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  • 201.
    Ali, Muhammad
    Umeå University, Faculty of Science and Technology, Department of Physics.
    RAMAN CHARACTERIZATION OF STRUCTURAL PROPERTIES OF THERMALLY MODIFIED NANOGRAPHITE2015Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Raman spectroscopy is highly sensitive to study the structural properties of nanographite (NG) materials. An experiment was conducted to assess the spectrum of multi-shell nanographite at different temperature and laser treatments. Four samples with different temperature were used. The range of temperature used was 1500-1650 oC. All samples were subjected to different laser treatments like 488, 514, 633 and 785 nm respectively. The spectrum of nanographite was observed by using the Raman spectroscopy. The 1st and 2nd order spectra of NG were evaluated by using the Voigt analysis. The variations in the intensities of D and G bands were analyzed. The decrease of D band width with heat treatment was observed. The peak 1523 cm-1 exhibited more and more reduction with increase in temperature treatments. Temperature induced the conversion of nanodiamond to nanographite.

  • 202. Ali, Qasim
    et al.
    Haider, Muhammad Zulqurnain
    Iftikhar, Wasif
    Jamil, Sidra
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Botany, Faculty of Science and Technology, Government College University, Faisalabad, Pakistan.
    Javed, M. Tariq
    Noman, Ali
    Iqbal, Muhammad
    Perveen, Rashida
    Drought tolerance potential of Vigna mungo L. lines as deciphered by modulated growth, antioxidant defense, and nutrient acquisition patterns2016In: Revista Brasileira de Botânica, ISSN 0100-8404, E-ISSN 1806-9959, Vol. 39, no 3, p. 801-812Article in journal (Refereed)
    Abstract [en]

    Water shortage is one of the major environmental constraints that hamper the crop productivity worldwide. The present study was aimed to examine the drought tolerance potential of seven cultivars/lines of Vigna mungo L. depending upon their germination behavior, seedling growth, antioxidative defense mechanism, and nutrient acquisition. An experiment was conducted in the growth chamber using petri-plates and laid out in a completely randomized design (CRD). Hoagland's nutrient solution supplemented with 12 % PEG-8000 (drought treatment) or without PEG-800 (control) was used. Drought stress significantly altered the germination attributes as well as biomass production of all the studied cultivars/lines. Least adversative effects of drought stress were recorded in lines M-01001-1 and M-6036-21, respectively. The studied cultivars/lines exhibited differential response for various biochemical attributes under drought stress. The maximum increase in MDA and SOD activities and protein content was recorded in line M-603621, while the maximum AsA was recorded in line M-01001-1. Drought stress resulted in a significant reduction of plant N, P, K, Ca, and Mg contents, while the plant iron (Fe) contents remained unaffected. Results revealed that cultivars/lines M-01001-1 and M-6036-21 exhibited enhanced performance in terms of nutrient acquisition when stressed by drought. Based upon seed germination behavior, plant biomass production, biochemical attributes and mineral elements, the cultivars/lines M-01001-1 and M-6036-21 were identified as drought tolerant, while M-97 and Arroj-II were identified as drought sensitive.

  • 203. Ali, S
    et al.
    Moslem, WM
    Shukla, Padma Kant
    Umeå University, Faculty of Science and Technology, Department of Physics. Institut für Theoretische Physik IV, Fakultät für Physik und Astronomie, Ruhr-Universität Bochum, D-44780 Bochum, Germany; Max-Planck Institut für extraterrestrische Physik, D-85741 Garching, Germany; GoLP/Instituto Superior Técnico, 1049-001 Lisbon, Portugal; CCLRC Centre for Fundamental Physics, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon 0X11 0QX, UK; SUPA Department of Physics, University of Strathclyde, Glasgow G 40NG, UK.
    Wake potential with mobile positive/negative ions in multicomponent dusty plasmas2008In: Physics Letters A, ISSN 0375-9601, E-ISSN 1873-2429, Vol. 372, no 44, p. 6650-6652Article in journal (Refereed)
    Abstract [en]

    We employ the test charge approach to calculate the electrostatic potential for a test charge in a multicomponent dusty plasma, whose constituents are the Boltzmann distributed electrons, mobile positive and negative ions, and immobile positive/negative charged dust particles. By using the modified dielectric constant of the dust-ion-acoustic (DIA) waves, the Debye screening and wake potentials are obtained. It is found that the presence of mobile negative ions significantly modify the DIA speed and the wake potential. The present results are relevant to polar mesosphere and microelectronic in the context of charged particle attraction and repulsion.

  • 204. Ali, S
    et al.
    Shukla, Padma K
    Umeå University, Faculty of Science and Technology, Department of Physics. Institut für Theoretische Physik IV, Fakultät für Physik und Astronomie, Ruhr-Universität Bochum, D-44780 Bochum, Germany; Max-Planck Institut für extraterrestrische Physik, D-85741 Garching, Germany, GoLP/Instituto Superior Técnico, 1049-001 Lisbon, Portugal, Centre for Fundamental Physics, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon 0X11 0QX, United Kingdom, and Department of Physics, University of Strathclyde, Glasgow, Scotland, United Kingdom .
    Dust acoustic solitary waves in a quantum plasma2006In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 13, no 2, article id 022313Article in journal (Refereed)
    Abstract [en]

    By employing one-dimensional quantum hydrodynamic (QHD) model for a three species quantum plasma, nonlinear properties of dust acoustic solitary waves are studied. For this purpose a Korteweg-de Vries (KdV) equation is derived, incorporating quantum corrections. The quantum mechanical effects are also examined numerically both on the profiles of the amplitude and the width of dust acoustic solitary waves. It is found that the amplitude remains constant but the width shrinks for different values of a dimensionless electron quantum parameter H-e=root(Z(d0)h(2)omega(2)(pd))/m(e)m(d)C(d)(4), where Z(d0) is the dust charge state, h is the Planck constant divided by 2 pi, omega(pd) is the dust plasma frequency, m(e) (m(d)) is the electron (dust) mass, and C-d is the dust acoustic speed.

  • 205. Ali, S
    et al.
    Shukla, Padma Kant
    Umeå University, Faculty of Science and Technology, Department of Physics. Institut für Theoretische Physik IV and Centre for Plasma Science and Astrophysics, Fakultät für Physik und Astronomie, Ruhr-Universität Bochum, D-44780 Bochum, Germany; Max-Planck Institut für extraterrestrische Physik, D-85741 Garching, Germany; GoLP/Instituto Superior Técnico, 1049-001 Lisbon, Portugal; Centre for Fundamental Physics, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon 0X11 0QX, United Kingdom; Department of Physics, University of Strathclyde, Glasgow, Scotland, United Kingdom.
    Dispersion properties of compressional electromagnetic waves in quantum dusty magnetoplasmas2006In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 13, no 5, article id 052113Article in journal (Refereed)
    Abstract [en]

    A new dispersion relation for low-frequency compressional electromagnetic waves is derived by employing quantum magnetohydrodynamic model and Maxwell equations in cold quantum dusty magnetoplasmas. The latter is composed of inertialess electrons, mobile ions, and immobile charged dust particulates. The dispersion relation for the low-frequency compressional electromagnetic modes is further analyzed for the waves propagating parallel, perpendicular, and oblique to the external magnetic field direction. It is found theoretically and numerically that the quantum parameter alpha(q)=(n(i0)/n(e0))h(2)/(4m(e)m(i)) affects the real angular frequencies and the phase speeds of the compressional electromagnetic modes. Here, n(i0) (n(e0)) is the equilibrium number density of the ions (electrons), m(e) (m(i)) is the electron (ion) mass, and h is the Plank constant divided by 2 pi.

  • 206.
    Ali, Shahid
    Umeå University, Faculty of Science and Technology, Physics.
    Waves and instabilities in quantum plasmas2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The study of waves and instabilities in quantum plasmas is of fundamental importance for understanding collective interactions in superdense astrophysical objects, in high intense laser-plasma/solid-matter interactions, in microelectronic devices and metallic nanostructures. In dense quantum plasmas, there are new pressure laws associated with the Fermi-Dirac distribution functions and new quantum forces associated with the quantum Bohm potential and the Bohr magnetization involving electron ½ spin. These forces significantly alter the collective behavior of dense quantum plasmas. This thesis contains six papers, considering several novel collective modes and instabilities at quantum scales. In Paper I, we have used the quantum hydrodynamical (QHD) model for studying the one-dimensional dust-acoustic (DA) waves incorporating the Fermi pressure law and the quantum Bohm potential. The latter modifies the DA wave dispersion relation in a collisional plasma. In Paper II, we have calculated the electrostatic potential of a test charge in an unmagnetized electron-ion quantum plasma. It is found that the Debye-Hückel and oscillatory wake potentials strongly depend upon the Fermi energy at quantum scales. The results can be of interest for explaining the charged particle attraction and repulsion in degenerate quantum plasmas, such as those in semiconductor and microelectronic devices. Paper III presents the parametric study of nonlinear electrostatic waves in two-dimensional collisionless quantum dusty plasmas. A reductive perturbation method has been employed to the QHD equations together with the Poisson equation, obtaining the cylindrical Kadomtsev-Petviashvili (CKP) equations and their stationary localized solutions. We have numerically examined the quantum mechanical and geometrical effects on the profiles of nonplanar quantum dust-ion-acoustic (DIA) and DA solitary waves. The role of static as well as mobile (negatively or positively charged) dust particles on the low-frequency electrostatic waves has also been highlighted for metallic nanostructures. Paper IV introduces the nonlinear properties of the ion-sound waves in a dense electron-ion Fermi magnetoplasma. The computational analysis of the nonlinear system reveals that the Sagdeev-like potential and the ion-sound density excitations are significantly affected by the wave direction cosine and the Mach number at quantum scales. Paper V considers the nonlinear interactions of electrostatic upper-hybrid (UH), ion-cyclotron (IC), lower-hybrid (LH), and Alfvén waves in a quantum magnetoplasma. The nonlinear dispersion relations have been analyzed analytically to obtain the growth rates for both the decay and modulational instabilities involving the dispersive IC, LH, and Alfvén waves. In Paper VI, we have identified a new drift-like dissipative instability in a collisional quantum plasma. The modified unstable drift-like mode can cause cross-field anomalous ion-diffusion at quantum scales.

