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Romance of the three domains:how cladistics transformed the classifi cation of cellular organisms

Protein & cell 2013年第9期4卷 664-676页

作者： chi-chun ho Susanna K.P.Lau Patrick c.Y.Woo department of Microbiology The University of Hong KongHong KongChina State Key Laboratory of Emerging Infectious Diseases The University of Hong KongHong KongChina Research centre of Infection and Immunology The University of Hong KongHong KongChina carol Yu centre of Infection The University of Hong KongHong KongChina

cladistics is a biological philosophy that uses genealogi-cal relationship among species and an inferred sequence of divergence as the basis of classifi *** review critically surveys the chronological development of bio-logical classification from Aristotle through our post-genomic era with a central focus on *** 1957,Julian Huxley coined cladogenesis to denote splitting from *** 1960,the English translation of Willi Hennig’s 1950 work,Systematic Phylogenetics,was published,which received strong opposition from phenet-icists,such as numerical taxonomists Peter Sneath and Robert Sokal,and evolutionary taxonomist,Ernst Mayr,and sparked acrimonious debates in *** 1977-1990,carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellu-lar life and established major prokaryotic *** has since dominated *** being compatible with modern microbiological observations,*** with unusual phenotypes,restricted expression of charac-teristics and occasionally being uncultivable,increasing recognition of pervasiveness and abundance of horizon-tal gene transfer has challenged relevance and validity of *** mosaic nature of eukaryotic and prokary-otic genomes was also gradually *** the mid-2000s,high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of *** genomics only indirectly leads to understanding of func-tional adaptations to ecological niches,computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be *** are not expected to settle as taxonomic classifi cations shall remain subjective to serve the human scientist,not the classifi ed.

关键词： cladistics phenetics phylogeny classifi ca-tion evolution

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Direct 4D printing of functionally graded hydrogel networks for biodegradable,untethered,and multimorphic soft robots

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International Journal of Extreme Manufacturing 2024年第2期6卷 407-416页

作者： Soo Young cho Dong Hae ho Sae Byeok Jo Jeong ho cho department of chemical and Biomolecular Engineering Yonsei UniversitySeoul 03722Republic of Korea department of Mechanical Engineering Virginia TechBlacksburgVA 24061United States of America School of chemical Engineering Sungkyunkwan UniversitySuwon 16419Republic of Korea SKKU Institute of Energy Science and Technology(SIEST) Sungkyunkwan UniversitySuwon 16419Republic of Korea

Recent advances in functionally graded additive manufacturing(FGAM)technology have enabled the seamless hybridization of multiple functionalities in a single *** robotics can become one of the largest beneficiaries of these advances,through the design of a facile four-dimensional(4D)FGAM process that can grant an intelligent stimuli-responsive mechanical functionality to the printed ***,we present a simple binder jetting approach for the 4D printing of functionally graded porous multi-materials(FGMM)by introducing rationally designed graded multiphase feeder *** graded cross-linking agents gradually form stable porous network structures within aqueous polymer particles,enabling programmable hygroscopic deformation without complex mechanical ***,a systematic bed design incorporating additional functional agents enables a multi-stimuli-responsive and untethered soft robot with stark stimulus *** biodegradability of the proposed 4D-printed soft robot further ensures the sustainability of our approach,with immediate degradation rates of 96.6%within 72 *** proposed 4D printing concept for FGMMs can create new opportunities for intelligent and sustainable additive manufacturing in soft robotics.

关键词： intelligent and sustainable additive manufacturing multi-material four-dimensional printing untethered soft robot multi-stimuli-responsive soft robot biodegradable soft robotics

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Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma

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World Journal of Gastroenterology 2013年第47期19卷 8873-8879页

作者： de-Leung Gu Yen-Hsieh chen Jou-ho Shih chi-Hung Lin Yuh-Shan Jou chian-Feng chen Institute of Biomedical Sciences Academia Sinica Institute of Microbiology and Immunology School of Life ScienceNational Yang-Ming University Bioinformatics Program Taiwan International Graduate ProgramAcademia Sinica Genome and Systems Biology degree Program National Taiwan University VYM Genome Research center National Yang-Ming University

