Browsing by Subject "AGGREGATION"

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  • Raerinne, Jani (2018)
    In addition to their core explanatory and predictive assumptions, scientific models include simplifying assumptions, which function as idealizations, approximations, and abstractions. There are methods to investigate whether simplifying assumptions bias the results of models, such as robustness analyses. However, the equally important issue - the focus of this paper - has received less attention, namely, what are the methodological and epistemic strengths and limitations associated with different simplifying assumptions. I concentrate on one type of simplifying assumption, the use of mega parameters as abstractions in ecological models. First, I argue that there are two kinds of mega parameters qua abstractions, sufficient parameters and aggregative parameters, which have gone unnoticed in the literature. The two are associated with different heuristics, holism and reductionism, which many view as incompatible. Second, I will provide a different analysis of abstractions and the associated heuristics than previous authors. Reductionism and holism and the accompanying abstractions have different methodological and epistemic functions, strengths, and limitations, and the heuristics should be viewed as providing complementary research perspectives of cognitively limited beings. This is then, third, used as a premise to argue for epistemic and methodological pluralism in theoretical ecology. Finally, the presented taxonomy of abstractions is used to comment on the current debate whether mechanistic accounts of explanation are compatible with the use of abstractions. This debate has suffered from an abstract discussion of abstractions. With a better taxonomy of abstractions the debate can be resolved.
  • Niemi, Tero; Kokkonen, Teemu; Sillanpää, Nora; Setälä, Heikki; Koivusalo, Harri (2019)
    Constructing hydrological models for large urban areas is time consuming and laborious due to the requirements for high-resolution data and fine model detail. An open-source algorithm using adaptive subcatchments is proposed to automate Storm Water Management Model (SWMM) construction. The algorithm merges areas with homogeneous land cover and a common outlet into larger subcatchments, while retaining small-scale details where land cover or topography is more heterogeneous. The method was tested on an 85-ha urban catchment in Helsinki, Finland. A model with adaptive subcatchments reproduced the observed discharge at the catchment outlet with high model-performance indices emphasizing the strength of the proposed method. Computation times of the adaptive model were substantially lower than those of a corresponding model with uniformly sized high-resolution subcatchments. Given that high-resolution land cover and topography data are available, the proposed algorithm provides an advanced method for implementing SWMM models automatically even for large urban catchments without a substantial manual workload. Simultaneously, the high-resolution land cover details of the catchments can be maintained where they matter the most. (c) 2019 American Society of Civil Engineers.
  • Kilpeläinen, Tommi; Julku, Ulrika; Svarcbahs, Reinis; Myöhänen, Timo (2019)
    Alpha-synuclein (aSyn) is the main component of Lewy bodies, the histopathological marker in Parkinson's disease (PD), and point mutations and multiplications of the aSyn coding SNCA gene correlate with early onset PD. Therefore, various transgenic mouse models overexpressing native or point-mutated aSyn have been developed. Although these models show highly increased aSyn expression they rarely capture dopaminergic cell loss and show a behavioural phenotype only at old age, whereas SNCA mutations are risk factors for PD with earlier onset. The aim of our study was to re-characterize a transgenic mouse strain carrying both A30P and A53T mutated human aSyn. Our study revealed decreased locomotor activity for homozygous transgenic mice starting from 3 months of age which was different from previous studies with this mouse strain that had behavioural deficits starting only after 7-9 months. Additionally, we found a decreased amphetamine response in locomotor activity and decreased extracellular dopaminergic markers in the striatum and substantia nigra with significantly elevated levels of aSyn oligomers. In conclusion, homozygous transgenic A30P*A53T aSyn mice capture several phenotypes of PD with early onset and could be a useful tool for aSyn studies.