  • 207.
    Ali-Eldin, Ahmed
    et al.
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Kihl, Maria
    Dept. of Electrical and Information Technology, Lund University, Lund, Sweden.
    Tordsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Elmroth, Erik
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Efficient provisioning of bursty scientific workloads on the cloud using adaptive elasticity control2012In: Proceedings of the 3rd workshop on Scientific Cloud Computing Date, Association for Computing Machinery (ACM), 2012, p. 31-40Conference paper (Refereed)
    Abstract [en]

    Elasticity is the ability of a cloud infrastructure to dynamically change theamount of resources allocated to a running service as load changes. We build anautonomous elasticity controller that changes the number of virtual machinesallocated to a service based on both monitored load changes and predictions offuture load. The cloud infrastructure is modeled as a G/G/N queue. This modelis used to construct a hybrid reactive-adaptive controller that quickly reactsto sudden load changes, prevents premature release of resources, takes intoaccount the heterogeneity of the workload, and avoids oscillations. Using simulations with Web and cluster workload traces, we show that our proposed controller lowers the number of delayed requests by a factor of 70 for the Web traces and 3 for the cluster traces when compared to a reactive controller. Ourcontroller also decreases the average number of queued requests by a factor of 3 for both traces, and reduces oscillations by a factor of 7 for the Web traces and 3 for the cluster traces. This comes at the expense of between 20% and 30% over-provisioning, as compared to a few percent for the reactive controller.

  • 208.
    Ali-Eldin, Ahmed
    et al.
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Tordsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Elmroth, Erik
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    An adaptive hybrid elasticity controller for cloud infrastructures2012In: 2012 IEEE Network operations and managent symposium (NOMS), IEEE Communications Society, 2012, p. 204-212Conference paper (Refereed)
    Abstract [en]

    Cloud elasticity is the ability of the cloud infrastructure to rapidly change the amount of resources allocated to a service in order to meet the actual varying demands on the service while enforcing SLAs. In this paper, we focus on horizontal elasticity, the ability of the infrastructure to add or remove virtual machines allocated to a service deployed in the cloud. We model a cloud service using queuing theory. Using that model we build two adaptive proactive controllers that estimate the future load on a service. We explore the different possible scenarios for deploying a proactive elasticity controller coupled with a reactive elasticity controller in the cloud. Using simulation with workload traces from the FIFA world-cup web servers, we show that a hybrid controller that incorporates a reactive controller for scale up coupled with our proactive controllers for scale down decisions reduces SLA violations by a factor of 2 to 10 compared to a regression based controller or a completely reactive controller.

  • 209.
    Alin, Lars
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Object Tracking withIphone 3Gs2010Independent thesis Advanced level (degree of Master (One Year)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    In June of 2007 Apple Inc. released the smartphone Iphone. It was a groundbreaking success that set a new standard for what a smartphone should be able to do. Apple has improved the Iphone every year since then and the 3Gs is the newest Iphone model. As the phones have improved, both when looking at hardware and software, the applications have improved as well. The Iphone 3Gs provides the possibility to use the camera as an application background and with that the possibility to analyze the surroundings, making it possible to track objects that the phone is pointed towards.This thesis examines how object tracking can be implemented in applications for Iphone 3Gs as well as providing a survey of four different areas of use that have been implemented in Xcode: an augmented reality car game, a letter tracking application, a face recognition application and an object recognition application.

  • 210.
    AliNazari, Mirian
    Umeå University, Faculty of Teacher Education, Department of Creative Studies.
    Kreativ Uppväxtmiljö: en studie av stadieteorier2007Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    I examensarbetet studerades bildutveckling som även jämförts med författarens egen uppväxtmiljö. Metoden har varit en litteraturstudie som behandlar ämnet estetiska uttrycksformer och kreativ uppväxt. Därtill har en granskning av författarens uppväxtmiljö gällande möjlighet till övande av kreativ förmåga tagits upp i relation till personlig utveckling. Jämförelse har gjorts med stadieteorier om utvecklande av barns bildanvändning. Genom dokumenterade av författarens egna bilder under tidiga år visades bildutveckling i de olika teckningsutvecklingsstadierna. Slutsatsen är att kreativ förmåga påverkas sannolikt av uppfostran fylld med möjligheten att få måla och teckna, något som bildlärare kan utveckla i arbetet med barn. Behov att som blivande lärare integrera bilden i de teoretiska ämnena kan utveckla dessa möjligheter ytterligare.

  • 211. Aljetlawi, A A
    et al.
    Albertsson, Jan
    Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
    Leonardsson, K
    Effect of food and sediment pre-treatment in experiments with a deposit-feeding amphipod, Monoporeia affinis2000In: Journal of Experimental Marine Biology and Ecology, ISSN 0022-0981, E-ISSN 1879-1697, Vol. 249, no 2, p. 263-280Article in journal (Refereed)
    Abstract [en]

    We experimentally investigated the effects of different pre-treatments of the sediment, and the effect of daily addition of fresh phytoplankton, on the growth and survival of 1-year-old (1 +) individuals of the deposit feeder Monoporeia affinis (Amphipoda). We used three different types of sieved sediment: pre-frozen muddy clay, non-pre-frozen muddy clay, and fine sand. The muddy clay contained phytoplankton originating from the surface sediment sampled in the field during the late spring bloom. No phytoplankton was initially present in sand. The experiment lasted for 18 days. M. affinis responded to the daily phytoplankton addition by increasing growth. Phytoplankton addition had no significant effects on the survival of M. affinis. Upon phytoplankton addition, the sandy and non-frozen muddy clay gave similar growth and survival responses. In contrast, the pre-frozen sediment resulted in significantly lower growth and survival. The growth was negative in all treatments without phytoplankton. Thus, the high initial chlorophyll content in the muddy clay was not of sufficient quality or concentration to allow a positive growth response in M. affinis. The growth of M. affinis was significantly correlated with the reduction of the chlorophyll. Our results indicated that M. affinis is capable of assimilating settled phytoplankton with no, or only a few days' time delay. (C) 2000 Elsevier Science BN: All rights reserved.

  • 212.
    Alkhori, Liza
    et al.
    Linköpings universitet, Avdelningen för cellbiologi.
    Öst, Anita
    Linköpings universitet, Avdelningen för cellbiologi.
    Alenius, Mattias
    Linköpings universitet, Avdelningen för cellbiologi.
    The corepressor Atrophin specifies odorant receptor expression in Drosophila2014In: The FASEB Journal, ISSN 0892-6638, E-ISSN 1530-6860, Vol. 28, no 3, p. 1355-1364Article in journal (Refereed)
    Abstract [en]

    In both insects and vertebrates, each olfactory sensory neuron (OSN) expresses one odorant receptor (OR) from a large genomic repertoire. How a receptor is specified is a tantalizing question addressing fundamental aspects of cell differentiation. Here, we demonstrate that the corepressor Atrophin (Atro) segregates OR gene expression between OSN classes in Drosophila. We show that the knockdown of Atro result in either loss or gain of a broad set of ORs. Each OR phenotypic group correlated with one of two opposing Notch fates, Notch responding, Nba (N(on)), and nonresponding, Nab (N(off)) OSNs. Our data show that Atro segregates ORs expressed in the Nba OSN classes and helps establish the Nab fate during OSN development. Consistent with a role in recruiting histone deacetylates, immunohistochemistry revealed that Atro regulates global histone 3 acetylation (H3ac) in OSNs and requires Hdac3 to segregate OR gene expression. We further found that Nba OSN classes exhibit variable but higher H3ac levels than the Nab OSNs. Together, these data suggest that Atro determines the level of H3ac, which ensures correct OR gene expression within the Nba OSNs. We propose a mechanism by which a single corepressor can specify a large number of neuron classes.-Alkhori, L., Öst, A., Alenius, M. The corepressor Atrophin specifies odorant receptor expression in Drosophila.

