@article{DreymannWuenscheSabrowskietal.2022, author = {Dreymann, Nico and Wuensche, Julia and Sabrowski, Wiebke and Moeller, Anja and Czepluch, Denise and Vu Van, Dana and F{\"u}ssel, Susanne and Menger, Marcus M.}, title = {Inhibition of Human Urokinase-Type Plasminogen Activator (uPA) Enzyme Activity and Receptor Binding by DNA Aptamers as Potential Therapeutics through Binding to the Different Forms of uPA}, series = {International journal of molecular sciences}, volume = {23}, journal = {International journal of molecular sciences}, number = {9}, publisher = {MDPI}, address = {Basel}, issn = {1661-6596}, doi = {10.3390/ijms23094890}, pages = {22}, year = {2022}, abstract = {Urokinase-type plasminogen activator is widely discussed as a marker for cancer prognosis and diagnosis and as a target for cancer therapies. Together with its receptor, uPA plays an important role in tumorigenesis, tumor progression and metastasis. In the present study, systematic evolution of ligands by exponential enrichment (SELEX) was used to select single-stranded DNA aptamers targeting different forms of human uPA. Selected aptamers allowed the distinction between HMW-uPA and LMW-uPA, and therefore, presumably, have different binding regions. Here, uPAapt-02-FR showed highly affine binding with a K-D of 0.7 nM for HMW-uPA and 21 nM for LMW-uPA and was also able to bind to pro-uPA with a K-D of 14 nM. Furthermore, no cross-reactivity to mouse uPA or tissue-type plasminogen activator (tPA) was measured, demonstrating high specificity. Suppression of the catalytic activity of uPA and inhibition of uPAR-binding could be demonstrated through binding with different aptamers and several of their truncated variants. Since RNA aptamers are already known to inhibit uPA-uPAR binding and other pathological functions of the uPA system, these aptamers represent a novel, promising tool not only for detection of uPA but also for interfering with the pathological functions of the uPA system by additionally inhibiting uPA activity.}, language = {en} } @article{ZhangHuYangetal.2022, author = {Zhang, Kai and Hu, Jiege and Yang, Shuai and Xu, Wei and Wang, Zhichao and Zhuang, Peiwen and Grossart, Hans-Peter and Luo, Zhuhua}, title = {Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1}, series = {Journal of hazardous materials}, volume = {437}, journal = {Journal of hazardous materials}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3894}, doi = {10.1016/j.jhazmat.2022.129406}, pages = {10}, year = {2022}, abstract = {Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80\% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.}, language = {en} } @article{RaffeinerUestuenGuerraetal.2022, author = {Raffeiner, Margot and {\"U}st{\"u}n, Suayib and Guerra, Tiziana and Spinti, Daniela and Fitzner, Maria and Sonnewald, Sophia and Baldermann, Susanne and B{\"o}rnke, Frederik}, title = {The Xanthomonas type-III effector XopS stabilizes CaWRKY40a to regulate defense responses and stomatal immunity in pepper (Capsicum annuum)}, series = {The plant cell}, volume = {34}, journal = {The plant cell}, number = {5}, publisher = {Oxford Univ. Press}, address = {Cary}, issn = {1040-4651}, doi = {10.1093/plcell/koac032}, pages = {1684 -- 1708}, year = {2022}, abstract = {As a critical part of plant immunity, cells that are attacked by pathogens undergo rapid transcriptional reprogramming to minimize virulence. Many bacterial phytopathogens use type III effector (T3E) proteins to interfere with plant defense responses, including this transcriptional reprogramming. Here, we show that Xanthomonas outer protein S (XopS), a T3E of Xanthomonas campestris pv. vesicatoria (Xcv), interacts with and inhibits proteasomal degradation of WRKY40, a transcriptional regulator of defense gene expression. Virus-induced gene silencing of WRKY40 in pepper (Capsicum annuum) enhanced plant tolerance to Xcv infection, indicating that WRKY40 represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets, which include salicylic acid-responsive genes and the jasmonic acid signaling repressor JAZ8. Xcv bacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery by Xcv, as well as ectopic expression of XopS in Arabidopsis thaliana or Nicotiana benthamiana, prevented stomatal closure in response to bacteria and biotic elicitors. Silencing WRKY40 in pepper or N. benthamiana abolished XopS's ability to prevent stomatal closure. This suggests that XopS interferes with both preinvasion and apoplastic defense by manipulating WRKY40 stability and downstream gene expression, eventually altering phytohormone crosstalk to promote pathogen proliferation.