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  • Qi, Lu; Vogel, Alexander L.; Esmaeilirad, Sepideh; Cao, Liming; Zheng, Jing; Jaffrezo, Jean-Luc; Fermo, Paola; Kasper-Giebl, Anne; Dällenbach, Kaspar; Chen, Mindong; Ge, Xinlei; Baltensperger, Urs; Prevot, Andre S. H.; Slowik, Jay G. (2020)
    The aerosol mass spectrometer (AMS), combined with statistical methods such as positive matrix factorization (PMF), has greatly advanced the quantification of primary organic aerosol (POA) sources and total secondary organic aerosol (SOA) mass. However, the use of thermal vaporization and electron ionization yields extensive thermal decomposition and ionization-induced fragmentation, which limit chemical information needed for SOA source apportionment. The recently developed extractive electrospray ionization time-of-flight mass spectrometer (EESI-TOF) provides mass spectra of the organic aerosol fraction with a linear response to mass and no thermal decomposition or ionization-induced fragmentation. However, the costs and operational requirements of online instruments make their use impractical for long-term or spatially dense monitoring applications. This challenge was overcome for AMS measurements by measuring re-nebulized water extracts from ambient filter samples. Here, we apply the same strategy for EESI-TOF measurements of 1 year of 24 h filter samples collected approximately every fourth day throughout 2013 at an urban site. The nebulized water extracts were measured simultaneously with an AMS. The application of positive matrix factorization (PMF) to EESI-TOF spectra resolved seven factors, which describe water-soluble OA: less and more aged biomass burning aerosol (LABB(EESI) and MABB(EESI), respectively), cigarette-smoke-related organic aerosol, primary biological organic aerosol, biogenic secondary organic aerosol, and a summer mixed oxygenated organic aerosol factor. Seasonal trends and relative contributions of the EESI-TOF OA sources were compared with AMS source apportionment factors, measured water-soluble ions, cellulose, and meteorological data. Cluster analysis was utilized to identify key factor-specific ions based on PMF. Both LABB and MABB contribute strongly during winter. LABB is distinguished by very high signals from C6H10O5 (levoglucosan and isomers) and C8H12O6, whereas MABB is characterized by a large number of CxHyOz and CxHyOzN species of two distinct populations: one with low H : C and high O : C and the other with high H : C and low O : C. Two oxygenated summertime SOA sources were attributed to terpene-derived biogenic SOA, a major summertime aerosol source in central Europe. Furthermore, a primary biological organic aerosol factor was identified, which was dominated by plant-derived fatty acids and correlated with free cellulose. The cigarette-smoke-related factor contained a high contribution of nicotine and high abundance of organic nitrate ions with low m/z.
  • Hu, Man; Lehtonen, Aleksi; Minunno, Francesco; Mäkelä, Annikki (2020)
    Tree structure equations derived from pipe model theory (PMT) are well-suited to estimate biomass allocation in Scots pine (Pinus sylvestrisL.) and Norway spruce (Picea abies[L.] Karst.). However, age dependence of parameters should be accounted for when applying the equations.
  • Laursen, Karsten; Moller, Anders Pape; Haugaard, Lars; Öst, Markus; Vainio, Jouni (2019)
    Capital breeders, such as the eider duck Somateria mollissima, accumulate resources before the start of breeding. Eiders preferentially feed on blue mussels Mytilus edulis to build up body condition during winter. We explored how body condition and gizzard mass of wintering eiders relate to mussel quality and quantity, winter climate and body condition of females at the breeding grounds. Body condition during winter (defined as scaled body mass index) of eiders increased during winter and the magnitude of the effect depended on age and mussel quality. Gizzard mass of eiders increased during winter with effects of mussel quality, mussel stocks and sex. Body condition in winter of adult females increased from the first half of January to the second half of February on average by 1.5%, equal to c. 96 g. During the same period gizzard mass of adult females increased by 12.2%, i.e., a nearly ten-fold increase compared to that observed in body condition in winter. Body condition of females at the breeding grounds in Finland (defined as body condition at hatching) was significantly positively correlated with gizzard mass in winter, but not significantly correlated with body condition in winter. Thus, eiders allocate body reserves to increase gizzard mass but less so to increase body condition in winter. This can be considered an adaptive migratory strategy of these eiders, whereby large winter (pre-migratory) gizzards increase food processing capacity, making it possible for eiders to arrive at the breeding grounds with superior body condition and a high reproductive potential.