  • 213. Allakhverdiev, Suleyman I.
    et al.
    Zharmukhamedov, Sergey K.
    Rodionova, Margarita V.
    Shuvalov, Vladimir A.
    Dismukes, Charles
    Shen, Jian-Ren
    Barber, James
    Samuelsson, Göran
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Govindjee,
    Vyacheslav (Slava) Klimov (1945-2017): A scientist par excellence, a great human being, a friend, and a Renaissance man2018In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 136, no 1, p. 1-16Article in journal (Other academic)
    Abstract [en]

    Vyacheslav Vasilevich (V.V.) Klimov (or Slava, as most of us called him) was born on January 12, 1945 and passed away on May 9, 2017. He began his scientific career at the Bach Institute of Biochemistry of the USSR Academy of Sciences (Akademy Nauk (AN) SSSR), Moscow, Russia, and then, he was associated with the Institute of Photosynthesis, Pushchino, Moscow Region, for about 50 years. He worked in the field of biochemistry and biophysics of photosynthesis. He is known for his studies on the molecular organization of photosystem II (PSII). He was an eminent scientist in the field of photobiology, a well-respected professor, and, above all, an outstanding researcher. Further, he was one of the founding members of the Institute of Photosynthesis in Pushchino, Russia. To most, Slava Klimov was a great human being. He was one of the pioneers of research on the understanding of the mechanism of light energy conversion and of water oxidation in photosynthesis. Slava had many collaborations all over the world, and he is (and will be) very much missed by the scientific community and friends in Russia as well as around the World. We present here a brief biography and some comments on his research in photosynthesis. We remember him as a friendly and enthusiastic person who had an unflagging curiosity and energy to conduct outstanding research in many aspects of photosynthesis, especially that related to PSII.

  • 214. Allan, Mohammed
    et al.
    Le Roux, Gael
    De Vleeschouwer, Francois
    Bindler, Richard
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Blaauw, Maarten
    Piotrowska, Natalia
    Sikorski, Jaroslaw
    Fagel, Nathalie
    High-resolution reconstruction of atmospheric deposition of trace metals and metalloids since AD 1400 recorded by ombrotrophic peat cores in Hautes-Fagnes, Belgium2013In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 178, p. 381-394Article in journal (Refereed)
    Abstract [en]

    The objective of our study was to determine the trace metal accumulation rates in the Misten bog, Hautes-Fagnes, Belgium, and assess these in relation to established histories of atmospheric emissions from anthropogenic sources. To address these aims we analyzed trace metals and metalloids (Pb, Cu, Ni, As, Sb, Cr, Co, V, Cd and Zn), as well as Pb isotopes, using XRF, Q-ICP-MS and MC-ICP-MS, respectively in two 40-cm peat sections, spanning the last 600 yr. The temporal increase of metal fluxes from the inception of the Industrial Revolution to the present varies by a factor of 5-50, with peak values found between AD 1930 and 1990. A cluster analysis combined with Pb isotopic composition allows the identification of the main sources of Pb and by inference of the other metals, which indicates that coal consumption and metallurgical activities were the predominant sources of pollution during the last 600 years.

    (c) 2013 Elsevier Ltd. All rights reserved.

  • 215. Allas, Ular
    et al.
    Toom, Lauri
    Selyutina, Anastasia
    Maeorg, Uno
    Medina, Ricardo
    Merits, Andres
    Rinken, Ago
    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, Nooruse 1, Tartu 50411, Estonia.
    Kaldalu, Niilo
    Tenson, Tanel
    Antibacterial activity of the nitrovinylfuran G1 (Furvina) and its conversion products2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 36844Article in journal (Refereed)
    Abstract [en]

    2-Bromo-5-(2-bromo-2-nitrovinyl) furan (G1 or Furvina) is an antimicrobial with a direct reactivity against thiol groups. It is active against Gram-positive and Gram-negative bacteria, yeasts and filamentous fungi. By reacting with thiol groups it causes direct damage to proteins but, as a result, is very short-living and interconverts into an array of reaction products. Our aim was to characterize thiol reactivity of G1 and its conversion products and establish how much of antimicrobial and cytotoxic effects are due to the primary activity of G1 and how much can be attributed to its reaction products. Stability of G1 in growth media as well as its conversion in the presence of thiols was characterized. The structures of G1 decomposition products were determined using NMR and mass-spectroscopy. Concentration-and time-dependent killing curves showed that G1 is bacteriostatic for Escherichia coli at the concentration of 16 mu g/ml and bactericidal at 32 mu g/ml. However, G1 is inefficient against non-growing E. coli. Addition of cysteine to medium reduces the antimicrobial potency of G1. Nevertheless, the reaction products of G1 and cysteine enabled prolonged antimicrobial action of the drug. Therefore, the activity of 2-bromo-5-(2-bromo-2-nitrovinyl) furan is a sum of its immediate reactivity and the antibacterial effects of the conversion products.

  • 216.
    Allegrini, Elisa
    et al.
    Technical University of Denmark, Department of Environmental Engineering.
    Boldrin, Alessio
    Tech Univ Technical University of Denmark, Department of Environmental Engineering.
    Jansson, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lundtorp, Kasper
    Babcock & Wilcox Vølund A/S, Göteborg, Sweden.
    Fruergaard Astrup, Thomas
    Technical University of Denmark, Department of Environmental Engineering.
    Quality and generation rate of solid residues in the boiler of a waste-to-energy plant2014In: Journal of Hazardous Materials, ISSN 0304-3894, E-ISSN 1873-3336, Vol. 270, p. 127-136Article in journal (Refereed)
    Abstract [en]

    The Danish waste management system relies significantly on waste-to-energy (WtE) plants. The ash produced at the energy recovery section (boiler ash) is classified as hazardous waste, and is commonly mixed with fly ash and air pollution control residues before disposal. In this study, a detailed characterization of boiler ash from a Danish grate-based mass burn type WtE was performed, to evaluate the potential for improving ash management. Samples were collected at 10 different points along the boiler's convective part, and analysed for grain size distribution, content of inorganic elements, polychlorinated dibenzo-. p-dioxins and dibenzofurans (PCDD and PCDF), and leaching of metals. For all samples, PCDD and PCDF levels were below regulatory limits, while high pH values and leaching of e.g. Cl were critical. No significant differences were found between boiler ash from individual sections of the boiler, in terms of total content and leaching, indicating that separate management of individual ash fractions may not provide significant benefits. 

  • 217. Allgardsson, Anders
    et al.
    Berg, Lotta
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Akfur, Christine
    Hörnberg, Andreas
    Worek, Franz
    Linusson, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ekström, Fredrik J.
    Structure of a prereaction complex between the nerve agent sarin, its biological target acetylcholinesterase, and the antidote HI-62016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 20, p. 5514-5519Article in journal (Refereed)
    Abstract [en]

    Organophosphorus nerve agents interfere with cholinergic signaling by covalently binding to the active site of the enzyme acetylcholinesterase (AChE). This inhibition causes an accumulation of the neurotransmitter acetylcholine, potentially leading to overstimulation of the nervous system and death. Current treatments include the use of antidotes that promote the release of functional AChE by an unknown reactivation mechanism. We have used diffusion trap cryocrystallography and density functional theory (DFT) calculations to determine and analyze prereaction conformers of the nerve agent antidote HI-6 in complex with Mus musculus AChE covalently inhibited by the nerve agent sarin. These analyses reveal previously unknown conformations of the system and suggest that the cleavage of the covalent enzyme-sarin bond is preceded by a conformational change in the sarin adduct itself. Together with data from the reactivation kinetics, this alternate conformation suggests a key interaction between Glu202 and the O-isopropyl moiety of sarin. Moreover, solvent kinetic isotope effect experiments using deuterium oxide reveal that the reactivation mechanism features an isotope-sensitive step. These findings provide insights into the reactivation mechanism and provide a starting point for the development of improved antidotes. The work also illustrates how DFT calculations can guide the interpretation, analysis, and validation of crystallographic data for challenging reactive systems with complex conformational dynamics.

  • 218.
    Almgren, Anton
    et al.
    Umeå University, Faculty of Social Sciences, Department of Psychology.
    Winbäck, Hannes
    Umeå University, Faculty of Social Sciences, Department of Psychology.
    Användbarhet inom människa-datorinteraktion i praktiken: En kartläggning av utvärderingsmetoder2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Studiens syfte är att kartlägga yrkesverksammas preferenser och användning av utvärderingsmetoder för användbarhet inom människa-datorinteraktion. En webbenkät distribuerades via epost till företag med minst en anställd som arbetar med användbarhet samt via sociala medier genom intresseorganisationen STIMDI och företaget Inuse. Totalt erhölls 104 svarande varav en räknades som bortfall då den ansågs vara en dubblett. Resultaten visar att ingen enskild eller kombination av metoder används oftast och rankas ge högst effekt på användbarhet. Angående vilka utvärderingsmetoder som används är intervju och tänka högt med användare de två metoder som nämns av flest deltagare. Resultaten visar även att nästan 80 % skattar användning av utvärderingsmetoder och involvering av användare i deras arbete som mycket viktigt. En tydlig preferens för att involvera användare och arbeta med kombinationer av metoder framgår i denna kartläggning. Forskning bör möjligtvis fokusera mer på hur användandet av utvärderingsmetoder sker i kombination. 