}, language = {en} } @article{HanniganNendelKrull2022, author = {Hannigan, Sara and Nendel, Claas and Krull, Marcos}, title = {Effects of temperature on the movement and feeding behaviour of the large lupine beetle, Sitona gressorius}, series = {Journal of pest science}, journal = {Journal of pest science}, publisher = {Springer}, address = {Heidelberg}, issn = {1612-4758}, doi = {10.1007/s10340-022-01510-7}, pages = {389 -- 402}, year = {2022}, abstract = {Even though the effects of insect pests on global agricultural productivity are well recognised, little is known about movement and dispersal of many species, especially in the context of global warming. This work evaluates how temperature and light conditions affect different movement metrics and the feeding rate of the large lupine beetle, an agricultural pest responsible for widespread damage in leguminous crops. By using video recordings, the movement of 384 beetles was digitally analysed under six different temperatures and light conditions in the laboratory. Bayesian linear mixed-effect models were used to analyse the data. Furthermore, the effects of temperature on the daily diffusion coefficient of beetles were estimated by using hidden Markov models and random walk simulations. Results of this work show that temperature, light conditions, and beetles' weight were the main factors affecting the flight probability, displacement, time being active and the speed of beetles. Significant variations were also observed in all evaluated metrics. On average, beetles exposed to light conditions and higher temperatures had higher mean speed and flight probability. However, beetles tended to stay more active at higher temperatures and less active at intermediate temperatures, around 20 degrees C. Therefore, both the diffusion coefficient and displacement of beetles were lower at intermediate temperatures. These results show that the movement behaviour and feeding rates of beetles can present different relationships in the function of temperature. It also shows that using a single diffusion coefficient for insects in spatially explicit models may lead to over- or underestimation of pest spread.}, language = {en} } @article{HilgersHartmannPfaenderetal.2022, author = {Hilgers, Leon and Hartmann, Stefanie and Pfaender, Jobst and Lentge-Maass, Nora and Marwoto, Ristiyanti M. and von Rintelen, Thomas and Hofreiter, Michael}, title = {Evolutionary divergence and radula diversification in two ecomorphs from an adaptive radiation of freshwater snails}, series = {Genes}, volume = {13}, journal = {Genes}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes13061029}, pages = {16}, year = {2022}, abstract = {(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin's finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.}, language = {en} } @phdthesis{Siebler2024, author = {Siebler, Lara}, title = {Identifying novel regulators of heat stress memory in Arabidopsis thaliana}, doi = {10.25932/publishup-63447}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-634477}, school = {Universit{\"a}t Potsdam}, pages = {135}, year = {2024}, abstract = {Heat stress (HS) is a major abiotic stress that negatively affects plant growth and productivity. However, plants have developed various adaptive mechanisms to cope with HS, including the acquisition and maintenance of thermotolerance, which allows them to respond more effectively to subsequent stress episodes. HS memory includes type II transcriptional memory which is characterized by enhanced re-induction of a subset of HS memory genes upon recurrent HS. In this study, new regulators of HS memory in A. thaliana were identified through the characterization of rein mutants. The rein1 mutant carries a premature stop in CYCLIN-DEPENDENT-KINASE 8 (CDK8) which is part of the cyclin kinase module of the Mediator complex. Rein1 seedlings show impaired type II transcriptional memory in multiple heat-responsive genes upon re-exposure to HS. Additionally, the mutants exhibit a significant deficiency in HS memory at the physiological level. Interaction studies conducted in this work indicate that CDK8 associates with the memory HEAT SHOCK FACTORs HSAF2 and HSFA3. The results suggest that CDK8 plays a crucial role in HS memory in plants together with other memory HSFs, which may be potential targets of the CDK8 kinase function. Understanding the role and interaction network of the Mediator complex during HS-induced transcriptional memory will be an exciting aspect of future HS memory research. The second characterized mutant, rein2, was selected based on its strongly impaired pAPX2::LUC re-induction phenotype. In gene expression analysis, the mutant revealed additional defects in the initial induction of HS memory genes. Along with this observation, basal thermotolerance was impaired similarly as HS memory at the physiological level in rein2. Sequencing of backcrossed bulk segregants with subsequent fine mapping narrowed the location of REIN2 to a 1 Mb region on chromosome 1. This interval contains the At1g65440 gene, which encodes the histone chaperone SPT6L. SPT6L interacts with chromatin remodelers and bridges them to the transcription machinery to regulate nucleosome and Pol II occupancy around the transcriptional start site. The EMS-induced missense mutation in SPT6L may cause altered HS-induced gene expression in rein2, possibly triggered by changes in the chromatin environment resulting from altered histone chaperone function. Expanding research on screen-derived factors that modify type II transcriptional memory has the potential to enhance our understanding of HS memory in plants. Discovering connections between previously identified memory factors will help to elucidate the underlying network of HS memory. This knowledge can initiate new approaches to improve heat resilience in crops.