  • Vuorio, Joni; Vattulainen, Ilpo; Martinez-Seara, Hector (2017)
    Hyaluronan is a polyanionic, megadalton-scale polysaccharide, which initiates cell signaling by interacting with several receptor proteins including CD44 involved in cell-cell interactions and cell adhesion. Previous studies of the CD44 hyaluronan binding domain have identified multiple widespread residues to be responsible for its recognition capacity. In contrast, the X-ray structural characterization of CD44 has revealed a single binding mode associated with interactions that involve just a fraction of these residues. In this study, we show through atomistic molecular dynamics simulations that hyaluronan can bind CD44 with three topographically different binding modes that in unison define an interaction fingerprint, thus providing a plausible explanation for the disagreement between the earlier studies. Our results confirm that the known crystallographic mode is the strongest of the three binding modes. The other two modes represent metastable configurations that are readily available in the initial stages of the binding, and they are also the most frequently observed modes in our unbiased simulations. We further discuss how CD44, fostered by the weaker binding modes, diffuses along HA when attached. This 1D diffusion combined with the constrained relative orientation of the diffusing proteins is likely to influence the aggregation kinetics of CD44. Importantly, CD44 aggregation has been suggested to be a possible mechanism in CD44-mediated signaling.
  • Jolma, Arttu; Zhang, Jilin; Mondragon, Estefania; Morgunova, Ekaterina; Kivioja, Teemu; Laverty, Kaitlin U.; Yin, Yimeng; Zhu, Fangjie; Bourenkov, Gleb; Morris, Quaid; Hughes, Timothy R.; Maher III, Louis James; Taipale, Jussi (2020)
    RNA-binding proteins (RBPs) regulate RNA metabolism at multiple levels by affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization, translation, and stability. Despite their central role in RNA function, the RNA-binding specificities of most RBPs remain unknown or incompletely defined. To address this, we have assembled a genome-scale collection of RBPs and their RNA-binding domains (RBDs) and assessed their specificities using high-through-put RNA-SELEX (HTR-SELEX). Approximately 70% of RBPs for which we obtained a motif bound to short linear sequenc-es, whereas similar to 30% preferred structured motifs folding into stem-loops. We also found that many RBPs can bind to multiple distinctly different motifs. Analysis of the matches of the motifs in human genomic sequences suggested novel roles for many RBPs. We found that three cytoplasmic proteins-ZC3H12A, ZC3H12B, and ZC3H12C-bound to motifs resembling the splice donor sequence, suggesting that these proteins are involved in degradation of cytoplasmic viral and/or unspliced transcripts. Structural analysis revealed that the RNA motif was not bound by the conventional C3H1 RNA-binding domain of ZC3H12B. Instead, the RNA motif was bound by the ZC3H12B's PilT N terminus (PIN) RNase domain, revealing a po-tential mechanism by which unconventional RBDs containing active sites or molecule-binding pockets could interact with short, structured RNA molecules. Our collection containing 145 high-resolution binding specificity models for 86 RBPs is the largest systematic resource for the analysis of human RBPs and will greatly facilitate future analysis of the various bi-ological roles of this important class of proteins.
  • Frege, Carla; Bianchi, Federico; Molteni, Ugo; Trostl, Jasmin; Junninen, Heikki; Henne, Stephan; Sipilä, Mikko; Herrmann, Erik; Rossi, Michel J.; Kulmala, Markku; Hoyle, Christopher R.; Baltensperger, Urs; Dommen, Josef (2017)
    The ion composition at high altitude (3454 m a.s.l.) was measured with an atmospheric pressure interface time-of-flight mass spectrometer (APi-TOF) during a period of 9 months, from August 2013 to April 2014. The negative mass spectra were dominated by the ions of sulfuric, nitric, malonic, and methanesulfonic acid (MSA) as well as SO5. The most prominent positive ion peaks were from amines. The other cations were mainly organic compounds clustered with a nitrogen-containing ion, which could be either NH4+ or an aminium. Occasionally the positive spectra were characterized by groups of compounds each differing by a methylene group. In the negative spectrum, sulfuric acid was always observed during clear sky conditions following the diurnal cycle of solar irradiation. On many occasions we also saw a high signal of sulfuric acid during nighttime when clusters up to the tetramer were observed. A plausible reason for these events could be evaporation from particles at low relative humidity. A remarkably strong correlation between the signals of SO5 and CH3SO3- was observed for the full measurement period. The presence of these two ions during both the day and the night suggests a non-photochemical channel of formation which is possibly linked to halogen chemistry. Halogenated species, especially Br- and IO3-, were frequently observed in air masses that originated mainly from the Atlantic Ocean and occasionally from continental areas based on back trajectory analyses. We found I2O5 clustered with an ion, a species that was proposed from laboratory and modeling studies. All halogenated ions exhibited an unexpected diurnal behavior with low values during daytime. New particle formation (NPF) events were observed and characterized by (1) highly oxygenated molecules (HOMs) and low sulfuric acid or (2) ammonia-sulfuric acid clusters. We present characteristic spectra for each of these two event types based on 26 nucleation episodes. The mass spectrum of the ammonia-sulfuric acid nucleation event compares very well with laboratory measurements reported from the CLOUD chamber. A source receptor analysis indicates that NPF events at the Jungfraujoch take place within a restricted period of time of 24-48 h after air masses have had contact with the boundary layer. This time frame appears to be crucial to reach an optimal oxidation state and concentration of organic molecules necessary to facilitate nucleation.
