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  • 13501.
    Zarin, Ru
    et al.
    Interactive Institute Swedish ICT.
    Fällman, Daniel
    Interactive Institute Swedish ICT.
    Through the Troll Forest: Exploring Tabletop Interaction Design for Children with Special Cognitive Needs2011In: Proceeding ACM CHI '11 Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, New York: ACM Digital Library, 2011, p. 3319-3322Conference paper (Refereed)
    Abstract [en]

    We describe the interaction design process of conceiving, designing, implementing, and testing Trollskogen, a purpose-built tabletop multitouch system featuring a range of small software applications, termed 'micro applications'. Each micro application is devised as a tool intended to improve or allow for exercise of social communication skills. Throughout the project, we have worked closely with a group of six children diagnosed with Autism Spectrum Disorder (ASD) or Down's syndrome, all in the age range of 5-8. The system has been designed together with the users, their teachers, and various experts as a complement to the current curricula. In this paper, the three main phases of our design process are described and we conclude the paper by reporting on and discussing some preliminary findings and observations from a small user study.

  • 13502. Zas, Rafael
    et al.
    Björklund, Niklas
    Sampedro, Luis
    Hellqvist, Claes
    Karlsson, Bo
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nordlander, Göran
    Genetic variation in resistance of Norway spruce seedlings to damage by the pine weevil Hylobius abietis2017In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 13, no 5, article id 111Article in journal (Refereed)
    Abstract [en]

    Regeneration of northern conifer forests is commonly performed by reforestation with genetically improved materials obtained from long-term breeding programs focused on productivity and timber quality. Sanitary threats can, however, compromise the realization of the expected genetic gain. Including pest resistance traits in the breeding programs may contribute to a sustainable protection. Here we quantified the variation in different components of resistance of Norway spruce to its main pest, the pine weevil Hylobius abietis. We followed insect damage in two large progeny trials (52 open-pollinated families with 100-200 individuals per family and trial) naturally infested by the pine weevil. Pine weevils damaged between 17 and 48% of the planted seedlings depending on the trial and year, and mortality due to weevil damage was up to 11.4%. The results indicate significant genetic variation in resistance to the pine weevil, and importantly, the variation was highly consistent across trials irrespective of contrasting incidence levels. Individual heritability estimates for the different components of seedling resistance were consistently low, but family heritabilities were moderate (0.53 to 0.81). While forward selections and breeding for higher resistance seem not feasible, backwards selections of the best parent trees emerge as a putative alternative to reduce weevil damage. A positive genetic correlation between early growth potential and probability of being attacked by the weevil was also observed, but the relationship was weak and appeared only in one of the trials. Overall, results presented here open the door to a new attractive way for reducing damage caused by this harmful pest.

  • 13503. Zbornikova, Eva
    et al.
    Knejzlik, Zdenek
    Hauryliuk, Vasili
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). University of Tartu, Institute of Technology, Tartu,Estonia.
    Krasny, Libor
    Rejman, Dominik
    Analysis of nucleotide pools in bacteria using HPLC-MS in HILIC mode2019In: Talanta: The International Journal of Pure and Applied Analytical Chemistry, ISSN 0039-9140, E-ISSN 1873-3573, Vol. 205, article id 120161Article in journal (Refereed)
    Abstract [en]

    Nucleotides, nucleosides and their derivatives are present in all cells at varying concentrations that change with the nutritional, and energetic status of the cell. Precise measurement of the concentrations of these molecules is instrumental for understanding their regulatory effects. Such measurement is challenging due to the inherent instability of these molecules and, despite many decades of research, the reported values differ widely. Here, we present a comprehensive and easy-to-use approach for determination of the intracellular concentrations of > 25 target molecular species. The approach uses rapid filtration and cold acidic extraction followed by high performance liquid chromatography (HPLC) in the hydrophilic interaction liquid chromatography (HILIC) mode using zwitterionic columns coupled with UV and MS detectors. The method reliably detects and quantifies all the analytes expected to be observed in the bacterial cell and paves the way for future studies correlating their concentrations with biological effects.

  • 13504.
    Zechner, Niklas
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    A novel approach to text classification2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis explores the foundations of text classification, using both empirical and deductive methods, with a focus on author identification and syntactic methods. We strive for a thorough theoretical understanding of what affects the effectiveness of classification in general. 

    To begin with, we systematically investigate the effects of some parameters on the accuracy of author identification. How is the accuracy affected by the number of candidate authors, and the amount of data per candidate? Are there differences in how methods react to the changes in parameters? Using the same techniques, we see indications that methods previously thought to be topic-independent might not be so, but that syntactic methods may be the best option for avoiding topic dependence. This means that previous studies may have overestimated the power of lexical methods. We also briefly look for ways of spotting which particular features might be the most effective for classification. Apart from author identification, we apply similar methods to identifying properties of the author, including age and gender, and attempt to estimate the number of distinct authors in a text sample. In all cases, the techniques are proven viable if not overwhelmingly accurate, and we see that lexical and syntactic methods give very similar results. 

    In the final parts, we see some results of automata theory that can be of use for syntactic analysis and classification. First, we generalise a known algorithm for finding a list of the best-ranked strings according to a weighted automaton, to doing the same with trees and a tree automaton. This result can be of use for speeding up parsing, which often runs in several steps, where each step needs several trees from the previous as input. Second, we use a compressed version of deterministic finite automata, known as failure automata, and prove that finding the optimal compression is NP-complete, but that there are efficient algorithms for finding good approximations. Third, we find and prove the derivatives of regular expressions with cuts. Derivatives are an operation on expressions to calculate the remaining expression after reading a given symbol, and cuts are an extension to regular expressions found in many programming languages. Together, these findings may be able to improve on the syntactic analysis which we have seen is a valuable tool for text classification.

  • 13505.
    Zechner, Niklas
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Derivatives of regular expressions with cuts2017Report (Other academic)
    Abstract [en]

    Derivatives of regular expressions are an operation which for a given expression produces an expression for what remains after a specific symbol has been read. This can be used as a step in transforming an expression into a finite string automaton. Cuts are an extension of the ordinary regular expressions; the cut operator is essentially a concatenation without backtracking, formalising a behaviour found in many programming languages. Just as for concatenation, we can also define an iterated cut operator. We show and derive expressions for the derivatives of regular expressions with cuts and iterated cuts.

  • 13506. Zegenhagen, Loreen
    et al.
    Weber, Elvira
    Kurade, Chaitanya
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology.
    Nair, Sharmila
    Överby, Anna K.
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Virology.
    Kroeger, Andrea
    Differential innate immune responses in various brain regions regulate antiviral response in the CNS during Tick-borne encephalitis virus infection2015In: Cytokine, ISSN 1043-4666, E-ISSN 1096-0023, Vol. 76, no 1, p. 91-91Article in journal (Other academic)
  • 13507. Zeh, Lilli
    et al.
    Limpens, Juul
    Erhagen, Björn
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bragazza, Luca
    Kalbitz, Karsten
    Plant functional types and temperature control carbon input via roots in peatland soils2019In: Plant and Soil, ISSN 0032-079X, E-ISSN 1573-5036, Vol. 438, no 1-2, p. 19-38Article in journal (Refereed)
    Abstract [en]

    Aims: Northern peatlands store large amounts of soil organic carbon (C) that can be very sensitive to ongoing global warming. Recently it has been shown that temperature-enhanced growth of vascular plants in these typically moss-dominated ecosystems may promote microbial peat decomposition by increased C input via root exudates. To what extent different plant functional types (PFT) and soil temperature interact in controlling root C input is still unclear. In this study we explored how root C input is related to the presence of ericoid shrubs (shrubs) and graminoid sedges (sedges) by means of a factorial plant clipping experiment (= PFT effect) in two peatlands located at different altitude (= temperature effect).

    Methods: By selective clipping of shrub and sedge shoots in mixed vegetation at two Alpine peatland sites we interrupted the above- to belowground translocation of C, thus temporarily inhibiting root C release. Subsequent measurements of soil respiration, dissolved organic carbon (DOC) concentration and stable isotope composition (13C) of DOC in pore water were used as proxies to estimate the above- to belowground transfer of C by different PFT.

    Results: We found that soil respiration rates and DOC concentrations temporarily decreased within 24 h after clipping, with the decrease in soil respiration being most pronounced at the 1.4 °C warmer peatland after clipping shrubs. The transient drop in DOC concentration coincided with a shift towards a heavier C isotope signature, indicating that the decrease was associated with inhibition of a light C source that we attribute to root exudates. Together these results imply that shrubs translocated more C into the peat than sedges, particularly at higher temperature.

    Conclusions: We showed that plant functional type and temperature interact in controlling root C input under field conditions in peatlands. Our results provide a mechanistic evidence that shrubs may potentially promote the release of stored soil C through root-derived C input.

