076 Tubingen Ger

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://***/. [GrAPHICS] .

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Genic C-Methylation in Soybean Is Associated with Gene Paralogs relocated to Transposable Element-rich Pericentromeres

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Molecular Plant 2018年第3期11卷 485-495页

作者： Moaine El Baidouri Kyung do Kim Brian Abernathy Ying-Hui Li Li-Juan Qiu Scott A. Jackson Center for Applied Genetic Technologies University of Georgia 111 Riverbend Road Athens GA 30602 USA Corporate R&D LG Chem LG Science Park 30 Magokjungang 10-ro Gangseo-gu Seoul 07796 Republic of Korea The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Institute of Crop Science Chinese Academy of Agricultural SciencesBeijing China These authors contributed equally to this article.

Most plants are polyploid due to whole-genome duplications （WGd） and can thus have duplicated genes. Following a WGd, paralogs are often fractionated （lost） and few duplicate pairs remain. Little attention has been paid to the role of dNA methylation in the functional divergence of paralogous genes. Using high- resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, dNA methylation likely contributed to the elimination of ge- netic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit partic- ular genomic features as they are often associated with proximal transposable elements （TEs） and are pref- erentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.

关键词： soybean paralog gene methylation proximal transposable element methylation spreading

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Genomic landscape of lung adenocarcinoma in East Asians

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NATUrE GENETICS 2020年第2期52卷 177-+页

作者： Chen, Jianbin Yang, Hechuan Teo, Audrey Su Min Amer, Lidyana Bte Sherbaf, Faranak Ghazi Tan, Chu Quan Alvarez, Jacob Josiah Santiago Lu, Bingxin Lim, Jia Qi Takano, Angela Nahar, rahul Lee, Yin Yeng Phual, Cheryl Zi Jin Chua, Khi Pin Suteja, Lisda Chen, Pauline Jieqi Chang, Mei Mei Koh, Tina Puay Theng Ong, Boon-Hean Anantham, devanand Hsu, Anne Ann Ling Gogna, Apoorva Too, Chow Wei Aung, Zaw Win Lee, Yi Fei Wang, Lanying Lim, Tony Kiat Hon Wilm, Andreas Choi, Poh Sum Ng, Poh Yong Toh, Chee Keong Lim, Wan-Teck Ma, Siming Lim, Bing Liu, Jin Tam, Wai Leong Skanderup, Anders Jacobsen Yeong, Joe Poh Sheng Tan, Eng-Huat Creasy, Caretha L. Tan, daniel Shao Weng Hillmer, Axel M. Zhai, Weiwei Agcy Sci Technol & Res Genome Inst Singapore Singapore Singapore Chinese Acad Sci Inst Zool Key Lab Zool Systemat & Evolut Beijing Peoples R China Singapore Gen Hosp Dept Anat Pathol Singapore Singapore Natl Canc Ctr Singapore Div Med Oncol Singapore Singapore Natl Canc Ctr Singapore Surg Oncol Singapore Singapore Natl Heart Ctr Singapore Dept Cardiothorac Surg Singapore Singapore Singapore Gen Hosp Dept Resp & Crit Care Med Singapore Singapore Singapore Gen Hosp Dept Vasc & Intervent Radiol Singapore Singapore Natl Canc Ctr Singapore Div Clin Trials & Epidemiol Sci Singapore Singapore Nanyang Technol Univ Sch Biol Sci Singapore Singapore Agcy Sci Technol & Res Inst Mol & Cell Biol Singapore Singapore Duke NUS Med Sch Ctr Quantitat Med Program Hlth Serv & Syst Res Singapore Singapore Natl Univ Singapore Canc Sci Inst Singapore Singapore Singapore Natl Univ Singapore Yong Loo Lin Sch Med Dept Biochem Singapore Singapore GlaxoSmithKline Oncol R&D Collegeville PA USA Natl Canc Ctr Singapore Div Med Sci Canc Therapeut Res Lab Singapore Singapore Univ Cologne Fac Med Inst Pathol Cologne Germany Univ Cologne Univ Hosp Cologne Cologne Germany Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming Yunnan Peoples R China

Lung cancer is the world's leading cause of cancer death and shows strong ancestry disparities. By sequencing and assembling a large genomic and transcriptomic dataset of lung adenocarcinoma (LUAd) in individuals of East Asian ancestry (EAS;n = 305), we found that East Asian LUAds had more stable genomes characterized by fewer mutations and fewer copy number alterations than LUAds from individuals of European ancestry. This difference is much stronger in smokers as compared to nonsmokers. Transcriptomic clustering identified a new EAS-specific LUAd subgroup with a less complex genomic profile and upregulated immune-related genes, allowing the possibility of immunotherapy-based approaches. Integrative analysis across clinical and molecular features showed the importance of molecular phenotypes in patient prognostic stratification. EAS LUAds had better prediction accuracy than those of European ancestry, potentially due to their less complex genomic architecture. This study elucidated a comprehensive genomic landscape of EAS LUAds and highlighted important ancestry differences between the two cohorts. Genomic and transcriptomic analysis of lung adenocarcinoma (LUAd) in Asia indicates that Asian LUAds have fewer mutations, lower driver prevalence and fewer copy number alterations than European LUAds.

关键词： data mining Genomics Non-small-cell lung cancer

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