Browsing by Subject "FLUORESCENCE"

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  • Kortesoja, Maarit; Trofin, Raluca Elena; Hanski, Leena (2020)
    The obligate intracellular bacterium, Chlamydia pneumoniae, has been identified as a risk factor for several chronic inflammatory diseases in addition to respiratory tract infections. The dissemination of C. pneumoniae from respiratory tract to secondary sites of infection occurs via infected monocyte / macrophage line cells, in which C. pneumoniae can persist as an antibiotic-refractory phenotype. To allow more detailed studies on the epithelium-monocyte/macrophage transition of the infection, new in vitro bioassays are needed. To this end, a coculture system with human continuous cell lines was established. Respiratory epithelial HL cells were infected with C. pneumoniae and THP-1 monocytes were added into the cultures at 67 h post infection. After a 5 h coculture, THP-1 cells were collected with a biotinylated HLA antibody and streptavidin-coated magnetic beads and C. pneumoniae genome copy numbers in THP-1 determined by quantitative PCR. The assay was optimized for cell densities, incubation time, THP-1 separation technique and buffer composition, and its robustness was demonstrated by a Z' value of 0.6. The mitogen-activated protein kinase (MAPK) inhibitors: SP600125 (JNK inhibitor), SB203580 (p38 inhibitor) and FR180204 (ERK inhibitor) suppressed the transfer of C. pneumoniae from HL to THP-1 cells, making them suitable positive controls for the assay. Based on analysis of separate steps of the process, the MAPK inhibitors suppress the bacterial entry to THP-1 cells. The transfer of C. pneumoniae from epithelium to phagocytes represents a crucial step in the establishment of persistent infections by this pathogen, and the presented methods enables future studies to block this process by therapeutic means.
  • Saarinen, Jukka Kalle Samuel; Gütter, Friederike; Lindman, Mervi M; Agopov, Mikael; Fraser-Miller, Sara J.; Scherließ, Regina; Jokitalo, Eija; Almeida Santos, Helder; Peltonen, Leena; Isomäki, Antti; Strachan, Clare J. (2019)
    A wide variety of nanoparticles are playing an increasingly important role in drug delivery. Label-free imaging techniques are especially desirable to follow the cellular uptake and intracellular fate of nanoparticles. The combined correlative use of different techniques, each with unique advantages, facilitates more detailed investigation about such interactions. The synergistic use of correlative coherent anti-Stokes Raman scattering and electron microscopy (C-CARS-EM) imaging offers label-free, chemically-specific, and (sub)-nanometer spatial resolution for studying nanoparticle uptake into cells as demonstrated in the current study. Coherent anti-Stokes Raman scattering (CARS) microscopy offers chemically-specific (sub)micron spatial resolution imaging without fluorescent labels while transmission electron microscopy (TEM) offers (sub)-nanometer scale spatial resolution and thus visualization of precise nanoparticle localization at the sub-cellular level. This proof-of-concept imaging platform with unlabeled drug nanocrystals and macrophage cells revealed good colocalization between the CARS signal and electron dense nanocrystals in TEM images. The correlative TEM images revealed subcellular localization of nanocrystals inside membrane bound vesicles, showing multivesicular body (MVB)-like morphology typical for late endosomes (LEs), endolysosomes, and phagolysosomes. C-CARS-EM imaging has much potential to study the interactions between a wide range of nanoparticles and cells with high precision and confidence.
  • Owen, Michael C.; Kulig, Waldemar; Rog, Tomasz; Vattulainen, Ilpo; Strodel, Birgit (2018)
    In an effort to delineate how cholesterol protects membrane structure under oxidative stress conditions, we monitored the changes to the structure of lipid bilayers comprising 30 mol% cholesterol and an increasing concentration of Class B oxidized 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) glycerophospholipids, namely, 1-palmitoyl-2-(9'-oxo-nonanoyl)-sn-glycero-3-phosphocholine (PoxnoPC), and 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC), using atomistic molecular dynamics simulations. Increasing the content of oxidized phospholipids (oxPLs) from 0 to 60 mol% oxPL resulted in a characteristic reduction in bilayer thickness and increase in area per lipid, thereby increasing the exposure of the membrane hydrophobic region to water. However, cholesterol was observed to help reduce water injury by moving into the bilayer core and forming more hydrogen bonds with the oxPLs. Cholesterol also resists altering its tilt angle, helping to maintain membrane integrity. Water that enters the 1-nm-thick core region remains part of the bulk water on either side of the bilayer, with relatively few water molecules able to traverse through the bilayer. In cholesterol-rich membranes, the bilayer does not form pores at concentrations of 60 mol% oxPL as was shown in previous simulations in the absence of cholesterol.