High-throughput short-read sequencing of exomes and whole cancer genomes in multiple human hepatocellular carcinoma(Hcc)cohorts confirmed previously identified frequently mutated somatic genes,such as TP53,cTNNB1 and AXIN1,and identified several novel genes with moderate mutation frequencies,including ARID1A,ARID2,MLL,MLL2,MLL3,MLL4,IRF2,ATM,cDKN2A,FGF19,PIK3ca,RPS6KA3,JAK1,KEAP1,NFE2L2,c16orf62,LEPR,RAc2,and *** classification of these mutated genes suggested that alterations in pathways participating in chromatin remodeling,Wnt/β-catenin signaling,JAK/STAT signaling,and oxidative stress play critical roles in Hcc ***,because there are few druggable genes used in Hcc therapy,the identification of new therapeutic targets through integrated genomic approaches remains an important *** a large amount of Hcc genomic data genotyped by high density single nucleotide polymorphism arrays is deposited in the public domain,copy number alteration(cNA)analyses of these arrays is a cost-effective way to reveal target genes through profiling of recurrent and overlapping amplicons,homozygous deletions and potentially unba.a.c.d chromosomal translocations accumulated during Hcc ***,integration of cNAs with other high-throughput genomic data,such as aberrantly coding transcriptomes and non-coding gene expression in human Hcc tissues and rodent Hcc models,provides lines of evidence that can be used to facilitate the identification of novel Hcc target genes with the potential of improving the survival of Hcc patients.

关键词： copy number alteration High-density single nucleotide polymorphism arrays Driver genes Hepatocellular carcinoma

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Synthesis,contact Printing,and device characterization of Ni-catalyzed,crystalline InAs Nanowires

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Nano Research 2008年第1期1卷 32-39页

作者： Alexandra c.Ford Johnny c.ho Zhiyong Fan Onur Ergen Virginia Altoe Shaul Aloni Haleh Razavi Ali Javey department of Electrical Engineering and computer Sciences University of California at BerkeleyBerkeleyCA 94720USA Materials Sciences Division Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA Molecular Foundry Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA

InAs nanowires have been actively explored as the channel material for high performance transistors owing to their high electron mobility and ease of ohmic metal contact *** catalytic growth of nonepitaxial InAs nanowires,however,has often relied on the use of Au colloids which is non-cMOS ***,we demonstrate the successful synthesis of crystalline InAs nanowires with high yield and tunable diameters by using Ni nanoparticles as the catalyst material on amorphous SiO_(2) *** nanowires show superb electrical properties with field-effect electron mobility~2700 cm^(2)/Vs and ION/IOFF>10^(3).The uniformity and purity of the grown InAs nanowires are further demonstrated by large-scale assembly of parallel arrays of nanowires on substrates via the contact printing process that enables high performance,“printable”transistors,capable of delivering 510 mA ON currents(~400 nanowires).

关键词： crystalline InAs nanowire Ni catalyst high-performance transistor

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Machine learning guided discovery of ternary compounds involving La and immiscible co and Pb elements

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npj computational Materials 2022年第1期8卷 2462-2470页

作者： Renhai Wang Weiyi Xia Tyler JSlade Xinyu Fan Huafeng Dong Kai-Ming ho Paul c.canfield cai-Zhuang Wang School of Physics and Optoelectronic Engineering Guangdong University of Technology510006GuangzhouChina department of Physics and Astronomy Iowa State UniversityAmesIA50011USA Ames Laboratory-USDOE Iowa State UniversityAmesIA50011USA department of Physics University of Science and Technology of China230026HefeiChina

Ternary compounds with an immiscible pair of elements are relatively unexplored but promising for novel quantum materials *** what third element and its ratio that can be added to make stable ternary compounds out of an immiscible pair of elements remains a great *** this work,we combine a machine learning(ML)method with ab initio calculations to efficiently search for the energetically favorable ternary La-co-Pb compounds containing immiscible elements co and *** previously reported structures are correctly captured by our ***,we predict a ground state La_(3)coPb compound and 57 low-energy La-co-Pb ternary *** to synthesize La_(3)coPb via multiple techniques produce mixed or multi-phases samples with,at best,ambiguous signals of the predicted lowest-energy La_(3)coPb and the second lowest-energy La_(18)co_(28)Pb_(3)*** calculated results of Gibbs free energy are consistent with experiments,and will provide very useful guidance for further experimental synthesis.