  • Witos, Joanna; Karjalainen, Erno; Tenhu, Heikki; Wiedmer, Susanne K. (2020)
    Amphiphilic diblock copolymers consisting of a hydrophobic core containing a polymerized ionic liquid and an outer shell composed of poly(N-isoprolylacrylamide) were investigated by capillary electrophoresis and asymmetrical flow-field flow fractionation. The polymerized ionic liquid comprised poly(2-(1-butylimidazolium-3-yl)ethyl methacrylate tetrafluoroborate) with a constant block length (n = 24), while the length of the poly(N-isoprolylacrylamide) block varied (n = 14; 26; 59; 88). Possible adsorption of the block copolymer on the fused silica capillary, due to alterations in the polymeric conformation upon a change in the temperature (25 and 45 degrees C), was initially studied. For comparison, the effect of temperature on the copolymer conformation/hydrodynamic size was determined with the aid of asymmetrical flow-field flow fractionation and light scattering. To get more information about the hydrophilic/hydrophobic properties of the synthesized block copolymers, they were used as a pseudostationary phase in electrokinetic chromatography for the separation of some model compounds, that is, benzoates and steroids. Of particular interest was to find out whether a change in the length or concentration of the poly(N-isoprolylacrylamide) block would affect the separation of the model compounds. Overall, our results show that capillary electrophoresis and asymmetrical flow-field flow fractionation are suitable methods for characterizing conformational changes of such diblock copolymers.
  • Banić, Martina; Uroić, Ksenija; Leboš Pavunc, Andreja; Novak, Jasna; Zorić, Katarina; Durgo, Ksenija; Petković, Hrvoje; Jamnik, Polona; Kazazić, Saša; Kazazić, Snježana; Radović, Slobodanka; Scalabrin, Simone; Hynönen, Ulla; Šušković, Jagoda; Kos, Blaženka (2018)
    Abstract S-layers represent the simplest biological membranes developed during the evolution and are one of the most abundant biopolymers on Earth. Current fundamental and applied research aim to reveal the chemical structure, morphogenesis and function of S-layer proteins (Slps). This is the first paper that describes the Slps of certain Lactobacillus brevis strain isolated from sauerkraut. The whole genome sequence (WGS) analysis of the L. brevis SF9B strain uncovered three genes encoding the putative Slps, but merely one, identified as similar to the SlpB of L. brevis ATCC 14869, was expressed. Slp-expressing SF9B cells exhibited increased survival in simulated gastrointestinal (GI) conditions and during freeze-drying. Their survival in stress conditions was additionally enhanced by microencapsulation, especially when using alginate with gelatine as a matrix. Thus prepared cells were subjected to simulated GI conditions and their mortality was only 0.28 ± 0.45 log CFU/mL. Furthermore, a correlation between the high surface hydrophobicity and the remarkable aggregative capacity of SF9B strain was established. The results indicate a prominent role of Slps in adhesion to mucin, extracellular matrix (ECM) proteins, and particularly to Caco-2 cells, where the removal of Slps utterly abolished the adhesiveness of SF9B cells for 7.78 ± 0.25 log CFU/mL.
  • Ruokonen, Suvi-Katriina; Sanwald, Corinna; Robciuc, Alexandra; Hietala, Sami; Rantamäki, Antti H.; Witos, Joanna; King, Alistair W. T.; Lämmerhofer, Michael; Wiedmer, Susanne K. (2018)
    This study aims at extending the understanding of the toxicity mechanism of ionic liquids (ILs) using various analytical methods and cytotoxicity assays. The cytotoxicity of eight ILs and one zwitterionic compound was determined using mammalian and bacterial cells. The time dependency of the IL toxicity was assessed using human corneal epithelial cells. Hemolysis was performed using human red blood cells and the results were compared with destabilization data of synthetic liposomes upon addition of ILs. The effect of the ILs on the size and zeta potential of liposomes revealed information on changes in the lipid bilayer. Differential scanning calorimetry was used to study the penetration of the ILs into the lipid bilayer. Pulsed field gradient nuclear magnetic resonance spectroscopy was used to determine whether the ILs occurred as unimers, micelles, or if they were bound to liposomes. The results show that the investigated ILs can be divided into three groups based on the cytotoxicity mechanism: cell wall disrupting ILs, ILs exerting toxicity through both cell wall penetration and metabolic alteration, and ILs affecting solely on cell metabolism.
