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Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis

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Molecular Plant 2017年第6期10卷 846-865页

作者： Victor Aguilar-Hernandez do-Young Kim Robert J. Stankey Mark Scalf Lloyd M. Smith richard d. Vierstra department of Biology Washington University in St. Louis Campus Box 1137 One Brookings Drive St. Louis MO 63130 USA department of Genetics 425-G Henry Mall department of Chemistry 1101 University Avenue University of Wisconsin-Madison Madison WI 53706 USA Advanced Bio Convergence Center Pohang Technopark Gyeong-Buk South Korea 37668

The switch from skotomorphogenesis to photomorphogenesis is a key developmental transition in the life of seed plants. While much of the underpinning proteome remodeling is driven by light-induced changes in gene expression, the proteolytic removal of specific proteins by the ubiquitin-26S proteasome system is also likely paramount. Through mass spectrometric analysis of ubiquitylated proteins affinity-purified from etiolated Arabidopsis seedlings before and after red-light irradiation, we identified a number of influential proteins whose ubiquitylation status is modified during this switch. We observed a substantial enrichment for proteins involved in auxin, abscisic acid, ethylene, and brassinosteroid signaling, peroxisome function, disease resistance, protein phosphorylation and light perception, including the phytochrome （Phy） A and phototropin photoreceptors. Soon after red-light treatment, PhyA becomes the dominant ubiquitylated species, with ubiquitin attachment sites mapped to six lysines. A PhyA mutant protected from ubiquitin addition at these sites is substantially more stable in planta upon photoconversion to Pfr and is hyperactive in driving photomorphogenesis. However, light still stimulates ubiquitylation and degradation of this mutant, implying that other attachment sites and/or proteolytic pathways exist. Collectively, we expand the catalog of ubiquitylation targets in Arabidopsis and show that this post- translational modification is central to the rewiring of plants for photoautotrophic growth.

关键词： Arabidopsis ubiquitin mass spectrometry photomorphogenesis phytochrome degradation

A study of process-induced grain structures during steady state and non-steady state electron-beam welding of a titanium alloy

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Journal of Materials Science & Technology 2022年第18期113卷 117-127页

作者： Yu Lu richard Turner Jeffery Brooks Hector Basoalto School of Metallurgy and Materials University of BirminghamBirminghamB152TTUnited Kingdom department of Materials Science and Engineering The University of SheffieldMappin StreetSheffieldS13JDUnited Kingdom

A detailed microstructural characterisation of the emerging weld-line grain structure,for bead-upon-plate welds in Ti-6Al-4V(Ti64)of differing plate thickness,was *** microstructure studied was formed during both steady state and non-steady state sections within the weld path,with the non-steady state portion being taken from the end of the plate as the weld bead and heat source overhang the edge of the *** allows for the effects of welding process conditions on the microstructural evolution to be *** weld pool geometry and 3d tomography of the weld-induced defects have been *** characterisation of microstructure and texture for different welding parameters and for steady and non-steady states have been used to identify physical parameters for the microstructure predictions that are difficult to obtain *** different states significantly affect the weld crown shape and formation,weld toe,weld bead depth and ***,the heat affected zone(HAZ)re-mains *** the microstructural evolution,both the steady and non-steady states have similar microstructure and *** defects were observed in the steady state section of welds,but sub-surface spherical pores have been observed in the non-steady state section of a *** element modelling to simulate the thermal-metallurgical-mechanical fields within the steady and non-steady state sections of the welds was considered,and the cooling rates predicted within steady state and non-steady sections were interrogated to improve the theoretical understanding of the microstructure and defect formation differences in these Ti64 EB weld regions.

关键词： Electron-beam fusion welding Processing Microstructure Ti-6Al-4V

Erbium-doped TeO2-coated Si3N4 waveguide amplifiers with 5 dB net gain

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Photonics Research 2020年第2期8卷 127-134页

作者： HENRY C.FRANKIS HAMIdU M.MBONdE dAWSON B.BONNEVILLE CHENGLIN ZHANG richard MATEMAN ARNE LEINSE JONATHAN d.B.BRAdLEY department of Engineering Physics Mc Master UniversityHamilton L8S 4L7Canada Lioni X International BV Enschede AL 7500The Netherlands