}, language = {en} } @misc{HermanussenSchefflerPulunganetal.2020, author = {Hermanussen, Michael and Scheffler, Christiane and Pulungan, Aman B. and Batubara, Jose R. L. and Julia, Madarina and Bogin, Barry}, title = {Response to the correspondence referring to our article "Stunting is not a synonym of malnutrition" (2018EJCN0997RR) by Conny Tanjung, Titis Prawitasari, Damayanti Rusli Sjarif}, series = {European journal of clinical nutrition}, volume = {74}, journal = {European journal of clinical nutrition}, number = {3}, publisher = {Nature Publ. Group}, address = {New York, NY}, issn = {0954-3007}, doi = {10.1038/s41430-020-0571-1}, pages = {529 -- 531}, year = {2020}, language = {en} } @article{PerkinsSantosRoseetal.2022, author = {Perkins, Anita K. and Santos, Isaac R. and Rose, Andrew L. and Schulz, Kai G. and Grossart, Hans-Peter and Eyre, Bradley D. and Kelaher, Brendan P. and Oakes, Joanne M.}, title = {Production of dissolved carbon and alkalinity during macroalgal wrack degradation on beaches}, series = {Biogeochemistry}, volume = {160}, journal = {Biogeochemistry}, number = {2}, publisher = {Springer}, address = {Dordrecht}, issn = {0168-2563}, doi = {10.1007/s10533-022-00946-4}, pages = {159 -- 175}, year = {2022}, abstract = {Marine macroalgae are a key primary producer in coastal ecosystems, but are often overlooked in blue carbon inventories. Large quantities of macroalgal detritus deposit on beaches, but the fate of wrack carbon (C) is little understood. If most of the wrack carbon is respired back to CO2, there would be no net carbon sequestration. However, if most of the wrack carbon is converted to bicarbonate (alkalinity) or refractory DOC, wrack deposition would represent net carbon sequestration if at least part of the metabolic products (e.g., reduced Fe and S) are permanently removed (i.e., long-term burial) and the DOC is not remineralised. To investigate the release of macroalgal C via porewater and its potential to contribute to C sequestration (blue carbon), we monitored the degradation of Ecklonia radiata in flow-through mesocosms simulating tidal flushing on sandy beaches. Over 60 days, 81\% of added E. radiata organic matter (OM) decomposed. Per 1 mol of detritus C, the degradation produced 0.48 +/- 0.34 mol C of dissolved organic carbon (DOC) (59\%) and 0.25 +/- 0.07 mol C of dissolved inorganic carbon (DIC) (31\%) in porewater, and a small amount of CO2 (0.3 +/- 0.0 mol C; ca. 3\%) which was emitted to the atmosphere. A significant amount of carbonate alkalinity was found in porewater, equating to 33\% (0.27 +/- 0.05 mol C) of the total degraded C. The degradation occurred in two phases. In the first phase (days 0-3), 27\% of the OM degraded, releasing highly reactive DOC. In the second phase (days 4-60), the labile DOC was converted to DIC. The mechanisms underlying E. radiata degradation were sulphate reduction and ammonification. It is likely that the carbonate alkalinity was primarily produced through sulphate reduction. The formation of carbonate alkalinity and semi-labile or refractory DOC from beach wrack has the potential to play an overlooked role in coastal carbon cycling and contribute to marine carbon sequestration.}, language = {en} } @article{TeraoGarattiniRomaoetal.2020, author = {Terao, Mineko and Garattini, Enrico and Rom{\~a}o, Maria Jo{\~a}o and Leimk{\"u}hler, Silke}, title = {Evolution, expression, and substrate specificities of aldehyde oxidase enzymes in eukaryotes}, series = {The journal of biological chemistry}, volume = {295}, journal = {The journal of biological chemistry}, number = {16}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Rockville}, issn = {0021-9258}, doi = {10.1074/jbc.REV119.007741}, pages = {5377 -- 5389}, year = {2020}, abstract = {Aldehyde oxidases (AOXs) are a small group of enzymes belonging to the larger family of molybdo-flavoenzymes, along with the well-characterized xanthine oxidoreductase. The two major types of reactions that are catalyzed by AOXs are the hydroxylation of heterocycles and the oxidation of aldehydes to their corresponding carboxylic acids. Different animal species have different complements of AOX genes. The two extremes are represented in humans and rodents; whereas the human genome contains a single active gene (AOX1), those of rodents, such as mice, are endowed with four genes (Aox1-4), clustering on the same chromosome, each encoding a functionally distinct AOX enzyme. It still remains enigmatic why some species have numerous AOX enzymes, whereas others harbor only one functional enzyme. At present, little is known about the physiological relevance of AOX enzymes in humans and their additional forms in other mammals. These enzymes are expressed in the liver and play an important role in the metabolisms of drugs and other xenobiotics. In this review, we discuss the expression, tissue-specific roles, and substrate specificities of the different mammalian AOX enzymes and highlight insights into their physiological roles.}, language = {en} } @article{KunstmannEngstroemWehleetal.2020, author = {Kunstmann, Ruth Sonja and Engstr{\"o}m, Olof and Wehle, Marko and Widmalm, G{\"o}ran and Santer, Mark and Barbirz, Stefanie}, title = {Increasing the affinity of an O-Antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein}, series = {Chemistry - A European Journal}, volume = {26}, journal = {Chemistry - A European Journal}, number = {32}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0947-6539}, doi = {10.1002/chem.202000495}, pages = {7263 -- 7273}, year = {2020}, abstract = {Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D H-1,H-1-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.}, language = {en} }