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SNARE-RNAi Results in Higher Terpene Emission from Ectopically Expressed Caryophyllene Synthase in Nicotiana benthamiana

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Molecular Plant 2015年第3期8卷 454-466页

作者： Hieng-Ming Ting Thierry L. Delatte Pim Kolkman Johana C. Misas-Villamil Renier A.L. van der Hoom Harro J. Bouwmeester alexander R. van der Krol Laboratory of Plant Physiology Wageningen University PO Box 658 6700 AR Wageningen The Netherlands plant Chemetics Laboratory Max Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany Plant Chemetics Laboratory Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK

Plants produce numerous terpenes and much effort has been dedicated to the identification and charac- terization of the terpene biosynthetic genes. However, little is known about how terpenes are transported within the cell and from the cell into the apoplast. To investigate a putative role of vesicle fusion in this pro- cess, we used Agrobacterium tumefaciens-mediated transient coexpression in Nicotiana benthamiana of an MtVAMP721e-RNAi construct （Vi） with either a caryophyllene synthase or a linalool synthase, respec- tively. Headspace analysis of the leaves showed that caryophyllene or linalool emission increased about five-fold when N. benthamiana VAMP72 function was blocked. RNA sequencing and protein ubiquitination analysis of the agroinflltrated N. benthamiana leaf extracts suggested that increased terpene emissions may be attributed to proteasome malfunction based on three observations： leaves with TPS＋Vi showed （1） a higher level of a DsRed marker protein, （2） a higher level of ubiquitinated proteins, and （3） coordinated induced expression of multiple proteasome genes, presumably caused by the lack of proteasome- mediated feedback regulation. However, caryophyllene or linalool did not inhibit proteasome-related pro- tease activity in the in vitro assays. While the results are not conclusive for a role of vesicle fusion in terpene transport, they do show a strong interaction between inhibition of vesicle fusion and ectopic expression of certain terpenes. The results have potential applications in metabolic engineering.

关键词： terpene transport vesicle-associated membrane proteins (VAMP72) caryophyllene synthase linaloolsynthase proteasome Nicotiana benthamiana

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Predicting localised corrosion and mechanical performance of a PEO surface modified rare earth magnesium alloy for implant use through in-silico modelling

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Bioactive Materials 2023年第8期26卷 437-451页

作者： Kerstin van Gaalen Conall Quinn Marek Weiler Felix Gremse Felix Benn Peter E.McHugh Ted J.Vaughan alexander Kopp Biomechanics Research Centre(BioMEC) Biomedical EngineeringSchool of EngineeringUniversity of GalwayGalwayIreland Meotec GmbH AachenGermany Institute for Experimental Molecular Imaging RWTH Aachen UniversityAachenGermany Gremse-IT GmbH AachenGermany School of Mechanical and Aerospace Engineering Queen’s University BelfastBelfastUnited Kingdom

In this study,the influence of a plasma electrolytic oxidation(PEO)surface treatment on a medical-grade WE43-based magnesium alloy is examined through an experimental and computational framework that considers the effects of localised corrosion features and mechanical properties throughout the corrosion ***,a comprehensive in-vitro immersion study was performed on WE43-based tensile specimens with and without PEO surface modification,which included fully automated spatial reconstruction of the phenomenological features of corrosion through micro-CT scanning,followed by uniaxial tensile *** the experimental data of both unmodified and PEO-modified groups were used to calibrate parameters of a finite element-based surface corrosion ***-vitro,it was found that the WE43-PEO modified group had a significantly lower corrosion rate and maintained significantly higher mechanical properties than the *** corrosion rates were~50%lower in the WE43-PEO modified specimens,the local geometric features of corroding surfaces remained similar to the unmodified WE43 group,however evolving after almost the double amount of *** were also able to quantitatively demonstrate that the PEO surface treatment on magnesium continued to protect samples from corrosion throughout the entire period tested,and not just in the early stages of *** the results from the testing framework,the model parameters of the surface-based corrosion model were identified for both *** enabled,for the first time,in-silico prediction of the physical features of corrosion and the mechanical performance of both unmodified and PEO modified magnesium *** simulation framework can enable future in-silico design and optimisation of bioabsorbable magnesium devices for load-bearing medical applications.

