Browsing by Subject "DEGRADATION"

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  • Kyostila, Kaisa; Syrja, Pernilla; Jagannathan, Vidhya; Chandrasekar, Gayathri; Jokinen, Tarja S; Seppala, Eija H.; Becker, Doreen; Drogemuller, Michaela; Dietschi, Elisabeth; Drogemuller, Cord; Lang, Johann; Steffen, Frank; Rohdin, Cecilia; Jaderlund, Karin H.; Lappalainen, Anu K.; Hahn, Kerstin; Wohlsein, Peter; Baumgartner, Wolfgang; Henke, Diana; Oevermann, Anna; Kere, Juha; Lohi, Hannes; Leeb, Tosso (2015)
    Inherited neurodegenerative disorders are debilitating diseases that occur across different species. We have performed clinical, pathological and genetic studies to characterize a novel canine neurodegenerative disease present in the Lagotto Romagnolo dog breed. Affected dogs suffer from progressive cerebellar ataxia, sometimes accompanied by episodic nystagmus and behavioral changes. Histological examination revealed unique pathological changes, including profound neuronal cytoplasmic vacuolization in the nervous system, as well as spheroid formation and cytoplasmic aggregation of vacuoles in secretory epithelial tissues and mesenchymal cells. Genetic analyses uncovered a missense change, c.1288G>A; p.A430T, in the autophagy-related ATG4D gene on canine chromosome 20 with a highly significant disease association (p = 3.8 x 10(-136)) in a cohort of more than 2300 Lagotto Romagnolo dogs. ATG4D encodes a poorly characterized cysteine protease belonging to themacroautophagy pathway. Accordingly, our histological analyses indicated altered autophagic flux in affected tissues. The knockdown of the zebrafish homologue atg4da resulted in a widespread developmental disturbance and neurodegeneration in the central nervous system. Our study describes a previously unknown canine neurological disease with particular pathological features and implicates the ATG4D protein as an important autophagy mediator in neuronal homeostasis. The canine phenotype serves as a model to delineate the disease-causing pathological mechanism(s) and ATG4D function, and can also be used to explore treatment options. Furthermore, our results reveal a novel candidate gene for human neurodegeneration and enable the development of a genetic test for veterinary diagnostic and breeding purposes.
  • Pflugmacher, Stephan; Tallinen, Saila; Kim, Young Jun; Kim, Sanghun; Esterhuizen, Maranda (2021)
    Plastic has been an environmental pollutant far longer than claimed by the first reports surfacing in 1979, meaning some plastic materials have been decaying in nature for decades. Nevertheless, the threat posed to biota is not fully understood, especially from aged microplastic. The question considered in this study was whether the adverse effects of new plastic differ from those of old plastic material. Therefore, the morphological and physiological effects on Lepidium sativum with exposure to both new and aged polycarbonate were considered against a known stressor leaching from polycarbonate with time, bisphenol-A. Exposure to new and short-term aged polycarbonate (up to 80 days) elicited the most severe effects such as germination inhibition, reduced seedling growth, decreased chlorophyll concentrations, and increased catalase activity. These adverse effects in L. sativum associated with polycarbonate exposure were reduced as a function of the ageing time applied to the polycarbonate. The chemical substances that lend new polycarbonate material its toxicity were likely leached with time during the ageing process. Based on the results obtained, temperature and humidity based artificial ageing significantly reduced the phytotoxicity of the microplastic particles
  • Liebmann, Jonathan; Sobanski, Nicolas; Schuladen, Jan; Karu, Einar; Hellen, Heidi; Hakola, Hannele; Zha, Qiaozhi; Ehn, Mikael; Riva, Matthieu; Heikkinen, Liine; Williams, Jonathan; Fischer, Horst; Lelieyeld, Jos; Crowley, John N. (2019)
    The formation of alkyl nitrates in various oxidation processes taking place throughout the diel cycle can represent an important sink of reactive nitrogen and mechanism for chain termination in atmospheric photo-oxidation cycles. The low-volatility alkyl nitrates (ANs) formed from biogenic volatile organic compounds (BVOCs), especially terpenoids, enhance rates of production and growth of secondary organic aerosol. Measurements of the NO3 reactivity and the mixing ratio of total alkyl nitrates (6 ANs) in the Finnish boreal forest enabled assessment of the relative importance of NO3-, O-3- and OH-initiated formation of alkyl nitrates from BVOCs in this environment. The high reactivity of the forest air towards NO3 resulted in reactions of the nitrate radical, with terpenes contributing substantially to formation of ANs not only during the night but also during daytime. Overall, night-time reactions of NO3 accounted for 49% of the local production rate of ANs, with contributions of 21 %, 18% and 12% for NO3, OH and O-3 during the day. The lifetimes of the gas-phase ANs formed in this environment were on the order of 2 h due to efficient uptake to aerosol (and dry deposition), resulting in the transfer of reactive nitrogen from anthropogenic sources to the forest ecosystem.
