Browsing by Subject "ENZYME-ACTIVITIES"

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  • Kekkonen, Riina A.; Holma, Reetta; Hatakka, Katja; Suomalainen, Tarja; Poussa, Tuija; Adlercreutz, Herman; Korpela, Riitta (2011)
  • Shapiguzov, Alexey; Vainonen, Julia; Hunter, Kerri Alyssa; Tossavainen, Helena P M; Tiwari, Arjun; Järvi, Sari; Hellman, Maarit Helena; Aarabi, Fayezeh; Alseekh, Saleh; Wybouw, Brecht; Van Der Kelen, Katrien; Nikkanen, Lauri; Krasensky-Wrzaczek, Julia; Sipari, Nina Hannele; Keinänen, Markku; Tyystjaervi, Esa; Rintamäki, Eevi; De Rybel, Bert; Salojärvi, Jarkko Tapani; Van Breusegem, Frank; Fernie, Alisdair R.; Brosche, Mikael Johan; Permi, Perttu Esko Ilari; Aro, Eva-Mari; Wrzaczek, Michael Alois; Kangasjärvi, Jaakko Sakari (2019)
    Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles.
  • Oskolkov, Nikolay; Santel, Malgorzata; Parikh, Hemang M.; Ekstrom, Ola; Camp, Gray J.; Miyamoto-Mikami, Eri; Strom, Kristoffer; Mir, Bilal Ahmad; Kryvokhyzha, Dmytro; Lehtovirta, Mikko; Kobayashi, Hiroyuki; Kakigi, Ryo; Naito, Hisashi; Eriksson, Karl-Fredrik; Nystedt, Bjorn; Fuku, Noriyuki; Treutlein, Barbara; Paabo, Svante; Hansson, Ola (2022)
    Background: Skeletal muscle fiber type distribution has implications for human health, muscle function, and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these studies. Here, we present a method based on muscle tissue RNA sequencing data (totRNAseq) to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for a larger number of individuals to be tested. Methods: By using single-nuclei RNA sequencing (snRNAseq) data as a reference, cluster expression signatures were produced by averaging gene expression of cluster gene markers and then applying these to totRNAseq data and inferring muscle fiber nuclei type via linear matrix decomposition. This estimate was then compared with fiber type distribution measured by ATPase staining or myosin heavy chain protein isoform distribution of 62 muscle samples in two independent cohorts (n = 39 and 22). Results: The correlation between the sequencing-based method and the other two were r(ATpas) = 0.44 [0.13-0.67], [95% CI], and r(myosin) = 0.83 [0.61-0.93], with p = 5.70 x 10(-3) and 2.00 x 10(-6), respectively. The deconvolution inference of fiber type composition was accurate even for very low totRNAseq sequencing depths, i.e., down to an average of similar to 10,000 paired-end reads. Conclusions: This new method ( consequently allows for measurement of fiber type distribution of a larger number of samples using totRNAseq in a cost and labor-efficient way. It is now feasible to study the association between fiber type distribution and e.g. health outcomes in large well-powered studies.
  • Glippa, Olivier; Engström-Öst, Jonna; Kanerva, Mirella; Rein, Anni; Vuori, Kristiina (2018)
    On a daily basis, planktonic organisms migrate vertically and thus experience widely varying conditions in their physico-chemical environment. In the Gulf of Finland, these changes are larger than values predicted by climate change scenarios predicted for the next century (up to 0.5 units in pH and 5 degrees C in temperature). In this work, we are interested in how temporal variations in physico-chemical characteristics of the water column on a daily and weekly scale influence oxidative stress level and antioxidant responses in the planktonic copepod of the genus Acartia. Responses were determined from samples collected during a two-week field survey in the western Gulf of Finland, Baltic Sea. Our results showed that GST (Glutathione-S-transferase) enzyme activity increased in the surface waters between Weeks I and II, indicating antioxidant defense mechanism activation. This is most likely due to elevating temperature, pH, and dissolved oxygen observed between these two weeks. During Week II also GSSG (oxidized glutathione) was detected, indicating that copepods responded to stressor(s) in the environment. Our results suggest that Acartia copepods seem fairly tolerant to weekly fluctuations in environmental conditions in coastal and estuarine areas, in terms of antioxidant defense and oxidative stress. This could be directly connected to a very efficient glutathione cycling system acting as antioxidant defense system for neutralizing ROS and avoiding elevated levels of LPX.
  • Adamczyk, Bartosz; Adamczyk, Sylwia; Smolander, Aino; Kitunen, Veikko; Simon, Judy (2018)
    Processes underlying soil organic matter (SOM) transformations are meeting growing interest as SOM contains more carbon (C) than global vegetation and the atmosphere combined. Therefore, SOM is a crucial element of the C cycle, especially in ecosystems rich in organic matter, such as boreal forests. However, climate change may shift the fate of this SOM from C sink into C source, accelerating global warming. These processes require a better understanding of the involved mechanisms driving both the C cycle and the interlinked nitrogen (N) cycle. SOM transformations are balanced by a network of interactions between biological, chemical and physical factors. In this review, we discuss the findings of the most recent studies to the current state of knowledge about the main drivers in SOM transformations. We focus on plant-derived secondary metabolites, as their biochemical traits, especially interactions with soil microbial communities, organic N compounds and enzymes make them potential regulators of SOM decomposition. However, these regulatory abilities of plant-derived compounds are not fully explored.