  • Elminen, Tuija; Zwingmann, Horst; Kaakinen, Anu (2018)
    Sheared sedimentary clay was found in a faulted fracture in crystalline bedrock in a tunnelling site at 60 m depth in southern Finland. Brittle faults are numerous in the Fennoscandian Palaeoproterozoic bedrock, but only some of them have relative age constraints, while absolute ages are nearly lacking. Sedimentary rocks altogether are uncommon in Finland and only sparsely dated by micropaleontological studies. This study reports K-Ar data of fresh, non-weathered authigenic illite and constrains a time framework for the local faulting and sedimentation. The Neoproterozoic Tonian to Cryogenian ages derived from the grains in diminishing grain-size order are c. 967, 947, 809 and 697 Ma. Results indicate that the formation of the extension fracture is related to the collapse of Sveconorwegian orogeny c. 1000 Ma; clay and mature quartz sand were deposited in this extension fracture in shallow water in an intracratonic basin followed by early diagenetic processes and neocrystallization of illite around 967-947 Ma. The Neoproterozoic 1000-700 Ma sedimentation documented in this study is rare in the Fennoscandian shield as a whole. Neocrystallization of authigenic illite in the finest 0.4 and <0.1 pm fractions c. 809-697 Ma ago is interpreted as resulting from reactivation in the fault due to the continental break-up on the western side of the craton as documented by arenite crosscutting relationships. The younger ages may also be attributed to a Caledonian thermal overprint ca. 410 Ma ago that would influence the 967 Ma age if sufficient thermal energy had been present.
  • Kwiatek, Grzegorz; Saarno, Tero; Ader, Thomas; Bluemle, Felix; Bohnhoff, Marco; Chendorain, Michael; Dresen, Georg; Heikkinen, Pekka; Kukkonen, Ilmo; Leary, Peter; Leonhardt, Maria; Malin, Peter; Martínez-Garzón, Patricia; Passmore, Kevin; Passmore, Paul; Valenzuela, Sergio; Wollin, Christopher (2019)
    We show that near–real-time seismic monitoring of fluid injection allowed control of induced earthquakes during the stimulation of a 6.1-km-deep geothermal well near Helsinki, Finland. A total of 18,160 m3 of fresh water was pumped into crystalline rocks over 49 days in June to July 2018. Seismic monitoring was performed with a 24-station borehole seismometer network. Using near–real-time information on induced-earthquake rates, locations, magnitudes, and evolution of seismic and hydraulic energy, pumping was either stopped or varied—in the latter case, between well-head pressures of 60 and 90 MPa and flow rates of 400 and 800 liters/min. This procedure avoided the nucleation of a project-stopping magnitude MW 2.0 induced earthquake, a limit set by local authorities. Our results suggest a possible physics-based approach to controlling stimulation-induced seismicity in geothermal projects.