  • Haliloglu, Kamil; Hosseinpour, Arash; Cinisli, Kağan Tolga; Ozturk, Halil Ibrahim; Ozkan, Guller; Pour-Aboughadareh, Alireza; Poczai, Péter (2020)
    Salinity is an edaphic stress that dramatically restricts worldwide crop production. Nanomaterials and plant growth-promoting bacteria (PGPB) are currently used to alleviate the negative effects of various stresses on plant growth and development. This study investigates the protective effects of different levels of zinc oxide nanoparticles (ZnO-NPs) (0, 20, and 40 mg L-1) and PGPBs (no bacteria, Bacillus subtilis, Lactobacillus casei, Bacillus pumilus) on DNA damage and cytosine methylation changes in the tomato (Solanum lycopersicum L. 'Linda') seedlings under salinity stress (250 mM NaCl). Coupled Restriction Enzyme Digestion-Random Amplification (CRED-RA) and Randomly Amplified Polymorphic DNA (RAPD) approaches were used to analyze changes in cytosine methylation and to determine how genotoxic effects influence genomic stability. Salinity stress increased the polymorphism rate assessed by RAPD, while PGPB and ZnO-NPs reduced the adverse effects of salinity stress. Genomic template stability was increased by the PGPBs and ZnO-NPs application; this increase was significant when Lactobacillus casei and 40 mg L-1 of ZnO-NPs were used.A decreased level of DNA methylation was observed in all treatments. Taken together, the use of PGPB and ZnO-NPs had a general positive effect under salinity stress reducing genetic impairment in tomato seedlings.
  • Scopetani, Costanza; Chelazzi, David; Cincinelli, Alessandra; Esterhuizen-Londt, Maranda (2019)
    In the last few years, several studies have investigated microplastics (MPs) in marine ecosystems, but data monitoring and assessing the occurrence in freshwater environments are still scarce. The present study aims to investigate the occurrence, distribution, and chemical composition of MP pollution in Vesijärvi lake and Pikku Vesijärvi pond close to the city of Lahti (Finland) in winter. Sediment, snow, and ice core samples were collected near the shore of these two aquatic systems. MPs were analysed and identified by a non-destructive method using Fourier transform infrared spectroscopy (FTIR) 2D imaging. The mean concentrations of MPs detected in sediment, snow, and ice samples were 395.5 ± 90.7 MPs/kg, 117.1 ± 18.4 MPs/L, and 7.8 ± 1.2 MPs/L, respectively. FTIR results showed the predominant abundance of microplastics, such as polyamides (up to 53.3%), polyethylene and polypropylene (up to 17.1%), and natural fragments such as cellulose (up to 45.8%) and wool (up 18.8%) in the same size range. The potential release of MPs arising from stormwaters and sport and recreational activities was evidenced.