  • 13508.
    Zelan, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Hagman, Henning
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Karlsson, Kristoffer
    Luleå University of Technology, EISLAB, 971 87 Luleå, Sweden..
    Dion, Claude
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Kastberg, Anders
    Laboratoire de Physique de la Matière Condensée, CNRS UMR 6622, Université de Nice-Sophia Antipolis, Parc Valrose, 06108 Nice Cedex 2, France.
    Fluctuation-induced drift in a gravitationally tilted optical lattice2010In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 82, no 3, p. 031136-Article in journal (Refereed)
    Abstract [en]

    Experimental and theoretical studies are made of Brownian particles trapped in a periodic potential, which is very slightly tilted due to gravity. In the presence of fluctuations, these will trigger a measurable average drift along the direction of the tilt. The magnitude of the drift varies with the ratio between the bias force and the trapping potential. This can be closely compared to a theoretical model system, based on a Fokker-Planck equation formalism. We show that the level of control and measurement precision we have in our system, which is based on cold atoms trapped in a three-dimensional dissipative optical lattice, makes the experimental setup suitable as a testbed for fundamental statistical physics. We simulate the system with a very simplified and general classical model, as well as with an elaborate semiclassical Monte Carlo simulation. In both cases, we achieve good qualitative agreement with experimental data.

  • 13509.
    Zelan, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Hagman, Henning
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Labaigt, Gabriel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Jonsell, Svante
    Stockholms universitet.
    Dion, Claude M.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Experimental measurement of the efficiency and the transport coherence of a cold-atom Brownian motor realized with cold atoms in optical lattices2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 83, no 2, article id 020102Article in journal (Refereed)
    Abstract [en]

    The rectification of noise into directed movement or useful energy is utilized by many different systems. The peculiar nature of the energy source and conceptual differences between such Brownian motor systems makes a characterization of the performance far from straightforward. In this work, where the Brownian motor consists of atoms interacting with dissipative optical lattices, we adopt existing theory and present experimental measurements for both the efficiency and the transport coherence. We achieve up to 0.3% for the efficiency and 0.01 for the Péclet number.

  • 13510. Zelent, B
    et al.
    Yano, T
    Ohlsson, P-I
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Smith, ML
    Paul, J
    Vanderkooi, JM
    Optical spectra of lactoperoxidase as a function of solvent2005In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 44, no 48, p. 15953-15959Article in journal (Refereed)
    Abstract [en]

    The iron of lactoperoxidase is predominantly high-spin at ambient temperature. Optical spectra of lactoperoxidase indicate that the iron changes from high-spin to low-spin in the temperature range from room temperature to 20 K. The transformation is independent of whether the enzyme is in glycerol/water or solid sugar glass. Addition of the inhibitor benzohydroxamic acid increases the amount of the low-spin form, and again the transformation is independent of whether the protein is in an aqueous solution or a nearly anhydrous sugar. In contrast to lactoperoxidase, horseradish peroxidase remains high-spin over the temperature excursion in both solvents and with addition of benzohydroxamic acid. We conclude that details of the heme pocket of lactoperoxidase allow ligation changes with temperature that are dependent upon the apoprotein but independent of solvent fluctuations. At low pH, lactoperoxidase shows a solvent-dependent transition; the high-spin form is predominant in anhydrous sugar glass, but in the presence of water, the low-spin form is also present in abundance. The active site of lactoperoxidase is not as tightly constrained at low pH as at neutrality, though the enzyme is active over a wide pH range.

  • 13511.
    Zemankova, Katerina
    et al.
    Prague 4, Czech Republic.
    Makoveichuk, Elena
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Physiological chemistry.
    Vlasakova, Zuzana
    Prague 4, Czech Republic.
    Olivecrona, Gunilla
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Physiological chemistry.
    Kovar, Jan
    Prague 4, Czech Republic.
    Acute alcohol consumption downregulates lipoprotein lipase activity in vivo2015In: Metabolism: Clinical and Experimental, ISSN 0026-0495, E-ISSN 1532-8600, Vol. 64, no 11, p. 1592-1596Article in journal (Refereed)
    Abstract [en]

    Objective. Acute alcohol consumption can induce hypertriglyceridemia. Such an effect could be explained in part by the influence of alcohol on lipoprotein lipase (LPL) - the key enzyme responsible for triglyceride hydrolysis in circulation. Therefore, we have studied the effects of acute moderate alcohol consumption on LPL activity and on the concentrations of angiopoietin-like proteins 3 and 4 (ANGPTL3 and ANGPTL4), which are known to inhibit LPL. Methods. Two experiments were carried out in 8 healthy volunteers. They received 25 g of alcohol (vodka) in one experiment and water in the other (control). The in vivo function of LPL was estimated using intravenous fat tolerance tests (IVFTT) carried out before, 2 and 4 hours after alcohol administration. At the end of each experiment, LPL activity and mass were measured in post-heparin plasma (PHP). The concentrations of ANGPTL3 and ANGPTL4 in blood were measured before alcohol consumption and at the end of the experiments. Results. LPL activity, as estimated using the IVFTT, was reduced by 25% and 24% two and four hours after the administration of alcohol, respectively, and was not affected in the control experiment. At the end of the experiment, LPL activity in PHP was 23% lower after alcohol consumption than in the controls. The concentrations of ANGPTL3 and ANGPTL4 had dropped to 67% and 86% of baseline values, respectively, at 280 min after alcohol consumption. These levels were not affected in the control experiment. The levels of ANGPTL4 but not those of ANGPTL3 were increased in PHP compared to both baseline values and values at 280 min. Conclusion. The capacity for triglyceride clearance seemed to be acutely reduced by alcohol consumption and the effect persisted for several hours. The levels of LPL activity in PHP were reduced to a similar extent. This reduction in LPL activity could not be explained by the changes in the levels of ANGPTL3 or ANGPTL4, which both decreased. (C) 2015 Elsevier Inc. All rights reserved.

  • 13512.
    Zeng, Qing-Yin
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Development of molecular techniques for fungal diagnostic research2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Fungi are present everywhere in indoor and outdoor environments. Many fungi are toxigenic or pathogenic that may cause various public health concerns. Rapid detection, quantification and characterization of fungi in living and working environments are essential for exposure risk assessment to safe guard public health.

    Rapid and accurate detection and identification of fungi using molecular method require specific markers. In this thesis, partial mt SSU and LSU rDNA were amplified and sequenced from 31 fungal species of 16 genera. Sequence alignments showed that fungal mt SSU and LSU rDNA contained sufficient amount of variation for the development of markers that can discriminate even among closely related species. Forty-eight probes were designed and were verified as highly specific to 25 fungal species commonly detected in living and working environments. These specific probes would have potential applications in clinical diagnosis and public health-related environmental monitoring.

    Nested PCR is a highly sensitive and specific method. Based on the nuclear 18S rDNA sequence variation pattern, three nested PCR systems were developed to detect the conifer tree pathogen Gremmeniella abietina, an ascomycete fungus that causes stem canker and shoot dieback in many conifer species. The three nested PCR systems showed high specificity and sensitivity. These methods could have broad applications in forest protection and disease management programs.

    Quantitative real-time PCR offers the ability of simultaneous detection and quantification of DNA of a specific microbe in one reaction. Based on the 18S rDNA sequence, two real-time PCR assays were developed to detect and quantify Wallemia sebi, a deuteromycete fungus commonly found in agricultural environments and is suspected to be a causative agent of farmer’s lung disease. Both PCR systems proved to be highly specific and sensitive for W. sebi detection even in a high background of other fungal DNAs. Application of the real-time PCR methods in the quantification of W. sebi in the aerosols of a farm revealed a high concentration of W. sebi spores (107/m3). The study indicates that W. sebi is a dominant fungus in agriculture environments.

    Cladosporium spores are important aeroallergens, and prolonged exposure to elevated spore concentrations can provoke chronic allergy and asthma. A TaqMan probe and a SYBR Green I based real-time PCR assay were developed to detect and quantify Cladosporium in aerosols. The two real-time PCR systems proved to be highly specific and sensitive for Cladosporium. These methods were employed to quantify Cladosporium in aerosols of five different indoor environments. High spore concentration of Cladosporium (107/m3) was observed in a cow barn. Cladosporium spore concentration in paper and pulp factory and countryside house also exceeded threshold value for clinical significance. Prolonged exposure in these environments could impose certain health risk. Thus, monitoring Cladosporium spore concentration in indoor environments is important for indoor air quality control.

  • 13513.
    Zeng, Qing-Yin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Westermark, Sven-Olof
    Rasmuson-Lestander, Åsa
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Wang, Xiao-Ru
    Detection and quantification of Cladosporium in aerosols by real-time PCR2006In: Journal of Environmental Monitoring, ISSN 1464-0325, E-ISSN 1464-0333, Vol. 8, no 1, p. 153-160Article in journal (Refereed)
    Abstract [en]

    Cladosporium is one of the most common airborne molds found in indoor and outdoor environments. Cladosporium spores are important aeroallergens, and prolonged exposure to elevated spore concentrations can provoke chronic allergy and asthma. To accurately quantify the levels of Cladosporium in indoor and outdoor environments, two real-time PCR systems were developed in this study. The two real-time PCR systems are highly specific and sensitive for Cladosporium detection even in a high background of other fungal DNAs. These methods were employed to quantify Cladosporium in aerosols of five different indoor environments. The investigation revealed a high spore concentration of Cladosporium (10(7) m(-3)) in a cow barn that accounted for 28-44% of the airborne fungal propagules. In a countryside house that uses firewood for heating and in a paper and pulp factory, Cladosporium was detected at 10(4) spores m(-3), which accounted for 2-6% of the fungal propagules in the aerosols. The concentrations of Cladosporium in these three indoor environments far exceeded the medical borderline level (3000 spores m(-3)). In a power station and a fruit and vegetable storage, Cladosporium was found to be a minor component in the aerosols, accounted for 0.01-0.1% of the total fungal propagules. These results showed that monitoring Cladosporium in indoor environments is more important than in outdoor environments from the public health point of view. Cladosporium may not be the dominant fungi in some indoor environments, but its concentration could still be exceeding the threshold value for clinical significance. The methods developed in this study could facilitate accurate detection and quantification of Cladosporium for public health related risk assessment.