We demonstrate 5dB net gain in an erbium-doped tellurium-oxide-coated silicon nitride *** amplifier design leverages the high refractive index and high gain in erbium-doped tellurite glass as well as the ultralow losses and mature,reliable,and low-cost fabrication methods of silicon nitride waveguide *** show that the waveguide platform demonstrates low background propagation losses of 0.25dB/cm based on a ring resonator device with a Q factor of 1.3×10^6 at 1640 *** measure 5dB peak net gain at 1558 nm and>3dB of net gain across the C band in a 6.7 cm long waveguide for 35 m W of launched 1470 nm pump *** per unit length of 1.7 and 1.4dB/cm is measured in a 2.2 cm long waveguide for 970 and 1470 nm pump wavelengths,*** simulations predict that>10dB gain can be achieved across the C band simply by optimizing waveguide length and fiber-chip *** results demonstrate a promising approach for the monolithic integration of compact erbium-doped waveguide amplifiers on silicon nitride chips and within silicon-based photonic integrated circuits.

关键词： waveguide pump amplifiers

dAM IMPACTS ON ANd RESTORATION OF AN ALLUVIAL RIVER-RIO GRANdE, NEW MEXICO

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International Journal of Sediment Research 2003年第2期18卷 89-96页

作者： Gigi richard,Pierre JULIEN department of Physical and Environmental Sciences Mesa State College Grand Junction CO department of Civil Engineering Engineering Research Center Colorado State University Fort Collins CO USA USA

The impact of construction of dams and reservoirs on alluvial rivers extends both upstream and downstream of the dam. downstream of dams, both the water and sediment supplies can be altered leading to adjustments in the river channel geometry and ensuing changes in riparian and aquatic habitats. The wealth of pre and post-regulation data on the Middle Rio Grande, New Mexico, provides an excellent case study of river regulation, channel adjustments, and restoration efforts. Cochiti dam was constructed on the main stem of the Rio Grande in 1973 for flood control and sediment retention. Prior to dam construction, the Rio Grande was a wide, sandy braided river. Following dam construction, the downstream channel bed degraded and coarsened to gravel size, and the planform shifted to a more meandering pattern. Ecological implications of the geomorphic changes include detachment of the river from the floodplain, reduced recruitment of riparian cottonwoods, encroachment of non-native saltcedar and Russian olive into the floodplain, and degraded aquatic habitat for the Rio Grande silvery minnow. Recent restoration strategies include removal of non-native riparian vegetation, mechanical lowering of floodplain areas, and channel widening.

关键词： River morphology Effects of dams Rio Grande

Computation of Local Fractal dimension Values of the Human Cerebral Cortex

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Applied Mathematics 2014年第12期5卷 1733-1740页

作者： richard d. King Center for Alzheimer’s Care Imaging and Research Department of Neurology University of Utah Salt Lake City USA

Objectives: The purpose of this paper is to describe a technique for computing the local fractal dimension of the human cerebral cortex as extracted from high-resolution magnetic resonance imaging scans. Methods: 3d models of the human cerebral cortex were extracted from high resolution magnetic resonance images of 10 healthy adult volunteers using FreeSurfer. The local fractal dimension of the cortex was computed using a custom-written cube-counting algorithm. The effect of constraining the maximum region size on the measured value of local fractal dimension was examined. A proof of principle was demonstrated by comparing an individual with Alzheimer’s disease to a healthy individual. Results: Local values of cortical fractal dimension can be obtained by constraining the size of the region over which the cube counting is performed. Cubic regions of intermediate size (30 × 30 × 30 mm) yielded a profile that demonstrated greater regional variability compared to smaller (15 × 15 × 15 mm) or larger (60 × 60 × 60 mm) region sizes. Conclusions: Local fractal dimension of the cerebral cortex is a novel measure that may yield additional, quantitative insight into the clinical meaning of cortical shape changes.

关键词： Fractal dimension Cortex Imaging Biomarkers Local

Routine use of thiopurines in maintaining remission in pediatric Crohn's disease

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World Journal of Gastroenterology 2014年第27期20卷 9185-9190页

作者： Brendan M Boyle Michael d Kappelman richard B Colletti Robert N Baldassano david E Milov Wallace V Crandall Nationwide Children’s Hospital department of Pediatrics University of North Carolina at Chapel Hill University of Vermont Children’s Hospital of Philadelphia Nemours Children’s Clinic

AIM: To evaluate the effectiveness of thiopurines in maintaining steroid-free remission in routine clinical practice.