  • Vus, Kateryna; Girych, Mykhailo; Trusova, Valeriya; Gorbenko, Galyna; Kurutos, Atanas; Vasilev, Aleksey; Gadjev, Nikolai; Deligeorgiev, Todor (2019)
    The potential of novel cyanine dyes to inhibit the insulin amyloid formation was evaluated using thioflavin T fluorescence assay, quantum-chemical calculations, molecular docking and molecular dynamics simulations. According to the ability to suppress the insulin fibrillization under physiological conditions the examined compounds were found to follow the order: trimethines > pentamethines > monomethines > heptamethines. Of these, the trimethines 3-3 and 3-5, and pentamethines 5-3 and 5-9 almost completely prevented the protein aggregation by retarding both nucleation (except 3-3) and elongation processes. The quantum-chemical calculations revealed a complex relationship between the dye structure and its inhibitory effects. The molecular docking studies showed that most cyanines bind specifically to the L17 ladder of the B chain, located at the dry steric zipper of the insulin fibril protofilament, and form the stable complexes with the helices of the insulin monomer. The molecular dynamics simulations provided evidence for the increase of insulin helicity in the presence of cyanines. Collectively, the presented findings highlight two possible mechanisms by which cyanines can inhibit the insulin fibrillization: i) stabilization of the native protein structure followed by the retardation of the protein nucleation (all dyes); and ii) blocking the lateral extension of beta-sheets via the dye-protein stacking interactions (3-3, 3-5, 5-3, 5-9). Overall, the obtained results may prove of importance for the design of small molecules capable of preventing amyloid fibril formation by insulin and other proteins. (C) 2018 Elsevier B.V. All rights reserved.
  • Laine, Outi; Joutsi-Korhonen, Lotta; Lassila, Riitta; Huhtala, Heini; Vaheri, Antti; Makela, Satu; Mustonen, Jukka (2016)
    We evaluated the mechanisms of thrombocytopenia and procoagulant changes in relation with clinical variables in a cohort of patients with acute hantavirus disease. Blood samples of 33 prospectively recruited, consecutive, hospitalized patients with acute Puumala virus-induced hemorrhagic fever with renal syndrome (HFRS) were collected acutely and at the recovery visit (control). Serum thrombopoietin (TPO) and activity of plasma microparticles (MPs) from various cell sources were measured with enzyme-linked immunosorbent assay-based methods. The results were related to data on platelet indices and functions, coagulation variables, and clinical disease. Serum TPO was nearly 4-fold higher acutely compared with the control (median 207pg/mL, range 56-1258pg/mL vs. median 58 pg/mL, range 11-241pg/mL, P Upregulated TPO together with high MPV and IPF% confirm active thrombopoiesis, but do not predict severity of HFRS. Simultaneously, elevated prothrombin fragments and D-dimer suggest increased consumption of platelets in patients with severe AKI. Activity of platelet-derived MPs in HFRS should be studied with flow cytometry in a larger cohort of patients.
  • Nissila, Eija; Douillard, Francois P.; Ritari, Jarmo; Paulin, Lars; Jarvinen, Hanna M.; Rasinkangas, Pia; Haapasalo, Karita; Meri, Seppo; Jarva, Hanna; de Vos, Willem M. (2017)
    Lactobacillus rhamnosus strains are ubiquitous in fermented foods, and in the human body where they are commensals naturally present in the normal microbiota composition of gut, vagina and skin. However, in some cases, Lactobacillus spp. have been implicated in bacteremia. The aim of the study was to examine the genomic and immunological properties of 16 clinical blood isolates of L. rhamnosus and to compare them to the well- studied L. rhamnosus probiotic strain GG. Blood cultures from bacteremic patients were collected at the Helsinki University Hospital laboratory in 2005-2011 and L. rhamnosus strains were isolated and characterized by genomic sequencing. The capacity of the L. rhamnosus strains to activate serum complement was studied using immunological assays for complement factor C3a and the terminal pathway complement complex (TCC). Binding of complement regulators factor H and C4bp was also determined using radioligand assays. Furthermore, the isolated strains were evaluated for their ability to aggregate platelets and to form biofilms in vitro. Genomic comparison between the clinical L. rhamnosus strains showed them to be clearly different from L. rhamnosus GG and to cluster in two distinct lineages. All L. rhamnosus strains activated complement in serum and none of them bound complement regulators. Four out of 16 clinical blood isolates induced platelet aggregation and/or formed more biofilms than L. rhamnosus GG, which did not display platelet aggregation activity nor showed strong biofilm formation. These findings suggest that clinical L. rhamnosus isolates show considerable heterogeneity but are clearly different from L. rhamnosus GG at the genomic level. All L. rhamnosus strains are still normally recognized by the human complement system.