关键词： Plasma electrolytic oxidation WE43MEO Degradation model Corrosion phenomenology Mechanical integrity

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A Heuristics-Based Cost Model for Scientic Workow Scheduling in Clou

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Computers, Materials & Continua 2021年第6期67卷 3265-3282页

作者： Ehab Nabiel Al-Khanak Sai Peck Lee Saif Ur Rehman Khan Navid Behboodian Osamah Ibrahim Khalaf alexander Verbraeck Hans van Lint Department of Transport and Planning Faculty of Civil Engineering and Geosciences(CiTG)Delft University of TechnologyDelftNetherlands Faculty of Computer Science and Information Technology University of MalayaKuala LumpurMalaysia Department of Computer Science COMSATS University Islamabad(CUI)IslamabadPakistan Faculty of Computing and Digital Technology HELP UniversityKuala LumpurMalaysia Al-Nahrain Nanorenewable Energy Research Centre Al-Nahrain UniversityBaghdadIraq Department Multi-Actor Systems Faculty of TechnologyPolicy and Management(TPM)Delft University of TechnologyDelftNetherlands

Scientic Workow Applications(SWFAs)can deliver collaborative tools useful to researchers in executing large and complex scientic ***,Scientic Workow Scheduling(SWFS)accelerates the computational procedures between the available computational resources and the dependent workow jobs based on the researchers’***,cost optimization is one of the SWFS challenges in handling massive and complicated tasks and requires determining an approximate(near-optimal)solution within polynomial computational *** by this,current work proposes a novel SWFS cost optimization model effective in solving this *** proposed model contains three main stages:(i)scientic workow application,(ii)targeted computational environment,and(iii)cost optimization *** model has been used to optimize completion time(makespan)and overall computational cost of SWFS in cloud computing for all considered scenarios in this research *** will ultimately reduce the cost for service *** the same time,reducing the cost has a positive impact on the protability of service providers towards utilizing all computational resources to achieve a competitive advantage over other cloud service *** evaluate the effectiveness of this proposed model,an empirical comparison was conducted by employing three core types of heuristic approaches,including Single-based(i.e.,Genetic Algorithm(GA),Particle Swarm Optimization(PSO),and Invasive Weed Optimization(IWO)),Hybrid-based(i.e.,Hybrid-based Heuristics Algorithms(HIWO)),and Hyper-based(i.e.,Dynamic Hyper-Heuristic Algorithm(DHHA)).Additionally,a simulation-based implementation was used for SIPHT SWFA by considering three different sizes of *** proposed model provides an efcient platform to optimally schedule workow tasks by handing data-intensiveness and computational-intensiveness of *** results reveal that the proposed cost optimization model attained an optimal Job completio

关键词： Scientic workow scheduling empirical comparison cost optimization model heuristic approach cloud computing

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Improving Railway Passengers Experience:Two Perspectives

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Journal of Traffic and Transportation Engineering 2019年第3期7卷 97-110页

作者： mark van Hagen Niels van Oort Research Department Dutch RailwaysPO Box 20252500 HAUtrechtthe Netherlands Department of Transport and Planning Delft University of TechnologyPO Box 50482600 GADelftthe Netherlands

This paper describes two perspectives to improve the passenger *** passenger satisfaction pyramid is introduced,consisting of the base of the pyramid(dissatisfiers)focusing on time well saved and the top of the pyramid(satisfiers)aiming at time well *** challenge in planning and design of public transport services is to find the most efficient(set of)design *** on the context this might either mean focusing on the top or on the bottom of the *** found that influencing and enhancing the qualities of the satisfiers is far more important than traditional studies showed *** stations,regression analyses show that dissatisfiers are responsible for explaining almost half of the total score of the station and satisfiers are responsible for the other half of the scores passengers give for the *** still have to put a lot of energy in getting the basics right,starting in the planning phase,but then we are not allowed to lean *** have to keep investing in qualities like ambience,comfort and experience which makes the customers truly happy at the end of the day.

