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A Light-Independent Allele of Phytochrome B Faithfully Recapitulates Photomorphogenic Transcriptional Networks

Molecular Plant 2009年第1期2卷 166-182页

作者： Wei Hu Yi-Shin Su j. clark lagarias Department of Molecular and Cellular Biology College of Biological Sciences University of California Davis CA 95616 USA Present address: Carnegie Institution of Washington -Department of Plant Biology Stanford CA 94305 USA

Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer lightindependent, constitutive photomorphogenic （cop） phenotypes to transgenic plants （Su and lagarias, 2007）. In the present study, comparative transcription profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole- genome transcription profiles of dark-grown phyAphyB seedlings expressing the Y^276H mutant of phyB （YHB） revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to but quantitatively greater than those of wild-type seedlings grown under 15 or 50 μmol m^-2 m^-1 continuous red light （Rc）. Among the 2977 genes statistically significant two-fold （SSTF） regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways, and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-regulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the maj.rity of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway（s） strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion.

关键词： light signaling signal transduction transcriptome analysis photomorphogenesis Arabidopsis phytochrome.

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Insights into the efficiency and stability of Cu-based nanowires for electrocatalytic oxygen evolution

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Nano Research 2018年第8期11卷 4323-4332页

作者： j.n Yu Qi Cao Bin Feng Changli Li j.ngyuan Liu j. Kenj. clark j.an-j.cques Delaunay Department of Mechanical Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan Institute of Engineering Innovation The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan School of Materials Science and Engineering Tsinghua University Beijing 100084 China Department of Chemical System Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan

Copper oxide nanowires with varying oxidation states are prepared and their activity for water oxidation is studied. The nanowires with a CuO phase are found to be the most active, and their degree of crystallinity is important in achieving efficient water oxidation. For the crystalline CuO nanowires in a weakly basic Na2CO3 electrolyte, a Tafel slope of 41 mV/decade, an overpotential of approximately 500 mV at - 10 mA/crn2 （without compensation for the solution resistance）, and a faradaic efficiency of nearly 100% are obtained. This electrode maintains a stable current for over 15 lx The low overpotential of 500 mV at 10 mA/cm2, small Tafel slope, long-term stability, and low cost make CuO one of the most promising catalysts for water oxidation. Moreover, the evolution of the CuO nanowire morphology over time is studied by electron microscop）-revealing that the diffusion of Cu ions from the interior of the nanowires to their surface causes the aggregation of individual nanowires over time. However, despite this aggregation, the current density remains nearly constant, because the total electrochemically active surface area of CuO does not change.

关键词： oxygen evolution reaction crystalline CuO active phase copper ion diffusion

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Synthetically engineered microbes reveal interesting principles of cooperation

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Frontiers of Chemical Science and Engineering 2017年第1期11卷 3-14页

作者： Michael D. Dressier Corey j. clark Chelsea A. Thachettu Yasmine Zakaria Omar Tonsi Eldakar Robert P. Smith Department of Marine Biology and Environmental Science Halmos College of Natural Sciences and Oceanography Nova Southeastern University Fort Lauderdale FL 33314-7796 USA Department of Biological Sciences Halmos College of Natural Sciences and Oceanography Nova Southeastern University Fort Lauderdale FL 33314-7796 USA

Cooperation is ubiquitous in biological sys- tems. However, if natural selection favors traits that confer an advantage to one individual over another, then helping others would be paradoxical. Nevertheless, cooperation persists and is critical in maintaining homeostasis in systems ranging from populations of bacteria to groupings of mammals. Developing an understanding of the dynamics and mechanisms by which cooperation operates is critical in understanding ecological and evolutionary relationships. Over the past decade, synthetic biology has emerged as a powerful tool to study social dynamics. By engineering rationally controlled and modulatable beha- vior into microbes, we have increased our overall under- standing of how cooperation enhances, or conversely constrains, populations. Furthermore, it has increased our understanding of how cooperation is maintained within populations, which may provide a useful framework to influence populations by altering cooperation. As many bacterial pathogens require cooperation to infect the host and survive, the principles developed using synthetic biology offer promise of developing novel tools and strategies to treat infections, which may reduce the use of antimicrobial agents. Overall, the use of engineered cooperative microbes has allowed the field to verify existing, and develop novel, theories that may govern cooperative behaviors at all levels of biology.

