TY - JOUR A1 - Höfs, Soraya A1 - Huelague, Deniz A1 - Bennet, Francesca A1 - Carl, Peter A1 - Flemig, Sabine A1 - Schmid, Thomas A1 - Schenk, Jorg A. A1 - Hodoroaba, Vasile-Dan A1 - Schneider, Rudolf J. T1 - Electrochemical immunomagnetic Ochratoxin A sensing BT - steps forward in the application of 3,3’,5,5’-Tetramethylbenzidine in amperometric assays JF - ChemElectroChem N2 - Electrochemical methods offer great promise in meeting the demand for user-friendly on-site devices for monitoring important parameters. The food industry often runs own lab procedures, for example, for mycotoxin analysis, but it is a major goal to simplify analysis, linking analytical methods with smart technologies. Enzyme-linked immunosorbent assays, with photometric detection of 3,3',5,5'-tetramethylbenzidine (TMB), form a good basis for sensitive detection. To provide a straightforward approach for the miniaturization of the detection step, we have studied the pitfalls of the electrochemical TMB detection. By cyclic voltammetry it was found that the TMB electrochemistry is strongly dependent on the pH and the electrode material. A stable electrode response to TMB could be achieved at pH 1 on gold electrodes. We created a smartphone-based, electrochemical, immunomagnetic assay for the detection of ochratoxin A in real samples, providing a solid basis for sensing of further analytes. KW - amperometry KW - cyclic voltammetry KW - immunoassays KW - screen-printed electrodes KW - 3,3′,5,5′-tetramethylbenzidine Y1 - 2021 U6 - https://doi.org/10.1002/celc.202100446 SN - 2196-0216 VL - 8 IS - 13 SP - 2597 EP - 2606 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Razaghi-Moghadam, Zahra A1 - Sokolowska, Ewelina A1 - Sowa, Marcin A. A1 - Skirycz, Aleksandra A1 - Nikoloski, Zoran T1 - Combination of network and molecule structure accurately predicts competitive inhibitory interactions JF - Computational and structural biotechnology journal N2 - Mining of metabolite-protein interaction networks facilitates the identification of design principles underlying the regulation of different cellular processes. However, identification and characterization of the regulatory role that metabolites play in interactions with proteins on a genome-scale level remains a pressing task. Based on availability of high-quality metabolite-protein interaction networks and genome-scale metabolic networks, here we propose a supervised machine learning approach, called CIRI that determines whether or not a metabolite is involved in a competitive inhibitory regulatory interaction with an enzyme. First, we show that CIRI outperforms the naive approach based on a structural similarity threshold for a putative competitive inhibitor and the substrates of a metabolic reaction. We also validate the performance of CIRI on several unseen data sets and databases of metabolite-protein interactions not used in the training, and demonstrate that the classifier can be effectively used to predict competitive inhibitory interactions. Finally, we show that CIRI can be employed to refine predictions about metabolite-protein interactions from a recently proposed PROMIS approach that employs metabolomics and proteomics profiles from size exclusion chromatography in E. coli to predict metaboliteprotein interactions. Altogether, CIRI fills a gap in cataloguing metabolite-protein interactions and can be used in directing future machine learning efforts to categorize the regulatory type of these interactions. KW - Metabolite-protein interactions KW - Genome-scale metabolic models KW - Supervised machine learning Y1 - 2021 U6 - https://doi.org/10.1016/j.csbj.2021.04.012 SN - 2001-0370 VL - 19 SP - 2170 EP - 2178 PB - Research Network of Computational and Structural Biotechnology (RNCSB) CY - Gotenburg ER - TY - JOUR A1 - Habel, Jan Christian A1 - Schmitt, Thomas A1 - Gros, Patrick A1 - Ulrich, Werner T1 - Breakpoints in butterfly decline in Central Europe over the last century JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Recent studies indicated severe decline of insect diversity and abundance across major parts of Central Europe. Theoretical studies showed that the drivers behind biodiversity loss vary considerably over time. However, these scenarios so far have been insufficiently approved by long-term and large-scale data. In this study we analysed the temporal trends of butterflies and Zygaenid moths across the federal state of Salzburg, northern Austria, from 1920 to 