  • 13514.
    Zeng, Qing-Yin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). National Institute for Working Life.
    Westermark, Sven-Olof
    Rasmuson-Lestander, Åsa
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Wang, Xiao-Ru
    Detection and quantification of Wallemia sebi in aerosols by real-time PCR, conventional PCR, and cultivation2004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, no 12, p. 7295-7302Article in journal (Refereed)
    Abstract [en]

    Wallemia sebi is a deuteromycete fungus commonly found in agricultural environments in many parts of the world and is suspected to be a causative agent of farmer's lung disease. The fungus grows slowly on commonly used culture media and is often obscured by the fast-growing fungi. Thus, its occurrence in different environments has often been underestimated. In this study, we developed two sets of PCR primers specific to W. sebi that can be applied in either conventional PCR or real-time PCR for rapid detection and quantification of the fungus in environmental samples. Both PCR systems proved to be highly specific and sensitive for W. sebi detection even in a high background of other fungal DNAs. These methods were employed to investigate the presence of W. sebi in the aerosols of a farm. The results revealed a high concentration of W. sebi spores, 10(7) m(-3) by real-time PCR and 10(6) m(-3) by cultivation, which indicates the prevalence of W. sebi in farms handling hay and grain and in cow barns. The methods developed in this study could serve as rapid, specific, and sensitive means of detecting W. sebi in aerosol and surface samples and could thus facilitate investigations of its distribution, ecology, clinical diagnosis, and exposure risk assessment.

  • 13515.
    Zetterström, Caroline E.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Small Molecules as Tools in Biological Chemistry: Effects of Synthetic and Natural Products on the Type III Secretion System2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The increasing use of antibiotics has led to a huge problem for society, as some bacteria have developed resistance towards many of the antibiotics currently available. To help find solutions to this problem we studied small molecules that inhibit bacterial virulence, the ability to cause disease. The type III secretion system (T3SS) is a conserved virulence system found in several gram-negative bacteria, including human and plants pathogens, such as Yersinia spp., Pseudomonas aeruginosa, Chlamydia spp., Salmonella spp., Shigella spp, enteropathogenic Escherichia coli (EPEC), enterohemorrhagic Escherichia coli (EHEC), and Erwinia spp. One class of virulence-blocking compounds is the salicylidene acylhydrazides. They were first identified in a screen towards the T3SS in Yersinia pseudotuberculosis and have since been shown to block the T3SS in a panel of gram-negative bacteria such as Chlamydia spp. Salmonella enterica, Shigella flexneri and EPEC.

    We designed and synthesized a library of 58 salicylidene acylhydrazides and evaluated their activity as virulence-blocking compounds in Y. pseudotuberculosis followed by calculations of quantitative structure activity relationships (QSARs). Four QSAR models were calculated, and when used in consensus they correctly classified between five out of eight compounds for Y. pseudotuberculosis as active or inactive and six out of eight compounds for C. trachomatis.

    Since the target and mode of action of the salicylidene acylhydrazides were unknown, we used solution and solid phase synthesis to synthesize three different affinity reagents. One of these affinity reagents was used in affinity chromatography experiments, where 19 putative target proteins from an E. coli O157 bacterial lysate were identified. We studied four of the proteins, Tpx, WrbA, FolX, and AdhE, in more detail in Y. pseudotuberculosis and E. coli O157. We believe that the salicylidene acylhydrazides act on multiple targets that together result in down-regulation of T3SS functions. A knockout of AdhE in E. coli O157 showed a similar phenotype as salicylidene acylhydrazide treated E. coli, suggesting that this protein may be particularly interesting as a drug target.

    Many of the antibiotics used today originate form natural sources. In contrast, most virulence-blocking compounds towards the T3SS are small synthetic organic molecules. Therefore, a prefractionated natural product library with marine and terrestrial biota samples was screened towards the T3SS in Y. pseudotuberculosis. Neohopeaphenol A was identified as a hit and shown to have micromolar activity towards Y. pseudotuberculosis and P. aeruginosa in cell-based infection models. 

  • 13516.
    Zetterström, Caroline E.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Hasselgren, Jenny
    Creative Antibiotics Sweden AB, Umeå, Sweden .
    Salin, Olli
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Department of Clinical Microbiology.
    Davis, Rohan A.
    Eskitis Institute, Griffith University, Brisbane, Australia.
    Quinn, Ronald J.
    Eskitis Institute, Griffith University, Brisbane, Australia.
    Sundin, Charlotta
    Creative Antibiotics Sweden AB, Umeå, Sweden .
    Elofsson, Mikael
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    The Resveratrol Tetramer (-)-Hopeaphenol Inhibits Type III Secretion in the Gram-Negative Pathogens Yersinia pseudotuberculosis and Pseudomonas aeruginosa2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 12, article id e81969Article in journal (Refereed)
    Abstract [en]

    Society faces huge challenges, as a large number of bacteria have developed resistance towards many or all of the antibiotics currently available. Novel strategies that can help solve this problem are urgently needed. One such strategy is to target bacterial virulence, the ability to cause disease e.g., by inhibition of type III secretion systems (T3SSs) utilized by many clinically relevant gram-negative pathogens. Many of the antibiotics used today originate from natural sources. In contrast, most virulence-blocking compounds towards the T3SS identified so far are small organic molecules. A recent high-throughput screening of a prefractionated natural product library identified the resveratrol tetramer (-)-hopeaphenol as an inhibitor of the T3SS in Yersinia pseudotuberculosis. In this study we have investigated the virulence blocking properties of (-)-hopeaphenol in three different gram-negative bacteria. (-)- Hopeaphenol was found to have micromolar activity towards the T3SSs in Yersinia pseudotuberculosis and Pseudomonas aeruginosa in cell-based infection models. In addition (-)-hopeaphenol reduced cell entry and subsequent intracellular growth of Chlamydia trachomatis.

  • 13517.
    Zetterström, Caroline E.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Uusitalo, Pia
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Qian, Weixing
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Hinch, Shannon
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Caraballo, Remi
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Grundström, Christin
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Elofsson, Mikael
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Screening for Inhibitors of Acetaldehyde Dehydrogenase (AdhE) from Enterohemorrhagic Escherichia coli (EHEC)2018In: SLAS Discovery, ISSN 2472-5552, Vol. 23, no 8, p. 815-822Article in journal (Refereed)
    Abstract [en]

    Acetaldehyde dehydrogenase (AdhE) is a bifunctional acetaldehyde-coenzyme A (CoA) dehydrogenase and alcohol dehydrogenase involved in anaerobic metabolism in gram-negative bacteria. This enzyme was recently found to be a key regulator of the type three secretion (T3S) system in Escherichia coli. AdhE inhibitors can be used as tools to study bacterial virulence and a starting point for discovery of novel antibacterial agents. We developed a robust enzymatic assay, based on the acetaldehyde-CoA dehydrogenase activity of AdhE using both absorption and fluorescence detection models (Z' > 0.7). This assay was used to screen similar to 11,000 small molecules in 384-well format that resulted in three hits that were confirmed by resynthesis and validation. All three compounds are noncompetitive with respect to acetaldehyde and display a clear dose-response effect with hill slopes of 1-2. These new inhibitors will be used as chemical tools to study the interplay between metabolism and virulence and the role of AdhE in T3S regulation in gram-negative bacteria, and as starting points for the development of novel antibacterial agents.

  • 13518.
    Zettervall, Niklas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Multi-scale methods for stochastic differential equations2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Standard Monte Carlo methods are used extensively to solve stochastic differential equations. This thesis investigates a Monte Carlo (MC) method called multilevel Monte Carlo that solves the equations on several grids, each with a specific number of grid points. The multilevel MC reduces the computational cost compared to standard MC. When using a fixed computational cost the variance can be reduced by using the multilevel method compared to the standard one. Discretization and statistical error calculations are also being conducted and the possibility to evaluate the errors coupled with the multilevel MC creates a powerful numerical tool for calculating equations numerically. By using the multilevel MC method together with the error calculations it is possible to efficiently determine how to spend an extended computational budget.