关键词： elements immiscible ternary

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Metal intercalation-induced selective adatom mass transport on graphene

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Nano Research 2016年第5期9卷 1434-1441页

作者： Xiaojie Liu cai-Zhuang Wang Myron Hupalo Hai-Qing Lin Kai-Ming ho Patricia A. Thiel Michael c. Tringides center for Quantum Science and School of Physics Northeast Normal University Changchun 730777 China Ames Laboratory-U.S. department of Energy and Department of Physics and Astronomy Iowa State University Ames IA 50011 USA Beijing computational Science Research center Beijing 100084 China Ames Laboratory-U.S. department of Energy Department of Chemistry and Department of Materials Science and Engineering Iowa State University Ames IA 50011 USA

Recent experiments indicate that metal intercalation is a very effective method to manipulate the graphene-adatom interaction and control metal nanostructure formation on graphene. A key question is mass transport, i.e., how atoms deposited uniformly on graphene populate different areas depending on the local intercalation. Using first-principles calculations, we show that partially intercalated graphene, with a mixture of intercalated and pristine areas, can induce an alternating electric field because of the spatial variations in electron doping, and thus, an oscillatory electrostatic potential. This alternating field can change normal stochastic adatom diffusion to biased diffusion, leading to selective mass transport and consequent nucleation, on either the intercalated or pristine areas, depending on the charge state of the adatoms.

关键词： graphene intercalation electrostatic potential selective adsorption first-principle calculation

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Regulatory mechanisms for abnormal expression of the human breast cancer specific gene 1 in breast cancer cells

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Science china(Life Sciences) 2006年第4期49卷 403-408页

作者： LU Aiping1, LI Qing1, LIU Jingwen2 1. department of Pathology, Peking University School of Oncology, Beijing cancer hospital, Beijing 100036, china 2. va Palo alto Health care System, Palo Alto, california, ca 94304, USA department of Pathology Peking University School of Oncology Beijing Cancer Hospital Beijing China va Palo alto Health care System Palo Alto USA

Breast cancer-specific gene 1 (BcSG1), also referred as synuclein γ, was originally iso-lated from a human breast cancer cDNA library and the protein is mainly localized to presynaptic terminals in the nervous system. BcSG1 is not expressed in normal or benign breast lesions, but expressed at an extremely high level in the vast majority of the advanced staged breast carcinomas and ovarian carcinomas. Overexpression of BcSG1 in cancer cells led to significant increase in cell proliferation, motility and invasiveness, and metastasis. To elucidate the molecular mechanism and regulation for abnormal transcription of BcSG1, a variety of BcSG1 promoter luciferase reporters were constructed including 3′ end deleted sequences, Sp1 deleted, and activator protein-1 (AP1) domains mutated. Transient transfection assay was used to detect the transcriptional activation of BcSG1 promoters. Results showed that the Sp1 sequence in 5′-flanking region was involved in the basal transcriptional activities of BcSG1 without cell-type specificity. In comparison to pGL3-1249, the reporter activities of pGL3-1553 in BcSG1-negative McF-7 cells and pGL3-1759 in HepG2 cells were notably decreased. Mutations at AP1 sites in BcSG1 intron 1 significantly reduced the promoter ac-tivity in all cell lines. Transcription factors, c-jun, c-fos and cyclin AMP-responsive element binding (cREB) protein, could markedly enhance the promoter activities. Thus, our results suggest that the abnormal expression of BcSG1 in breast cancer cells is likely regulated by multiple mechanisms. The 5′ flanking region of BcSG1 provides the basal transcriptional activity without cell type specificity. A critical promoter element involved in abnormal expression of BcSG1 presents in the first exon. The cell type specificity of BcSG1 transcription is probably affected through intronic cis-regulatory se-quences. AP1 domains in the first intron play an important role in control of BcSG1 transcription.

关键词： breast cancer-specific gene 1, promoter, transcriptional activity.

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Vlodeling information exchange between living and artificial cells

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Frontiers of Electrical and Electronic Engineering in china 2017年第1期5卷 76-89页

作者： Keith c.Heyde Mary Joe K. Rice Sung-ho Paek Felicia Y. Scott Ruihua Zhang Warren c. Ruder department of Mechanical Engineering Carnegie Mellon University Pittsburgh PA 15213 USA department of Mechanical Engineering Virginia Polytechnic Institute and State University Blacksburg VA 24061 USA department of Biological Systems Engi-neering Virginia Polytechnic Institute and State University Black sburg VA 24061 USA department of Bioengineering University of Pittsburgh Pittsburgh PA 15219 USA