  • Lu, Yiqun; Liu, Ling; Ning, An; Yang, Gan; Liu, Yiliang; Kurten, Theo; Vehkamäki, Hanna; Zhang, Xiuhui; Wang, Lin (2020)
    Sulfuric acid (SA)-dimethylamine (DMA)-H2O cluster formation has been proven to be responsible for a significant part of new particle formation (NPF) in a Chinese megacity. However, the possible involvement of common atmospheric acids in the subsequent growth of SA-DMA clusters remains elusive. We simulated formation and growth of clusters using atmospheric relevant concentrations of SA, DMA, and trifluoroacetic acid (TFA), a commonly observed atmospheric perfluorocarboxylic acid, using Density Functional Theory combined with Atmospheric Cluster Dynamics Code. The presence of TFA leads to complex cluster formation routes and an enhancement of NPF rates by up to 2.3 ([TFA] = 5.0 x 10(6) molecules cm(-3), [SA] = 1.0 x 10(6) molecules cm(-3), and [DMA] = 1.5 x 10(9) molecules cm(-3)). The agreement of (SA)(1)center dot(DMA)(1-2)center dot(TFA)(1) concentrations between simulations and ambient measurements during NPF events validates model predictions and implies that perfluorocarboxylic acids could potentially boost atmospheric SA-DMA NPF rates.
  • Kalam, Kristjan; Seemen, Helina; Ritslaid, Peeter; Rähn, Mihkel; Tamm, Aile; Kukli, Kaupo; Kasikov, Aarne; Link, Joosep; Stern, Raivo; Duenas, Salvador; Castan, Helena; Garcia, Hector (2018)
    Thin solid films consisting of ZrO2 and Fe2O3 were grown by atomic layer deposition (ALD) at 400 degrees C. Metastable phases of ZrO2 were stabilized by Fe2O3 doping. The number of alternating ZrO2 and Fe2O3 deposition cycles were varied in order to achieve films with different cation ratios. The influence of annealing on the composition and structure of the thin films was investigated. Additionally, the influence of composition and structure on electrical and magnetic properties was studied. Several samples exhibited a measurable saturation magnetization and most of the samples exhibited a charge polarization. Both phenomena were observed in the sample with a Zr/Fe atomic ratio of 2.0.
  • Cooper, Helen M.; Yang, Yang; Ylikallio, Emil; Khairullin, Rafil; Woldegebriel, Rosa; Lin, Kai-Lan; Euro, Liliya; Palin, Eino; Wolf, Alexander; Trokovic, Ras; Isohanni, Pirjo; Kaakkola, Seppo; Auranen, Mari; Lonnqvist, Tuula; Wanrooij, Sjoerd; Tyynismaa, Henna (2017)
    De novo mutations in ATAD3A (ATPase family AAA-domain containing protein 3A) were recently found to cause a neurological syndrome with developmental delay, hypotonia, spasticity, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy. Using whole-exome sequencing, we identified a dominantly inherited heterozygous variant c.1064G > A (p.G355D) in ATAD3A in a mother presenting with hereditary spastic paraplegia (HSP) and axonal neuropathy and her son with dyskinetic cerebral palsy, both with disease onset in childhood. HSP is a clinically and genetically heterogeneous disorder of the upper motor neurons. Symptoms beginning in early childhood may resemble spastic cerebral palsy. The function of ATAD3A, a mitochondrial inner membrane AAA ATPase, is yet undefined. AAA ATPases form hexameric rings, which are catalytically dependent on the co-operation of the subunits. The dominant-negative patient mutation affects the Walker A motif, which is responsible for ATP binding in the AAA module of ATAD3A, and we show that the recombinant mutant ATAD3A protein has a markedly reduced ATPase activity. We further show that overexpression of the mutant ATAD3A fragments the mitochondrial network and induces lysosome mass. Similarly, we observed altered dynamics of the mitochondrial network and increased lysosomes in patient fibroblasts and neurons derived through differentiation of patient-specific induced pluripotent stem cells. These alterations were verified in patient fibroblasts to associate with upregulated basal autophagy through mTOR inactivation, resembling starvation. Mutations in ATAD3A can thus be dominantly inherited and underlie variable neurological phenotypes, including HSP, with intrafamiliar variability. This finding extends the group of mitochondrial inner membrane AAA proteins associated with spasticity.