关键词： Passenger experience service reliability perception behaviour

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Cerebral magnetic resonance imaging in quiescent Crohn's disease patients with fatigue

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World Journal of Gastroenterology 2017年第6期23卷 1018-1029页

作者： Sanne van Erp Ece Ercan Perla Breedveld Lianne Brakenhoff Eidrees Ghariq Sophie Schmid Matthias van Osch mark van Buchem Bart Emmer Jeroen van der Grond Ron Wolterbeek Daniel Hommes Herma Fidder Nic van der Wee Tom Huizinga Désirée van der Heijde Huub Middelkoop Itamar Ronen Andrea van der Meulen-de Jong Department of Gastroenterology and Hepatology Leiden University Medical Center C.J.Gorter Center Leiden University Medical Center Department of Radiology Leiden University Medical Center Department of Medical Statistics Leiden University Medical Center Center for Inflammatory Bowel Diseases University of California Los Angeles Department of Gastroenterology and Hepatology University Medical Center Utrecht Department of Psychiatry Leiden University Medical Center Department of Rheumatology Leiden University Medical Center Department of Neuropsychology Leiden University Medical Center Department of Radiology Leiden University Medical CenterLeiden

To evaluate brain involvement in quiescent Crohn’s disease (CD) patients with fatigue using quantitative magnetic resonance imaging (MRI).METHODSMultiple MRI techniques were used to assess cerebral changes in 20 quiescent CD patients with fatigue (defined with at least 6 points out of an 11-point numeric rating scale compared with 17 healthy age and gender matched controls without fatigue. Furthermore, mental status was assessed by cognitive functioning, based on the neuropsychological inventory including the different domains global cognitive functioning, memory and executive functioning and in addition mood and quality of life scores. Cognitive functioning and mood status were correlated with MRI findings in the both study *** glutamate + glutamine (Glx = Glu + Gln) concentrations (P = 0.02) and ratios to total creatine (P = 0.02) were found in CD patients compared with controls. Significant increased Cerebral Blood Flow (P = 0.05) was found in CD patients (53.08 ± 6.14 mL/100 g/min) compared with controls (47.60 ± 8.62 mL/100 g/min). CD patients encountered significantly more depressive symptoms (P 1-weighted analysis. In addition, no correlation was found between mental status and MRI *** work shows evidence for perfusion, neurochemical and mental differences in the brain of CD patients with fatigue compared with healthy controls.

关键词： Magnetic resonance imaging Systemic inflammation Fatigue Crohn’s disease Cognition

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Sustainable Application of a Novel Water Cycle Using Seawater for Toilet Flushing

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Engineering 2016年第4期2卷 460-469页

作者： Xiaoming Liu Ji Dai Di Wu Feng Jiang Guanghao Chen Ho-Kwong Chui mark C. M. van Loosdrecht Department of Civil and Environmental Engineering The Hong Kong University of Science and Technology Hong Kong China Water Technology Center The Hong Kong University of Science and Technology Hong Kong China Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (Hong Kong Branch) The Hong Kong University of Science and Technology l-long Kong China School of Chemistry and Environment South China Normal University Guangzhou 510006 China Department of Biotechnology Delft University of Technology Delft2629 HZ the Netherlands

Global water security is a severe issue that threatens human health and well-being. Finding sustainable alternative water resources has become a matter of great urgency. For coastal urban areas, desalinated seawater could serve as a freshwater supply. However, since 20%-30% of the water supply is used for flushing waste from the city, seawater with simple treatment could also partly replace the use of freshwater. In this work, the freshwater saving potential and environmental impacts of the urban water system （water-wastewater closed loop） adopting seawater desalination, seawater for toilet flushing （SWTF）, or reclaimed water for toilet flushing （RWTF） are compared with those of a conventional freshwater system, through a life-cycle assessment and sensitivity analysis. The potential applications of these processes are also assessed. The results support the environmental sustainability of the SWTF approach, but its potential application depends on the coastal distance and effective population density of a city. Developed coastal cities with an effective population density exceeding 3000 ***-2 and located less than 30 km from the seashore （for the main pipe supplying seawater to the city） would benefit from applying SWTF, regardless of other impact parameters. By further applying the sulfate reduction, autotrophic denitrification, and nitrification integrated （SANI） process for wastewater treatment, the maximum distance from the seashore can be extended to 60 km. Considering that most modern urbanized cities fulfill these criteria, the next generation of water supply systems could consist of a freshwater supply coupled with a seawater supply for sustainable urban development.