  • Haraguchi, Lumi; Asmala, Eero; Jakobsen, Hans H.; Carstensen, Jacob (2019)
    Dissolved organic matter (DOM) is an important component of nutrient cycling, but the role of different organisms controlling the processing of autochthonous DOM remains poorly understood. Aiming to characterize phytoplankton-derived DOM and the effects of complex pelagic communities on its dynamics, we incubated natural plankton communities from a temperate mesohaline estuary under controlled conditions for 18 days. The incubations were carried out in contrasting seasons (spring and autumn) and changes in the planktonic community (phytoplankton, bacteria and microzooplankton), nutrients and DOM were assessed. Our results highlight the complexity of DOM production and fate in natural planktonic communities. Small changes in DOM composition were observed in the experiments relative to the orders-of-magnitude variations experienced in the phytoplankton assembly. We argue that the tight coupling between microbial processing and DOM production by phytoplankton and grazers stabilizes variations in quantity and characteristics of autochthonous DOM, resulting in apparently homogeneous semi-labile DOM pool throughout the experiments. However, seasonal differences in the production and processing of DOM were observed, reflecting differences in the nutrient regimes and initial DOM characteristics in each experiment, but also likely influenced by changes in the successional status of the pelagic community. Acknowledging that characteristics of the DOM derived from phytoplankton growth can vary broadly, heterotrophic processing and successional status of the community are synergistically important factors for shaping those characteristics, and thus affecting the seasonal signature of the semi-labile autochthonous DOM pool.
  • Wang, Linping; Saarela, Jani; Poque, Sylvain; Valkonen, Jari P. T. (2020)
    The class 1 ribonuclease III (RNase III) encoded by Sweet potato chlorotic stunt virus (CSR3) suppresses RNA silencing in plant cells and thereby counters the host antiviral response by cleaving host small interfering RNAs, which are indispensable components of the plant RNA interference (RNAi) pathway. The synergy between sweet potato chlorotic stunt virus and sweet potato feathery mottle virus can reduce crop yields by 90%. Inhibitors of CSR3 might prove efficacious to counter this viral threat, yet no screen has been carried out to identify such inhibitors. Here, we report a novel high-throughput screening (HTS) assay based on fluorescence resonance energy transfer (FRET) for identifying inhibitors of CSR3. For monitoring CSR3 activity via HTS, we used a small interfering RNA substrate that was labelled with a FRET-compatible dye. The optimized HTS assay yielded 109 potential inhibitors of CSR3 out of 6,620 compounds tested from different small-molecule libraries. The three best inhibitor candidates were validated with a dose-response assay. In addition, a parallel screen of the selected candidates was carried out for a similar class 1 RNase III enzyme from Escherichia coli (EcR3), and this screen yielded a different set of inhibitors. Thus, our results show that the CSR3 and EcR3 enzymes were inhibited by distinct types of molecules, indicating that this HTS assay could be widely applied in drug discovery of class 1 RNase III enzymes.
  • Mõttus, Matti; Aragão, Luiz; Bäck, Jaana; Clemente, Rocío Hernandez; Maeda, Eduardo Eiji; Markiet, Vincent Robert Leon; Nichol, Caroline; Oliveira, Raimundo Cosme; Restrepo-Coupe, Natalia (2019)
    The spectral properties of plant leaves relate to the state of their photosynthetic apparatus and the surrounding environment. An example is the well known photosynthetic downregulation, active on the time scale from minutes to hours, caused by reversible changes in the xanthophyll cycle pigments. These changes affect leaf spectral absorption and are frequently quantified using the photochemical reflectance index (PRI). This index can be used to remotely monitor the photosynthetic status of vegetation, and allows for a global satellite-based measurement of photosynthesis. Such earth observation satellites in near-polar orbits usually cover the same geographical location at the same local solar time at regular intervals. To facilitate the interpretation of these instantaneous remote PRI measurements and upscale them temporally, we measured the daily course of leaf PRI in two evergreen biomes—a European boreal forest and an Amazon rainforest. The daily course of PRI was different for the two locations: At the Amazonian forest, the PRI of Manilkara elata leaves was correlated with the average photosynthetic photon flux density (PPFD) ( R2=0.59 ) of the 40 minutes preceding the leaf measurement. In the boreal location, the variations in Pinus sylvestris needle PRI were only weakly ( R2=0.27) correlated with mean PPFD of the preceding two hours; for Betula pendula, the correlation was insignificant regardless of the averaging period. The measured daily PRI curves were specific to species and/or environmental conditions. Hence, for a proper interpretation of satellite-measured instantaneous photosynthesis, the scaling of PRI measurements should be supported with information on its correlation with PPFD.