  • 13519. Zhan, Jiasui
    et al.
    Ericson, Lars
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Burdon, Jeremy J.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. State Key Laboratory for Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; CSIRO Agriculture & Food, Canberra, ACT, Australia.
    Climate change accelerates local disease extinction rates in a long-term wild host-pathogen association2018In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 24, no 8, p. 3526-3536Article in journal (Refereed)
    Abstract [en]

    Pathogens are a significant component of all plant communities. In recent years, the potential for existing and emerging pathogens of agricultural crops to cause increased yield losses as a consequence of changing climatic patterns has raised considerable concern. In contrast, the response of naturally occurring, endemic pathogens to a warming climate has received little attention. Here, we report on the impact of a signature variable of global climate change - increasing temperature - on the long-term epidemiology of a natural host-pathogen association involving the rust pathogen Triphragmium ulmariae and its host plant Filipendula ulmaria. In a host-pathogen metapopulation involving approximately 230 host populations growing on an archipelago of islands in the Gulf of Bothnia we assessed changes in host population size and pathogen epidemiological measures over a 25-year period. We show how the incidence of disease and its severity declines over that period and most importantly demonstrate a positive association between a long-term trend of increasing extinction rates in individual pathogen populations of the metapopulation and increasing temperature. Our results are highly suggestive that changing climatic patterns, particularly mean monthly growing season (April-November) temperature, are markedly influencing the epidemiology of plant disease in this host-pathogen association. Given the important role plant pathogens have in shaping the structure of communities, changes in the epidemiology of pathogens have potentially far-reaching impacts on ecological and evolutionary processes. For these reasons, it is essential to increase understanding of pathogen epidemiology, its response to warming, and to invoke these responses in forecasts for the future.

  • 13520. Zhan, Xuejia
    et al.
    Hu, Guangzhi
    Umeå University, Faculty of Science and Technology, Department of Physics. Laboratory of Environmental Science and Technology, The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, People’s Republic of China .
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Zhan, Shenshan
    Xu, Hanchu
    Zhou, Pei
    Electrochemical aptasensor for tetracycline using a screen-printed carbon electrode modified with an alginate film containing reduced graphene oxide and magnetite (Fe3O4) nanoparticles2016In: Microchimica Acta, ISSN 0026-3672, E-ISSN 1436-5073, Vol. 183, no 2, p. 723-729Article in journal (Refereed)
    Abstract [en]

    The authors describe a label-free electrochemical aptasensor for tetracycline (TET). The TET-binding aptamer was immobilized on a composite consisting of reduced graphene oxide, magnetite (Fe3O4) and sodium alginate, and this material was used to modify the surface of a screen-printed carbon electrode (SPCE). Cyclic voltammetry was carried out to characterize the single steps in the preparation of the modified electrode and to optimize the conditions for detection. Differential pulse voltammetry (DPV) was then used to monitor the interaction between aptamer and TET by applying the electrochemical probe thionine. Under optimal conditions, TET can be quantified by DPV in the 1 nM to 5 mu M concentration range, with a detection limit as low as 0.6 nM (at an S/N ratio of 3). The method is rapid, cost-efficient, highly sensitive and specific, and therefore is considered to be a viable platform for TET analysis in food, environmental, and clinical samples.

  • 13521. Zhan, Xuejia
    et al.
    Hu, Guangzhi
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Zhang, Dongwei
    Zhou, Pei
    A Label-Free Electrochemical Aptasensor for the Rapid Detection of Tetracycline Based on Ordered Mesoporous Carbon-Fe3O42018In: Australian journal of chemistry (Print), ISSN 0004-9425, E-ISSN 1445-0038, Vol. 71, no 2-3, p. 170-176Article in journal (Refereed)
    Abstract [en]

    A novel aptasensor based on a tetracycline (TET) aptamer immobilized by physical adsorption on an ordered mesoporous carbon-Fe3O4 (OMC-Fe3O4)-modified screen-printed electrode surface was successfully fabricated. OMC-Fe3O4 was characterized by scanning electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. The modification procedure of the aptasensor was characterized by cyclic voltammetry. Interaction between the TET aptamer and target was determined by differential pulse voltammetry. Under optimal conditions, the proposed aptasensor exhibited good electrochemical sensitivity to TET in a concentration range of 5 nM to 10 μM, with a detection limit of 0.8 nM (S/N =3D 3). This aptasensor exhibited satisfactory specificity, reproducibility, and stability.

  • 13522. Zhang, B
    et al.
    Miskolczi, P. C.
    Escamez, Sacha
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Turumtay, H
    Vanholme, R
    Hedenström, M
    Cao, Y
    Ma, L
    Bhalerao, R. P.
    Boerjan, W
    Tuominen, H
    PIRIN2 controls chromatin modification of lignin biosynthetic genes and modulates the non-cell autonomous xylem lignification in Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 13523. Zhang, Bo
    et al.
    Holmlund, Mattias
    Lorrain, Severine
    Norberg, Mikael
    Bakó, László
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Fankhauser, Christian
    Nilsson, Ove
    BLADE-ON-PETIOLE proteins act in an E3 ubiquitin ligase complex to regulate PHYTOCHROME INTERACTING FACTOR 4 abundance2017In: eLIFE, E-ISSN 2050-084X, Vol. 6, article id e26759Article in journal (Refereed)
    Abstract [en]

    Both light and temperature have dramatic effects on plant development. Phytochrome photoreceptors regulate plant responses to the environment in large part by controlling the abundance of PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. However, the molecular determinants of this essential signaling mechanism still remain largely unknown. Here, we present evidence that the BLADE-ON-PETIOLE (BOP) genes, which have previously been shown to control leaf and flower development in Arabidopsis, are involved in controlling the abundance of PIF4. Genetic analysis shows that BOP2 promotes photo-morphogenesis and modulates thermomorphogenesis by suppressing PIF4 activity, through a reduction in PIF4 protein level. In red-light-grown seedlings PIF4 ubiquitination was reduced in the bop2 mutant. Moreover, we found that BOP proteins physically interact with both PIF4 and CULLIN3A and that a CULLIN3-BOP2 complex ubiquitinates PIF4 in vitro. This shows that BOP proteins act as substrate adaptors in a CUL3BOP1/BOP2 E3 ubiquitin ligase complex, targeting PIF4 proteins for ubiquitination and subsequent degradation.

  • 13524.
    Zhang, Bo
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sztojka, Bernadette
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Escamez, Sacha
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Vanholme, Ruben
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wang, Yin
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gorzsás, András
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Boerjan, Wout
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    PIRIN2 suppresses S-type lignin accumulation in a noncell-autonomous manner in Arabidopsis xylem elements2019In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137Article in journal (Refereed)
    Abstract [en]
    • PIRIN (PRN) genes encode cupin domain‐containing proteins that function as transcriptional co‐regulators in humans but that are poorly described in plants. A previous study in xylogenic cell cultures of Zinnia elegans suggested a role for a PRN protein in lignification. This study aimed to identify the function of Arabidopsis (Arabidopsis thaliana) PRN proteins in lignification of xylem tissues.
    • Chemical composition of the secondary cell walls was analysed in Arabidopsis stems and/or hypocotyls by pyrolysis–gas chromatography/mass spectrometry, 2D‐nuclear magnetic resonance and phenolic profiling. Secondary cell walls of individual xylem elements were chemotyped by Fourier transform infrared and Raman microspectroscopy.
    • Arabidopsis PRN2 suppressed accumulation of S‐type lignin in Arabidopsis stems and hypocotyls. PRN2 promoter activity and PRN2:GFP fusion protein were localised specifically in cells next to the vessel elements, suggesting a role for PRN2 in noncell‐autonomous lignification of xylem vessels. Accordingly, PRN2 modulated lignin chemistry in the secondary cell walls of the neighbouring vessel elements.
    • These results indicate that PRN2 suppresses S‐type lignin accumulation in the neighbourhood of xylem vessels to bestow G‐type enriched lignin composition on the secondary cell walls of the vessel elements. Gene expression analyses suggested that PRN2 function is mediated by regulation of the expression of the lignin‐biosynthetic genes.
  • 13525.
    Zhang, Bo
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Tremousaygue, Dominique
    Denancé, Nicolas
    van Esse, H. Peter
    Hörger, Anja C.
    Dabos, Patrick
    Goffner, Deborah
    Thomma, Bart P. H. J.
    van der Hoorn, Renier A. L.
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    PIRIN2 stabilizes cysteine protease XCP2 and increases susceptibility to the vascular pathogen Ralstonia solanacearum in Arabidopsis2014In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 79, no 6, p. 1009-1019Article in journal (Refereed)
    Abstract [en]

    PIRIN (PRN) is a member of the functionally diverse cupin protein superfamily. There are four members of the Arabidopsis thaliana PRN family, but the roles of these proteins are largely unknown. Here we describe a function of the Arabidopsis PIRIN2 (PRN2) that is related to susceptibility to the bacterial plant pathogen Ralstonia solanacearum. Two prn2 mutant alleles displayed decreased disease development and bacterial growth in response to R. solanacearum infection. We elucidated the underlying molecular mechanism by analyzing PRN2 interactions with the papain-like cysteine proteases (PLCPs) XCP2, RD21A, and RD21B, all of which bound to PRN2 in yeast two-hybrid assays and in Arabidopsis protoplast co-immunoprecipitation assays. We show that XCP2 is stabilized by PRN2 through inhibition of its autolysis on the basis of PLCP activity profiling assays and enzymatic assays with recombinant protein. The stabilization of XCP2 by PRN2 was also confirmed in planta. Like prn2 mutants, an xcp2 single knockout mutant and xcp2 prn2 double knockout mutant displayed decreased susceptibility to R.solanacearum, suggesting that stabilization of XCP2 by PRN2 underlies susceptibility to R.solanacearum in Arabidopsis.