  • Toledo, Miriam; Batista-Gonzalez, Ana; Merheb, Emilio; Aoun, Marie Louise; Tarabra, Elena; Feng, Daorong; Sarparanta, Jaakko; Merlo, Paola; Botre, Francesco; Schwartz, Gary J.; Pessin, Jeffrey E.; Singh, Rajat (2018)
    The circadian clock coordinates behavioral and circadian cues with availability and utilization of nutrients. Proteasomal degradation of clock repressors, such as cryptochrome (CRY) 1, maintains periodicity. Whether macroautophagy, a quality control pathway, degrades circadian proteins remains unknown. Here we show that circadian proteins BMAL1, CLOCK, REV-ERB alpha, and CRY1 are lysosomal targets, and that macroautophagy affects the circadian clock by selectively degrading CRY1. Autophagic degradation of CRY1, an inhibitor of gluconeogenesis, occurs in a diurnal window when rodents rely on gluconeogenesis, suggesting that CRY1 degradation is timeimprinted to maintenance of blood glucose. High-fat feeding accelerates autophagic CRY1 degradation and contributes to obesity-associated hyperglycemia. CRY1 contains several light chain 3 (LC3)-interacting region (LIR) motifs, which facilitate the interaction of cargo proteins with the autophagosome marker LC3. Using mutational analyses, we identified two distinct LIRs on CRY1 that exert circadian glycemic control by regulating CRY1 degradation, revealing LIRs as potential targets for controlling hyperglycemia.
  • Hanemaaijer, Evelyn S.; Panahi, Mahmod; Swaddiwudhipong, Nol; Tikka, Saara; Winblad, Bengt; Viitanen, Matti; Piras, Antonio; Behbahani, Homira (2018)
    Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a familial progressive degenerative disorder and is caused by mutations in NOTCH3 gene. Previous study reported that mutant NOTCH3 is more prone to form aggregates than wild-type NOTCH3 and the mutant aggregates are resistant to degradation. We hypothesized that aggregation or accumulation of NOTCH3 could be due to impaired lysosomal-autophagy machinery in VSMC. Here, we investigated the possible cause of accumulation/aggregation of NOTCH3 in CADASIL using cerebral VSMCs derived from control and CADASIL patients carrying NOTCH3(RI33C) mutation. Thioflavin-S-staining confirmed the increased accumulation of aggregated NOTCH3 in VSMCR133C compared to VSMCWT. Increased levels of the lysosomal marker, Lamp2, were detected in VSMCR133C, which also showed co-localization with NOTCH3 using double-immunohistochemistry. Increased level of LC3-II/LC3-I ratio was observed in VSMCR133C suggesting an accumulation of autophagosomes. This was coupled with the decreased co-localization of NOTCH3 with LC3, and Lamp2 and, further, increase of p62/SQSTM1 levels in VSMCR133C compared to the VSMCWT. In addition, Western blot analysis indicated phosphorylation of p-ERK, p-S6RP, and p-P70 S6K. Altogether, these results suggested a dysfunction in the autophagy-lysosomal pathway in VSMCR133C. The present study provides an interesting avenue of the research investigating the molecular mechanism of CADASIL.