  • Saponaro, Giulia; Kolmonen, Pekka; Sogacheva, Larisa; Rodriguez, Edith; Virtanen, Timo; De Leeuw, Gerrit (2017)
    Retrieved from the Moderate Resolution Imaging Spectroradiometer (MODIS) on-board the Aqua satellite, 12 years (2003-2014) of aerosol and cloud properties were used to statistically quantify aerosol-cloud interaction (ACI) over the Baltic Sea region, including the relatively clean Fennoscandia and the more polluted central-eastern Europe. These areas allowed us to study the effects of different aerosol types and concentrations on macro-and microphysical properties of clouds: cloud effective radius (CER), cloud fraction (CF), cloud optical thickness (COT), cloud liquid water path (LWP) and cloud-top height (CTH). Aerosol properties used are aerosol optical depth (AOD), Angstrom exponent (AE) and aerosol index (AI). The study was limited to low-level water clouds in the summer. The vertical distributions of the relationships between cloud properties and aerosols show an effect of aerosols on low-level water clouds. CF, COT, LWP and CTH tend to increase with aerosol loading, indicating changes in the cloud structure, while the effective radius of cloud droplets decreases. The ACI is larger at relatively low cloud-top levels, between 900 and 700 hPa. Most of the studied cloud variables were unaffected by the lower-tropospheric stability (LTS), except for the cloud fraction. The spatial distribution of aerosol and cloud parameters and ACI, here defined as the change in CER as a function of aerosol concentration for a fixed LWP, shows positive and statistically significant ACI over the Baltic Sea and Fennoscandia, with the former having the largest values. Small negative ACI values are observed in central-eastern Europe, suggesting that large aerosol concentrations saturate the ACI.
  • Vanninen, Paula; Östin, Anders; Beldowski, Jacek; Pedersen, Erik A.; Söderström, Martin; Szubska, Marta; Grabowski, Milosz; Siedlewicz, Grzegorz; Czub, Michal; Popiel, Stanislaw; Dziedzic, Daniel; Jakacki, Jaromir; Paczek, Bartlomiej; Nawala, Jakub (2020)
    About 50 000 tons of chemical weapons (CW) were dumped to the Baltic Sea after the Second World War. Munitions are located in the deep areas of the Baltic Sea, and there they act as a point source of contamination to the ecosystem. Corroded munitions release chemical warfare agents (CWAs) to nearby water and sediments. In this study we investigated known dumpsites (Bornholm, Gotland and Gdansk Deep) and dispersed chemical munitions, to evaluate the extent of contamination of nearby sediments, as well as to assess the degradation process of released CWA. It was found that CWA-related phenylarsenic chemicals (Clark I, Clark II and Adamsite) and sulfur mustard are released to the sediments and undergo environmental degradation to chemicals, of which some remain toxic. The extent of pollution of released CWAs and their corresponding degradation products reaches more than 250 m from the CW objects, and seem to follow a power curve decrease of concentration from the source. Bornholm Deep is characterised with the highest concentration of CWAs in sediments, but occasional concentration peaks are also observed in the Gdansk Deep and close to dispersed munitions. Detailed investigation of spreading pattern show that the range of pollution depends on bottom currents and topography.
  • Lan, Hangzhen; Holopainen, Jani; Hartonen, Kari; Jussila, Matti; Ritala, Mikko; Riekkola, Marja-Liisa (2019)
    Comprehensive and time-dependent information (e.g., chemical composition, concentration) of volatile organic compounds (VOCs) in atmospheric, indoor, and breath air is essential to understand the fundamental science of the atmosphere, air quality, and diseases diagnostic. Here, we introduced a fully automated online dynamic in-tube extraction (ITEX)-gas chromatography/mass spectrometry (GC/MS) method for continuous and quantitative monitoring of VOCs in air. In this approach, modified Cycle Composer software and a PAL autosampler controlled and operated the ITEX preconditioning, internal standard (ISTD) addition, air sampling, and ITEX desorption sequentially to enable full automation. Air flow passed through the ITEX with the help of an external pump, instead of plunger up-down strokes, to allow larger sampling volumes, exhaustive extraction, and consequently lower detection limits. Further, in order to evaluate the ITEX system stability and to develop the corresponding quantitative ITEX method, two laboratory-made permeation systems (for standard VOCs and ISTD) were constructed. The stability and suitability of the developed system was validated with a consecutive 19 day atmospheric air campaign under automation. By using an electrospun polyacrylonitrile nanofibers packed ITEX, selective extraction of some VOCs and durability of over 1500 extraction and desorption cycles were achieved. Especially, the latter step is critically important for on-site long-term application at remote regions. This ITEX method provided 2-3 magnitudes lower quantitation limits than the headspace dynamic ITEX method and other needle trap methods. Our results proved the excellence of the fully automated online dynamic ITEX-GC/MS system for tracking VOCs in the atmospheric air.