  • Valiev, R. R.; Nasibullin, R. T.; Cherepanov, V. N.; Baryshnikov, G.; Sundholm, D.; Ågren, H.; Minaev, B. F.; Kurten, T. (2020)
    A new method for calculating internal conversion rate constants (k_(IC)), including anharmonic effects and using the Lagrangian multiplier technique, is proposed. The deuteration effect on k_(IC) is investigated for naphthalene, anthracene, free-base porphyrin (H2P) and tetraphenylporphyrin (H2TPP). The results show that anharmonic effects are important when calculating k_(IC) for transitions between electronic states that are energetically separated (Delta E) by more than 20 000-25 000 cm(-1). Anharmonic effects are also important when Delta E <20 000-25 000 cm(-1) and when the accepting modes are X-H stretching vibrations with a frequency larger than 2000 cm(-1). The calculations show that there is mixing between the S-1 and S-2 states of naphthalene induced by non-adiabatic interactions. The non-adiabatic interaction matrix element between the S-1 and S-2 states is 250 cm(-1) and 50 cm(-1) for the normal and fully deuterated naphthalene structure and this difference significantly affects the estimated fluorescence quantum yield. Besides aromatic hydrocarbons H2P and H2TPP, the k_(IC) rate constant is also calculated for pyrometene (PM567) and tetraoxa[8]circulene (4B) with a detailed analysis of the effect of the vibrational anharmonicity.
  • Valiev, R. R.; Cherepanov, V. N.; Baryshnikov, G. V.; Sundholm, D. (2018)
    A method for calculating the rate constants for internal-conversion (k(IC)) and intersystem-crossing (k(ISC)) processes within the adiabatic and Franck-Condon (FC) approximations is proposed. The applicability of the method is demonstrated by calculation of k(IC) and k(ISC) for a set of organic and organometallic compounds with experimentally known spectroscopic properties. The studied molecules were pyrromethene-567 dye, psoralene, hetero[8]circulenes, free-base porphyrin, naphthalene, and larger polyacenes. We also studied fac-Alq(3) and fac-Ir(ppy)(3), which are important molecules in organic light emitting diodes (OLEDs). The excitation energies were calculated at the multi-configuration quasi-degenerate second-order perturbation theory (XMC-QDPT2) level, which is found to yield excitation energies in good agreement with experimental data. Spin-orbit coupling matrix elements, non-adiabatic coupling matrix elements, Huang-Rhys factors, and vibrational energies were calculated at the time-dependent density functional theory (TDDFT) and complete active space self-consistent field (CASSCF) levels. The computed fluorescence quantum yields for the pyrromethene-567 dye, psoralene, hetero[8]circulenes, fac-Alq(3) and fac-Ir(ppy)(3) agree well with experimental data, whereas for the free-base porphyrin, naphthalene, and the polyacenes, the obtained quantum yields significantly differ from the experimental values, because the FC and adiabatic approximations are not accurate for these molecules.