2019. Our study area covers a large variety of habitats and altitudes. Various changes of land use and intensification occurred during and shortly before our studied period, with a first wave of habitat destruction starting in the late 19th century, followed by the deterioration of habitat quality since the mid-20th century. We used 59,870 presence-only data of 168 butterfly and burnet moth species. Each of these species was classified according to ecological characteristics. Break point analyses for non-linear temporal trends in the community composition returned two major time windows. These time windows coincide with periods characterized by severe habitat destruction and the deterioration of habitat quality due to agricultural intensification. We found significant reductions of the proportion of species requiring specific habitats since 1920 and until today. We identified additional break points for species requiring high habitat qualities, endangered butterfly species, and sedentary species, particularly after a main break point in the 1960s. Our findings underline that, apart from habitat destruction, the deterioration of habitat quality is a main driver of biodiversity loss in general. Therefore, nature conservation should focus on maintaining the highest possible habitat quality. KW - biodiversity crisis KW - time series KW - species community assembly KW - species richness KW - relative abundance KW - trait assemblages KW - break points KW - multiple drivers Y1 - 2022 U6 - https://doi.org/10.1016/j.scitotenv.2022.158315 SN - 0048-9697 SN - 1879-1026 VL - 851 IS - Part 2 PB - Elsevier Science CY - Amsterdam ER - TY - GEN A1 - Thirumalaikumar, Venkatesh P. A1 - Gorka, Michal A1 - Schulz, Karina A1 - Masclaux-Daubresse, Celine A1 - Sampathkumar, Arun A1 - Skirycz, Aleksandra A1 - Vierstra, Richard D. A1 - Balazadeh, Salma T1 - Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1 T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1343 KW - Arabidopsis thaliana KW - heat stress KW - HSFA2 KW - HSP90.1 KW - NBR1 KW - ROF1 KW - selective autophagy KW - stress memory KW - stress recovery Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-538186 SN - 1866-8372 IS - 1343 SP - 2184 EP - 2199 ER - TY - GEN A1 - Tran, Quan Hong A1 - Bui, Ngoc Hong A1 - Kappel, Christian A1 - Dau, Nga Thi Ngoc A1 - Nguyen, Loan Thi A1 - Tran, Thuy Thi A1 - Khanh, Tran Dang A1 - Trung, Khuat Huu A1 - Lenhard, Michael A1 - Vi, Son Lang T1 - Mapping-by-sequencing via MutMap identifies a mutation in ZmCLE7 underlying fasciation in a newly developed EMS mutant population in an elite tropical maize inbred T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Induced point mutations are important genetic resources for their ability to create hypo- and hypermorphic alleles that are useful for understanding gene functions and breeding. However, such mutant populations have only been developed for a few temperate maize varieties, mainly B73 and W22, yet no tropical maize inbred lines have been mutagenized and made available to the public to date. We developed a novel Ethyl Methanesulfonate (EMS) induced mutation resource in maize comprising 2050 independent M2 mutant families in the elite tropical maize inbred ML10. By phenotypic screening, we showed that this population is of comparable quality with other mutagenized populations in maize. To illustrate the usefulness of this population for gene discovery, we performed rapid mapping-by-sequencing to clone a fasciated-ear mutant and identify a causal promoter deletion in ZmCLE7 (CLE7). Our mapping procedure does not require crossing to an unrelated parent, thus is suitable for mapping subtle traits and ones affected by heterosis. This first EMS population in tropical maize is expected to be very useful for the maize research community. Also, the EMS mutagenesis and rapid mapping-by-sequencing pipeline described here illustrate the power of performing forward genetics in diverse maize germplasms of choice, which can lead to novel gene discovery due to divergent genetic backgrounds. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1401 KW - EMS KW - MutMap KW - mutagenesis KW - CLE7 KW - tropical maize KW - fasciation KW - mapping Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515677 SN - 1866-8372 IS - 3 ER - TY - JOUR A1 - Glaw, Frank A1 - Kohler, Jorn A1 - Hawlitschek, Oliver A1 - Ratsoavina, Fanomezana M. A1 - Rakotoarison, Andolalao A1 - Scherz, Mark D. A1 - Vences, Miguel T1 - Extreme miniaturization of a new amniote vertebrate and insights into the evolution of genital size in chameleons JF - Scientific reports N2 - Evolutionary reduction of adult body size (miniaturization) has profound consequences for organismal biology and is an important subject of evolutionary research. Based on two individuals we describe a new, extremely miniaturized chameleon, which may be the world's smallest reptile species. The male holotype of Brookesia nana sp. nov. has a snout-vent length of 13.5 mm (total length 21.6 mm) and has large, apparently fully developed hemipenes, making it apparently the smallest mature male amniote ever recorded. The female paratype measures 19.2 mm snout-vent length (total length 28.9 mm) and a micro-CT scan revealed developing eggs in the body cavity, likewise indicating sexual maturity. The new chameleon is only known from a degraded montane rainforest in northern Madagascar and might be threatened by extinction. Molecular phylogenetic analyses place it as sister to B. karchei, the largest species in the clade of miniaturized Brookesia species, for which we resurrect Evoluticauda Angel, 1942 as subgenus name. The genetic divergence of B. nana sp. nov. is rather strong (9.914.9% to all other Evoluticauda species in the 16S rRNA gene). A comparative study of genital length in Malagasy chameleons revealed a tendency for the smallest chameleons to have the relatively largest hemipenes, which might be a consequence of a reversed sexual size dimorphism with males substantially smaller than females in the smallest species. The miniaturized males may need larger hemipenes to enable a better mechanical fit with female genitals during copulation. Comprehensive studies of female genitalia are needed to test this hypothesis and to better understand the evolution of genitalia in reptiles. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-020-80955-1 SN - 2045-2322 VL - 11 IS - 1 PB - SPringer Nature CY - Berlin ER - TY - JOUR A1 - Wicaksono, Wisnu Adi A1 - Egamberdieva, Dilfuza A1 - Berg, Christian A1 - Mora, Maximilian A1 - Kusstatscher, Peter A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Function-based rhizosphere assembly along a gradient of desiccation in the former Aral Sea JF - mSystems N2 - The desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches.IMPORTANCE The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. Here, we investigated bacterial and archaeal communities in the rhizosphere of pioneer plants by combining classic molecular methods with amplicon sequencing as well as metagenomics for functional insights. By implementing a desiccation gradient, we observed (i) remarkable differences in the archaeon-bacterium ratio of plant rhizosphere samples, (ii) replacement of archaeal indicator taxa during succession, and (iii) the presence of specific, potentially plant-beneficial biosynthetic pathways in archaea present during the early stages. In addition, our results provide hitherto-undescribed insights into the functional redundancy between plant-associated archaea and bacteria. The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. KW - Aral Sea KW - microbiome KW - desiccation KW - nutrient cycling KW - soil microorganisms KW - revegetation KW - archaea KW - bacteria KW - metagenome Y1 - 2022 U6 - https://doi.org/10.1128/msystems.00739-22 SN - 2379-5077 VL - 7 IS - 6 PB - American Society for Microbiology CY - Washington, DC ER - TY - JOUR A1 - Vyse, Stuart A. A1 - Herzschuh, Ulrike A1 - Pfalz, Gregor A1 - Pestryakova, Lyudmila A. A1 - Diekmann, Bernhard A1 - Nowaczyk, Norbert A1 - Biskaborn, Boris K. T1 - Sediment and carbon accumulation in a glacial lake in Chukotka (Arctic Siberia) during the Late Pleistocene and Holocene BT - combining hydroacoustic profiling and down-core analyses JF - Biogeosciences N2 - Lakes act as important sinks for inorganic and organic sediment components. However, investigations of sedimentary carbon budgets within glacial lakes are currently absent from Arctic Siberia. The aim of this paper is to provide the first reconstruction of accumulation rates, sediment and carbon budgets from a lacustrine sediment core from Lake Rauchuagytgyn, Chukotka (Arctic Siberia). We combined multiple sediment biogeochemical and sedimentological parameters from a radiocarbon-dated 6.5m sediment core with lake basin hydroacoustic data to derive sediment stratigraphy, sediment volumes and infill budgets. Our results distinguished