  • Reckling, Moritz; Döring, Thomas F.; Bergkvist, Göran; Stoddard, Frederick L.; Watson, Christine A.; Seddig, Sylvia; Chmielewski, Frank-M.; Bachinger, Johann (2018)
    Grain legumes produce high-quality protein for food and feed, and potentially contribute to sustainable cropping systems, but they are grown on only 1.5% of European arable land. Low temporal yield stability is one of the reasons held responsible for the low proportion of grain legumes, without sufficient quantitative evidence. The objective of this study was to compare the yield stability of grain legumes with other crop species in a northern European context and accounting for the effects of scale in the analysis and the data. To avoid aggregation biases in the yield data, we used data from long-term field experiments. The experiments included grain legumes (lupin, field pea, and faba bean), other broad-leaved crops, spring, and winter cereals. Experiments were conducted in the UK, Sweden, and Germany. To compare yield stability between grain legumes and other crops, we used a scale-adjusted yield stability indicator that accounts for the yield differences between crops following Taylor's Power Law. Here, we show that temporal yield instability of grain legumes (30%) was higher than that of autumn-sown cereals (19%), but lower than that of other spring-sown broad-leaved crops (35%), and only slightly greater than spring-sown cereals (27%). With the scale-adjusted yield stability indicator, we estimated 21% higher yield stability for grain legumes compared to a standard stability measure. These novel findings demonstrate that grain legume yields are as reliable as those of other spring-sown crops in major production systems of northern Europe, which could influence the current negative perception on grain legume cultivation. Initiatives are still needed to improve the crops agronomy to provide higher and more stable yields in future.
  • Prebble, Dale W; Voser, Vanja; Er, Safak; Hlushchuk, Irena; Domanskyi, Andrii; Airavaara, Mikko; Ekins, Merrick G; Mellick, George D; Carroll, Anthony R (2022)
    During a high-throughput screen of 300 Australian marine invertebrate extracts, the extract of the marine sponge Clathria (Thalysias) cf. hesperia was identified with α-synuclein binding activity. The bioassay-guided purification of this extract resulted in the isolation of 1-methyl-1,2,7,8-tetrahydro-2,8-dioxoadenosine (2) as the α-syn binder along with one new compound, hesperine (1), and five known compounds, indole-3-carboxaldehyde (3), (Z)-2'-demethylaplysinopsin (4), 2-amino-4'-hydroxyacetophenone (5), 4-hydroxybenzoic acid (6) and 4-hydroxybenzaldehyde (7). Herein, we report the structure elucidation of hesperine (1) and α-syn binding activity of 1-methyl-1,2,7,8-tetrahydro-2,8-dioxoadenosine (2).
  • Virta, Miisa; Huitu, Otso; Heikkinen, Juha; Holmala, Katja; Jokelainen, Pikka (2022)
    In Finland, free-ranging Eurasian lynx (Lynx lynx) population has grown from 30 to 40 individuals to 2800 individuals since the species became partly protected in 1962. Changes in host population size are known to have an impact on host-parasite dynamics, and the Eurasian lynx population in Finland provides a unique opportunity for studying the potential effects of dramatic population increase and expansion of a solitary apex predator on their parasite prevalence and abundance. Toxocara cati is a zoonotic gastrointestinal parasite infecting domestic cats and wild felids worldwide. We studied T. cati infection prevalence and worm burden in 2756 Eurasian lynx individuals from Finland, covering the years 1999-2015. Toxocara cati worms that had been collected from intestinal contents were identified based on morphology. We performed regression analyses to investigate possible associations of age, sex, and host population density with T. cati infection. We found T. cati from 2324 (84.3%, 95% confidence interval 82.9-86.0) of the examined lynx. Each year, the infection prevalence was higher than 75% and not density dependent. The parasites were strongly aggregated, with older individuals harboring fewer T. cati than younger ones did. Old females aged 9-15 years had higher T. cati abundance than males of the same age group. Our results indicate that T. cati was a common and abundant parasite of Eurasian lynx throughout the study period, regardless of the changing population size and density.