  • Cruz, Cristina D; Wrigstedt, Pauli; Moslova, Karina; Iashin, Vladimir; Mäkkylä, Heidi; Ghemtio, Leo; Heikkinen, Sami; Tammela, Päivi; Perea-Buceta, Jesus Enrique (2021)
    N-aryl-oxazolidinones is a prominent family of antimicrobials used for treating infections caused by clinically prevalent Gram-positive bacteria. Recently, boron-containing compounds have displayed intriguing potential in the antibiotic discovery setting. Herein, we report the unprecedented introduction of a boron-containing moiety such as an aryl boronic acid in the external region of the oxazolidinone structure via a chemoselective acyl coupling reaction. As a result, we accessed a series of analogues with a distal aryl boronic pharmacophore on the oxazolidinone scaffold. We identified that a peripheric linear conformation coupled with freedom of rotation and no further substitution on the external aryl boronic ring, an amido linkage with hydrogen bonding character, in addition to a para-relative disposition between boronic group and linker, are the optimal combination of structural features in this series for antimicrobial activity. In comparison to linezolid, the analogue comprising all those features, compound 20b, displayed levels of antimicrobial activity augmented by an eight-fold to a thirty-two-fold against a panel of Gram-positive strains, and a near one hundred-fold against Escherichia coli JW5503, a Gram-negative mutant strain with a defective efflux capability.
  • Mamali, D.; Mikkilä, J.; Henzing, B.; Spoor, R.; Ehn, M.; Petäjä, T.; Russchenberg, H.; Biskos, G. (2018)
    Long-term measurements of PM2.5 mass concentrations and aerosol particle size distributions from 2008 to 2015, as well as hygroscopicity measurements conducted over one year (2008-2009) at Cabauw, The Netherlands, are compiled here in order to provide a comprehensive dataset for understanding the trends and annual variabilities of the atmospheric aerosol in the region. PM2.5 concentrations have a mean value of 14.4 mu g m(-3) with standard deviation 2.1 mu g m(-3), and exhibit an overall decreasing trend of -0.74 mu g m(-3) year(-1). The highest values are observed in winter and spring and are associated with a shallower boundary layer and lower precipitation, respectively, compared to the rest of the seasons. Number concentrations of particles smaller than 500 nm have a mean of 9.2 x 10(3) particles cm(-3) and standard deviation 4.9x10(3) particles cm(-3), exhibiting an increasing trend between 2008 and 2011 and a decreasing trend from 2013 to 2015. The particle number concentrations exhibit highest values in spring and summer (despite the increased precipitation) due to the high occurrence of nucleation-mode particles, which most likely are formed elsewhere and are transported to the observation station. Particle hygroscopicity measurements show that, independently of the air mass origin, the particles are mostly externally mixed with the more hydrophobic mode having a mean hygroscopic parameter kappa of 0.1 while for the more hydrophilic mode kappa is 0.35. The hygroscopicity of the smaller particles investigated in this work (i.e., particles having diameters of 35 nm) appears to increase during the course of the nucleation events, reflecting a change in the chemical composition of the particles. (C) 2017 Elsevier B.V. All rights reserved.
  • Koivu, Maija; Huotarinen, Antti; Scheperjans, Filip; Laakso, Aki; Kivisaari, Riku; Pekkonen, Eero (2018)
    Objectives: To evaluate the efficacy and adverse effects of subthalamic deep brain stimulation (STN-DBS) in patients with advanced Parkinson's disease (PD) and the possible correlation between electrode location and clinical outcome. Methods: We retrospectively reviewed 87 PD-related STN-DBS operations at Helsinki University Hospital (HUH) from 2007 to 2014. The changes of Unified Parkinson's Disease Rating Scale (UPDRS) part III score, Hoehn & Yahr stage, antiparkinson medication, and adverse effects were studied. We estimated the active electrode location in three different coordinate systems: direct visual analysis of MRI correlated to brain atlas, location in relation to the nucleus borders and location in relation to the midcommisural point. Results: At 6 months after operation, both levodopa equivalent doses (LEDs; 35%, Wilcoxon signed-rank test = 0.000) and UPDRS part III scores significantly decreased (38%, Wilcoxon signed-rank test = 0.000). Four patients (5%) suffered from moderate DBS-related dysarthria. The generator and electrodes had to be removed in one patient due to infection (1%). Electrode coordinates in the three coordinate systems correlated well with each other. On the left side, more ventral location of the active contact was associated with greater LED decrease. Conclusions: STN-DBS improves motor function and enables the reduction in anti-parkinson medication with an acceptable adverse effect profile. More ventral location of the active contact may allow stronger LED reduction. Further research on the correlation between contact location, clinical outcome, and LED reduction is warranted.