  • Silva, Luis; Calleja, Maria Ll.; Ivetic, Snjezana; Huete-Stauffer, Tamara; Roth, Florian; Carvalho, Susana; Moran, Xose Anxelu G. (2021)
    In coral reefs, dissolved organic matter (DOM) cycling is a critical process for sustaining ecosystem functioning. However, global and local stressors have caused persistent shifts from coral- to algae-dominated benthic communities. The influence of such phase shifts on DOM nature and its utilization by heterotrophic bacterioplankton remains poorly studied. Every second month for one year, we retrieved seawater samples enriched in DOM produced by coral- and algae-dominated benthic communities in a central Red Sea reef during a full annual cycle. Seawater incubations were conducted in the laboratory under in situ temperature and light conditions by inoculating enriched DOM samples with bacterial assemblages collected in the surrounding waters. Dissolved organic carbon (DOC) concentrations were higher in the warmer months (May-September) in both communities, resulting in higher specific growth rates and bacterial growth efficiencies (BGE). However, these high summer values were significantly enhanced in algal-DOM relative to coral-DOM, suggesting the potential for bacterioplankton biomass increase in reefs with algae replacing healthy coral cover under warmer conditions. The potential exacerbation of heterotrophic bacterial activity in the ongoing widespread regime shift from coral- to algae-dominated communities may have detrimental consequences for the overall health of tropical coral reefs. (C) 2020 The Authors. Published by Elsevier B.V.
  • Koivuniemi, Artturi; Fallarero, Adyary; Bunker, Alex (2019)
    The development of antimicrobial agents that target and selectively disrupt biofilms is a pressing issue since, so far, no antibiotics have been developed that achieve this effectively. Previous experimental work has found a promising set of antibacterial peptides: β2,2-amino acid derivatives, relatively small molecules with common structural elements composed of a polar head group and two non-polar hydrocarbon arms. In order to develop insight into possible mechanisms of action of these novel antibacterial agents, we have performed an in silico investigation of four leading β2,2-amino acid derivatives, interacting with models of both bacterial (target) and eukaryotic (host) membranes, using molecular dynamics simulation with a model with all-atom resolution. We found an unexpected result that could shed light on the mechanism of action of these antimicrobial agents: the molecules assume a conformation where one of the hydrophobic arms is directed downward into the membrane core while the other is directed upwards, out of the membrane and exposed above the position of the membrane headgroups; we dubbed this conformation the “can-can pose”. Intriguingly, the can-can pose was most closely linked to the choice of headgroup. Also, the compound previously found to be most effective against biofilms displayed the strongest extent of this behavior and, additionally, this behavior was more pronounced for this compound in the bacterial than in the eukaryotic membrane. We hypothesize that adopting the can-can pose could possibly disrupt the protective peptidoglycan macronet found on the exterior of the bacterial membrane.
  • Kerst, Thomas; Toivonen, Juha (2018)
    Luminescence in air induced by alpha particle emitters can be used to optically detect radioactive contamination from distances that surpass the range of the alpha radiation itself. Alpha particles excite nitrogen molecules in air and the relaxation creates a faint light emission. When the composition of the gases surrounding the alpha particle emitter is altered then the luminescence spectrum changes. In this work. we report the creation of an intense light emission in the wavelength regime below 300 nm originating from alpha particle excited nitric oxide (NO). The light yield has been investigated as a function of the NO concentration in an N-2 atmosphere. Unlike the emission from molecular nitrogen, NO emits at wavelengths shorter than 300 nm, where solar background and artificial lighting am negligible, thus enabling optical detection of alpha radiation even under bright lighting conditions. We show that the radioactively induced NO emission reaches its maximum intensity at a concentration of 50 ppm of NO diluted in N-2. At this concentration, the strongest emission line of NO is about 25 times more intense than the most intense line of N-2 radioluminescence. Lastly, we discuss potential applications and limitations of the technique. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
  • Rowe, Owen F.; Dinasquet, Julie; Paczkowska, Joanna; Figueroa, Daniela; Riemann, Lasse; Andersson, Agneta (2018)
    Dissolved organic matter (DOM) in marine waters is a complex mixture of compounds and elements that contribute substantially to the global carbon cycle. The large reservoir of dissolved organic carbon (DOC) represents a vital resource for heterotrophic bacteria. Bacteria can utilise, produce, recycle and transform components of the DOM pool, and the physicochemical characteristics of this pool can directly influence bacterial activity; with consequences for nutrient cycling and primary productivity. In the present study we explored bacterial transformation of naturally occurring DOM across an extensive brackish water gradient in the Baltic Sea. Highest DOC utilisation (indicated by decreased DOC concentration) was recorded in the more saline southerly region where waters are characterised by more autochthonous DOM. These sites expressed the lowest bacterial growth efficiency (BGE), whereas in northerly regions, characterised by higher terrestrial and allochthonous DOM, the DOC utilisation was low and BGE was highest. Bacterial processing of the DOM pool in the south resulted in larger molecular weight compounds and compounds associated with secondary terrestrial humic matter being degraded, and a processed DOM pool that was more aromatic in nature and contributed more strongly to water colour; while the opposite was true in the north. Nutrient concentration and stoichiometry and DOM characteristics affected bacterial activity, including metabolic status (BGE), which influenced DOM transformations. Our study highlights dramatic differences in DOM characteristics and microbial carbon cycling in sub-basins of the Baltic Sea. These findings are critical for our understanding of carbon and nutrient biogeochemistry, particularly in light of climate change scenarios.
