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Frontispiece: The Fourth Alloying Mode by Way of Anti-Galvanic Reaction

Angewandte Chemie International Edition 2018年第17期57卷

作者： Dr. Min Zhu Dr. Pu Wang Nan Yan Xiaoqi Chai Lizhong He Yan Zhao Nan Xia Chuanhao Yao Prof. Dr. Jin Li Prof. Dr. Haiteng Deng Prof. Dr. Yan Zhu Prof. Dr. Yong Pei Prof. Dr. Zhikun Wu Key Laboratory of Materials Physics Anhui Key Laboratory of Nanomaterials and Nanotechnology CAS Center for Excellence in Nanoscience Institute of Solid State Physics Chinese Academy of Sciences Hefei 230031 China Institute of Physical Science and Information Technology Anhui University Hefei 230031 China University of Science and Technology of China Hefei 230026 China Department of Chemistry Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education Xiangtan University Hunan Province Xiangtan 411105 China Key Lab of Mesoscopic Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210093 China Tsinghua University-Peking University Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing 100084 China MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China

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Frontispiz: The Fourth Alloying Mode by Way of Anti‐Galvanic Reaction

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Angewandte Chemie 2018年第17期130卷

作者： Min Zhu Pu Wang Nan Yan Xiaoqi Chai Lizhong He Yan Zhao Nan Xia Chuanhao Yao Jin Li Haiteng Deng Yan Zhu Yong Pei Zhikun Wu Key Laboratory of Materials Physics Anhui Key Laboratory of Nanomaterials and Nanotechnology CAS Center for Excellence in Nanoscience Institute of Solid State Physics Chinese Academy of Sciences Hefei 230031 China Institute of Physical Science and Information Technology Anhui University Hefei 230031 China University of Science and Technology of China Hefei 230026 China Department of Chemistry Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education Xiangtan University Hunan Province Xiangtan 411105 China Key Lab of Mesoscopic Chemistry School of Chemistry and Chemical Engineering Nanjing University Nanjing 210093 China Tsinghua University-Peking University Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing 100084 China MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China

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The Fourth Alloying Mode by Way of Anti‐Galvanic Reaction

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Angewandte Chemie 2018年第17期130卷

Anti‐galvanic reaction (AGR) not only defies classic galvanic theory but is a promising method for tuning the compositions, structures, and properties of noble‐metal nanoparticles. Employing AGR for the preparation of alloy nanoparticles has recently received great interest. Herein, we report an unprecedented alloying mode by way of AGR, in which foreign atoms induce structural transformation of the mother nanoparticles and enter the nanoparticles in a non‐replacement fashion. A novel, active‐metal‐doped, gold nanoparticle was synthesized by this alloying mode, and its structure resolved. A CdSH motif was found in the protecting staples of the bimetal nanoparticle. DFT calculations revealed that the Au 20 Cd 4 (SH)(SR) 19 nanoparticle is a 8e superatom cluster. Furthermore, although the Cd‐doping does not essentially alter the absorption spectrum of the mother nanocluster, it distinctly enhances the stability and catalytic selectivity of the mother nanoclusters.

关键词： Antigalvanische Reaktion (AGR) Gold Kristallstrukturen Legierungen Nanopartikel

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Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

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NATURE 2021年第7856期592卷 E24-E24页