  • Lv, Xia; Xia, Yangliu; Finel, Moshe; Wu, Jingjing; Ge, Guangbo; Yang, Ling (2019)
    Uridine-diphosphate glucuronosyltransferase 1A1 (UGT1A1) is an important conjugative enzyme in mammals that is responsible for the conjugation and detoxification of both endogenous and xenobiotic compounds. Strong inhibition of UGT1A1 may trigger adverse drug/herb-drug interactions, or result in metabolic disorders of endobiotic metabolism. Therefore, both the US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) have recommended assaying the inhibitory potential of drugs under development on the human UGT1A1 prior to approval. This review focuses on the significance, progress and challenges in discovery and characterization of UGT1A1 inhibitors. Recent advances in the development of UGT1A1 probes and their application for screening UGT1A1 inhibitors are summarized and discussed in this review for the first time. Furthermore, a long list of UGT1A1 inhibitors, including information on their inhibition potency, inhibition mode, and affinity, has been prepared and analyzed. Challenges and future directions in this field are highlighted in the final section. The information and knowledge that are presented in this review provide guidance for rational use of drugs/herbs in order to avoid the occurrence of adverse effects via UGT1A1 inhibition, as well as presenting methods for rapid screening and characterization of UGT1A1 inhibitors and for facilitating investigations on UGT1A1-ligand interactions. (C) 2019 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V.
  • Urbanova, Zuzana; Straková, Petra; Kastovska, Eva (2018)
    Various peatland restoration strategies developed during the last two decades have aimed to stop degradation and bring back the original hydrology, biodiversity and other peatland functions. This study evaluated progress 6-15 years after rewetting in vegetation development, physicochemical properties of peat, soil organic matter (SOM) quality and microbial activity in previously long-term drained bogs and spruce swamp forests (SSF) in comparison with pristine and long-term drained sites in the Bohemian Forest, Czech Republic. Long-term drainage led to overall ecosystem degradation, indicated by a change in vegetation composition, reduced decomposability of peat, with high content of recalcitrant compounds and decreased pH, and reduced soil microbial biomass and activity. The degradation was more pronounced in SSF, while bogs seemed to be relatively resistant to environmental changes caused by drainage. Post-rewetting progress has occurred with regard to vegetation composition, peat pH, microbial biomass and potential anaerobic CO2 and CH4 production, all of which tending towards characteristics of the pristine sites. However, overall SOM quality has not yet responded significantly, indicating that some peat properties and functions, such as C accumulation, need much longer periods of time to return to the original level.
  • Zhou, Xuan; Sun, Hui; Pumpanen, Jukka; Sietiö, Outi-Maaria; Heinonsalo, Jussi; Köster, Kajar; Berninger, Frank (2019)
    Wildfires thaw near-surface permafrost soils in the boreal forest, making previously frozen organic matter available to microbes. The short-term microbial stoichiometric dynamics following a wildfire are critical to understanding the soil element variations in thawing permafrost. Thus, we selected a boreal wildfire chronosequence in a region of continuous permafrost, where the last wildfire occurred 3, 25, 46, and > 100 years ago (set as the control) to explore the impact of wildfire on the soil chemistry, soil microbial stoichiometry, and the fungal-to-bacterial gene ratio (F:B ratio). We observed the microbial biomass C:N:P ratio remained constant in distinct age classes indicating that microbes are homeostatic in relation to stoichiometric ratios. The microbial C:N ratios were independent of the shifts in the fungal-to-bacterial ratio when C:N exceeded 12. Wildfire-induced reduction in vegetation biomass positively affected the fungal, but not the bacterial, gene copy number. The decline in microbial biomass C, N, and P following a fire, primarily resulted from a lack of soil available C and nutrients. Wildfire affected neither the microbial biomass nor the F:B ratios at a soil depth of 30 cm. We conclude that microbial stoichiometry does not always respond to changes in the fungal-to-bacterial ratio and that wildfire-induced permafrost thawing does not accelerate microbial respiration.
  • Pontes, Maria Victoria Aguilar; Patyshakuliyeva, Aleksandrina; Post, Harm; Jurak, Edita; Hilden, Kristiina; Altelaar, Maarten; Heck, Albert; Kabel, Mirjam A.; de Vries, Ronald P.; Mäkelä, Miia R. (2018)
    The white button mushroom Agaricus bisporus is one of the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. bisporus strains for their potential to convert the components that are poorly utilized by the commercial strain A15. We therefore focused our analysis on the stages where the fungus is producing fruiting bodies. Growth profiling was used to identify A. bisporus strains with different abilities to use plant biomass derived polysaccharides, as well as to transport and metabolize the corresponding monomeric sugars. Six wild-type isolates with diverse growth profiles were compared for mushroom production to A15 strain in semi-commercial cultivation conditions. Transcriptome and proteome analyses of the three most interesting wild-type strains and A15 indicated that the unrelated A. bisporus strains degrade and convert plant biomass polymers in a highly similar manner. This was also supported by the chemical content of the compost during the mushroom production process. Our study therefore reveals a highly conserved physiology for unrelated strains of this species during growth in compost.