  • 13526.
    Zhang, Chang
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Construction and Calibration of a Watt Balance2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    We build a calibration system for a Watt balance. The Watt balance uses the Lorentz force acting on a current-carrying coil attached to the weighing pan and placed in a radial magnetic field to balance the gravitational force acting on the measured object. To calibrate the balance, we determine the constant value BL (where B is the total magnetic flux through the coil and L is the total length of the wire around the coil) for the coil A and coil B installed under the weighing pans. We perform two modes of operation to measure BL: velocity mode by applying Faraday's law of induction, and force mode, using magnetic force acting on the coil carrying a current and a set of reference masses.

    We find that BL from the velocity mode for coil A is 4.2±0.2 [(Vs)/m] and 3.9±0.1 [(Vs)/m] for coil B, while from force mode, BL is 3.91±0.04 [(Vs)/m] for coil A and 3.42±0.04 [(Vs)/m] for coil B. Considering the error from reference masses, we use the results of the velocity mode as the most accurate value of BL for the coils.

  • 13527. Zhang, Feng
    et al.
    Nilsson, Christer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Xu, Zhenzhu
    Zhou, Guangsheng
    Evaluation of restoration approaches on the Inner Mongolian Steppe based on criteria of the Society for Ecological Restoration2019In: Land Degradation and Development, ISSN 1085-3278, E-ISSN 1099-145XArticle in journal (Refereed)
    Abstract [en]

    Ecological restoration is becoming an increasingly common management tool worldwide. However, a challenge still exists on how to effectively monitor restoration outcomes and evaluate restoration success for ecological restoration managers. In this review, the goal is to evaluate whether the research in a degraded area has been sufficient for fostering efficient restoration measures and follow-up of restoration success based on the Society for Ecological Restoration (SER) criteria. We selected the Inner Mongolian Steppe (IMS) in China as a model system. This area has been the subject of substantial research over the most recent years to understand degradation processes and restoration outcomes. We put together the variables used to assess degradation and restoration needs in the IMS and analyzed restoration results based on SER's nine criteria for evaluating restoration success. We found that the accomplished research in the IMS only partially supplied the data needed for evaluation of restoration success. The available results were sufficient for a proper evaluation of species composition and tentatively supported assessments of another seven criteria but not self-sustainability. Grazing exclusion led to the fastest and most successful recovery of degraded steppe, but landscape-scale processes during restoration in the IMS are still incompletely known. Our review supports large-scale restoration of the IMS and emphasizes the need for long-time monitoring for a more complete evaluation of the outcome of the IMS restoration following all SER's criteria.

  • 13528. Zhang, Feng
    et al.
    Zhou, Guangsheng
    Nilsson, Christer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Remote estimation of the fraction of absorbed photosynthetically active radiation for a maize canopy in Northeast China2015In: Journal of Plant Ecology, ISSN 1752-9921, E-ISSN 1752-993X, Vol. 8, no 4, p. 429-435Article in journal (Refereed)
    Abstract [en]

    Aims Accurate remote estimation of the fraction of absorbed photosynthetically active radiation (fAPAR) is essential for the light use efficiency (LUE) models. Currently, one challenge for the LUE models is lack of knowledge about the relationship between fAPAR and the normalized difference vegetation index (NDVI). Few studies have tested this relationship against field measurements and evaluated the accuracy of the remote estimation method. This study aimed to reveal the empirical relationship between NDVI and fAPAR and to improve algorithms for remote estimation of fAPAR.

    Methods To investigate the method of remote estimation of fAPAR seasonal dynamics, the CASA (Carnegie-Ames-Stanford Approach) model and spectral vegetation indices (VIs) were used for in situ measurements of spectral reflectance and fAPAR during the growing season of a maize canopy in Northeast China.

    Important Findings The results showed that the fAPAR increased rapidly with the day of year during the vegetative stage, it remained relatively stable at the stage of reproduction, and finally decreased slowly during the senescence stage. In addition, fAPAR(green) [fAPAR(green) = fAPAR x (green LAI/green LAI(max))] showed clearer seasonal trends than fAPAR. The NDVI, red-edge NDVI, wide dynamic range vegetation index, red-edge position (REP) and REP with Sentinel-2 bands derived from hyperspectral remote sensing data were all significantly positively related to fAPAR(green) during the entire growing season. In a comparison of the predictive performance of VIs for the whole growing season, REP was the most appropriate spectral index, and can be recommended for monitoring seasonal dynamics of fAPAR in a maize canopy.

  • 13529. Zhang, Feng
    et al.
    Zhou, Guangsheng
    Wang, Yu
    Yang, Fulin
    Nilsson, Christer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Evapotranspiration and crop coefficient for a temperate desert steppe ecosystem using eddy covariance in Inner Mongolia, China2012In: Hydrological Processes, ISSN 0885-6087, E-ISSN 1099-1085, Vol. 26, no 3, p. 379-386Article in journal (Refereed)
    Abstract [en]

    Evapotranspiration (ET), which links water, energy and the carbon cycle in terrestrial ecosystems, is an important eco-hydrological process, especially in arid and semi-arid regions. To determine the crop coefficient (K-c) over a 2-year period for a temperate desert steppe in Inner Mongolia, China, ET was measured using the eddy covariance method and the reference evapotranspiration (ET0) was estimated from site meteorological data. The results showed that the seasonal variation of ET differed on an annual timescale between the 2 consecutive years, exhibiting a multi-peak curve in 2008 and a single peak in 2009. The mean daily K-c values were 0.15 and 0.17 in 2 years, varying from 0.009 to 0.75 in 2008 and from 0.005 to 0.58 in 2009. The 5-day moving average for K-c values was mainly affected by SWC10cm and R-n, and the regression coefficients (R-2) were 58.9 and 69.5%, respectively. These results will aid in making accurate and quantitative assessments of the vulnerability of the sparse vegetation to climate change.

    Copyright (C) 2011 John Wiley & Sons, Ltd.

  • 13530. Zhang, Guobin
    et al.
    Zhao, Miao
    Yan, Chunli
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Sun, Bing
    Wu, Zonggang
    Chang, Hudong
    Jin, Zhi
    Sun, Jie
    Liu, Honggang
    Thermal Analysis of AlGaN/GaN High-Electron-Mobility Transistors with Graphene2018In: Journal of Nanoscience and Nanotechnology, ISSN 1533-4880, E-ISSN 1533-4899, Vol. 18, no 11, p. 7578-7583Article in journal (Refereed)
    Abstract [en]

    A thermal analysis of AlGaN/GaN high electron mobility transistors (HEMTs) with Graphene is investigated using Silvaco and Finite Element Method. Two thermal management solutions are adopted; first of all, graphene is used as dissipation material between SiC substrate and GaN buffer layer to reduce thermal boundary resistance of the device. At the same time, graphene is also used as a thermal spread material on the top of the source contacts to reduce thermal resistance of the device. The thermal analysis results show that the temperature rise of device adopting graphene decreases by 46.5% in transistors operating at 13.86 W/mm. Meanwhile, the thermal resistance of GaN HEMTs with graphene is 6.8 K/W, which is much lower than the device without graphene, which is 18.5 K/W. The thermal management solutions are useful for integration of large-scale graphene into practical devices for effective heat spreading in AlGaN/GaN HEMT.

  • 13531.
    Zhang, Hanqing
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Construction of an Optical Tweezers Instrumentation and Validation of Brownian motion2011Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    We constructed a standalone optical trapping system that was steerable in three dimensions and allowed for sufficient imaging of one цm particles with a CCD camera. The motion of the trapped particles was monitored by both a position sensitive detector as well with the CCD camera. The trap stiffness was evaluated by the power spectrum method and the equipartition theorem. For calibration of the stiffness of the trap, we found that the power spectrum method with data assessed by the PSD was most straightforward and accurate. The equipartition method was compromised by noise, low resolution and the bandwidth of the detector. With a HeNe laser run at 10 mW output power the trap strength of our system reached ~2 pN/um. The results also showed a decrease in the trap stiffness and particle's position variance when the size of trapped particles increased.

  • 13532.
    Zhang, Hanqing
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Digital holography and image processing methods for applications in biophysics2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Understanding dynamic mechanisms, morphology and behavior of bacteria are important to develop new therapeutics to cure diseases. For example, bacterial adhesion mechanisms are prerequisites for initiation of infections and for several bacterial strains this adhesion process is mediated by adhesive surface organelles, also known as fimbriae. Escherichia coli (E. coli) is a bacterium expressing fimbriae of which pathogenic strains can cause severe diseases in fluidic environments such as the urinary tract and intestine. To better understand how E. coli cells attach and remain attached to surfaces when exposed to a fluid flow using their fimbriae, experiments using microfluidic channels are important; and to assess quantitative information of the adhesion process and cellular information of morphology, location and orientation, the imaging capability of the experimental technique is vital.