作者： Feng, Shaohong Stiller, Josefin Deng, Yuan Armstrong, Joel Fang, Qi Reeve, Andrew Hart Xie, Duo Chen, Guangji Guo, Chunxue Faircloth, Brant C. Petersen, Bent Wang, Zongji Zhou, Qi Diekhans, Mark Chen, Wanjun Andreu-Sanchez, Sergio Margaryan, Ashot Howard, Jason Travis Parent, Carole Pacheco, George Sinding, Mikkel-Holger S. Puetz, Lara Cavill, Emily Ribeiro, Angela M. Eckhart, Leopold Fjeldsa, Jon Hosner, Peter A. Brumfield, Robb T. Christidis, Les Bertelsen, Mads F. Sicheritz-Ponten, Thomas Tietze, Dieter Thomas Robertson, Bruce C. Song, Gang Borgia, Gerald Claramunt, Santiago Lovette, Irby J. Cowen, Saul J. Njoroge, Peter Dumbacher, John Philip Ryder, Oliver A. Fuchs, Jerome Bunce, Michael Burt, David W. Cracraft, Joel Meng, Guanliang Hackett, Shannon J. Ryan, Peter G. Jonsson, Knud Andreas Jamieson, Ian G. da Fonseca, Rute R. Braun, Edward L. Houde, Peter Mirarab, Siavash Suh, Alexander Hansson, Bengt Ponnikas, Suvi Sigeman, Hanna Stervander, Martin Frandsen, Paul B. van der Zwan, Henriette van der Sluis, Rencia Visser, Carina Balakrishnan, Christopher N. Clark, Andrew G. Fitzpatrick, John W. Bowman, Reed Chen, Nancy Cloutier, Alison Sackton, Timothy B. Edwards, Scott V. Foote, Dustin J. Shakya, Subir B. Sheldon, Frederick H. Vignal, Alain Soares, Andre E. R. Shapiro, Beth Gonzalez-Solis, Jacob Ferrer-Obiol, Joan Rozas, Julio Riutort, Marta Tigano, Anna Friesen, Vicki Dalen, Love Urrutia, Araxi O. Szekely, Tamas Liu, Yang Campana, Michael G. Corvelo, Andre Fleischer, Robert C. Rutherford, Kim M. Gemmell, Neil J. Dussex, Nicolas Mouritsen, Henrik Thiele, Nadine Delmore, Kira Liedvogel, Miriam Franke, Andre Hoeppner, Marc P. Krone, Oliver Fudickar, Adam M. Mila, Borja Ketterson, Ellen D. Fidler, Andrew Eric Friis, Guillermo Parody-Merino, Angela M. Battley, Phil F. Cox, Murray P. Lima, Nicholas Costa Barroso Prosdocimi, Francisco Parchman, Thomas Lee Schlinger, Barney A. Loiselle, Bette A. Blake, John G. Lim, Haw Chuan Day, Lainy B. Fuxjager, Matthew J. Baldwin, Maude W. Braun, Michael J. Wirthlin, Morgan Dikow, China National GeneBank BGI-Shenzhen Shenzhen China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China BGI-Shenzhen Shenzhen China Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen Copenhagen Denmark BGI Education Center University of Chinese Academy of Sciences Shenzhen China MOE Laboratory of Biosystems Homeostasis and Protection Life Sciences Institute Zhejiang University Hangzhou China Department of Neuroscience and Developmental Biology University of Vienna Vienna Austria Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China James D. Watson Institute of Genome Sciences Hangzhou China UC Santa Cruz Genomics Institute UC Santa Cruz Santa Cruz CA USA Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark Center for Macroecology Evolution and Climate GLOBE Institute University of Copenhagen Copenhagen Denmark Department of Biological Sciences Louisiana State University Baton Rouge LA USA Museum of Natural Science Louisiana State University Baton Rouge LA USA Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio) Faculty of Applied Sciences AIMST University Kedah Malaysia Section for Evolutionary Genomics The GLOBE Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Institute of Molecular Biology National Academy of Sciences Yerevan Armenia University Museum Norwegian University of Science and Technology Trondheim Norway Center for Reproductive Medicine The 2nd Affiliated Hospital School of Medicine Zhejiang University Hangzhou China Novogene Durham NC USA Duke University Medical Center Durham NC USA The Rockefeller University New York NY USA Howard Hughes Medical Institute Chevy Chase MD USA Department of Dermatology Medical University of Vienna Vienna Austria

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Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

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Science China(Life Sciences) 2014年第1期57卷 22-35页

作者： YANG YuCheng UMETSU Jumpei LU Zhi John MOE Key Lab of Bioinformatics School of Life Sciences Tsinghua University Department of Biological Information Tokyo Institute of TechnologyTokyo 152-8850 Japan

Protein binding is essential to the transport,decay and regulation of almost all RNA ***,the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly ***,we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins(RBPs)and structured RNAs in yeast at single-nucleotide *** found that on average,in terms of percent total lengths,~15%of mRNA untranslated regions(UTRs),~37%of canonical non-coding RNAs(ncRNAs)and^11%of long ncRNAs(lncRNAs)are bound by *** RBP binding sites,in general,tend to occur at single-stranded loops,with evolutionarily conserved signatures,and often facilitate a specific RNA structure conformation in *** found that four nucleotide modifications of tRNA are significantly associated with RBP *** also identified various structural motifs bound by RBPs in the UTRs of mRNAs,associated with localization,degradation and stress ***,we identified>200 novel lncRNAs bound by RBPs,and about half of them contain conserved secondary *** present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome,emphasizing their structural context and cellular functions.