  • Savijärvi, Hannu; Paton, Mark; Harri, Ari-Matti (2018)
    Boundary layer simulations are shown for the first sols of the two Viking landers (VL1, VL2) on Mars. The column model (with cloud/radiation interaction and Prandtl slope wind terms), used successfully for Phoenix and Curiosity, is equipped here with an adsorption-diffusion scheme for water vapor transport in porous regolith. The model's 1.6 m temperatures and winds are quite close to those observed by the two landers; in particular the weak summer slope winds of VL2 are excellently reproduced. The model predicts for both sites diffusion and adsorption of water into regolith in the evening, very thin ground frost deposition from about midnight, and an early morning fog with an inflection in T1.6 m slightly weaker than observed. At the moister VL2 site fog increases optical depth as observed. Fogs and frosts sublimate away after sunrise, allowing desorption and diffusion of water off the sun-heated regolith. For porosity of 22% column water is approximately conserved from sol to sol at both sites with only little diurnal variation, as the depleted layer of air moisture is quite shallow. In simulations without adsorption frost forms early and it grows thick. At VL2 fog now forms earlier and the jump in optical depth is larger than observed. At the drier VL1 fog still forms nearly as with adsorption, so observations could also be explained without adsorption. On the other hand VL1 certainly landed onto porous regohth and frost was not observed. Hence it is suggested that adsorption is likely at both VL sites in summer. (C) 2017 Elsevier Inc. All rights reserved.
  • Li, Yuanyuan; Nie, Wei; Liu, Yuliang; Huang, Dandan; Xu, Zheng; Peng, Xiang; George, Christian; Yan, Chao; Tham, Yee Jun; Yu, Chuan; Xia, Men; Fu, Xiao; Wang, Xinfeng; Xue, Likun; Wang, Zhe; Xu, Zhengning; Chi, Xuguang; Wang, Tao; Ding, Aijun (2020)
    Titanium dioxide (TiO2) is extensively used with the process of urbanization and potentially influences atmospheric chemistry, which is yet unclear. In this work, we demonstrated strong production of Cl-2 from illuminated KCl-coated TiO2 membranes and suggested an important daytime source of chlorine radicals. We found that water and oxygen were required for the reactions to proceed, and Cl-2 production increased linearly with the amount of coated KCl, humidity of the carrier gas, and light intensity. These results suggested that water promotes the reactivity of coated KCl via interaction with the crystal lattice to release free chloride ions (Cl-). The free Cl- transfer charges to O-2 via photoactivated TiO2 to form Cl-2 and probably the O-2(-) radical. In addition to Cl-2, ClO and HOCl were also observed via the complex reactions between Cl/Cl-2 and HOx. An intensive campaign was conducted in Shanghai, during which evident daytime peaks of Cl-2 were observed. Estimated Cl-2 production from TiO2 photocatalysis can be up to 0.2 ppb/h when the TiO2-containing surface reaches 20% of the urban surface, and highly correlated to the observed Cl-2. Our results suggest a non-negligible role of TiO2 in atmospheric photochemistry via altering the radical budget.
  • van der Meijden, Els; Horvath, Barbara; Nijland, Marcel; de Vries, Karin; Raez, Emoke; Diercks, Gilles F.; de Weerd, Annelies E.; Clahsen-van Groningen, Marian C.; van der Blij-de Brouwer, Caroline S.; van der Zon, Arnulfo J.; Kroes, Aloys C. M.; Hedman, Klaus; van Kampen, Jeroen J. A.; Riezebos-Brilman, Annelies; Feltkamp, Mariet C. W. (2017)
    Classic human polyomaviruses (JC and BK viruses) become pathogenic when reactivating from latency. For the rare skin disease trichodysplasia spinulosa, we show that manifestations of the causative polyomavirus (TSPyV) occur during primary infection of the immunosuppressed host. High TSPyV loads in blood and cerebrospinal fluid, sometimes coinciding with cerebral lesions and neuroendocrine symptoms, marked the acute phase of trichodysplasia spinulosa, whereas initiation and maturation of TSPyV seroresponses occurred in the convalescent phase. TSPyV genomes lacked the rearrangements typical for reactivating polyomaviruses. These findings demonstrate the clinical importance of primary infection with this rapidly expanding group of human viruses and explain the rarity of some novel polyomavirus-associated diseases.