    In-line digital holographic microscopy (DHM) is a powerful imaging technique that can be realized around a conventional light microscope. It is a non-invasive technique without the need of staining or sectioning of the sample to be observed in vitro. DHM provides holograms containing three-dimensional (3D) intensity and phase information of cells under study with high temporal and spatial resolution. By applying image processing algorithms to the holograms, quantitative measurements can provide information of position, shape, orientation, optical thickness of the cell, as well as dynamic cell properties such as speed, growing rate, etc.

    In this thesis, we aim to improve the DHM technique and develop image processing methods to track and assess cellular properties in microfluidic channels to shed light on bacterial adhesion and cell morphology. To achieve this, we implemented a DHM technique and developed image processing algorithms to provide for a robust and quantitative analysis of holograms. We improved the cell detection accuracy and efficiency in DHM holograms by developing an algorithm for detection of cell diffraction patterns. To improve the 3D detection accuracy using in-line digital holography, we developed a novel iterative algorithm that use multiple-wavelengths. We verified our algorithms using synthetic, colloidal and cell data and applied the algorithms for detecting, tracking and analysis. We demonstrated the performance when tracking bacteria with sub-micrometer accuracy and kHz temporal resolution, as well as how DHM can be used to profile a microfluidic flow using a large number of colloidal particles. We also demonstrated how the results of cell shape analysis based on image segmentation can be used to estimate the hydrodynamic force on tethered capsule-shaped cells in micro-fluidic flows near a surface.

  • 13533.
    Zhang, Hanqing
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Stangner, Tim
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wiklund, Krister
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Object plane detection and phase retrieval from single-shot holograms using multi-wavelength in-line holographyManuscript (preprint) (Other academic)
    Abstract [en]

    Phase retrieval and the twin-image problem in digital in-line holographic microscopy can be resolvedby iterative reconstruction routines. However, recovering the phase properties of an object in a hologramneeds an object plane to be chosen correctly for reconstruction. In this work, we present a novelmulti-wavelength Gerchberg-Saxton algorithm to determine the object plane using single-shot hologramsrecorded with multiple wavelengths in an in-line holographic microscope. For micro-sized objects, weverify the object positioning capabilities of the method for various shapes and derive the phase informationusing synthetic and experimental data. Experimentally, we built a compact digital in-line holographicmicroscopy setup around a standard optical microscope with a regular RGB-CCD camera andacquire holograms of micro-spheres, E. coli and red blood cells, that are illuminated using three lasersoperating at 491nm, 532nm and 633nm, respectively. We demonstrate that our method provides accurateobject plane detection and phase retrieval under noisy conditions, e.g., using low-contrast hologramswithout background normalization. This method allows for automatic positioning and phase retrievalsuitable for holographic particle velocimetry, and object tracking in biophysical or colloidal research.

  • 13534.
    Zhang, Hanqing
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Stangner, Tim
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wiklund, Krister
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Object plane detection and phase retrieval from single-shot holograms using multi-wavelength in-line holography2018In: Applied Optics, ISSN 1559-128X, E-ISSN 2155-3165, Vol. 57, no 33, p. 9855-9862Article in journal (Refereed)
    Abstract [en]

    Phase retrieval and the twin-image problem in digital in-line holographic microscopy can be resolved by iterative reconstruction routines. However, recovering the phase properties of an object in a hologram requires an object plane to be chosen correctly for reconstruction. In this work, we present a novel multi-wavelength iterative algorithm to determine the object plane using single-shot holograms recorded at multiple wavelengths in an in-line holographic microscope. Using micro-sized objects, we verify the object positioning capabilities of the method for various shapes and derive the phase information using synthetic and experimental data. Experimentally, we built a compact digital in-line holographic microscopy setup around a standard optical microscope with a regular RGB-CCD camera and acquired holograms of micro-spheres, E. coli, and red blood cells, which are illuminated using three lasers operating at 491 nm, 532 nm, and 633 nm, respectively. We demonstrate that our method provides accurate object plane detection and phase retrieval under noisy conditions, e.g., using low-contrast holograms with an inhomogeneous background. This method allows for automatic positioning and phase retrieval suitable for holographic particle velocimetry, and object tracking in biophysical or colloidal research. 

  • 13535.
    Zhang, Hanqing
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Stangner, Tim
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wiklund, Krister
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rodrigues, Alvaro
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    UmUTracker: a versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data2017In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 219, p. 390-399Article in journal (Refereed)
    Abstract [en]

    We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the 2D lateral positions of particles with an algorithm based on the isosceles triangle transform, and reconstructs their 3D axial positions by a fast implementation of the Rayleigh-Sommerfeld model using a radial intensity profile. To validate the accuracy and performance of our program, we first track the 2D position of polystyrene particles using bright field and digital holographic microscopy. Second, we determine the 3D particle position by analyzing synthetic and experimentally acquired holograms. Finally, to highlight the full program features, we profile the microfluidic flow in a 100 gm high flow chamber. This result agrees with computational fluid dynamic simulations. On a regular desktop computer UmUTracker can detect, analyze, and track multiple particles at 5 frames per second for a template size of 201 x 201 in a 1024 x 1024 image. To enhance usability and to make it easy to implement new functions we used object-oriented programming. UmUTracker is suitable for studies related to: particle dynamics, cell localization, colloids and microfluidic flow measurement.

    Program summary

    Program title: UmUTracker Program Files doi: http://dx.doi.org/10.17632/fkprs4s6xp.1

    Licensing provisions: Creative Commons by 4.0 (CC by 4.0)

    Programming language: MATLAB Nature of problem: 3D multi-particle tracking is a common technique in physics, chemistry and biology. However, in terms of accuracy, reliable particle tracking is a challenging task since results depend on sample illumination, particle overlap, motion blur and noise from recording sensors. Additionally, the computational performance is also an issue if, for example, a computationally expensive process is executed, such as axial particle position reconstruction from digital holographic microscopy data. Versatile robust tracking programs handling these concerns and providing a powerful post-processing option are significantly limited.

    Solution method: UmUTracker is a multi-functional tool to extract particle positions from long video sequences acquired with either light microscopy or digital holographic microscopy. The program provides an easy-to-use graphical user interface (GUI) for both tracking and post-processing that does not require any programming skills to analyze data from particle tracking experiments. UmUTracker first conduct automatic 2D particle detection even under noisy conditions using a novel circle detector based on the isosceles triangle sampling technique with a multi-scale strategy. To reduce the computational load for 3D tracking, it uses an efficient implementation of the Rayleigh-Sommerfeld light propagation model. To analyze and visualize the data, an efficient data analysis step, which can for example show 4D flow visualization using 3D trajectories, is included. Additionally, UmUTracker is easy to modify with user customized modules due to the object-oriented programming style.

    Additional comments: Program obtainable from https://sourceforge.net/projects/umutracker/

  • 13536.
    Zhang, Hanqing
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Söderholm, Niklas
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Sandblad, Linda
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Wiklund, Krister
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    DSeg: a dynamic image segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures2019In: Microscopy and Microanalysis, ISSN 1431-9276, E-ISSN 1435-8115, Vol. 25, no 3, p. 711-719Article in journal (Refereed)
    Abstract [en]

    Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. It is even more problematic if these structures continuously grow when recording a time-series of images. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. The program includes a robust binary level-set algorithm modified to use size constraints, edge intensity, and past information. We verify our algorithms using synthetic data, differential interference contrast images of filamentous prokaryotes, and transmission electron microscopy images of bacterial adhesion fimbriae. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available at Sourceforge.

  • 13537. Zhang, Hao
    et al.
    Yoshizawa, Susumu
    Sun, Ying
    Huang, Yongjie
    Chu, Xiao
    Gonzalez, Jose M.
    Pinhassi, Jarone
    Luo, Haiwei
    Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 2, p. 648-666Article in journal (Refereed)
    Abstract [en]

    The taxonomy of marine and non-marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean-to-land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non-marine adaptive genes. This included various Na+-dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non-marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K+ scavenging ATPase was repeatedly gained whereas the corresponding low-affinity transporter repeatedly lost upon transitions, reflecting K+ ions are less available to non-marine bacteria. Strikingly, the central metabolism Na+-translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H+-translocating counterpart was repeatedly gained in non-marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non-marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non-marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.

  • 13538.
    Zhang, Hong
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Jiangsu Univ, Dept Math, Zhenjiang 212013, Jiangsu, Peoples R China.
    Georgescu, Paul
    The global properties of an age-dependent SI model involving pathogenic virus release and defence mechanisms for pests2010In: Mathematical and computer modelling, ISSN 0895-7177, E-ISSN 1872-9479, Vol. 52, no 1-2, p. 37-54Article in journal (Refereed)
    Abstract [en]

    Insect pests are common but undesirable elements in ecosystems and represent thorny problems for most developing countries. To prevent pest outbreaks, growers often resort to insect-pathogenic viruses rather than to pesticides which affect human health and the environment. The purpose of this paper is to investigate a new age-structured pest management model which describes the interaction between susceptible insect pests, infected insect pests, pathogenic viruses and defence immunity mechanisms. A feature of this model is that it accounts for the dependence of the amount of pathogenic viruses released and of the efficiency of the defence mechanisms upon the so-called age of infection. First, the asymptotic behavior of the system is established via a monotonicity argument which makes use of several integral inequalities, being shown that the infection ultimately dies out, while under certain circumstances the susceptible pests also become extinct. By means of the Michailov criterion, one then analyzes the linearized stability of the trivial equilibrium and of the semi-trivial infected pest-free equilibrium. In this regard, it is observed that the defence mechanisms and maximal length of the infective period play important roles in the dynamics of the system. Several pest controls strategies are further investigated by means of numerical simulations, which show that when the dose of pathogenic viruses released initially is larger than a certain amount the profile of the response of defence mechanisms can be modified by changing this dose. Finally, the paper is concluded with a discussion on the biological significance of the mathematical results and framework.