  • Moiseev, Dmitry; Lautaportti, Susanna; Alku, Laura; Tabakova, Ksenia; O'Connor, Ewan; Leskinen, Matti; Kulmala, Markku (2019)
    Abstract: Eleven years of dual-polarization weather radar data, complemented by satellite and lidar observations, were used to investigate the origin of areas of localized intensification of precipitation spotted in the vicinity of Helsinki-Vantaa airport. It was observed that existing precipitation is enhanced locally on spatial scales from a few kilometers to several tens of kilometers. The precipitation intensity in these localized areas was 6-14 times higher than the background large-scale precipitation rate. Surface observations and dual-polarization radar data indicate that snowflakes within the ice portion of the falling precipitation in the intensification regions are larger and more isotropic than in the surrounding precipitation. There appears to be an increase in the ice particle number concentration within the intensification region. The observed events were linked to arriving or departing air traffic. We advocate that the mechanism responsible for intensification is aircraft-produced ice particles boosting the aggregation growth of snowflakes. Plain Language Summary: By analyzing 11 years of dual-polarization weather radar observations in the Helsinki region, we have discovered that airplanes landing in or departing from the Helsinki-Vantaa airport could locally increase precipitation rate by as much as 14 times. The observed phenomenon is related to the hole-punch clouds, which are also forming with the help of airplanes. The reported observations allow us to have a better understanding of precipitation formation processes that take place in ice and mixed phase clouds. They show that falling ice crystals from upper clouds could seed lower clouds and therefore increase rain or snowfall intensity through the process called snowflake aggregation. During snowflake aggregation bigger faster falling particles are formed by ice particles colliding and sticking together.
  • Erkkilä, Arja T.; Manninen, Suvi; Fredrikson, Linda; Bhalke, Monika; Holopainen, Minna; Ruuth, Maija; Lankinen, Maria; Käkelä, Reijo; Öörni, Katariina; Schwab, Ursula S. (2021)
    Background: There is little knowledge on the effects of alpha-linolenic acid (ALA) and n-3 long chain polyunsaturated fatty acids (n-3 LCPUFA) on the LDL lipidome and aggregation of LDL particles. Objective: We examined if consumption of Camelina sativa oil (CSO) as a source of ALA, fatty fish (FF) as a source of n-3 LCPUFA and lean fish (LF) as a source of fish protein affect the lipidome of LDL as compared to a control diet. Methods: Participants with impaired glucose tolerance (39 women and 40 men) were randomized to 4 study groups (CSO providing 10 g/d ALA, FF and LF [both 4 fish meals/wk] and control limiting their fish and ALA intake) in a 12-week, parallel trial. Diets were instructed and dietary fats were provided to the participants. The lipidome of LDL particles isolated from samples collected at baseline and after intervention was analyzed with electrospray ionization-tandem mass spectrometry. Results: In the CSO group, the relative concentrations of saturated and monounsaturated cholesteryl ester species in LDL decreased and the species with ALA increased. In the FF group, LDL phosphatidylcholine (PC) species containing n-3 LCPUFA increased. There was a significant positive correlation between the change in total sphingomyelin and change in LDL aggregation, while total PC and triunsaturated PC species were inversely associated with LDL aggregation when all the study participants were included in the analysis. Conclusion: Dietary intake of CSO and FF modifies the LDL lipidome to contain more polyunsaturated and less saturated lipid species. The LDL surface lipids are associated with LDL aggregation. (c) 2021 National Lipid Association. Published by Elsevier Inc. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )
  • Kneifel, Stefan; Moisseev, Dmitri (2020)
    Riming is an efficient process of converting liquid cloud water into ice and plays an important role in the formation of precipitation in cold clouds. Due to the rapid increase in ice particle mass, riming enhances the particle's terminal velocity, which can be detected by ground-based vertically pointing cloud radars if the effect of vertical air motions can be sufficiently mitigated. In our study, we first revisit a previously published approach to relate the radar mean Doppler velocity (MDV) to rime mass fraction (FR) using a large ground-based in situ dataset. This relation is then applied to multiyear datasets of cloud radar observations collected at four European sites covering polluted central European, clean maritime, and Arctic climatic conditions. We find that riming occurs in 1%-8% of the nonconvective ice containing clouds with median FR between 0.5 and 0.6. Both the frequency of riming and FR reveal relatively small variations for different seasons. In contrast to previous studies, which suggested enhanced riming for clean environments, our statistics indicate the opposite; however, the differences between the locations are overall small. We find a very strong relation between the frequency of riming and temperature. While riming is rare at temperatures lower than -12 degrees C, it strongly increases toward 0 degrees C. Previous studies found a very similar temperature dependence for the amount and droplet size of supercooled liquid water, which might be closely connected to the riming signature found in this study. In contrast to riming frequency, we find almost no temperature dependence for FR.