  • Yan, Lijuan; Penttinen, Petri; Mikkonen, Anu; Lindstrom, Kristina (2018)
    We investigated bacterial community dynamics in response to used motor oil contamination and perennial crop cultivation by 16S rRNA gene amplicon sequencing in a 4-year field study. Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were the major bacterial phyla, and Rhodococcus was the most abundant genus. Initially, oil contamination decreased the overall bacterial diversity. Actinobacteria, Betaproteobacteria, and Gammaproteobacteria were sensitive to oil contamination, exhibiting clear succession with time. However, bacterial communities changed over time, regardless of oil contamination and crop cultivation. The abundance difference of most OTUs between oil-contaminated and non-contaminated plots remained the same in later sampling years after the initial abundance difference induced by oil spike. The abundances of three oil-favored actinobacteria (Lysinimonas, Microbacteriaceae, and Marmoricola) and one betaproteobacterium (Aquabacterium) changed in different manner over time in oil-contaminated and non-contaminated soil. We propose that these taxa are potential bio-indicators for monitoring recovery from motor oil contamination in boreal soil. The effect of crop cultivation on bacterial communities became significant only after the crops achieved stable growth, likely associated with plant material decomposition by Bacteroidetes, Armatimonadetes and Fibrobacteres.
  • Syrjä, Pernilla; Anwar, Tahira; Pääkkönen, Tarja; Kyöstilä, Kaisa; Hultin Jäderlund, Karin; Cozzi, Francesca; Rohdin, Cecilia; Hahn, Kerstin; Wohlsein, Peter; Baumgärtner, Wolfgang; Henke, Diana; Oevermann, Anna; Sukura, Antti; Leeb, Tosso; Lohi, Hannes; Eskelinen, Eeva-Liisa (2017)
    A missense variant in the autophagy-related ATG4D-gene has been associated with a progressive degenerative neurological disease in Lagotto Romagnolo (LR) dogs. In addition to neural lesions, affected dogs show an extraneural histopathological phenotype characterized by severe cytoplasmic vacuolization, a finding not previously linked with disturbed autophagy in animals. Here we aimed at testing the hypothesis that autophagy is altered in the affected dogs, at reporting the histopathology of extraneural tissues and at excluding lysosomal storage diseases. Basal and starvation-induced autophagy were monitored by Western blotting and immunofluorescence of microtubule associated protein 1A/B light chain3 (LC3) in fibroblasts from 2 affected dogs. The extraneural findings of 9 euthanized LRs and skin biopsies from 4 living affected LRs were examined by light microscopy, electron microscopy, and immunohistochemistry (IHC), using antibodies against autophagosomal membranes (LC3), autophagic cargo (p62), and lysosomal membranes (LAMP2). Biochemical screening of urine and fibroblasts of 2 affected dogs was performed. Under basal conditions, the affected fibroblasts contained significantly more LC3-II and LC3-positive vesicles than did the controls. Morphologically, several cells, including serous secretory epithelium, endothelial cells, pericytes, plasma cells, and macrophages, contained cytoplasmic vacuoles with an ultrastructure resembling enlarged amphisomes, endosomes, or multivesicular bodies. IHC showed strong membranous LAMP2 positivity only in sweat glands. The results show that basal but not induced autophagy is altered in affected fibroblasts. The ultrastructure of affected cells is compatible with altered autophagic and endo-lysosomal vesicular traffic. The findings in this spontaneous disease provide insight into possible tissue-specific roles of basal autophagy.