  • 13539.
    Zhang, Hong
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Department of Mathematics, Jiangsu University, Zhenjiang, 212013, Jiangsu Province, P. R. China.
    Georgescu, Paul
    Nieto, Juan J
    Chen, Lan-sun
    Impulsive perturbation and bifurcation of solutions for a model of chemostat with variable yield2009In: Applied mathematics and mechanics, ISSN 0253-4827, E-ISSN 1573-2754, Vol. 30, no 7, p. 933-944Article in journal (Refereed)
    Abstract [en]

    In this paper, we consider a variable yield model of a single-species growth in a well-stirred tank containing fresh medium, assuming the instances of time as triggering factors in which the nutrient refilling process and the removal of microorganisms by the uptake of lethal external antibiotic are initiated. It is also assumed that the periodic nutrient refilling and the periodic antibiotic injection occur with the same periodicity, but not simultaneously. The model is then formulated in terms of autonomous differential equations subject to impulsive perturbations. It is observed that either the population of microorganisms essentially washes out, or more favorably, the system is permanent. To describe this dichotomy, some biologically significant integral conditions are introduced. Further, it is shown that in a certain critical situation, a nontrivial periodic solution emerges via a bifurcation phenomenon. Finally, the dynamics of the model is illustrated with numerical experiments and computer simulations.

  • 13540. Zhang, Hong
    et al.
    Georgescu, Paul
    Zhang, Lai
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Periodic patterns and Pareto efficiency of state dependent impulsive controls regulating interactions between wild and transgenic mosquito populations2016In: Communications in nonlinear science & numerical simulation, ISSN 1007-5704, E-ISSN 1878-7274, Vol. 31, no 1-3, p. 83-107Article in journal (Refereed)
    Abstract [en]

    It is conceivable that genetically modified mosquitoes could stop the spread of malaria, by outcompeting the wild mosquitoes and interfering with their reproductive processes, and genetically inheriting and further transmitting a diminished potential to carry Plasmodium. To get insight into the possible outcomes, we formulate an ODE model for the interactions between wild and transgenic mosquito populations, which is subject to state-dependent impulsive perturbations. By first investigating the dynamics of the unperturbed system, we determine certain sufficient conditions for the existence and orbital stability of positive order-1 solution of the model system with state-dependent impulsive perturbations. Their feasibility is then illustrated by means of numerical simulations. In addition, to adequately control the wild mosquito population, we use a multi-target approach which, in addition to accounting for the total costs, keeps track of the total size of the wild mosquito population. To trade off these objectives, we consider the concept of Pareto efficiency to determine suitable control strategies which are near-optimal. Finally, we carry out numerical simulations to illustrate the Pareto frontier and then characterize the detailed Pareto efficient control regime. (C) 2015 Elsevier B.V. All rights reserved.

  • 13541.
    Zhang, Hui
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Digital holographic imaging using a point source - Investigation of microparticles diffusion2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The aim of this project was build a digital holographic microscopy setup to measure the diffusion coefficient of polystyrene micro-particles in water under room temperature. We used a laser operating with a wavelength of 633 nm, a pinhole to create spherical wave. We made a sample consisting of polystyrene micro-particles with a diameter of 2 μm, an objective with a magnification factor of 40, a CMOS camera as a detector, to build a digital in-line holographic microscopy setup to record holograms. These holograms carried the information of the objects and we could derive the 3D coordinates of those microparticles by using a numerical reconstruction algorithm. We can calculated the mean squared displacement (MSD) by using the particle’s trajectories and determine the diffusion coefficient with the slope of MSD over time. We found the diffusion coefficient in X axis and Y to be 1.86810·10-13 m2/s, and 2.55210·10-13 m2/s, respectively. And the relative error of the diffusion coefficient in our measurement is 0.73% for X axis and 37.6% for Y axis, compared with the theoretical diffusion coefficient 1.8545·10-13 m2/s.

  • 13542.
    Zhang, Hui
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Measurement of the emission spectrum from a super luminescent white diode with a Fourier transform spectrometer2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    A Fourier transform spectrometer (FTS) was constructed to analyze the light of a white LED. The spectrometer utilizes re-sampling with the help of a reference interferogram from a HeNe laser. The resolution was estimated from the measured line width of the re-sampled HeNe laser and was found to be in the order of 0.4 nm. The spectrum collated from the white diode had a signal to noise ratio of 350 which was more than sufficient for our purposes. The measured spectrum point towards the light being produced by a combination of red and blue LED:s and a phosphor layer of YAG:Ce providing the green-yellow colors.

  • 13543.
    Zhang, Huichun
    et al.
    College of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China.
    Dorr, Gary
    Faculty of Science, The University of Queensland, Brisbane 4343, Australia.
    Zhang, Jiaqiang
    College of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China.
    Zhou, Hongping
    College of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Wind tunnel experiment and regression model for spray drift2015In: Transactions of the Chinese Society of Agricultural Engineering, ISSN 1002-6819, Vol. 31, no 3, p. 94-100Article in journal (Refereed)
    Abstract [en]

    With greater environmental awareness, the movement of pesticides within and off of a spray target area is acritical public concern. Ideally, all of the material applied should be deposited within the targeted swath on the intendedpest or plant. But realistically, a portion of the spray remains airborne and is carried downwind to non-target areas.Airborne spray leaving the targeted area reduces the applied dosage, and could cause damage to neighboring plant andwater source or other detrimental environmental impacts. To study the influences of nozzle type, spray mixture and windspeed on spray drift, experiments were conducted using a wind tunnel. Spray drift risk was assessed by adding a tracer tothe spray mixture and measuring the quantities of spray deposited downwind from the nozzle on horizontal polythenelines with 2 mm diameter perpendicular to the wind direction in a vertical and a horizontal array. At a distance of 2 mdownwind from the static nozzle, five collector lines (V1 to V5) were positioned one above the other at the spacing of0.1 m to provide an estimate of the spray still airborne through this vertical profile. An additional five sampling collectorstrings (H1 to H5) were placed in a horizontal array with one-meter horizontal spacing at 0.1 m height to determine thefallout volumes and gradients of the spray from 2 to 6 m downwind. A water-soluble fluorescent tracer was dissolvedinto tap water as the spray liquid, and after the experiments, the collecting lines were washed with deionized water tomeasure deposit and drift. The results indicated that deposits on sampling collector decreased with increased verticalelevation and horizontal distance. Average fallout and airborne deposit resulting from the different spray applicationswere shown in the paper. These figures showed the expected fallout and airborne profiles for all tested nozzle types andsizes. The highest fallout deposits were measured at a position closest to the nozzle (H1) with a systematic decrease withthe distance from the nozzle. The highest airborne deposits were found at the lowest sampling collector (V1) with asystematic decrease with increasing height above the wind tunnel floor. Airborne spray drift was affected by wind speed.At all sample positions, deposits on collectors were reduced at lower wind speed. Nozzle’s structure was also found toinfluence droplet’s size, so injector/pre-orifice nozzle produced coarser droplets and reduced spray drift. The amount ofspray recovered is based on the amount of active ingredient of spray mixture within each droplet rather than the totaldroplet volume. On that basis, a multiple non-linear model for statistical drift prediction including four independent,non-correlated variables (target distance, wind speed, nozzle type and chemical type) was established. The regressionmodel provided a drift evaluation approach, and it was important in the interpretation of wind tunnel data for differentnozzle types, chemical types and sampling methodologies.

  • 13544.
    Zhang, Jin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Begum, Afshan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brännström, Kristoffer
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Grundström, Christin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Iakovleva, Irina
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Olofsson, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Sauer-Eriksson, A. Elisabeth
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Andersson, Patrik L.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Structure-based Virtual Screening Protocol for in silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin2016In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 50, no 21, p. 11984-11993Article in journal (Refereed)
    Abstract [en]

    Thyroid disruption by xenobiotics is associated with a broad spectrum of severe adverse outcomes. One possible molecular target of thyroid hormone disrupting chemicals (THDCs) is transthyretin (TTR), a thyroid hormone transporter in vertebrates. To better understand the interactions between TTR and THDCs, we determined the crystallographic structures of human TTR in complex with perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), and 2,2',4,4'-tetrahydroxybenzophenone (BP2). The molecular interactions between the ligands and TTR were further characterized using molecular dynamics simulations. A structure-based virtual screening (VS) protocol was developed with the intention of providing an efficient tool for the discovery of novel TTR-binders from the Tox21 inventory. Among the 192 predicted binders, 12 representatives were selected, and their TTR binding affinities were studied with isothermal titration calorimetry, of which seven compounds had binding affinities between 0.26 and 100 mu M. To elucidate structural details in their binding to TTR, crystal structures were determined of TTR in complex with four of the identified compounds including 2,6-dinitro-p-cresol, bisphenol S, clonixin, and triclopyr. The compounds were found to bind in the TTR hormone binding sites as predicted. Our results show that the developed VS protocol is able to successfully identify potential THDCs, and we suggest that it can be used to propose THDCs for future toxicological evaluations.