  • 219.
    Almqvist, Saga
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Nore, Lana
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Where to Stack the Chocolate?: Mapping and Optimisation of the Storage Locations with Associated Transportation Cost at Marabou2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Today, inventory management at Marabou is organised in such way that articles are stored based on which production line they belong to and are sent to storage locations close to their production line. However, some storage locations are not optimised, insofar articles are stored out of pure habit and follow what is considered most convenient. This means that the storage locations are not based on any fixed instructions or standard. In this report, we propose optimal storage locations with respect to transportation cost by modelling the problem mathematically as a minimal cost matching problem, which we solve using the so-called Hungarian algorithm. To be able to implement the Hungarian algorithm, we collected data regarding the stock levels of articles in the factory throughout 2016. We adjusted the collected data by turning the articles into units of pallets. We considered three different implementations of the Hungarian algorithm. The results from the different approaches are presented together with several suggestions regarding pallet optimisation. In addition to the theoretical background, our work is based on an empirical study through participant observations as well as qualitative interviews with factory employees. In addition to our modelling work, we thus offer several further suggestions for efficiency savings or improvements at the factory, as well as for further work building on this report.

  • 220. Almroth, Bethanie M. Carney
    et al.
    Gunnarsson, Lina M.
    Cuklev, Filip
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kristiansson, Erik
    Larsson, D. G. Joakim
    Waterborne beclomethasone dipropionate affects the physiology of fish while its metabolite beclomethasone is not taken up2015In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 511, p. 37-46Article in journal (Refereed)
    Abstract [en]

    Asthma is commonly treated with inhalable glucocorticosteroids, including beclomethasone dipropionate (BDP). This is a synthetic prodrug which is metabolized to the more active monopropionate (BMP) and free beclomethasone in humans. To evaluate potential effects of residual drugs on fish, we conducted a 14 day flow-through exposure experiment with BDP and beclomethasone using rainbow trout, and analyzed effects on plasma glucose, hepatic glutathione and catalase activity together with water and body concentrations of the BDP, BMP and beclomethasone. We also analyzed hepatic gene expression in BDP-exposed fish by micro-array and quantitative PCR Beclomethasone (up to 0.65 mu g/L) was not taken up in the fish while BDP (0.65 and 0.07 mu g/L) resulted in accumulation of both beclomethasone, BMP and BDP in plasma, reaching levels up to those found in humans during therapy. Accordingly, exposure to 0.65 mu g/L of BDP significantly increased blood glucose as well as oxidized glutathione levels and catalase activity in the liver. Exposure to beclomethasone or the low concentration of BDP had no effect on these endpoints. Both exposure concentrations of BDP resulted in significantly higher transcript abundance of phosphoenolpyruvate carboxykinase involved in gluconeogenesis, and of genes involved in immune responses. As only the rapidly metabolized prodrug was potent in fish, the environmental risks associated with the use of BDP are probably small. However, the observed physiological effects in fish of BDP at plasma concentrations known to affect human physiology provides valuable input to the development of read-across approaches in the identification of pharmaceuticals of environmental concern.

  • 221.
    Al-Naser, Mohammad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Söderström, Ulrik
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Reconstruction of occluded facial images using asymmetrical Principal Component Analysis2012In: Integrated Computer-Aided Engineering, ISSN 1069-2509, E-ISSN 1875-8835, Vol. 19, no 3, p. 273-283Article in journal (Refereed)
    Abstract [en]

    When only non-occluded image parts are available for facial images it is difficult or impossible to correctly recognize the person in the image. The problem addressed in this work is reconstruction of the occluded parts in facial images; e. g. eyes covered with sunglasses. Asymmetrical Principal Component Analysis (aPCA) allows estimation of occluded facial parts based on the content of the facial parts which are visible. aPCA is used to estimate full non-occluded faces from 3 kinds of occlusion with 2 different reconstruction methods in this work and we present the results with both objective and subjective evaluation. The subjective evaluation shows that clear and sharp image regions are preferred even if this results in visible edges in the images. The method also performs well when a different facial expression than the one in the database is used to calculate the reconstruction parameters.

  • 222.
    Al-Naseri, Haidar
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Quantum kinetic relativistic theory of linearized waves in magnetized plasmas2018Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In this work we have studied linear wave propagation in magnetized plasmas using a fully relativistic kinetic equation of spin-1/2 particles in the long scale approximation. The linearized kinetic equation is very long and complicated, hence we worked with restricted geometries in order to simplify the calculations. The dispersion relation of the relativistic model was calculated and compared with a dispersion relation from a previous work at the semi-relativistic limit.

    Moreover, a new mode was discovered that survives in the zero temperature limit. The origin of the mode in the kinetic equation was discussed and derived from a non-relativistic kinetic equation from a previous work.

  • 223. Alonso, Carlos
    et al.
    Roman, Alfonso
    Bejarano, Maria Dolores
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Garcia de Jalon, Diego
    Carolli, Mauro
    A graphical approach to characterize sub-daily flow regimes and evaluate its alterations due to hydropeaking2017In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 574, p. 532-543Article in journal (Refereed)
    Abstract [en]

    Most flow regime characterizations focus on long time scale flow patterns, which are not precise enough to capture key components of short-term flow fluctuations. Recent proposed methods describing sub-daily flow fluctuations are focused on limited components of the flow regime being unable to fully represent it, or on the identification of peaking events based on subjectively defined thresholds, being unsuitable for evaluations of short-term flow regime alterations through comparisons between regulated and free-flowing rivers. This study aims to launch an innovative approach based on the visual display of quantitative information to address the challenge of the short-term hydrologic characterization and evaluation of alteration resulting from hydropeaking. We propose a graphical method to represent a discrete set of ecologically relevant indices that characterize and evaluate the alteration of sub-daily flow regimes. The frequency of occurrence of classified values of a descriptive hydrological variable is represented in a map-like graph where longitude, latitude and altitude represent the Julian day, the value of the variable and the frequency of occurrence, respectively. Subsequently, we tested the method on several rivers, both free-flowing and subjected to hydropower production. The advantages of our approach compared to other analytical methods are: (i) it displays a great amount of information without oversimplification; (ii) it takes into account changes in the intensity, timing and frequency of the sub-daily flows, without needing a priori defined thresholds to identify hydropeaking events; and (iii) it supports the Water Framework Directive goal. Specifically, results from applications of our graphical method agree with Sauterleute and Charmasson (2014) analytical method.

  • 224. Alonso-Mori, R.
    et al.
    Asa, K.
    Bergmann, U.
    Brewster, A. S.
    Chatterjee, R.
    Cooper, J. K.
    Frei, H. M.
    Fuller, F. D.
    Goggins, E.
    Gul, S.
    Fukuzawa, H.
    Iablonskyi, D.
    Ibrahim, M.
    Katayama, T.
    Kroll, T.
    Kumagai, Y.
    McClure, B. A.
    Messinger, Johannes
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Motomura, K.
    Nagaya, K.
    Nishiyama, T.
    Saracini, C.
    Sato, Y.
    Sauter, N. K.
    Sokaras, D.
    Takanashi, T.
    Togashi, T.
    Ueda, K.
    Weare, W. W.
    Weng, T-C
    Yabashi, M.
    Yachandra, V. K.
    Young, I. D.
    Zouni, A.
    Kern, J. F.
    Yano, J.
    Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs2016In: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 194, p. 621-638Article in journal (Refereed)
    Abstract [en]

    The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.

  • 225. Alonso-Mori, Roberto
    et al.
    Kern, Jan
    Gildea, Richard J
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Lassalle-Kaiser, Benedikt
    Tran, Rosalie
    Hattne, Johan
    Laksmono, Hartawan
    Hellmich, Julia
    Glöckner, Carina
    Echols, Nathaniel
    Sierra, Raymond G
    Schafer, Donald W
    Sellberg, Jonas
    Kenney, Christopher
    Herbst, Ryan
    Pines, Jack
    Hart, Philip
    Herrmann, Sven
    Grosse-Kunstleve, Ralf W
    Latimer, Matthew J
    Fry, Alan R
    Messerschmidt, Marc M
    Miahnahri, Alan
    Seibert, M Marvin
    Zwart, Petrus H
    White, William E
    Adams, Paul D
    Bogan, Michael J
    Boutet, Sébastien
    Williams, Garth J
    Zouni, Athina
    Messinger, Johannes
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Glatzel, Pieter
    Sauter, Nicholas K
    Yachandra, Vittal K
    Yano, Junko
    Bergmann, Uwe
    Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 47, p. 19103-19107Article in journal (Refereed)
    Abstract [en]

    The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this "probe-before-destroy" approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kβ(1,3) XES spectra of Mn(II) and Mn(2)(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.