  • Ruohoalho, Johanna; Aro, Katri; Makitie, Antti A.; Atula, Timo; Haapaniemi, Aaro; Keski-Santti, Harri; Kylanpaa, Leena; Takala, Annika; Back, Leif J. (2017)
    Percutaneous endoscopic gastrostomy (PEG) is often the treatment of choice in head and neck cancer (HNC) patients needing long-term nutritional support. Prospective studies on PEG tube placement in an otorhinolaryngologist service are lacking. At our hospital, otolaryngologist-head and neck (ORL-HN) surgeons-have performed PEG insertions for HNC patients since 2008. We prospectively analyzed 127 consecutive HNC patients who received their PEG tubes at the Department of Otorhinolaryngology-head and neck surgery, and evaluated the outcome of PEG tube insertions performed by ORL-HN surgeons. To compare time delays before and after, PEG placement service was transferred from gastrointestinal surgeons to ORL-HN surgeons, and we retrospectively analyzed a separate group of 110 HNC patients who had earlier received PEG tubes at the Department of Gastrointestinal Surgery. ORL-HN surgeons' success rate in PEG insertion was 97.6%, leading to a final prospective study group of 124 patients. Major complications occurred in four (3.2%): two buried bumper syndromes, one subcutaneous hemorrhage leading to an abscess in the abdominal wall, and one metastasis at the PEG site. The most common minor complication was peristomal granulomatous tissue affecting 23 (18.5%) patients. After the change in practice, median time delay before PEG insertion decreased from 13 to 10 days (P <0.005). The proportion of early PEG placements within 0-3 days increased from 3.6 to 14.6% (P <0.005). PEG tube insertion seems to be a safe procedure in the hands of an ORL-HN surgeon. Independence from gastrointestinal surgeons' services reduced the time delay and improved the availability of urgent PEG insertions.
  • Haapanen, Outi; Sharma, Vivek (2021)
    Respiratory complex I is a key enzyme in the electron transport chains of mitochondria and bacteria. It transfers two electrons to quinone and couples this redox reaction to proton pumping to electrically charge the membrane it is embedded in. The charge and pH gradient across the membrane drives the synthesis of ATP. The redox reaction and proton pumping in complex I are separated in space and time, which raises the question of how the two reactions are coupled so efficiently. Here, we focus on the unique similar to 35 angstrom long tunnel of complex I, which houses the binding site of quinone reduction. We discuss the redox and protonation reactions that occur in this tunnel and how they influence the dynamics of protein and substrate. On the basis of recent structural data and results from molecular simulations, we review how quinone reduction and dynamics may be coupled to proton pumping in complex I.
  • Syed, Shahan; Hakala, Pipsa; Singh, Anirudh K.; Lapatto, Helena A. K.; King, Samantha J.; Meri, Seppo; Jokiranta, T. Sakari; Haapasalo, Karita (2019)
    The most frequent form of hemolytic-uremic syndrome (HUS) is associated with infections caused by Shiga-like toxin-producing Enterohaemorrhagic Escherichia coli (STEC). In rarer cases HUS can be triggered by Streptococcus pneumoniae. While production of Shiga-like toxins explains STEC-HUS, the mechanisms of pneumococcal HUS are less well known. S. pneumoniae produces neuraminidases with activity against cell surface sialic acids that are critical for factor H-mediated complement regulation on cells and platelets. The aim of this study was to find out whether S. pneumoniae neuraminidase NanA could trigger complement activation and hemolysis in whole blood. We studied clinical S. pneumoniae isolates and two laboratory strains, a wild-type strain expressing NanA, and a NanA deletion mutant for their ability to remove sialic acids from various human cells and platelets. Red blood cell lysis and activation of complement was measured ex vivo by incubating whole blood with bacterial culture supernatants. We show here that NanA expressing S. pneumoniae strains and isolates are able to remove sialic acids from cells, and platelets. Removal of sialic acids by NanA increased complement activity in whole blood, while absence of NanA blocked complement triggering and hemolytic activity indicating that removal of sialic acids by NanA could potentially trigger pHUS.