  • Palmio, Johanna; Jonson, Per Harald; Inoue, Michio; Sarparanta, Jaakko; Bengoechea, Rocio; Savarese, Marco; Vihola, Anna; Jokela, Manu; Nakagawa, Masanori; Noguchi, Satoru; Olivé, Montse; Masingue, Marion; Kerty, Emilia; Hackman, Peter; Weihl, Conrad C.; Nishino, Ichizo; Udd, Bjarne (2020)
    Eight patients from five families with undiagnosed dominant distal myopathy underwent clinical, neurophysiological and muscle biopsy examinations. Molecular genetic studies were performed using targeted sequencing of all known myopathy genes followed by segregation of the identified mutations in the affected families using Sanger sequencing. Two novel mutations in DNAJB6 J domain, c.149C>T (p.A50V) and c.161A>C (p.E54A), were identified as the cause of disease. The muscle involvement with p.A50V was distal calf-predominant, and the p.E54A was more proximo-distal. Histological findings were similar to those previously reported in DNAJB6 myopathy. In line with reported pathogenic mutations in the glycine/phenylalanine (G/F) domain of DNAJB6, both the novel mutations showed reduced anti-aggregation capacity by filter trap assay and TDP-43 disaggregation assays. Modeling of the protein showed close proximity of the mutated residues with the G/F domain. Myopathy-causing mutations in DNAJB6 are not only located in the G/F domain, but also in the J domain. The identified mutations in the J domain cause dominant distal and proximo-distal myopathy, confirming that mutations in DNAJB6 should be considered in distal myopathy cases.
  • Tonali, Nicolo; Hericks, Loreen; Schroeder, David C.; Kracker, Oliver; Krzemieniecki, Radoslaw; Kaffy, Julia; Le Joncour, Vadim; Laakkonen, Pirjo; Marion, Antoine; Ongeri, Sandrine; Dodero, Veronica I.; Sewald, Norbert (2021)
    In peptidotriazolamers every second peptide bond is replaced by a 1H-1,2,3-triazole. Such foldamers are expected to bridge the gap in molecular weight between small-molecule drugs and protein-based drugs. Amyloid beta (A beta) aggregates play an important role in Alzheimer's disease. We studied the impact of amide bond replacements by 1,4-disubstituted 1H-1,2,3-triazoles on the inhibitory activity of the aggregation "hot spots" (KLVFF20)-L-16 and G(39)VVIA(42) in A beta(1-42). We found that peptidotriazolamers act as modulators of the A beta(1-42) oligomerization. Some peptidotriazolamers are able to interfere with the formation of toxic early A beta oligomers, depending on the position of the triazoles, which is also supported by computational studies. Preliminary in vitro results demonstrate that a highly active peptidotriazolamer is also able to cross the blood-brain-barrier.
  • Cui, Hengjing; Norrbacka, Susanna Maria; Myöhänen, Timo (2022)
    The accumulation of aggregated alpha-synuclein (alpha-syn) has been identified as the primary component of Lewy bodies that are the pathological hallmarks of Parkinson's disease (PD). Several preclinical studies have shown alpha-syn aggregation, and particularly the intermediates formed during the aggregation process to be toxic to cells. Current PD treatments only provide symptomatic relief, and alpha-syn serves as a promising target to develop a disease-modifying therapy for PD. Our previous studies have revealed that a small-molecular inhibitor for prolyl oligopeptidase (PREP), KYP-2047, increases alpha-syn degradation by accelerating macroautophagy (MA) leading to disease-modifying effects in preclinical PD models. However, alpha-syn is also degraded by chaperone-mediated autophagy (CMA). In the present study, we tested the effects of PREP inhibition or deletion on CMA activa-tion and alpha-syn degradation. HEK-293 cells were transfected with alpha-syn and incubated with 1 & 10 mu M KYP-2047 for 24 h. Both 1 & 10 mu M KYP-2047 increased LAMP-2A levels, induced alpha-syn degradation and reduced the expression of Hsc70, suggesting that the PREP inhibitor prevented alpha-syn aggregation by activating the CMA pathway. Similarly, KYP-2047 increased the LAMP-2A immunoreactivity and reduced the Hsc70 levels in mouse primary cortical neurons. When LAMP-2A was silenced by a siRNA, KYP-2047 increased the LC3BII/LC3BI ratio and accelerated the clearance of alpha-syn. Additionally, KYP-2047 induced CMA effectively also when MA was blocked by bafilomycin A1. Based on our results, we suggest that PREP might function as a core network node in MA-CMA crosstalk, and PREP inhibition can reduce alpha-syn levels via both main autophagy systems.