  • 226.
    Alpay, Aylin
    Umeå University, Faculty of Science and Technology, Umeå Institute of Design.
    Untangling Road Trip Experiences with Conected Car: Planning and bringing it to the car2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    With developing technologies and growing infrastructures, connected experiences are expanding their realms towards various devices and scenarios in our lives. One of the areas, which is going under a big change due to this connectivity is the car related experiences. As connectivity is intrinsically enabler of different experiences and services, it is foreseen that it will bring a different dimension to car and driving related experiences as well.By investigating the future trends and possibilities that connectivity can provide to car and driving related experiences, this thesis aims for imagining the near future scenarios with an explorative approach, focusing on one and addressing to the rising issues with a design proposal that is meaningful to both users and the industry.The result, Tripcloud, contributes to the future scenario of having a road trip with the car, with a new digital platform that aims for supporting the users throughout the planning and bringing the plans into the car experience seamlessly and safely. It aims for reducing today’s existing complexity in terms of interaction and cognition to provide a better experience and avoid driver distraction. With providing organised information pieces, information exchange between people and automated links with mobile devices and car, Tripcloud offers easier an more convenient alternative for road trip planing and bringing the plans into car experiences for the near future.

  • 227. Alriksson, Björn
    et al.
    Horváth, Ilona Sárvári
    Jönsson, Leif J
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biomedical Sciences, Karlstad University.
    Overexpression of Saccharomyces cerevisiae transcription factor and multidrug resistance genes conveys enhanced resistance to lignocellulose-derived fermentation inhibitors2010In: Process Biochemistry, ISSN 1359-5113, E-ISSN 1873-3298, Vol. 45, no 2, p. 264-271Article in journal (Refereed)
    Abstract [en]

    The presence of fermentation inhibitors in lignocellulose hydrolysates is an obstacle for achieving efficient fermentation of lignocellulose hydrolysates to ethanol and other commodities. In this investigation, the possibility of generating more inhibitor-resistant Saccharomyces cerevisiae by genetic engineering was explored. Based on previous results from studies of deletion mutants, three S. cerevisiae genes (ATR1, FLR1, YAP1) involved in multidrug resistance and stress response of yeast were selected for overexpression in three S. cerevisiae strains. The resistance of the transformed strains to lignocellulose-derived fermentation inhibitors and a dilute-acid spruce hydrolysate was evaluated in fermentation experiments. Overexpression of FLR1 resulted in enhanced resistance to the phenolic inhibitor coniferyl aldehyde and the furan aldehyde HMF (5-hydroxymethyl-2-furaldehyde). Overexpression of ATR1 conferred increased resistance to coniferyl aldehyde. Strains overexpressing YAP1, which encodes a transcription factor, displayed increased resistance to coniferyl aldehyde, HMF, and the spruce hydrolysate. An ethanol productivity of 0.17 g ethanol × l−1 × h−1 was achieved for a YAP1-overexpressing transformant cultivated in spruce hydrolysate, whereas a control transformant, which did not overexpress YAP1, only reached a productivity of 0.05 g ethanol × l−1 × h−1

  • 228. Althuizen, Inge H. J.
    et al.
    Lee, Hanna
    Sarneel, Judith M
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Ecology and Biodiversity Group and Plant Ecophysiology Group, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.
    Vandvik, Vigdis
    Long-Term climate regime modulates the impact of short-term climate variability on decomposition in alpine grassland soils2018In: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 21, no 8, p. 1580-1592Article in journal (Refereed)
    Abstract [en]

    Decomposition of plant litter is an important process in the terrestrial carbon cycle and makes up approximately 70% of the global carbon flux from soils to the atmosphere. Climate change is expected to have significant direct and indirect effects on the litter decomposition processes at various timescales. Using the TeaBag Index, we investigated the impact on decomposition of short-term direct effects of temperature and precipitation by comparing temporal variability over years, versus long-term climate impacts that incorporate indirect effects mediated through environmental changes by comparing sites along climatic gradients. We measured the initial decomposition rate (k) and the stabilization factor (S; amount of labile litter stabilizing) across a climate grid combining three levels of summer temperature (6.5-10.5 degrees C) with four levels of annual precipitation (600-2700 mm) in three summers with varying temperature and precipitation. Several (a)biotic factors were measured to characterize environmental differences between sites. Increased temperatures enhanced k, whereas increased precipitation decreased k across years and climatic regimes. In contrast, S showed diverse responses to annual changes in temperature and precipitation between climate regimes. Stabilization of labile litter fractions increased with temperature only in boreal and sub-alpine sites, while it decreased with increasing precipitation only in sub-alpine and alpine sites. Environmental factors such as soil pH, soil C/N, litter C/N, and plant diversity that are associated with long-term climate variation modulate the response of k and S. This highlights the importance of long-term climate in shaping the environmental conditions that influences the response of decomposition processes to climate change.

  • 229.
    Alvarez, Laura
    et al.
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Hernandez, Sara B
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    de Pedro, Miguel A
    Cava, Felipe
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Ultra-sensitive, high-resolution liquid chromatography methods for the high-throughput quantitative analysis of bacterial cell wall chemistry and structure2016In: Bacterial cell wall homeostasis: methods and protocols /edited by Hee-Jeon Hong / [ed] Hee-Jeon Hong, New York: Humana Press, 2016, Vol. 1440, p. 11-27Chapter in book (Refereed)
    Abstract [en]

    High-performance liquid chromatography (HPLC) analysis has been critical for determining the structural and chemical complexity of the cell wall. However this method is very time consuming in terms of sample preparation and chromatographic separation. Here we describe (1) optimized methods for peptidoglycan isolation from both Gram-negative and Gram-positive bacteria that dramatically reduce the sample preparation time, and (2) the application of the fast and highly efficient ultra-performance liquid chromatography (UPLC) technology to muropeptide separation and quantification. The advances in both analytical instrumentation and stationary-phase chemistry have allowed for evolved protocols which cut run time from hours (2-3 h) to minutes (10-20 min), and sample demands by at least one order of magnitude. Furthermore, development of methods based on organic solvents permits in-line mass spectrometry (MS) of the UPLC-resolved muropeptides. Application of these technologies to high-throughput analysis will expedite the better understanding of the cell wall biology.

  • 230.
    Alvarez, Laura
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid- Consejo Superior de Investigaciones Científicas, Madrid, Spain.
    Sanchez-Hevia, Dione
    Sanchez, Mercedes
    Berenguer, Jose
    A new family of nitrate/nitrite transporters involved in denitrification2019In: International Microbiology, ISSN 1139-6709, E-ISSN 1618-1905, Vol. 22, no 1, p. 19-28Article in journal (Refereed)
    Abstract [en]

    Denitrifying bacteria carry out nitrate and nitrite respiration inside and outside the cell, respectively. In Thermus thermophilus, nitrate and nitrite transport processes are carried out by major facilitator superfamily (MFS) transporters. The sequence of the nar operon of nitrate-only respiring strains of T. thermophilus includes two tandemly organized MFS transporter genes (narK and narT) of the NarK1 and NarK2 families. Both can function as nitrate/nitrite antiporters, but NarK has been proposed as more specific for nitrate whereas NarT more specific for nitrite. In some nitrate- and nitrite-respiring strains of the same species, a single MFS transporter (NarO) belonging to a different MFS subfamily appears. To analyze the role of this single MFS in the same genetic context, we transferred the two types of nar operon to the aerobic strain HB27, and further included in both of them the ability to respire nitrite. The new denitrifying strains HB27dn, with two MFS, and HB27dp, with a single one, were used to isolate mutants devoid of transporters. Through in trans complementation experiments, we demonstrate that the NarO single MFS works efficiently in the transport of both nitrate and nitrite.

  • 231. Alves-Martins, Fernanda
    et al.
    Calatayud, Joaquín
    Umeå University, Faculty of Science and Technology, Department of Physics. Departament of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.
    Medina, Nagore G.
    De Marco, Paulo
    Juen, Leandro
    Hortal, Joaquin
    Drivers of regional and local diversity of Amazonian stream Odonata2019In: Insect Conservation and Diversity, ISSN 1752-458X, E-ISSN 1752-4598, Vol. 12, no 3, p. 251-261Article in journal (Refereed)
    Abstract [en]

    Large Amazonian rivers may act as dispersal barriers for animals with low dispersal abilities, limiting their distribution to certain interfluves. Consequently, the distribution of these taxa would be less affected by macroclimatic gradients. Conversely, high-dispersal taxa would be less constrained by large rivers and may track suitable climates. We evaluate whether Zygoptera and Anisoptera, two Odonata suborders with different dispersal abilities, show differences in distribution patterns across Amazonian interfluves. We further assess the relative importance of macroclimatic and habitat factors in their community assembly. We used network modularity analyses to identify biogeographic species pools and spatial buffers to define metacommunity species pools. Then, we used structural equationmodels to estimate the relative importance of multi-scale factors on species richness patterns. Zygoptera communities are more similar in species composition within than between interfluves, suggesting that large Amazonian rivers indeed limit the distribution of Zygoptera species. Conversely, the distribution of Anisoptera extends across Amazonian interfluves. Seasonality has a strong positive effect on Zygoptera and Anisoptera richness across scales. In addition, habitat integrity is negatively correlated with the regional species richness and abundance of Anisoptera and positively correlated with Zygoptera local richness. The contrasting effects of habitat integrity on Anisoptera and Zygoptera suggest that the former is favored in open habitats, whereas the latter is so in forests. Despite these differences, both suborders appear to follow similar community assembly mechanisms in Amazonia, with a strong climatic control across scales and an effect of habitat filters on local communities.