关键词： Alternative water resources Seawater toilet flushing SANIUrban water system Life-cycle assessment

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Design and thermodynamic analysis of a pathway enabling anaerobic production of poly-3-hydroxybutyrate in Escherichia coli

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Synthetic and Systems Biotechnology 2023年第4期8卷 629-639页

作者： Karel Olavarria Marco V.Becker Diana Z.Sousa mark C.M.van Loosdrecht S.Aljoscha Wahl Laboratory of Microbiology Wageningen University and ResearchStippenenweg 46708 WEWageningenThe Netherlands Centre for Living Technologies Eindhoven-Wageningen-Utrecht AlliancePrincetonlaan 63584 CBUtrechtThe Netherlands Department of Biotechnology Applied Sciences FacultyDelft University of Technologyvan der Maasweg 92629 HZDelftThe Netherlands Lehrstuhl für Bioverfahrenstechnik Friedrich-Alexander-Universit¨atPaul-Gordan-Strasse 391052ErlangenGermany

Utilizing anaerobic metabolisms for the production of biotechnologically relevant products presents potential advantages,such as increased yields and reduced energy ***,lower energy dissipation may indicate that certain reactions are operating closer to their thermodynamic *** stoichiometric analyses and genetic modifications are frequently employed in metabolic engineering,the use of thermodynamic tools to evaluate the feasibility of planned interventions is less *** this study,we propose a novel metabolic engineering strategy to achieve an efficient anaerobic production of poly-(R)-3-hydroxybutyrate(PHB)in the model organism Escherichia *** approach involves re-routing of two-thirds of the glycolytic flux through non-oxidative glycolysis and coupling PHB synthesis with NADH *** complemented our stoichiometric analysis with various thermodynamic approaches to assess the feasibility and the bottlenecks in the proposed engineered *** to our calculations,the main thermodynamic bottleneck are the reactions catalyzed by the acetoacetyl-CoAβ-ketothiolase(EC 2.***.1.9)and the acetoacetyl-CoA reductase(EC 1.***.1.36).Furthermore,we calculated thermodynamically consistent sets of kinetic parameters to determine the enzyme amounts required for sustaining the conversion *** the case of the engineered conversion route,the protein pool necessary to sustain the desired fluxes could account for 20%of the whole cell dry weight.

关键词： Pathway feasibility analysis Protein cost Anaerobic metabolism Engineered pathways Metabolite concentrations

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Hepatocyte cytoskeleton during ischemia and reperfusion -influence of ANP-mediated p38 MAPK activation

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World Journal of Gastroenterology 2005年第47期11卷 7418-7429页

作者： Melanie Keller alexander L Gerbes Stefanie Kulhanek-Heinze Tobias Gerwig Uwe Grützner Nico van Rooijen Angelika M Vollmar Alexandra K Kiemer Department of Pharmacy Centre of Drug ResearchUniversity of MunichButenandtstr. 5-1381377 MunichGermany Department of Medicine Ⅱ Klinikum GroβhadernUniversity of MunichMarchionistr. 1781377 MunichGermany Angelika M Vollmar Alexandra K KiemerDepartment of PharmacyCentre of Drug ResearchUniversity of MunichButenandtstr. 5-1381377 MunichGermany Department of Pharmacy Centre of Drug ResearchUniversity of MunichButenandtstr. 5-1381377 MunichGermany Department of Medicine ⅡKlinikum GroβhadernUniversity of MunichMarchionistr. 1781377 MunichGermany Institute for Surgical Research Klinikum GroβhadernUniversity of MunichMarchionistr. 1781377 MunichGermany Vrije Universiteit VUMCDepartment of Molecular Cell BiologyFaculty of Medicine1081 BT AmsterdamThe Netherlands

AIM： To determine functional consequences of this activation, whereby we focused on a potential regulation of the hepatocyte cytoskeleton during ischernia and reperfusion. METHODS： For in vivo experiments, animals received ANP （5 μg/kg） intravenously. In a different experimental setting, isolated rat livers were perfused with KH-buffer ＋ANP （200 nmol/L）＋SB203580 （2 μmol/L）. Livers were then kept under ischernic conditions for 24 h, and either transplanted or reperfused. Actin, Hsp27, and phosphorylated Hsp27 were determined by Western blotting, p38 MAPK activity by in vitro phosphorylation assay. F-actin distribution was determined by confocal microscopy. RESULTS： We first confirmed that ANP preconditioning leads to an activation of p38 MAPK and observed alterations of the cytoskeleton in hepatocytes of ANP- preconditioned organs. ANP induced an increase of hepatic F-actin after ischemia, which could be prevented by the p38 MAPK inhibitor SB203580 but had no effect on bile flow. After ischemia untreated livers showed a translocation of Hsp27 towards the cytoskeleton and an increase in total Hsp27, whereas ANP preconditioning prohibited translocation but caused an augmentation of Hsp27 phosphorylation. This effect is also mediated via p38 MAPK, since it was abrogated by the p38 MAPK inhibitor SB203580. CONCLUSION： This study reveals that ANP-mediated p38 MAPK activation leads to changes in hepatocyte cytoskeleton involving an elevation of phosphorylated Hsp27 and thereby for the first time shows functional consequences of ANP-induced hepatic p38 MAPK activation.