  • Takamiya, Masanari; Xu, Feng; Suhonen, Heikki; Gourain, Victor; Yang, Lixin; Nga Yu Ho, [Tuntematon]; Helfen, Lukas; Schroeck, Anne; Etard, Christelle; Grabher, Clemens; Rastegar, Sepand; Schlunck, Guenther; Reinhard, Thomas; Baumbach, Tilo; Straehle, Uwe (2016)
    Altered levels of trace elements are associated with increased oxidative stress that is eventually responsible for pathologic conditions. Oxidative stress has been proposed to be involved in eye diseases, including cataract formation. We visualized the distribution of metals and other trace elements in the eye of zebrafish embryos by micro X-ray fluorescence (mu-XRF) imaging. Many elements showed highest accumulation in the retinal pigment epithelium (RPE) of the zebrafish embryo. Knockdown of the zebrafish brown locus homologues tyrp1a/b eliminated accumulation of these elements in the RPE, indicating that they are bound by mature melanosomes. Furthermore, albino (slc45a2) mutants, which completely lack melanosomes, developed abnormal lens reflections similar to the congenital cataract caused by mutation of the myosin chaperon Unc45b, and an in situ spin trapping assay revealed increased oxidative stress in the lens of albino mutants. Finally transplanting a wildtype lens into an albino mutant background resulted in cataract formation. These data suggest that melanosomes in pigment epithelial cells protect the lens from oxidative stress during embryonic development, likely by buffering trace elements.
  • Morales, Luis O.; Shapiguzov, Alexey; Safronov, Omid; Leppälä, Johanna; Vaahtera, Lauri; Yarmolinsky, Dmitry; Kollist, Hannes; Brosche, Mikael (2021)
    Tropospheric ozone (O-3) is a major air pollutant that decreases yield of important crops worldwide. Despite long-lasting research of its negative effects on plants, there are many gaps in our knowledge on how plants respond to O-3. In this study, we used natural variation in the model plant Arabidopsis (Arabidopsis thaliana) to characterize molecular and physiological mechanisms underlying O-3 sensitivity. A key parameter in models for O-3 damage is stomatal uptake. Here we show that the extent of O-3 damage in the sensitive Arabidopsis accession Shahdara (Sha) does not correspond with O-3 uptake, pointing toward stomata-independent mechanisms for the development of O-3 damage. We compared tolerant (Col-0) versus sensitive accessions (Sha, Cvi-0) in assays related to photosynthesis, cell death, antioxidants, and transcriptional regulation. Acute O-3 exposure increased cell death, development of lesions in the leaves, and decreased photosynthesis in sensitive accessions. In both Sha and Cvi-0, O-3-induced lesions were associated with decreased maximal chlorophyll fluorescence and low quantum yield of electron transfer from Photosystem II to plastoquinone. However, O-3-induced repression of photosynthesis in these two O-3-sensitive accessions developed in different ways. We demonstrate that O-3 sensitivity in Arabidopsis is influenced by genetic diversity given that Sha and Cvi-0 developed accession-specific transcriptional responses to O-3. Our findings advance the understanding of plant responses to O-3 and set a framework for future studies to characterize molecular and physiological mechanisms allowing plants to respond to high O-3 levels in the atmosphere as a result of high air pollution and climate change.