  • 232.
    Amcoff Nyström, Christina
    Umeå University, Faculty of Social Sciences, Department of Informatics.
    Design rules for intranets according to the viable system model2006In: Systemic Practice and Action Research, ISSN 1094-429X, E-ISSN 1573-9295, Vol. 19, no 6, p. 523-535Article in journal (Refereed)
    Abstract [en]

    The Viable System Model, VSM, by Stafford Beer is a model used for diagnosing and designing organizational structure and communication to facilitate necessary and sufficient conditions for viability. The model has been used for diagnosing different kinds of organizations at different levels where its use highlights existing or missing communication patterns and information flows in different communication channels and relates findings to a viable system. In a previous article, VSM and Intranet have been discussed and examples of advantages of combining the two concepts when designing organizations, has been given. In this article, VSM is combined with Intranet and possible functions in an intranet that support information exchange between different systems are identified and described. The suggested functions identified in this article are finally related to Intranet use modes, and the concepts of Empowerment vs. control.

  • 233.
    Amer, Ayad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Costa, Tiago
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Farag, Salah
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Avican, Ummehan
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Forsberg, Åke
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Francis, Matthew
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Genetically engineered frameshifted YopN-TyeA chimeras influence type III secretion system function in Yersinia pseudotuberculosis2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 10, article id e77767Article in journal (Refereed)
    Abstract [en]

    Type III secretion is a tightly controlled virulence mechanism utilized by many gram negative bacteria to colonize their eukaryotic hosts. To infect their host, human pathogenic Yersinia spp. translocate protein toxins into the host cell cytosol through a preassembled Ysc-Yop type III secretion device. Several of the Ysc-Yop components are known for their roles in controlling substrate secretion and translocation. Particularly important in this role is the YopN and TyeA heterodimer. In this study, we confirm that Y. pseudotuberculosis naturally produce a 42 kDa YopN-TyeA hybrid protein as a result of a +1 frame shift near the 3 prime of yopN mRNA, as has been previously reported for the closely related Y. pestis. To assess the biological role of this YopN-TyeA hybrid in T3SS by Y. pseudotuberculosis, we used in cis site-directed mutagenesis to engineer bacteria to either produce predominately the YopN-TyeA hybrid by introducing +1 frame shifts to yopN after codon 278 or 287, or to produce only singular YopN and TyeA polypeptides by introducing yopN sequence from Y. enterocolitica, which is known not to produce the hybrid. Significantly, the engineered 42 kDa YopN-TyeA fusions were abundantly produced, stable, and were efficiently secreted by bacteria in vitro. Moreover, these bacteria could all maintain functionally competent needle structures and controlled Yops secretion in vitro. In the presence of host cells however, bacteria producing the most genetically altered hybrids (+1 frameshift after 278 codon) had diminished control of polarized Yop translocation. This corresponded to significant attenuation in competitive survival assays in orally infected mice, although not at all to the same extent as Yersinia lacking both YopN and TyeA proteins. Based on these studies with engineered polypeptides, most likely a naturally occurring YopN-TyeA hybrid protein has the potential to influence T3S control and activity when produced during Yersinia-host cell contact.

  • 234.
    Amer, Ayad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Gurung, Jyoti
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Costa, Tiago
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Ruuth, Kristina
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Zavialov, Anton
    Joint Biotechnology Laboratory, Department of Chemistry, University of Turku, Turku, Finland.
    Forsberg, Åke
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Francis, Matthew S
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    YopN and TyeA Hydrophobic Contacts Required for Regulating Ysc-Yop Type III Secretion Activity by Yersinia pseudotuberculosis2016In: Frontiers in Cellular and Infection Microbiology, E-ISSN 2235-2988, Vol. 6, article id 66Article in journal (Refereed)
    Abstract [en]

    Yersinia bacteria target Yop effector toxins to the interior of host immune cells by the Ysc-Yop type III secretion system. A YopN-TyeA heterodimer is central to controlling Ysc-Yop targeting activity. A + 1 frameshift event in the 3-prime end of yopN can also produce a singular secreted YopN-TyeA polypeptide that retains some regulatory function even though the C-terminal coding sequence of this YopN differs greatly from wild type. Thus, this YopN C-terminal segment was analyzed for its role in type III secretion control. Bacteria producing YopN truncated after residue 278, or with altered sequence between residues 279 and 287, had lost type III secretion control and function. In contrast, YopN variants with manipulated sequence beyond residue 287 maintained full control and function. Scrutiny of the YopN-TyeA complex structure revealed that residue W279 functioned as a likely hydrophobic contact site with TyeA. Indeed, a YopNW279G mutant lost all ability to bind TyeA. The TyeA residue F8 was also critical for reciprocal YopN binding. Thus, we conclude that specific hydrophobic contacts between opposing YopN and TyeA termini establishes a complex needed for regulating Ysc-Yop activity.

  • 235.
    Amer, Ayad
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Åhlund, Monika
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Bröms, Jeanette
    Department of Medical Countermeasures, Swedish Defense Research Agency, Division of NBC12 Defense, Umeå, Sweden.
    Forsberg, Åke
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Francis, Matthew
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Impact of the N-terminal secretor domain on YopD translocator function in Yersinia pseudotuberculosis type III secretion2011In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 193, no 23, p. 6683-6700Article in journal (Refereed)
    Abstract [en]

    Type III secretion systems (T3SSs) secrete needle components, pore-forming translocators, and the translocated effectors. In part, effector recognition by a T3SS involves their N-terminal amino acids and their 5′ mRNA. To investigate whether similar molecular constraints influence translocator secretion, we scrutinized this region within YopD from Yersinia pseudotuberculosis. Mutations in the 5′ end of yopD that resulted in specific disruption of the mRNA sequence did not affect YopD secretion. On the other hand, a few mutations affecting the protein sequence reduced secretion. Translational reporter fusions identified the first five codons as a minimal N-terminal secretion signal and also indicated that the YopD N terminus might be important for yopD translation control. Hybrid proteins in which the N terminus of YopD was exchanged with the equivalent region of the YopE effector or the YopB translocator were also constructed. While the in vitro secretion profile was unaltered, these modified bacteria were all compromised with respect to T3SS activity in the presence of immune cells. Thus, the YopD N terminus does harbor a secretion signal that may also incorporate mechanisms of yopD translation control. This signal tolerates a high degree of variation while still maintaining secretion competence suggestive of inherent structural peculiarities that make it distinct from secretion signals of other T3SS substrates.

  • 236. Ames, William
    et al.
    Pantazis, Dimitrios A
    Krewald, Vera
    Cox, Nicholas
    Messinger, Johannes
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lubitz, Wolfgang
    Neese, Frank
    Theoretical Evaluation of Structural Models of the S(2) State in the Oxygen Evolving Complex of Photosystem II: Protonation States and Magnetic Interactions2011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 49, p. 19743-19757Article in journal (Refereed)
    Abstract [en]

    Protonation states of water ligands and oxo bridges are intimately involved in tuning the electronic structures and oxidation potentials of the oxygen evolving complex (OEC) in Photosystem II, steering the mechanistic pathway, which involves at least five redox state intermediates S(n) (n = 0-4) resulting in the oxidation of water to molecular oxygen. Although protons are practically invisible in protein crystallography, their effects on the electronic structure and magnetic properties of metal active sites can be probed using spectroscopy. With the twin purpose of aiding the interpretation of the complex electron paramagnetic resonance (EPR) spectroscopic data of the OEC and of improving the view of the cluster at the atomic level, a complete set of protonation configurations for the S(2) state of the OEC were investigated, and their distinctive effects on magnetic properties of the cluster were evaluated. The most recent X-ray structure of Photosystem II at 1.9 Å resolution was used and refined to obtain the optimum structure for the Mn(4)O(5)Ca core within the protein pocket. Employing this model, a set of 26 structures was constructed that tested various protonation scenarios of the water ligands and oxo bridges. Our results suggest that one of the two water molecules that are proposed to coordinate the outer Mn ion (Mn(A)) of the cluster is deprotonated in the S(2) state, as this leads to optimal experimental agreement, reproducing the correct ground state spin multiplicity (S = 1/2), spin expectation values, and EXAFS-derived metal-metal distances. Deprotonation of Ca(2+)-bound water molecules is strongly disfavored in the S(2) state, but dissociation of one of the two water ligands appears to be facile. The computed isotropic hyperfine couplings presented here allow distinctions between models to be made and call into question the assumption that the largest coupling is always attributable to Mn(III). The present results impose limits for the total charge and the proton configuration of the OEC in the S(2) state, with implications for the cascade of events in the Kok cycle and for the water splitting mechanism.