three principal sediment and carbon accumulation regimes that could be identified across all measured environmental proxies including early Marine Isotope Stage 2 (MIS2) (ca. 29-23.4 ka cal BP), mid-MIS2-early MIS1 (ca. 23.4-11.69 ka cal BP) and the Holocene (ca. 11.69-present). Estimated organic carbon accumulation rates (OCARs) were higher within Holocene sediments (average 3.53 gOCm(-2) a(-1)) than Pleistocene sediments (average 1.08 gOCm(-2) a(-1)) and are similar to those calculated for boreal lakes from Quebec and Finland and Lake Baikal but significantly lower than Siberian thermokarst lakes and Alberta glacial lakes. Using a bootstrapping approach, we estimated the total organic carbon pool to be 0.26 +/- 0.02 Mt and a total sediment pool of 25.7 +/- 1.71 Mt within a hydroacoustically derived sediment volume of ca. 32 990 557m(3). The total organic carbon pool is substantially smaller than Alaskan yedoma, thermokarst lake sediments and Alberta glacial lakes but shares similarities with Finnish boreal lakes. Temporal variability in sediment and carbon accumulation dynamics at Lake Rauchuagytgyn is controlled predominantly by palaeoclimate variation that regulates lake ice-cover dynamics and catchment glacial, fluvial and permafrost processes through time. These processes, in turn, affect catchment and within-lake primary productivity as well as catchment soil development. Spatial differences compared to other lake systems at a trans-regional scale likely relate to the high-latitude, mountainous location of Lake Rauchuagytgyn. Y1 - 2021 U6 - https://doi.org/10.5194/bg-18-4791-2021 SN - 1726-4170 SN - 1726-4189 VL - 18 IS - 16 SP - 4791 EP - 4816 PB - Copernicus CY - Katlenburg-Lindau ER - TY - JOUR A1 - Sedaghatmehr, Mastoureh A1 - Stüwe, Benno A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Heat shock factor HSFA2 fine-tunes resetting of thermomemory via plastidic metalloprotease FtsH6 JF - Journal of experimental botany N2 - The transcription factor HSFA2 fine-tunes a balance between prolongation and resetting of thermomemory in Arabidopsis via the regulation of both memory-supporting and memory-resetting genes. Plants 'memorize' stressful events and protect themselves from future, often more severe, stresses. To maximize growth after stress, plants 'reset' or 'forget' memories of stressful situations, which requires an intricate balance between stress memory formation and the degree of forgetfulness. HEAT SHOCK PROTEIN 21 (HSP21) encodes a small heat shock protein in plastids of Arabidopsis thaliana. HSP21 functions as a key component of thermomemory, which requires a sustained elevated level of HSP21 during recovery from heat stress. A heat-induced metalloprotease, filamentation temperature-sensitive H6 (FtsH6), degrades HSP21 to its pre-stress abundance, thereby resetting memory during the recovery phase. The transcription factor heat shock factor A2 (HSFA2) activates downstream genes essential for mounting thermomemory, acting as a positive regulator in the process. Here, using a yeast one-hybrid screen, we identify HSFA2 as an upstream transactivator of the resetting element FtsH6. Constitutive and inducible overexpression of HSFA2 increases expression of FtsH6, whereas it is drastically reduced in the hsfa2 knockout mutant. Chromatin immunoprecipitation reveals in planta binding of HSFA2 to the FtsH6 promoter. Importantly, overexpression of HSFA2 improves thermomemory more profoundly in ftsh6 than wild-type plants. Thus, by activating both memory-supporting and memory-resetting genes, HSFA2 acts as a cellular homeostasis factor during thermomemory. KW - Arabidopsis thaliana KW - FtsH6 KW - heat stress KW - HSFA2 KW - HSP21 KW - thermomemory; KW - thermorecovery Y1 - 2022 U6 - https://doi.org/10.1093/jxb/erac257 SN - 0022-0957 SN - 1460-2431 VL - 73 IS - 18 SP - 6394 EP - 6404 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Baumas, Chloe M. J. A1 - Le Moigne, Frédéric A. C. A1 - Garel, Marc A1 - Bhairy, Nagib A1 - Guasco, Sophie A1 - Riou, Virginie A1 - Armougom, Fabrice A1 - Grossart, Hans-Peter A1 - Tamburini, Christian T1 - Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions JF - The ISME journal : multidisciplinary journal of microbial ecology N2 - The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes. Y1 - 2021 U6 - https://doi.org/10.1038/s41396-020-00880-z SN - 1751-7362 SN - 1751-7370 VL - 15 IS - 6 SP - 1695 EP - 1708 PB - Nature Publishing Group CY - Basingstoke ER -