  • Göbüz, Göker; Liu, Chang; Jiang, Zhong-qing; Pulkkinen, Marjo; Piironen, Vieno; Sontag-Strohm, Tuula; Heinonen, Marina (2018)
    The course of protein-lipid co-oxidation was investigated in oil-in-water emulsions stabilized with proteins extracted from microwave-treated (MWT) and conventional thermal-treated (CTT) faba beans stored at 37 degrees C for 7days. Emulsions prepared with proteins from untreated (UT) faba beans and soy protein isolate (SP) were monitored for comparison. Lipid oxidation was detected through formation of primary and secondary oxidation products while protein oxidation was examined via tryptophan fluorescence degradation in interface and aqueous phase. Oxidation of proteins was more emphasized in the interfacial layers of MWT, CTT, and SP emulsions than in UT emulsions due to the prominence of radical chain-driven co-oxidation mechanism while lipoxygenase (LOX) activity in UT and MWT emulsions resulted in high amounts of hydroperoxides and abundance in lipid oxidation volatiles. Conventional thermal treatment provided better oxidative stability than microwave treatment reflected in lower levels of hydroperoxides and relative lack of diversity in lipid volatiles. Among detected volatiles, formation of ketones was more distinguished in MWT, CTT, and SP emulsions while UT emulsions contained a more diverse range of alkenals and alkanals. Ketones are known to form mainly through radical recombination reactions which combined with the results of protein oxidation supports that radical transfer reactions between proteins and lipids were the driving force behind oxidation in MWT, CTT, and SP emulsions. Treatments of faba beans resulted in increased oxidative stability of emulsified lipids and lower degradation of aqueous phase proteins.
  • Sun, Linghui; Baker, Jessica; Gloor, Emanuel; Spracklen, Dominick; Boesch, Hartmut; Somkuti, Peter; Maeda, Eduardo Eiji; Buermann, Wolfgang (2019)
    We analyzed seasonal and spatial variations of evapotranspiration (ET) for five Amazon sub-basins and their response to the 2015/16 El Nino episode using a recently developed water-budget approach. ET varied typically between similar to 7 and 10 cm/month with exception of the Xingu basin for which it varied between 10 and 15 cm/month. Outstanding features of ET seasonality are (i) generally weak seasonality, (ii) two ET peaks for the two very wet catchments Solimoes and Negro, with one occurring during the wet season and one during the drier season, and (iii) a steady increase of ET during the second half of the dry season for the three drier catchments (Madeira, Tapajos, Xingu). Peak ET occurs during the first half of the wet season consistent with leaf flush occurring before the onset of the wet season. With regards to inter-annual variation, we found firstly that for the Solimoes and Madeira catchments the period with large positive wet season anomalies (2012-2015) is associated with negative ET anomalies, and negative SIF (solar induced fluorescence) anomalies. Furthermore, we found negative ET of several cm/months and SIF (up to 50%) anomalies for most of the Amazon basin during the 2015/16 El Nino event suggesting down-regulation of productivity as a main factor of positive carbon flux anomalies during anomalously hot and dry conditions. These results are of interest in view of predicted warmer and more erratic future climate conditions.
  • Siirila, Joonas; Karesoja, Mikko; Pulkkinen, Petri; Malho, Jani-Markus; Tenhu, Heikki (2019)
    Soft poly(N-vinylcaprolactam) (PNVCL) based nanogels were prepared and surface-decorated with gold nanoparticles (AuNPs). The applicability of the hybrid nanogels (PNVCL-AuNPs) as carriers for low molar mass substances was of special interest. AuNPs protected with a mixture of 11-azidoundecanothiol and 11-mercaptoundecanoic acid were bound to propargyl functionalized PNVCL based nanogels. Acidic groups on the surfaces of AuNPs and PNVCL based nanogels stabilize the particle dispersions against precipitation above the phase transition temperature of PNVCL. Both the neat PNVCL nanogels and the PVCL-AuNPs shrink upon heating the dispersions. Even though the AuNPs are mainly located in the soft surface layer of the nanogels, the PNVCL-AuNPs respond to visible light as well as to radio-frequency (RF) irradiation by shrinking due to the AuNPs acting as nanoheaters. Interactions of linear PNVCL, PNVCL nanogels and PNVCL-AuNPs with two fluorescent probes were studied as function of increasing temperature. Once bound to the polymer the fluorescent probe may or may not be released from it, depending on its polarity and water solubility. Presence of AuNPs changed the release behavior of the water soluble charged fluorescent probe from the nanogels.