  • 237.
    Amman, Nahom
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    PROTECTION AND DESORPTION OF CLAY-BOUND DNA2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 238. Amorim, Gisele C
    et al.
    Cisneros, David A.
    Unité de Génétique Moléculaire, Département de MicrobiologieInstitut Pasteur, Paris Cedex 15 France; CNRS, ERL 3526, Paris, France.
    Delepierre, Muriel
    Francetic, Olivera
    Izadi-Pruneyre, Nadia
    ¹H, ¹⁵N and ¹³C resonance assignments of PpdD, a type IV pilin from enterohemorrhagic Escherichia coli2014In: Biomolecular NMR Assignments, ISSN 1874-2718, E-ISSN 1874-270X, Vol. 8, no 1, p. 43-46Article in journal (Refereed)
    Abstract [en]

    Bacterial type 4 pili (T4P) are long flexible fibers involved in adhesion, DNA uptake, phage transduction, aggregation and a flagella-independent movement called "twitching motility". T4P comprise thousands of copies of the major pilin subunit, which is initially inserted in the plasma membrane, processed and assembled into dynamic helical filaments. T4P are crucial for host colonization and virulence of many Gram-negative bacteria. In enterohemorrhagic Escherichia coli the T4P, called hemorrhagic coli pili (HCP) promote cell adhesion, motility, biofilm formation and signaling. To understand the mechanism of HCP assembly and function, we analyzed the structure of the major subunit prepilin peptidase-dependent protein D (PpdD) (also called HcpA), a 15 kDa pilin with two potential disulfide bonds. Here we present the (1)H, (15)N and (13)C backbone and side chain resonance assignments of the C-terminal globular domain of PpdD as a first step to its structural determination.

  • 239. Amotchkina, Tatiana
    et al.
    Trubetskov, Michael K.
    Pervak, Yurij
    Veisz, Laszlo
    Max-Planck-Institut für Quantenoptik, D-85748 Garching, Germany.
    Pervak, Vladimir
    Stress compensation with antireflection coatings for ultrafast laser applications: from theory to practice2014In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 24, p. 30387-30393Article in journal (Refereed)
    Abstract [en]

    Each complicated coating, in particular, a dispersive mirror consists of dozens of layers. Thin films layers have mechanical stresses. After summing up stresses from all layers, the resulting stress is high enough to bend even a relatively thick substrate. To avoid this effect we suggest depositing an antireflection coating (AR) at the back-side of the substrate which together with suppression of unwanted reflections from the back side will also compensate this stress. We demonstrate unique, extremely thick and sophisticated AR coating consisting of 71 layers with the total physical thickness of 7.5 µm. This AR coating completely compensates stress from the dispersive mirror coated on the front side and minimizes unwanted reflections.

  • 240. Ampel, Linda
    et al.
    Bigler, Christian
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wohlfarth, Barbara
    Risberg, Jan
    Lotter, André F
    Veres, Daniel
    Modest summer temperature variability during DO cycles in western Europe2010In: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 29, no 11/12, p. 1322-1327Article in journal (Refereed)
    Abstract [en]

    Abrupt climatic shifts between cold stadials and warm interstadials, termed Dansgaard-Oeschger (DO) cycles, occurred frequently during the Last Glacial. Their imprint is registered in paleorecords worldwide, but little is known about the actual temperature change both annually and seasonally in different regions. A recent hypothesis based on modelling studies, suggests that DO cycles were characterised by distinct changes in seasonality in the Northern Hemisphere. The largest temperature change between stadial and interstadial phases would have occurred during the winter and spring seasons, whereas the summer seasons would have experienced a rather muted temperature shift. Here we present a temporally high-resolved reconstruction of summer temperatures for eastern France during a sequence of DO cycles between 36 and 18 thousand years before present. The reconstruction is based on fossil diatom assemblages from the paleolake Les Echets and indicates summer temperature changes of ca 0.5–2 °C between stadials and interstadials. This study is the first to reconstruct temperatures with a sufficient time resolution to investigate DO climate variability in continental Europe. It is therefore also the first proxy record that can test and support the hypothesis that temperature changes during DO cycles were modest during the summer season.

  • 241.
    Amundsson, Katharina
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Control of marine plankton respiration: High temperature sensitivity at low temperatures influenced by substrate availability2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Temperature dependence of marine plankton respiration is an important factor in understanding the function and changes in the ecosystem of the ocean. The aim of this study is to test the temperature sensitivity (Q10) of plankton respiration. The oxygen optode method was used to measure plankton respiration. Natural water samples from the Baltic Sea was incubated at short (in situ +1, +2, +3°C) and long (in situ +5, +10, +20°C) temperature intervals with influence of dissolved organic matter (DOC). The Arrhenius equation and Q10-model was used to determine the temperature dependence (Q10) of respiration at different temperatures. There was a significant difference in Q10 between short temperature intervals at low temperatures (p=0,008) and long temperature intervals at higher temperatures. There was no significant difference between long and short temperature intervals when DOC was added (p=0,094). A significant effect could be seen with the DOC enrichment at low temperatures, where the Q10-values became significantly lower (p=0,002) after DOC addition. This effect could, however, not be seen at higher temperatures (p=0,117). Together with results from earlier studies it was concluded that the difference in temperature depends on the actual temperature and not the length of the interval. Lowered temperature dependence at raised DOC concentration, was the opposite of what was expected. The results suggest that the importance of temperature for CO2 emissions and development of hypoxia in the sea may have been underestimated.

  • 242.
    Anani, Adi
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    M-learning in review: Technology, standard and evaluation2008In: Journal of Communication and Computer, ISSN 1548-7709, Vol. 5, no 11, p. 1-6Article in journal (Refereed)
    Abstract [en]

    Nowadays E-learning as a form of learning depending on networks and computer devices has been expanding by leaps and bounds. As a special kind of E-learning, M-learning (mobile learning) aims at the use of mobile devices anywhere at anytime by anybody. In this paper, the technologies to develop a M-learning system is deeply analyzed according to the layer model at first. Secondly, from the view of application, the standardization in M-learning is researched in order to accelerate the development and popularization of M-learning. Finally, quality estimation of M-learning system is discussed from the view of QoE (quality of experiences). The experience form end-user is the sole effective norm to judge the result of M-learning technology. It is no doubt that technologies, standardization and evaluation will play very important parts in the course of M-learning development.

  • 243.
    Anderl, Ines
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Activation of the Cellular Immune Response in Drosophila melanogaster Larvae2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During the last 40 years, Drosophila melanogaster has become an invaluable tool in understanding innate immunity. The innate immune system of Drosophila consists of a humoral and a cellular component. While many details are known about the humoral immune system, our knowledge about the cellular immune system is comparatively small. Blood cells or hemocytes constitute the cellular immune system. Three blood types have been described for Drosophila larvae. Plasmatocytes are phagocytes with a plethora of functions. Crystal cells mediate melanization and contribute to wound healing. Plasmatocytes and crystal cells constitute the blood cell repertoire of a healthy larva, whereas lamellocytes are induced in a demand-adapted manner after infection with parasitoid wasp eggs. They are involved in the melanotic encapsulation response against parasites and form melanotic nodules that are also referred to as tumors.

    In my thesis, I focused on unraveling the mechanisms of how the immune system orchestrates the cellular immune response. In particular, I was interested in the hematopoiesis of lamellocytes.

    In Article I, we were able to show that ectopic expression of key components of a number of signaling pathways in blood cells induced the development of lamellocytes, led to a proliferative response of plasmatocytes, or to a combination of lamellocyte activation and plasmatocyte proliferation.

    In Article II, I combined newly developed fluorescent enhancer-reporter constructs specific for plasmatocytes and lamellocytes and developed a “dual reporter system” that was used in live microscopy of fly larvae. In addition, we established flow cytometry as a tool to count total blood cell numbers and to distinguish between different blood cell types. The “dual reporter system” enabled us to differentiate between six blood cell types and established proliferation as a central feature of the cellular immune response. The combination flow cytometry and live imaging increased our understanding of the tempo-spatial events leading to the cellular immune reaction.

    In Article III, I developed a genetic modifier screen to find genes involved in the hematopoiesis of lamellocytes. I took advantage of the gain-of-function phenotype of the Tl10b mutation characterized by an activated cellular immune system, which induced the formation blood cell tumors. We screened the right arm of chromosome 3 for enhancers and suppressors of this mutation and uncovered ird1.

    Finally in Article IV, we showed that the activity of the Toll signaling pathway in the fat body, the homolog of the liver, is necessary to activate the cellular immune system and induce lamellocyte hematopoiesis.