  • 13545.
    Zhang, Jin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Grundström, Christin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brännström, Kristoffer
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Iakovleva, Irina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindberg, Mikael J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Olofsson, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Andersson, Patrik L.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sauer-Eriksson, A. Elisabeth
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Interspecies variation between fish and human transthyretins in their binding of thyroid-disrupting chemicals2018In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 52, no 20, p. 11865-11874Article in journal (Refereed)
    Abstract [en]

    Thyroid-disrupting chemicals (TDCs) are xenobiotics that can interfere with the endocrine system and cause adverse effects in organisms and their offspring. TDCs affect both the thyroid gland and regulatory enzymes associated with thyroid hormone homeostasis. Transthyretin (TTR) is found in the serum and cerebrospinal fluid of vertebrates, where it transports thyroid hormones. Here, we explored the interspecies variation in TDC binding to human and fish TTR (exemplified by Gilthead seabream (Sparus aurata)). The in vitro binding experiments showed that TDCs bind with equal or weaker affinity to seabream TTR than to the human TTR, in particular, the polar TDCs (>500-fold lower affinity). Crystal structures of the seabream TTR TDC complexes revealed that all TDCs bound at the thyroid binding sites. However, amino acid substitution of Ser117 in human TTR to Thr117 in seabream prevented polar TDCs from binding deep in the hormone binding cavity, which explains their low affinity to seabream TTR Molecular dynamics and in silico alanine scanning simulation also suggested that the protein backbone of seabream TTR is more rigid than the human one and that Thr117 provides fewer electrostatic contributions than Ser117 to ligand binding. This provides an explanation for the weaker affinities of the ligands that rely on electrostatic interactions with Thr117. The lower affinities of TDCs to fish TTR, in particular the polar ones, could potentially lead to milder thyroid-related effects in fish.

  • 13546.
    Zhang, Jin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kamstra, Jorke H.
    Ghorbanzadeh, Mehdi
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Weiss, Jana M.
    Hamers, Timo
    Andersson, Patrik L.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    In Silico Approach To Identify Potential Thyroid Hormone Disruptors among Currently Known Dust Contaminants and Their Metabolites2015In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 49, no 16, p. 10099-10107Article in journal (Refereed)
    Abstract [en]

    Thyroid hormone disrupting chemicals (THDCs) interfere with the thyroid hormone system and may induce multiple severe physiological disorders. Indoor dust ingestion is a major route of THDCs exposure in humans, and one of the molecular targets of these chemicals is the hormone transporter transthyretin (TTR). To virtually screen indoor dust contaminants and their metabolites for THDCs targeting TTR, we developed a quantitative structure activity relationship (QSAR) classification model. The QSAR model was applied to an in-house database including 485 organic dust contaminants reported from literature data and their 433 in silico derived metabolites. The model predicted 37 (7.6%) dust contaminants and 230 (53.1%) metabolites as potential TTR binders. Four new THDCs were identified after testing 23 selected parent dust contaminants in a radio-ligand TTR binding assay; 2,2',4,4'-tetrahydroxybenzophenone, perfluoroheptanesulfonic acid, 3,5,6-trichloro-2-pyridinol, and 2,4,5-trichlorophenoxyacetic acid. These chemicals competitively bind to TTR with 50% inhibition (IC50) values at or below 10 mu M. Molecular docking studies suggested that these THDCs interacted similarly with TTR via the residue Ser117A, but their binding poses were dissimilar to the endogenous ligand T4. This study identified new THDCs using an in silico approach in combination with bioassay testing and highlighted the importance of metabolic activation for TTR binding.

  • 13547.
    Zhang, Jin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mucs, Daniel
    Norinder, Ulf
    Svensson, Fredrik
    LightGBM: An Effective and Scalable Algorithm for Prediction of Chemical Toxicity-Application to the Tox21 and Mutagenicity Data Sets2019In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 59, no 10, p. 4150-4158Article in journal (Refereed)
    Abstract [en]

    Machine learning algorithms have attained widespread use in assessing the potential toxicities of pharmaceuticals and industrial chemicals because of their faster speed and lower cost compared to experimental bioassays. Gradient boosting is an effective algorithm that often achieves high predictivity, but historically the relative long computational time limited its applications in predicting large compound libraries or developing in silico predictive models that require frequent retraining. LightGBM, a recent improvement of the gradient boosting algorithm, inherited its high predictivity but resolved its scalability and long computational time by adopting a leaf-wise tree growth strategy and introducing novel techniques. In this study, we compared the predictive performance and the computational time of LightGBM to deep neural networks, random forests, support vector machines, and XGBoost. All algorithms were rigorously evaluated on publicly available Tox21 and mutagenicity data sets using a Bayesian optimization integrated nested 10-fold cross-validation scheme that performs hyperparameter optimization while examining model generalizability and transferability to new data. The evaluation results demonstrated that LightGBM is an effective and highly scalable algorithm offering the best predictive performance while consuming significantly shorter computational time than the other investigated algorithms across all Tox21 and mutagenicity data sets. We recommend LightGBM for applications of in silico safety assessment and also other areas of cheminformatics to fulfill the ever-growing demand for accurate and rapid prediction of various toxicity or activity related end points of large compound libraries present in the pharmaceutical and chemical industry.

  • 13548.
    Zhang, Jingpu
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Larsson, Jan
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Rasmuson-Lestander, Åsa
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Expression preference of the S-adenosylmethionine synthetase (SamS) gene in Drosophila melanogaster1997In: Dev Rep Biol, Vol. 6, p. 7-17Article in journal (Other (popular science, discussion, etc.))
  • 13549.
    Zhang, Lai
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Technical University of Denmark, Denmark ; International Institute for Applied Systems Analysis, Laxenburg, Austria.
    Andersen, Ken H.
    Dieckmann, Ulf
    Brannstrom, Ake
    Four types of interference competition and their impacts on the ecology and evolution of size-structured populations and communities2015In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 380, p. 280-290Article in journal (Refereed)
    Abstract [en]

    We investigate how four types of interference competition which alternatively affect foraging, metabolism, survival, and reproduction impact the ecology and evolution of size-structured populations. Even though all four types of interference competition reduce population biomass, interference competition at intermediate intensity sometimes significantly increases the abundance of adult individuals and the population's reproduction rate. We find that foraging and metabolic interference evolutionarily favor smaller maturation size when interference is weak and larger maturation size when interference is strong. The evolutionary response to survival interference and reproductive interference is always larger maturation size. We also investigate how the four types of interference competition impact the evolutionary dynamics and resultant diversity and trophic structure of size-structured communities. Like other types of trait-mediated competition, all four types of interference competition can induce disruptive selection and thus promote initial diversification. Even though foraging interference and reproductive interference are more potent in promoting initial diversification, they catalyze the formation of diverse communities with complex trophic structure only at high levels of interference intensity. By contrast, survival interference does so already at intermediate levels, while reproductive interference can only support relatively smaller communities with simpler trophic structure. Taken together, our results show how the type and intensity of interference competition jointly affect coexistence patterns in structured population models. (C) 2015 Elsevier Ltd. All rights reserved.

  • 13550.
    Zhang, Lai
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Dieckmann, Ulf
    Brännström, Åke
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Evolution and Ecology Program, International Institute for Applied Systems Analysis, A-2361 Laxenburg, Austria.
    On the performance of four methods for the numerical solution of ecologically realistic size-structured population models2017In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 8, no 8, p. 948-956Article in journal (Refereed)
    Abstract [en]

    1. Size-structured population models (SSPMs) are widely used in ecology to account for intraspecific variation in body size. Three characteristic features of size-structured populations are the dependence of life histories on the entire size distribution, intrinsic population renewal through the birth of new individuals, and the potential accumulation of individuals with similar body sizes due to determinate or stunted growth. Because of these three features, numerical methods that work well for structurally similar transport equations may fail for SSPMs and other transport-dominated models with high ecological realism, and thus their computational performance needs to be critically evaluated.

    2. Here, we compare the performance of four numerical solution schemes, the fixed-mesh upwind (FMU) method, the moving-mesh upwind (MMU) method, the characteristic method (CM), and the Escalator Boxcar Train (EBT) method, in numerically solving three reference problems that are representative of ecological systems in the animal and plant kingdoms. The MMU method is here applied for the first time to SSPMs, whereas the three other methods have been employed by other authors.

    3. Our results show that the EBT method performs best, except for one of the three reference problems, in which size-asymmetric competition affects individual growth rates. For that reference problem, the FMU method performs best, closely followed by the MMU method. Surprisingly, the CM method does not perform well for any of the three reference problems.

    4. We conclude that life-history features should be carefully considered when choosing the numerical method for analyzing ecologically realistic size-structured population models.

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