关键词： Crohn's disease Pediatric Remission Thiopurines Mercaptopurine

diapause development in early and late emerging phenotypes of delia floralis

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Insect Science 2014年第1期21卷 103-113页

作者： Tor J. Johansen richard Meadow Arctic Agriculture and Land Use division Bioforsk - Norwegian Institute for Agricultural and Environmental Research Tromsm plant Health and Plant Protection division Bioforsk - Norwegian Institute for Agricultural and Environmental Research As Norway

The turnip fly, delia floralis Fall6n （diptera： Anthomyiidae） is an important insect pest of brassica vegetable crops in the holarctic region. different populations have strongly varying temperature requirements for fly emergence, a challenge for accurate prediction of activity. This study focused on diapause development in one early and one late emerging phenotype. The physiological state after various treatments was deduced from emergence data. Our results showed a slow diapause progression at chilling conditions for both populations and diapause ended about 7 months after pupae were formed for the early population. For the late population held at 4℃ diapause did not end, no matter how long the duration of chilling. These pupae required a period with elevated temperatures above 6~C to continue development. At constant non-chilling conditions （18℃） from the time pupae were formed both populations completed diapause most rapidly. These results indicate that chilling delayed, rather than accelerated development and was not a prerequisite for diapause development. For post-diapause, results indicated a linear relationship between rate of development and temperature within the range of 6-18℃and a theoretical base temperature for development of about 2℃ for both populations. In conclusion, d. floralis pupae are in diapause throughout a long winter period, and delayed emergence of the late population appears to be caused by prolonged diapause regulated by a developmental temperature threshold. The study has added information on the biology of turnip fly populations, a prerequisite for improved pest control.

关键词： brassica chilling emergence hibernation quiescence

Evaluating Peptide Mass Fingerprinting-based Protein Identification

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Genomics, Proteomics & Bioinformatics 2007年第3期5卷 152-157页

作者： Senthilkumar damodaran Troy d.Wood Priyadharsini Nagarajan richard A.Rabin department of Pharmacology and Toxicology School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNY 14214USA department of Chemistry University at BuffaloBuffaloNY 14260USA department of Biochemistry School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNY 14214USA.

Identification of proteins by mass spectrometry （MS） is an essential step in proteomic studies and is typically accomplished by either peptide mass fingerprinting （PMF） or amino acid sequencing of the peptide. Although sequence information from MS/MS analysis can be used to validate PMF-based protein identification, it may not be practical when analyzing a large number of proteins and when highthroughput MS/MS instrumentation is not readily available. At present, a vast majority of proteomic studies employ PMF. However, there are huge disparities in criteria used to identify proteins using PMF. Therefore, to reduce incorrect protein identification using PMF, and also to increase confidence in PMF-based protein identification without accompanying MS/MS analysis, definitive guiding principles are essential. To this end, we propose a value-based scoring system that provides guidance on evaluating when PMF-based protein identification can be deemed sufficient without accompanying amino acid sequence data from MS/MS analysis.

关键词： peptide mass fingerprinting Mowse Mascot ProFound proteomics

development of a CO_2 Tolerant Fischer-Tropsch Catalyst:from Laboratory to Commercial-Sca1e demonstration in Alaska

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Journal of Natural Gas Chemistry 2004年第1期13卷 1-9页

作者： Joep J H M Font Freide Tim d Gamlin J richard Hensman Barry Nay Christopher Sharp BP Exploration Operating Company Chertsey RoadSunbury on ThamesMiddlesexTWl6 7LNEnglandDavy Process Technology Lid 20 Eastbourne TerraceLondon W2 6LEEnglandDavy Process Technology Lid 20 Eastbourne TerraceLondon W2 6LEEnglandBP Chemicals LtdChertsey RoadSunbury on ThamesMiddlesexTW16 7LLEnglandBP Chemicals LtdChertsey RoadSunbury on ThamesMiddlesexTW16 7LLEngland

This article describes the development of BP's Fischer-Tropsch catalyst, used for the conversion of carbon monoxide and hydrogen into liquid hydrocarbons. It covers the 18 year period from the early eighties, when laboratory scale preparations and micro-reactors were heavily used, right through to the present day with the commercial scale manufacture and proving of the finished catalyst in BP's new ＄86 million gas to liquids demonstration facility in Nikiski, Alaska. Extensive performance testing and scale-up experiments have been successfully carried out, all proof that a laboratory preparation can indeed be translated into a commercial manufacturing process. In addition, the resulting catalyst does not only meet the process design targets, but also exhibits enhanced stability and is tolerant to carbon dioxide. Above all, a commercial scale, fixed bed Fischer-Tropsch catalyst is now available and ready for licensing. Manufacturing procedures and quality control have all been successfully detailed and transferred to the commercial manufacturer.

关键词： carbon dioxide Fisher-Tropsch development syngas commercial catalyst