  • 244.
    Anderl, Ines
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Infection-induced proliferation is a central hallmark of the activation of the cellular immune response in Drosophila larvae.Manuscript (preprint) (Other academic)
    Abstract [en]

    Blood cells have important roles in immune reactions in all metazoan species. In Drosophila melanogaster larvae, phagocytic plasmatocytes are the main blood cell (hemocyte) type. Lamellocytes participate in encapsulating foreign objects and are formed in response to parasitoid wasps laying their eggs into the hemocoel of the larvae. The immune reaction against wasps requires controlled recruitment and action of hemocytes from the lymph glands, sessile islets and circulation. However, the contribution of these different hematopoietic compartments to the immune-induced hemocyte pool remains unclear. We used eater-GFP and MSNF9MO-mCherry to fluorescently tag plasmatocytes and lamellocytes, respectively, and utilized flow cytometry and in vivo imaging to assess the hemocyte numbers and types in circulation and in sessile compartments after infection by three wasp species of the genus Leptopilina. We detected five different hemocyte types based on fluorescence, and a population of non-fluorescent cells. While non-infected larvae generally had only one, eaterGFP-high plasmatocyte population, early after wasp infection a new, eaterGFP-low cell population appeared in circulation. EaterGFP-high and –low cells both accumulated msnCherry during the immune response, and formed two cell lineages. Whereas the eaterGFP-low cells gradually lost GFP, the eaterGFP-high cells retained it at high levels. We suggest that eaterGFP-low cells represent an immune-induced hemocyte precursor cell pool, which, via a prelamellocyte stage, gives rise to lamellocytes. EaterGFP-high plasmatocytes also differentiated into large, msnCherry-positive hemocytes on wasp eggs, but these cells retain plasmatocyte identity. Importantly, all hemocyte types, except for lamellocytes, were able to divide after wasp infection, contributing to the increased hemocyte numbers after infection. We conclude that orchestrated differentiation and division of different hemocyte types in circulation and in sessile compartment is key to a successful immune response against parasitoid wasps.

  • 245.
    Andersdotter Persson, Anna
    Umeå University, Faculty of Social Sciences, Department of Statistics.
    Kalibrering som ett sätt att hantera bortfall: Vilken korrelation krävs mellan hjälp- och responsvariabler?2010Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
  • 246. Andersen, G. Neumann
    et al.
    Andersen, M.
    Nagaeva, Olga
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Immunology.
    Wikberg, J. E. S.
    Mincheva-Nilsson, Lucia
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Immunology.
    Dermal Melanocortin Receptor Rebound in Diffuse Systemic Sclerosis after Anti-TGF ss 1 Antibody Therapy2012In: Scandinavian Journal of Immunology, ISSN 0300-9475, E-ISSN 1365-3083, Vol. 76, no 5, p. 478-482Article in journal (Refereed)
    Abstract [en]

    Disturbed transforming growth factor beta (TGF beta) signalling leads to enhanced synthesis of extracellular matrix (ECM), which is manifested as systemic sclerosis (SSc), but this may be attenuated by the melanocortin system. Here, we report of rebound reaction in the gene expression of melanocortin receptor (MCR) subtypes and of the precursor of these receptors ligands, the pro-opio-melanocortin protein (POMC), in the acute skin lesion of diffuse systemic sclerosis (dSSc) after treatment with a recombinant human anti-TGF beta 1 antibody. Biopsies, taken from the leading edge of the skin lesion, before and after treatment of a patient with recent onset dSSc, were examined. Before treatment, increased levels of TGF beta mRNA and suppressed levels of POMC mRNA and MCR subtypes MC1-3, 5R mRNAs were seen in the lesion, compared with healthy controls. After treatment, there was a rebound expression of POMC, MC2, 3, 5R mRNAs. As the melanocortin system regulates collagen and melanin production, our findings add a new understanding to the pathogenetic mechanisms involved in the acute skin lesion of dSSc, which is characterized by enhanced ECM formation and changes in skin pigmentation.

  • 247.
    Andersen, K. H.
    et al.
    Tech Univ Denmark, Denmark.
    Berge, T.
    Tech Univ Denmark, Denmark ; Univ Copenhagen, Denmark.
    Goncalves, R. J.
    Tech Univ Denmark, Denmark ;Consejo Nacl Invest Cient & Tecn, Argentina ; Estn Fotobiol Playa Union, Argentina.
    Hartvig, M.
    Tech Univ Denmark, Denmark ; Univ Copenhagen, Denmark ; Univ Göttingen, Germany.
    Heuschele, J.
    Tech Univ Denmark, Denmark.
    Hylander, Samuel
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Jacobsen, N. S.
    Tech Univ Denmark, Denmark.
    Lindemann, C.
    Tech Univ Denmark, Denmark.
    Martens, E. A.
    Tech Univ Denmark, Denmark ; Univ Copenhagen, Denmark.
    Neuheimer, A. B.
    Tech Univ Denmark, Denmark ; Univ Hawaii Manoa, USA.
    Olsson, K.
    Tech Univ Denmark, Denmark.
    Palacz, A.
    Tech Univ Denmark, Denmark.
    Prowe, A. E. F.
    Tech Univ Denmark, Denmark ; GEOMAR Helmholtz Ctr Ocean Res Kiel, Germany.
    Sainmont, J.
    Tech Univ Denmark, Denmark.
    Traving, S. J.
    Tech Univ Denmark, Denmark ; Univ Copenhagen, Denmark.
    Visser, A. W.
    Tech Univ Denmark, Denmark.
    Wadhwa, N.
    Tech Univ Denmark, Denmark.
    Kiorboe, T.
    Tech Univ Denmark, Denmark.
    Characteristic Sizes of Life in the Oceans, from Bacteria to Whales2016In: Annual Review of Marine Science, ISSN 1941-1405, E-ISSN 1941-0611, Vol. 8, p. 217-241Article in journal (Refereed)
    Abstract [en]

    The size of an individual organism is a key trait to characterize its physiology and feeding ecology. Size-based scaling laws may have a limited size range of validity or undergo a transition from one scaling exponent to another at some characteristic size. We collate and review data on size-based scaling laws for resource acquisition, mobility, sensory range, and progeny size for all pelagic marine life, from bacteria to whales. Further, we review and develop simple theoretical arguments for observed scaling laws and the characteristic sizes of a change or breakdown of power laws. We divide life in the ocean into seven major realms based on trophic strategy, physiology, and life history strategy. Such a categorization represents a move away from a taxonomically oriented description toward a trait-based description of life in the oceans. Finally, we discuss life forms that transgress the simple size-based rules and identify unanswered questions.

  • 248. Anderson, James V.
    Ramos-Sánchez, José M.
    Conde, Daniel
    Ibáñez, Christian
    Takata, Naoki
    Allona, Isabel
    Eriksson, Maria E.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Role of the Circadian Clock in Cold Acclimation and Winter Dormancy in Perennial Plants2015Collection (editor) (Refereed)
    Abstract [en]

    Seasonal variation is a strong cue directing the growth and development of plants. It is particularly important for perennials growing in temperate and boreal regions where woody plants must become dormant to survive freezing winter temperatures. Shortening of the photoperiod induces growth cessation, bud set and a first degree of cold acclimation in most woody plants. The subsequent drop in temperature then produces a greater tolerance to cold and, in deciduous trees, leaf senescence and fall. Trees must time their periods of dormancy accurately with their environment. Circadian clocks underlie this ability, allowing organisms to predict regular, daily changes in their environment as well as longer term seasonal changes. This chapter provides an update on the plant clock in a model annual, thale cress (Arabidopsis thaliana), and further summarizes recent advances about the clock in perennial plants and its involvement in their annual growth cycles, which allows trees to withstand cold and freezing temperatures. Moreover, we outline our views on areas where future work on the circadian clock is necessary to gain insight into the life of a tree.

  • 249. Anderson, K. E.
    et al.
    Nisbet, R. M.
    Diehl, S.
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Spatial scaling of consumer-resource interactions in advection-dominated systems2006In: American Naturalist, Vol. 168, no 3, p. 358-372Article in journal (Refereed)
    Abstract [en]

    Ecologists studying consumer-resource interactions in advection-dominated systems such as streams and rivers frequently seek to link the results of small-scale experiments with larger-scale patterns of distribution and abundance. Accomplishing this goal requires determining the characteristic scale, termed the response length, at which there is a shift from local dynamics dominated by advective dispersal to larger-scale dynamics dominated by births and deaths. Here, we model the dynamics of consumer-resource systems in a spatially variable, advective environment and show how consumer-resource interactions alter the response length relative to its single-species value. For one case involving a grazer that emigrates in response to high predator density, we quantify the changes using published data from small-scale experiments on aquatic invertebrates. Using Fourier analysis, we describe the responses of advection-dominated consumer-resource systems to spatially extended environmental variability in a way that involves explicit consideration of the response length. The patterns we derive for different consumer-resource systems exhibit important similarities in how component populations respond to spatial environmental variability affecting dispersal as opposed to demographic parameters.

  • 250. Anderson, K. E.
    et al.
    Nisbet, R. M.
    Diehl, S.
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Cooper, S. D.
    Scaling population responses to spatial environmental variability in advection-dominated systems2005In: Ecology Letters, Vol. 8, no 9, p. 933-943Article in journal (Refereed)
    Abstract [en]

    We model the spatial dynamics of an open population of organisms that disperse solely through advection in order to understand responses to multiscale environmental variability. We show that the distance over which a population responds to a localized perturbation, called the response length, can be characterized as an organisms average lifetime dispersal distance, unless there is strong density-dependence in demographic or dispersal rates. Continuous spatial fluctuations in demographic rates at scales smaller than the response length will be largely averaged in the population distribution, whereas those in per capita emigration rates will be strongly tracked. We illustrate these results using a parameterized example to show how responses to environmental variability may differ in streams with different average current velocities. Our model suggests an approach to linking local dynamics dominated by dispersal processes to larger-scale dynamics dominated by births and deaths.

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