  • Mazzoni, Annalisa; Maravic, Tatjana; Tezvergil-Mutluay, Arzu; Tjäderhane, Leo; Scaffa, Polliana Mendes Candia; Seseogullari-Dirihan, Roda; Bavelloni, Alberto; Gobbi, Pietro; Pashley, David H.; Tay, Franklin R.; Breschi, Lorenzo (2018)
    Objectives: Matrix metalloproteinases (MMPs) are dentinal endogenous enzymes claimed to have a vital role in dentin organic matrix breakdown. The aim of the study was to investigate presence, localization and distribution of MMP-7 in sound human dentin. Methods: Dentin was powdered, demineralized and dissolved in isoelectric focusing buffer. Resolved proteins were transferred to nitrocellulose membranes for western blotting (WB) analyses. For the zymographic analysis, aliquots of dentin protein were electrophoresed in 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis containing fluorescently labeled gelatin. Further, the concentrations of dentinal MMPs were measured using Fluorescent Microsphere Immunoassay with a human MMP-MAP multiplex kit. Pre- and post-embedding immunolabeling technique was used to investigate the localization and distribution of MMP-7 in dentin. Dentin was cryo-fractured, the fragments partially decalcified and labeled with a primary monoclonal anti-MMP-7 and a secondary antibody conjugated with gold nanoparticles. MMP-7 labelings were identified in the demineralized dentin matrix as highly electron-dense dispersed gold particles. Results: WB and zymographic analysis of extracted dentin proteins showed presence of MMP-7 (similar to 20-28 KDa). Further, MMP-7 was found in the supernatants of the incubated dentin beams using Fluorescent Microsphere Immunoassay. FEI-SEM and TEM analyses established MMP-7 as an intrinsic constituent of the human dentin organic matrix. Conclusion: This study demonstrated that MMP-7 is an endogenous component of the human dentin fibrillar network. Clinical significance: It is pivotal to understand the underlying processes behind dentin matrix remodeling and degradation in order to develop the most optimal clinical protocols and ensure the longevity of dental restorations.
  • Simpanen, Suvi; Dahl, Mari; Gerlach, Magdalena; Mikkonen, Anu; Malk, Vuokko; Mikola, Juha; Romantschuk, Martin (2016)
    The use of in situ techniques in soil remediation is still rare in Finland and most other European countries due to the uncertainty of the effectiveness of the techniques especially in cold regions and also due to their potential side effects on the environment. In this study, we compared the biostimulation, chemical oxidation, and natural attenuation treatments in natural conditions and pilot scale during a 16-month experiment. A real fuel spill accident was used as a model for experiment setup and soil contamination. We found that biostimulation significantly decreased the contaminant leachate into the water, including also the non-aqueous phase liquid (NAPL). The total NAPL leachate was 19 % lower in the biostimulation treatment that in the untreated soil and 34 % lower in the biostimulation than oxidation treatment. Soil bacterial growth and community changes were first observed due to the increased carbon content via oil amendment and later due to the enhanced nutrient content via biostimulation. Overall, the most effective treatment for fresh contaminated soil was biostimulation, which enhanced the biodegradation of easily available oil in the mobile phase and consequently reduced contaminant leakage through the soil. The chemical oxidation did not enhance soil cleanup and resulted in the mobilization of contaminants. Our results suggest that biostimulation can decrease or even prevent oil migration in recently contaminated areas and can thus be considered as a potentially safe in situ treatment also in groundwater areas.
  • Lindholm, Dan; Pham, Dan D.; Cascone, Annunziata; Eriksson, Ove; Wennerberg, Krister; Saarma, Mart (2016)
    Parkinson's disease (PD) is a progressive neurodegenerative disorder causing movement disabilities and several non-motor symptoms in afflicted patients. Recent studies in animal models of PD and analyses of brain specimen from PD patients revealed an increase in the level and activity of the non-receptor tyrosine kinase Abelson (c-Abl) in dopaminergic neurons with phosphorylation of protein substrates, such as alpha-synuclein and the E3 ubiquitin ligase, Parkin. Most significantly inhibition of c-Abl kinase activity by small molecular compounds used in the clinic to treat human leukemia have shown promising neuroprotective effects in cell and animal models of PD. This has raised hope that similar beneficial outcome may also be observed in the treatment of PD patients by using c-Abl inhibitors. Here we highlight the background for the current optimism, reviewing c-Abl and its relationship to pathophysiological pathways prevailing in PD, as well as discussing issues related to the pharmacology and safety of current c-Abl inhibitors. Clearly more rigorously controlled and well-designed trials are needed before the c-Abl inhibitors can be used in the neuroclinic to possibly benefit an increasing number of PD patients.