关键词： RNA binding protein non-coding RNA UTR RNA structure Saccharomyces cerevisiae

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Benzene containing polyhydroxyalkanoates homo-and copolymers synthesized by genome edited Pseudomonas entomophila

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Science China(Life Sciences) 2014年第1期57卷 4-10页

作者： SHEN Rui CAI LongWei MENG DeChuan WU LinPing GUO Kai DONG GuoXing LIU Lei CHEN JinChun WU Qiong CHEN GuoQiang MOE Key Lab of Bioinformatics Department of Biological Science and Biotechnology School of Life Science Tsinghua-Peking Center for Life Sciences Tsinghua University Department of Pharmaceutics and Analytical Chemistry Faculty of Pharmaceutical Sciences University of Copenhagen Copenhagen 2100Denmark Nanjing University of Technology College of Biotechnology & Pharmaceutical Engineering Department of Chemistry Tsinghua-Peking Center for Life Sciences Tsinghua University Center for Nano and Micro Mechanics Tsinghua University

Microbial synthesis of functional polymers has become increasingly important for industrial biotechnology. For the first time, it became possible to synthesize controllable composition of poly（3-hydroxyalkanoate）（P3HA） consisting of 3-hydroxydodec- anoate （3HDD） and phenyl group on the side-chain when chromosome of Pseudomonas entomophila was edited to weaken its t-oxidation. Cultured in the presence of 5-phenylvaleric acid （PVA）, the edited P. entomophila produced only homopolymer poly（3-hydroxy-5-phenylvalerate） or P（3HPhV）. While copolyesters P（3HPhV-co-3HDD） of 3-hydroxy-5-phenylvalerate （3HPhV） and 3-hydroxydodecanoate （3HDD） were synthesized when the strain was grown on mixtures of PVA and dodecanoic acid （DDA）. Compositions of 3HPhV in P（3HPhV-co-3HDD） were controllable ranging from 3% to 32% depending on DDDA/PVA ratios. Nuclear magnetic resonance （NMR） spectra clearly indicated that the polymers were homopolymer of P（3HPhV） and random copolymers of 3HPhV and 3HDD. Their mechanical and thermal properties varied dramatically de- pending on the monomer ratios. Our results demonstrated the possibility to produce tailor-made, novel functional PHA using the chromosome edited P. entomophila.

关键词： polyhydroxyalkanoates PHB Pseudomonas entomophila β-oxidation synthetic biology

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MEDICAL APPLICATIONS OF BIOPOLYESTERS POLYHYDROXYALKANOATES

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Chinese Journal of Polymer Science 2013年第5期31卷 719-736页

作者：陈国强汪洋 MOE Key Lab of Bioinformatics and Systems Biology Department of Biological Science and BiotechnologySchool of Life SciencesTsinghua-Peking Center for Life SciencesTsinghua University Center for Nano and Micro Mechanics Tsinghua University State Key Laboratory of Plant Physiology and Biochemistry National Plant Gene Research CentreCollege of Biological SciencesChina Agricultural University

Microbial polyhydroxyalkanoates （PHAs） are a family of biopolyesters produced by many wild type and engineered bacteria. PHAs have diverse structures accompanied by flexible thermal and mechanical properties. Combined with their in vitro biodegradation, cell and tissue compatibility, PHAs have been studied for medical applications, especially medical implants applications, including heart valve tissue engineering, vascular tissue engineering, bone tissue engineering, cartilage tissue engineering, nerve conduit tissue engineering as well as esophagus tissue engineering. Most studies have been conducted in the authors＇ lab in the past 20＋ years. Recently, mechanism on PHA promoted tissue regeneration was revealed to relate to cell responses to PHA biodegradation products and cell-material interactions mediated by microRNA. Very importantly, PHA implants were found not to cause carcinogenesis during long-term implantation. Thus, PHAs should have a bright future in biomedical areas.

关键词： PHB PHA Polyhydroxyalkanoates Tissue engineering Biomaterials Implants.