  • Myöhänen, Timo T.; Norrbacka, Susanna; Savolainen, Mari H. (2017)
    Lewy bodies, the histopathological hallmarks of Parkinson's disease (PD), contain insoluble and aggregated alpha-synuclein (aSyn) and many other proteins, proposing a role for failure in protein degradation system in the PD pathogenesis. Proteasomal dysfunction has indeed been linked to PD and aSyn oligomers have been shown to inhibit proteasomes and autophagy. Our recent studies have shown that inhibitors of prolyl oligopeptidase (PREP) can prevent the aggregation and enhance the clearance of accumulated aSyn, and therefore, we wanted to study if PREP inhibition can overcome the aSyn aggregation and toxicity induced by lactacystin, a proteasomal inhibitor. The cells overexpressing human A30P or A53T mutated aSyn were incubated with lactacystin and a PREP inhibitor, KYP-2047, for 48 h. Theafter, the cells were fractioned, and the effects of lactacystin with/without 1 mu M KYP-2047 on aSyn aggregation and ubiquitin accumulation, cell viability and on autophagic markers (p62, Beclin1 and LC3BII) were studied. We found that KYP-2047 attenuated lactacystin-induced cell death in mutant aSyn overexpressing cells but not in non-overexpressing control cells. KYP-2047 reduced significantly SDS-insoluble high-molecular-weight aSyn oligomers that were in line with the cell viability results. In addition, significant reduction in protein accumulation marker, p62, was seen in SDS fraction while LC3BII, a marker for autophagosome formation, was increased, indicating to enhanced autophagy. Our results further streghten the possibilities for PREP inhibitors as a potential drug therapy against synucleinopathies and other protein aggregating diseases. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
  • Eteläinen, T.; Kulmala, Soile; Svarcbahs, R.; Jäntti, M.; Myohänen, T. T. (2021)
    Oxidative stress (OS) is a common toxic feature in various neurodegenerative diseases. Therefore, reducing OS could provide a potential approach to achieve neuroprotection. Prolyl oligopeptidase (PREP) is a serine protease that is linked to neurodegeneration, as endogenous PREP inhibits autophagy and induces the accumulation of detrimental protein aggregates. As such, inhibition of PREP by a small-molecular inhibitor has provided neuroprotection in preclinical models of neurodegenerative diseases. In addition, PREP inhibition has been shown to reduce production of reactive oxygen species (ROS) and the absence of PREP blocks stress-induced ROS production. However, the mechanism behind PREP-related ROS regulation is not known. As we recently discovered PREP's physiological role as a protein phosphatase 2A (PP2A) regulator, we wanted to characterize PREP inhibition as an approach to reduce OS. We studied the impact of a PREP inhibitor, KYP-2047, on hydrogen peroxide and ferrous chloride induced ROS production and on cellular antioxidant response in HEK-293 and SHSY5Y cells. In addition, we used HEK-293 and SH-SY5Y PREP knock-out cells to validate the role of PREP on stress-induced ROS production. We were able to show that absence of PREP almost entirely blocks the stressinduced ROS production in both cell lines. Reduced ROS production and smaller antioxidant response was also seen in both cell lines after PREP inhibition by 10 mu M KYP-2047. Our results also revealed that the OS reducing mechanism of PREP inhibition is related to reduced activation of ROS producing NADPH oxidase through enhanced PP2A activation. In conclusion, our results suggest that PREP inhibition could also provide neuroprotection by reducing OS, thus broadening the scope of its beneficial effects on neurodegeneration.