  • de Moura, Yhasmin Mendes; Balzter, Heiko; Galvão, Lênio S.; Dalagnol, Ricardo; Espírito-Santo, Fernando; Santos, Erone G.; Garcia, Mariano; Bispo, Polyanna Da Conceição; Oliveira, Raimundo C.; Shimabukuro, Yosio E. (2020)
    Tropical forests hold significant amounts of carbon and play a critical role on Earth ' s climate system. To date, carbon dynamics over tropical forests have been poorly assessed, especially over vast areas of the tropics that have been affected by some type of disturbance (e.g., selective logging, understory fires, and fragmentation). Understanding the multi-temporal dynamics of carbon stocks over human-modified tropical forests (HMTF) is crucial to close the carbon cycle balance in the tropics. Here, we used multi-temporal and high-spatial resolution airborne LiDAR data to quantify rates of carbon dynamics over a large patch of HMTF in eastern Amazon, Brazil. We described a robust approach to monitor changes in aboveground forest carbon stocks between 2012 and 2018. Our results showed that this particular HMTF lost 0.57 myr(-1) in mean forest canopy height and 1.38 MgCha(-1)yr(-1) of forest carbon between 2012 and 2018. LiDAR-based estimates of Aboveground Carbon Density (ACD) showed progressive loss through the years, from 77.9 MgCha(-1) in 2012 to 53.1 MgCha(-1) in 2018, thus a decrease of 31.8%. Rates of carbon stock changes were negative for all time intervals analyzed, yielding average annual carbon loss rates of -1.34 MgCha(-1)yr(-1). This suggests that this HMTF is acting more as a source of carbon than a sink, having great negative implications for carbon emission scenarios in tropical forests. Although more studies of forest dynamics in HMTFs are necessary to reduce the current remaining uncertainties in the carbon cycle, our results highlight the persistent effects of carbon losses for the study area. HMTFs are likely to expand across the Amazon in the near future. The resultant carbon source conditions, directly associated with disturbances, may be essential when considering climate projections and carbon accounting methods.
  • Bitu, Carolina C.; Kauppila, Joonas H.; Bufalino, Andreia; Nurmenniemi, Sini; Teppo, Susanna; Keinanen, Meeri; Vilen, Suvi-Tuuli; Lehenkari, Petri; Nyberg, Pia; Coletta, Ricardo D.; Salo, Tuula (2013)
  • Pitkänen, S.; Paakinaho, K.; Pihlman, H.; Ahola, N.; Hannula, M.; Asikainen, S.; Manninen, M.; Morelius, M.; Keränen, P.; Hyttinen, J.; Kellomäki, M.; Laitinen-Vapaavuori, O.; Miettinen, S. (2019)
    Most synthetic bone grafts are either hard and brittle ceramics or paste-like materials that differ in applicability from the gold standard autologous bone graft, which restricts their widespread use. Therefore, the aim of the study was to develop an elastic, highly porous and biodegradable beta-tricalciumphosphate/poly(L-lactide-co-epsilon-caprolactone) (beta-TCP/PLCL) composite for bone applications using supercritical CO2 foaming. Ability to support osteogenic differentiation was tested in human adipose stem cell (hASC) culture for 21 d. Biocompatibility was evaluated for 24 weeks in a rabbit femur-defect model. Foamed composites had a high ceramic content (50 wt%) and porosity (65-67 %). After 50 % compression, in an aqueous environment at 37 degrees C, tested samples returned to 95 % of their original height. Hydrolytic degradation of beta-TCP/PLCL composite, during the 24-week follow-up, was very similar to that of porous PLCL scaffold both in vitro and in vivo. Osteogenic differentiation of hASCs was demonstrated by alkaline phosphatase activity analysis, alizarin red staining, soluble collagen analysis, immunocytochemical staining and qRT-PCR. In vitro, hASCs formed a pronounced mineralised collagen matrix. A rabbit femur defect model confirmed biocompatibility of the composite. According to histological Masson-Goldner's trichrome staining and micro-computed tomography, beta-TCP/PLCL composite did not elicit infection, formation of fibrous capsule or cysts. Finally, native bone tissue at 4 weeks was already able to grow on and in the beta-TCP/PLCL composite. The elastic and highly porous beta-TCP/PLCL composite is a promising bone substitute because it is osteoconductive and easy-to-use and mould intraoperatively.