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Population dynamics of cancer cells with cell state conversions

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Frontiers of Electrical and Electronic Engineering in China 2013年第3期8卷 201-208页

作者： Da Zhou Dingming Wu Zhe Li Minping Qian Michael Q. Zhang MOE Key Laboratory of Bioinformatics Bioinformatics Division/Center for Synthetic & Systems Biology TNLIST Department of Automation Tsinghua University Beijing 100084 China Computational Neuroscience Lab School of Medicine Tsinghua University Beijing 100084 China School of Mathematical Sciences Peking University Beijing 100871 China Department of Molecular and Cell Biology Center for Systems Biology The University of Texas at Dallas Richardson TX 75080. USA

Cancer stem cell （CSC） theory suggests a cell-lineage structure in tumor cells in which CSCs are capable of giving rise to the other non-stem cancer cells （NSCCs） but not vice versa. However, an alternative scenario of bidirectional interconversions between CSCs and NSCCs was proposed very recently. Here we present a general population model of cancer cells by integrating conventional cell divisions with direct conversions between different cell states, namely, not only can CSCs differentiate into NSCCs by asymmetric cell division, NSCCs can also dedifferentiate into CSCs by cell state conversion. Our theoretical model is validated when applying the model to recent experimental data. It is also found that the transient increase in CSCs proportion initiated from the purified NSCCs subpopulation cannot be well predicted by the conventional CSC model where the conversion from NSCCs to CSCs is forbidden, implying that the cell state conversion is required especially for the transient dynamics. The theoretical analysis also gives the condition such that our general model can be equivalently reduced into a simple Markov chain with only cell state transitions keeping the same cell proportion dynamics.

关键词： Breast Cancer Cell Line Cancer Stem Cell Cell State Markov Chain Model Transient Dynamic

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Production of Poly（3-hydroxybutyrate-co-3-hydroxyhexanoate） by Recombinant Pseudomonas stutzeri 1317 from Unrelated Carbon Sources

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Chinese Journal of Chemical Engineering 2013年第9期21卷 1057-1061页

作者：魏晓星刘峰简嘉王瑞妍陈国强 Depanent of Basic Medicine Medical College of Qinghai University Xining 810016 China MOE Key Lab of Bioinformatics and Systems Biology Department of Biological Science and Biotechnology School of Life Sciences Tsinghua-Peking Center for Life Sciences Tsinghua University Beijing 100084 China Tuspark Kunshan Biotech Science Park Development Center 4/F Science & Technology Plaza Tsinghua Science Park Kunshan Jiangsu 215347 China Center for Nano and Micro Mechanics Tsinghua University Beijing 100084 China

Synthetic biology promises to simplify the construction of metabolic pathways by assembling the de- tached modules of the whole pathway. This gives new approaches for the microbial production of industrial products such as polyhydroxyalkanoates （PHA）. In this study, to produce poly（3-hydroxybutyrate-co-3-hydroxyhexanoate）（PHBHHx） by Pseudomonas stutzeri 1317 from unrelated carbon sources such as glucose, the phaCl-phaZ-phaC2 operon of P. stutzeri 1317 was knocked out to generate the PHA deficient mutant P. stutzeri 1317LF. Then three modules containing phaCahAReBRe, phaCahBReGep and phaCAhPah were introduced into P. stutzeri 1317LF separately The shake flask results indicated that the precursor supply and PHA synthase activity were the vital factors for the PHBHHx accumulation of P. stutzeri 1317LF. Furthermore, the PHBHHx accumulation of the recombinants from different carbon resources were performed. The highest PHBHHx content was 23.7% （by mass） with 58.6% （by mole） 3HB fraction. These results provide basis for further improving the PHBHHx accumulation of P. stutzeri from unrelated carbon sources.

关键词： Pseudomonas stutzeri 1317 PHBHHx unrelated carbon sources

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incRNA:Characterizing novel ncRNAs by integrating high-throughput data and structure predictions

incRNA:Characterizing novel ncRNAs by integrating high-throu...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：鲁志 MOE Key Lab of Bioinformatics School of Life ScienceTsinghua University

I will present an integrative,machine-learning method,incRNA,for whole-genome identification of non-coding RNAs(ncRNAs).It combines a large amount of expression data,epigenetics data,RNA secondary-structure stability,and evolutionary conservation at the protein and nucleic-acid *** this model,we were able to separate known ncRNAs from coding sequences and other genomic elements with high accuracy(>93% AUC on an independent validation set),and find thousands of novel ncRNA candidates in *** and Arabidopsis. In addition,we characterized the novel ncRNA candidates and found that they have distinct expression patterns across developmental stages,tend to use novel RNA structural families,and are targeted by specific transcription ***,our study identifies many new potential ncRNAs in different systems.

关键词： incRNA:Characterizing novel ncRNAs by integrating high-throughput data and structure predictions

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