关键词： Hormonal preconditioning Atrial natriuretic peptide Hsp 27 Actin Polymerization

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A crowd-sourced genomic project to assess hybrid content in a rare avian vagrant(Azure Tit Cyanistes cyanus(Pallas,1770))

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Avian Research 2023年第4期14卷 545-552页

作者： Martin Irestedt Filip Thorn Per G.P.Ericson Hein van Grouw Yaroslav A.Red'kin alexander Hellquist Frank Johansson Johan A.A.Nylander Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryStockholmSweden Department of Zoology Stockholm University Sweden Bird Group Department of Life SciencesNatural History MuseumTringUnited Kingdom Zoological Museum Lomonosov Moscow State UniversityMoscowRussia Institute of Biological Problems of Cryolithozone SB RAS YakutskRussia Department of Women's and Children's Health Uppsala UniversitySweden Department of Ecology and Genetics Uppsala UniversityUppsalaSweden

The aim of this study was to correlate plumage variation with the amount of genomic hybrid content in hybrids between Azure Tits Cyanistes cyanus(Pallas,1770)and European Blue Tit Cyanistes caeruleus(Linnaeus,1758),by re-sequencing the genomes of museum specimens of non-hybrids and presumed hybrids with varying *** project was funded by crowdsourcing and initiated when two presumed Azure Tits,observed by hundreds of Swedish birdwatchers,were rejected as hybrids based on minor plumage deviations assumed to indicate hybrid contents from the European Blue *** results confirm that hybrids with intermediate plumages,so called Pleske’s Tits,are first generation hybrids(F1 hybrids).Individuals,whose plumages are similar to Azure Tits,but assessed as hybrids based on minor plumage deviations,are all backcrosses but vary in their degree of hybrid ***,some individuals morphologically recognized as pure Azure Tits expressed similar degrees of hybrid *** results indicate that:(1)hybrid content may be widespread in Azure Tits in the western part of its habitat distribution;(2)plumage deviation in backcrosses is not linearly correlated with the genetic degree of hybrid origin;and(3)all Azure Tits observed in Europe outside its natural distribution may have some degree of hybrid *** therefore suggest that it is very difficult to phenotypically single out hybrids beyond first generation *** argue that decreased sequencing costs and improved analytical tools open the doors for museomic crowd-sourced projects that may not address outstanding biological questions but have a major interest for lay citizens such as birdwatchers.

关键词： Crowdsourcing Cyanistes cyanus Hybridization Museomics

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Arabidopsis Coordinates the Diurnal Regulation of Carbon Allocation and Growth across a Wide Range of Photoperiods

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Molecular Plant 2014年第1期7卷 137-155页

作者： Ronan Sulpice Anna Flis alexander A. Ivakov Federico Apelt Nicole Krohn Beatrice Encke Christin Abel Regina Feil John E. Lunn mark Stitt Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany National University of Galway Plant Systems Biology Lab Plant and AgriBiosciences Research Centre Botany and Plant Science Galway Ireland

In short photoperiods, plants accumulate starch more rapidly in the light and degrade it more slowly at night, ensuring that their starch reserves last until dawn. To investigate the accompanying changes in the timing of growth, Arabidopsis was grown in a range of photoperiods and analyzed for rosette biomass, photosynthesis, respiration, ribosome abundance, polysome loading, starch, and over 40 metabolites at dawn and dusk. The data set was used to model growth rates in the daytime and night, and to identify metabolites that correlate with growth. Modeled growth rates and polysome loading were high in the daytime and at night in long photoperiods, but decreased at night in short photoperiods. Ribosome abundance was similar in all photoperiods. It is discussed how the amount of starch accumulated in the light period, the length of the night, and maintenance costs interact to constrain growth at night in short photoperiods, and alter the strategy for optimizing ribosome use. Significant correlations were found in the day- time and the night between growth rates and the levels of the sugar-signal trehalose 6-phosphate and the amino acid biosynthesis intermediate shikimate, identifying these metabolites as hubs in a network that coordinates growth with diurnal changes in the carbon supply.

关键词： Arabidopsis diurnal growth photoperiod ribosomes trehalose-6-phosphate starch

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