关键词： synthetic biology engineered bacteria coop-eration cheater quorum sensing

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Null Controllability of Some Reaction-Diffusion Systems with Only One Control Force in Moving Domains

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Chinese Annals of Mathematics,Series B 2016年第1期37卷 29-52页

作者： j. LIMACO M. clark A. MARINHO S. B. de MENEZES A. T. LOUREDO Universidade Federal Fluminense IM RJ Brazil Universidade Federal do Piaui DM PI Brazil Universidade Federal do Piaui DM PI Brazil Universidade Federal do Ceara DM CE Brazil Universidade Estadual da Pavaiba DM PB Brazil.

In this article, the authors establish the local null controllability property for semilinear parabolic systems in a domain whose boundary moves in time by a single control force acting on a prescribed subdomain. The proof is based on Kakutani＇s fixed point theorem combined with observability estimates for the associated lineaxized system.

关键词： Kakutani's fixed point theorem Unique continuation Null controllability

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Wing, tail, and vocal contributions to the complex acoustic signals of courting Calliope hummingbirds

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Current Zoology 2011年第2期57卷 187-196页

作者： Christopher j.mes clark Peabody Museum of Natural History Yale University PO Box 208106 New Haven CT 06511 USA Museum of Vertebrate Zoology University of California- Berkeley Berkeley CA USA

Multi-component signals contain multiple signal parts expressed in the same physical modality. One way to identify individual components is if they are produced by different physical mechanisms. Here, I studied the mechanisms generating acoustic signals in the courtship displays of the Calliope hummingbird Stellula calliope. Display dives consisted of three synchronized sound elements, a high-frequency tone （hfl）, a low frequency tone （lft）, and atonal sound pulses （asp）, which were then followed by a frequency-modulated fall. Manipulating any of the rectrices （tail-feathers） of wild males impaired production of the lft and asp but not the hfl or fall, which are apparently vocal. I tested the sound production capabilities of the rectrices in a wind tunnel. Single rectrices could generate the lft but not the asp, whereas multiple rectrices tested together produced sounds sitlfilar to the asp when they fluttered and collided with their neighbors percussively, representing a previously unknown mechanism of sound production. During the shuttle display, a trill is generated by the wings during pulses in which the wingbeat frequency is elevated to 95 Hz, 40% higher than the typical hovering wingbeat frequency. The Calliope hummingbird courtship displays include sounds produced by three independent mechanisms, and thus include a minimum of three acoustic signal components. These acoustic mechanisms have different constraints and thus potentially contain different messages. Producing multiple acoustic signals via multiple mechanisms may be a way to escape the constraints present in any single mechanism .

关键词： Calliope Hummingbird Courtship Multicomponent Signal Sonation Wind Tunnel

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Surfactant protein A (SP-A) binds to phosphatidylserine and competes with annexin V binding on late apoptotic cells

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Protein & Cell 2010年第2期1卷 188-197页

作者： Anne j.kel Kenneth B.M.Reid Howard clark Department of Pharmacology University of OxfordMansfield RoadOxford OX13QTUK MRC Immunochemistry Unit Department of BiochemistryUniversity of OxfordSouth Parks RoadOxford OX13QUUK University of Southampton MP 803 Level FSouth BlockSouthampton General HospitalSouthampton SO166YDUK

The role of surfactant protein A(SP-A)in the recognition and clearance of apoptotic cells is well established,but to date,it is still not clear which surface molecules of apoptotic cells are involved in the *** we present evidence that phosphatidylserine(PS)is a relevant binding molecule for human *** binding is Ca^(2+)-dependent and is not inhibited by mannose,suggesting that the sugar-binding site of the carbohydrate recognition domain(CRD)of SP-A is not *** cytometry studies on apoptotic j.rkat cells revealed apparent inhibition of annexin V binding by increasing concentrations of SP-A in late apoptotic but not early apoptotic cells,and this was consistent for j.rkat cells and *** these data,confocal microscopy results show a co-localisation of annexin V and SP-A in late apoptotic but not early apoptotic ***,we cannot conclude that this inhibition is exclusively due to the binding of SP-A to PS on the cell surface,as annexin V is not wholly specific for PS and SP-A also interacts with other phospholipids that might become exposed on the apoptotic cell surface.

关键词： surfactant proteins phosphatidylserine apoptotic cells

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Non-Local Density Functional Description of Poly-Para-Phenylene Vinylene

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Chinese Physics Letters 2007年第3期24卷 807-810页

作者：郑广 clark S. j.Brand S. Abram R. A. School of Mathematics and Physics China University of Geosciences Wuhan 430074 Department of Physics University of Durham Durham DHI 3LE United Kingdom

A fully non-local exchange-correlation formalism the weighted density approximation （WDA）, has within the framework of density functional theory, known as been applied to the conj.gated polymer poly-para-phenylene vinylene （PPV） and is shown to lead to a marked improvement in the agreement of theory and experiment for the electronic band structure of the conj.gated polymer. In particular, some new model WDA functions are developed, which substantially increase the electronic band gap of the polymer relative to those obtained with the local density approximation and generalized gradient approximation. The calculated band gap of PPV is quantitatively or atleast semiquantitatively in agreement with the experimental data.