  • Lubbers, Ronnie J. M.; Dilokpimol, Adiphol; Navarro, Jorge; Peng, Mao; Wang, Mei; Lipzen, Anna; Ng, Vivian; Grigoriev, Igor V.; Visser, Jaap; Hildén, Kristiina S.; de Vries, Ronald P. (2019)
    Cinnamic acid is an aromatic compound commonly found in plants and functions as a central intermediate in lignin synthesis. Filamentous fungi are able to degrade cinnamic acid through multiple metabolic pathways. One of the best studied pathways is the non-oxidative decarboxylation of cinnamic acid to styrene. In Aspergillus niger, the enzymes cinnamic acid decarboxylase (CdcA, formally ferulic acid decarboxylase) and the flavin prenyltransferase (PadA) catalyze together the non-oxidative decarboxylation of cinnamic acid and sorbic acid. The corresponding genes, cdcA and padA, are clustered in the genome together with a putative transcription factor previously named sorbic acid decarboxylase regulator (SdrA). While SdrA was predicted to be involved in the regulation of the non-oxidative decarboxylation of cinnamic acid and sorbic acid, this was never functionally analyzed. In this study, A. niger deletion mutants of sdrA, cdcA, and padA were made to further investigate the role of SdrA in cinnamic acid metabolism. Phenotypic analysis revealed that cdcA, sdrA and padA are exclusively involved in the degradation of cinnamic acid and sorbic acid and not required for other related aromatic compounds. Whole genome transcriptome analysis of ΔsdrA grown on different cinnamic acid related compounds, revealed additional target genes, which were also clustered with cdcA, sdrA, and padA in the A. niger genome. Synteny analysis using 30 Aspergillus genomes demonstrated a conserved cinnamic acid decarboxylation gene cluster in most Aspergilli of the Nigri clade. Aspergilli lacking certain genes in the cluster were unable to grow on cinnamic acid, but could still grow on related aromatic compounds, confirming the specific role of these three genes for cinnamic acid metabolism of A. niger.
  • Karjalainen, Olli; Aalto, Juha; Luoto, Miska; Westermann, Sebastian; Romanovsky, Vladimir E.; Nelson, Frederick E.; Etzelmueller, Bernd; Hjort, Jan (2019)
    Ongoing climate change is causing fundamental changes in the Arctic, some of which can be hazardous to nature and human activity. In the context of Earth surface systems, warming climate may lead to rising ground temperatures and thaw of permafrost. This Data Descriptor presents circumpolar permafrost maps and geohazard indices depicting zones of varying potential for development of hazards related to near-surface permafrost degradation, such as ground subsidence. Statistical models were used to predict ground temperature and the thickness of the seasonally thawed (active) layer using geospatial data on environmental conditions at 30 arc-second resolution. These predictions, together with data on factors (ground ice content, soil grain size and slope gradient) affecting permafrost stability, were used to formulate geohazard indices. Using climate-forcing scenarios (Representative Concentration Pathways 2.6, 4.5 and 8.5), permafrost extent and hazard potential were projected for the 2041-2060 and 2061-2080 time periods. The resulting data (seven permafrost and 24 geohazard maps) are relevant to near-future infrastructure risk assessments and for targeting localized geohazard analyses.