  • Huovelin, J.; Vainio, R.; Kilpua, E.; Lehtolainen, A.; Korpela, S.; Esko, E.; Muinonen, K.; Bunce, E.; Martindale, A.; Grande, M.; Andersson, H.; Nenonen, S.; Lehti, J.; Schmidt, W.; Genzer, M.; Vihavainen, T.; Saari, J.; Peltonen, J.; Valtonen, E.; Talvioja, M.; Portin, P.; Narendranath, S.; Järvinen, R.; Okada, T.; Milillo, A.; Laurenza, M.; Heino, E.; Oleynik, P. (2020)
    The Solar Intensity X-ray and particle Spectrometer (SIXS) on the BepiColombo Mercury Planetary Orbiter ("Bepi") measures the direct solar X-rays, energetic protons, and electrons that bombard, and interact with, the Hermean surface. The interactions result in X-ray fluorescence and scattering, and particle induced X-ray emission (PIXE), i.e. "glow" of the surface in X-rays. Simultaneous monitoring of the incident and emitted radiation enables derivation of the abundances of some chemical elements and scattering properties of the outermost surface layer of the planet, and it may reveal other sources of X-ray emission, due to, for example, weak aurora-like phenomena in Mercury's exosphere. Mapping of the Hermean X-ray emission is the main task of the MIXS instrument onboard BepiColombo. SIXS data will also be used for investigations of the solar X-ray corona and solar energetic particles (SEP), both in the cruise phase and the passes of the Earth, Venus and Mercury before the arrival at Mercury's orbit, and the final science phase at Mercury's orbit. These observations provide the first-ever opportunity for in-situ measurements of the propagation of SEPs, their interactions with the interplanetary magnetic field, and space weather phenomena in multiple locations throughout the inner solar system far away from the Earth, and more extensively at Mercury's orbit. In this paper we describe the scientific objectives, design and calibrations, operational principles, and scientific performance of the final SIXS instrument launched to the mission to planet Mercury onboard BepiColombo. We also provide the first analysis results of science observations with SIXS, that were made during the Near-Earth Commissioning Phase and early cruise phase operations in 2018-19, including the background X-ray sky observations and "first light" observations of the Sun with the SIXS X-ray detection system (SIXS-X), and in-situ energetic electron and proton observations with the SIXS Particle detection system (SIXS-P).
  • Song, Chengfang; Shan, Shengdao; Yang, Chao; Zhang, Cheng; Zhou, Xiaoqing; Ma, Qi; Yrjälä, Kim; Zheng, Huabao; Cao, Yucheng (2020)
    Dissolved organic matter (DOM) has an important effect on soil fertility, activity of microorganisms and transport of contaminants. In this study, DOM released by the hydrochar and biochar prepared under various conditions from pig manure, was assessed using a combination of UV–Visible spectroscopy, fluorescence excitation-emission (EEM) spectrophotometry and 1H-nuclear magnetic resonance (1H NMR). The dissolved organic carbon (DOC) extracted from the hydrochar and biochar ranged from 3.34–11.96% and 0.38–0.48%, respectively, and the highest DOM was released by HCK0.5 (180 °C and 0.5% KOH). The aliphatic compounds were most common in DOM which mainly included three humic acid-like and one protein-like substance. The hydrochar-DOM had a larger molecular weight and lower aromaticity than biochar-DOM, but the effect of temperature on the DOM characteristics of hydrochar and biochar was opposite. The acidic treatment increased the content of functional groups containing oxygen and nitrogen in hydrochar-DOM, and alkaline treatment increased the content of aliphatic compounds. The results obtained are beneficial to select carbonation process and guide the rational application of hydrochar and biochar from pig manure in soil remediation field.
  • Edlund, Petra; Takala, Heikki; Claesson, Elin; Henry, Leocadie; Dods, Robert; Lehtivuori, Heli; Panman, Matthijs; Pande, Kanupriya; White, Thomas; Nakane, Takanori; Berntsson, Oskar; Gustavsson, Emil; Bath, Petra; Modi, Vaibhav; Roy-Chowdhury, Shatabdi; Zook, James; Berntsen, Peter; Pandey, Suraj; Poudyal, Ishwor; Tenboer, Jason; Kupitz, Christopher; Barty, Anton; Fromme, Petra; Koralek, Jake D.; Tanaka, Tomoyuki; Spence, John; Liang, Mengning; Hunter, Mark S.; Boutet, Sebastien; Nango, Eriko; Moffat, Keith; Groenhof, Gerrit; Ihalainen, Janne; Stojkovic, Emina A.; Schmidt, Marius; Westenhoff, Sebastian (2016)
    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 angstrom resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 angstrom resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.