关键词： INHOMOGENEOUS ELECTRON-SYSTEMS CONj.GATED POLYMERS HARTREE-FOCK APPROXIMATION EXCHANGE 1ST-PRINCIPLES FORMALISM MOLECULES SEMICONDUCTORS DYNAMICS

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BUILDINGS ALIVE!ESTABLISHING THE COST OF LIVING BUILDINGS STRIVING FOR NET ZERO PERFORMANCE

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j.urnal of Green Building 2009年第3期4卷 61-71页

作者： Elizabeth j.Heider clark Brockman Skanska USA Building United States SERA Architects Inc United States

INTRODUCTION Innovative ideas have helped bring us some of the most incredible technological advances the world has *** ideas have ranged from the practical—“classic”inventions like the telephone—to the *** would have believed 15 years ago that today,in 2009,we are literally on the cusp of space *** incredible as the thinking was behind those innovations,there is another element that affects whether or not inventions catch on in a meaningful *** remarkable as many inventions are,we know that it takes more than innovation to bring big ideas into reality—it takes a deep understanding of what things cost,and of the value that obj.cts or ideas will deliver over time.

关键词： telephone meaningful invention

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Calculation and interpretation of classical turning surfaces in solids

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npj.Computational Materials 2021年第1期7卷 229-238页

作者： Aaron D.Kaplan Stewart j.clark Kieron Burke j.hn P.Perdew Department of Physics Temple UniversityPhiladelphiaPA 19122USA Centre for Materials Physics Durham UniversityDurham DH13LEUK Departments of Chemistry and Physics University of CaliforniaIrvineCA 92697USA Departments of Physics and Chemistry Temple UniversityPhiladelphiaPA 19122USA

Classical turning surfaces of Kohn–Sham potentials separate classically allowed regions(CARs)from classically forbidden regions(CFRs).They are useful for understanding many chemical properties of molecules but need not exist in solids,where the density never decays to *** equilibrium geometries,we find that CFRs are absent in perfect metals,rare in covalent semiconductors at equilibrium,but common in ionic and molecular *** all materials,CFRs appear or grow as the internuclear distances are uniformly *** can also appear at a monovacancy in a *** with several approximate density functionals and codes confirm these behaviors.A classical picture of conduction suggests that CARs should be connected in metals,and disconnected in wide-gap insulators,and is confirmed in the limits of extreme compression and ***,many semiconductors have no CFR at equilibrium,a key finding for density functional ***,a strong correlation with insulating behavior can still be ***,equilibrium bond lengths for all cases can be estimated from the bond type and the sum of the classical turning radii of the free atoms or ions.

关键词： turning solids expanded

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The Shishugou Fauna of the Middle-Late j.rassic Transition Period in the j.nggar Basin of Western China

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Acta Geologica Sinica(English Edition) 2022年第4期96卷 1115-1135页

作者： XU Xing j.mes M.clark David A.EBERTH Philip j.CURRIE Centre for Vertebrate Evolutionary Biology Yunnan UniversityKunming 650500China Key Laboratory of Vertebrate Evolution and Human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China Department of Biological Sciences George Washington UniversityWashington DC20052USA Royal Tyrrell Museum of Palaeontology Box 7500DrumhellerAlberta T0J 0Y0Canada Department of Biological Sciences University of Alberta 116 Street and 85 AvenueEdmontonAB T6G 2R3Canada

The Middle-Late j.rassic transition period is a critical period for the evolution of terrestrial vertebrates,but the global fossil record from this time is relatively *** Shishugou Fauna of this period has recently produced significant fossil remains of dinosaurs and other vertebrate groups,some representing the earliest known members of several dinosaurian groups and other vertebrate groups and some representing the best-known specimens of their *** discoveries are significant for our understanding of the origin and evolution of several vertebrate *** dating indicates that the fauna is aged approximately 159-164 *** with other similarly-aged terrestrial faunas such as Shaximiao and Yanliao show both taxonomic similarities and differences between these faunas and indicate that the j.nggar deposits might have preserved the most complete vertebrate fossil record for a Middle-Late j.rassic Laurasian terrestrial fauna.

关键词： Middle-Late j.rassic Shishugou Fauna Shishugou Formation terrestrial ecosystem Shaximiao Yanliao j.nggar Basin

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