Background： The tools of synthetic biology have enabled researchers to explore multiple scientific phenomena by directly engineering signaling pathways within living cells and artificial protoeells. Here, we explored the potential for engineered living cells themselves to assemble signafing pathways for non-living protocells. This analysis serves as a preliminary investigation into a potential origin of processes that may be utilized by complex living systems. Specifically, we suggest that if living cells can be engineered to direct the assembly of genetic signaling pathways from genetic biomaterials in their environment, then insight can be gained into how naturally occurring living systems might behave similarly. Methods： To this end, we have modeled and simulated a system consisting of engineered cells that control the assembly of DNA monomers on microparticle scaffolds. These DNA monomers encode genetic circuits, and therefore, these microparticles can then be encapsulated with minimal transcription and translation systems to direct protocell phenotype. The modeled system relies on multiple previously established synthetic systems and then links these together to demonstrate system feasibility. Results： In this specific model, engineered cells are induced to synthesize biotin, which competes with biotinylated, circuit-encoding DNA monomers for an avidinized-microparticle scaffold. We demonstrate that multiple synthetic motifs can be controlled in this way and can be tuned by manipulating parameters such as inducer and DNA concentrations. conclusions： We expect that this system will provide insight into the origin of living systems as well as serve as a tool for engineering living cells that assemble complex biomaterials in their environment.

关键词： synthetic biology artificial cells biotin microparticles

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Luminescent cyclometalated iridium(Ⅲ) dipyridoquinoxaline indole complexes as biological probes

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Science china chemistry 2010年第10期53卷 2091-2098页

作者： LO Kenneth Kam-Wing LEUNG Arthur ho-hon department of Biology and chemistry City University of Hong Kong

Four luminescent cyclometalated iridium(Ⅲ) dipyridoquinoxaline complexes appended with an indole moiety [Ir(N^c)2(N^N)] (PF6) (HN^c = 2-phenylpyridine, Hppy; N^N = 2-(N-(2-(indole-3-acetamido)ethyl)aminocarbonyl)dipyrido[3,2-f:2′,3′-h]quinox- aline, dpqc2indole (1a), N^N = 2-(N-(6-(indole-3-acetamido)hexyl)aminocarbonyl)dipyrido[3,2-f:2′,3′-h]quinoxaline, dpqc6indole (1b); HN^c = 7,8-benzoquinoline, Hbzq, N^N = dpqc2indole (2a), N^N = dpqc6indole (2b)) have been synthesized and characterized. Upon irradiation, all the complexes displayed moderately intense and long-lived luminescence under ambient condi-tions and in 77 K glass. On the basis of the photophysical data, the emission of the complexes has been assigned to an excited state of triplet metal-to-ligand charge-transfer (3MLcT) ((dπ(Ir)→π*(N^N)) character. cyclic voltammetric studies revealed indole-based and iridium-based oxidations at ca. +1.10 V and +1.24 V vs. ScE, respectively, and ligand-based reductions at ca. -1.07 to-2.29 V vs. ScE. The interactions of the complexes with an indole-binding protein, bovine serum albumin (BSA), have been examined by emission titrations.

关键词： binding indole iridium luminescence probes

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Surgical palliation of unresectable pancreatic head cancer in elderly patients

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World Journal of Gastroenterology 2009年第8期15卷 978-982页

作者： Sang Il Hwang Hyung Ook Kim Byung ho Son chang Hak Yoo Hungdai Kim Jun ho Shin department of Surgery Kangbuk Samsung Hospital Sungkyunkwan University School of Medicine Seoul 110-746 South Korea

AIM: To determine if surgical biliary bypass would provide improved quality of residual life and safe palliation in elderly patients with unresectable pancreatic head cancer. METhoDS: Nineteen patients, 65 years of age or older, were managed with surgical biliary bypass (Group A). These patients were compared with 19 patients under 65 years of age who were managed with surgical biliary bypass (Group B). In addition, the results for group A were compared with those obtained from 17 patients, 65 years of age or older (Group c), who received percutaneous transhepatic biliary drainage to evaluate the quality of residual life. RESULTS: Five patients (26.0%) in Group A had complications, including one intraabdominal abscess, one pulmonary atelectasis, and three wound infections. One death (5.3%) occurred on postoperative day 3. With respect to morbidity, mortality, and postoperative hospitalization, no statistically significant difference was noted between Groups A and B. The number of readmissions and the rate of recurrent jaundice were lower in Group A than in Group c, to a statistically significant degree (P = 0.019, P = 0.029, respectively). The median hospital-free survival period and themedian overall survival were also signifi cantly longer in Group A (P = 0.001 and P ctively). cONcLUSION: Surgical palliation does not increase the morbidity or mortality rates, but it does increase the survival rate and improve the quality of life in elderly patients with unresectable pancreatic head cancer.

关键词： Adenocarcinoma Elderly Palliative surgery Pancreas neoplasms

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