@article{HoefsHuelagueBennetetal.2021, author = {H{\"o}fs, Soraya and Huelague, Deniz and Bennet, Francesca and Carl, Peter and Flemig, Sabine and Schmid, Thomas and Schenk, Jorg A. and Hodoroaba, Vasile-Dan and Schneider, Rudolf J.}, title = {Electrochemical immunomagnetic Ochratoxin A sensing}, series = {ChemElectroChem}, volume = {8}, journal = {ChemElectroChem}, number = {13}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {2196-0216}, doi = {10.1002/celc.202100446}, pages = {2597 -- 2606}, year = {2021}, abstract = {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.}, language = {en} } @article{RazaghiMoghadamSokolowskaSowaetal.2021, author = {Razaghi-Moghadam, Zahra and Sokolowska, Ewelina and Sowa, Marcin A. and Skirycz, Aleksandra and Nikoloski, Zoran}, title = {Combination of network and molecule structure accurately predicts competitive inhibitory interactions}, series = {Computational and structural biotechnology journal}, volume = {19}, journal = {Computational and structural biotechnology journal}, publisher = {Research Network of Computational and Structural Biotechnology (RNCSB)}, address = {Gotenburg}, issn = {2001-0370}, doi = {10.1016/j.csbj.2021.04.012}, pages = {2170 -- 2178}, year = {2021}, abstract = {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.}, language = {en} } @article{HabelSchmittGrosetal.2022, author = {Habel, Jan Christian and Schmitt, Thomas and Gros, Patrick and Ulrich, Werner}, title = {Breakpoints in butterfly decline in Central Europe over the last century}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {851}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, number = {Part 2}, publisher = {Elsevier Science}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2022.158315}, pages = {9}, year = {2022}, abstract = {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.}, language = {en} } @article{GlawKohlerHawlitscheketal.2021, author = {Glaw, Frank and Kohler, Jorn and Hawlitschek, Oliver and Ratsoavina, Fanomezana M. and Rakotoarison, Andolalao and Scherz, Mark D. and Vences, Miguel}, title = {Extreme miniaturization of a new amniote vertebrate and insights into the evolution of genital size in chameleons}, series = {Scientific reports}, volume = {11}, journal = {Scientific reports}, number = {1}, publisher = {SPringer Nature}, address = {Berlin}, issn = {2045-2322}, doi = {10.1038/s41598-020-80955-1}, pages = {14}, year = {2021}, abstract = {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.}, language = {en} } @article{WicaksonoEgamberdievaBergetal.2022, author = {Wicaksono, Wisnu Adi and Egamberdieva, Dilfuza and Berg, Christian and Mora, Maximilian and Kusstatscher, Peter and Cernava, Tomislav and Berg, Gabriele}, title = {Function-based rhizosphere assembly along a gradient of desiccation in the former Aral Sea}, series = {mSystems}, volume = {7}, journal = {mSystems}, number = {6}, publisher = {American Society for Microbiology}, address = {Washington, DC}, issn = {2379-5077}, doi = {10.1128/msystems.00739-22}, pages = {16}, year = {2022}, abstract = {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.}, language = {en} } @article{VyseHerzschuhPfalzetal.2021, author = {Vyse, Stuart A. and Herzschuh, Ulrike and Pfalz, Gregor and Pestryakova, Lyudmila A. and Diekmann, Bernhard and Nowaczyk, Norbert and Biskaborn, Boris K.}, title = {Sediment and carbon accumulation in a glacial lake in Chukotka (Arctic Siberia) during the Late Pleistocene and Holocene}, series = {Biogeosciences}, volume = {18}, journal = {Biogeosciences}, number = {16}, publisher = {Copernicus}, address = {Katlenburg-Lindau}, issn = {1726-4170}, doi = {10.5194/bg-18-4791-2021}, pages = {4791 -- 4816}, year = {2021}, abstract = {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.}, language = {en} } @article{SedaghatmehrStueweMuellerRoeberetal.2022, author = {Sedaghatmehr, Mastoureh and St{\"u}we, Benno and M{\"u}ller-R{\"o}ber, Bernd and Balazadeh, Salma}, title = {Heat shock factor HSFA2 fine-tunes resetting of thermomemory via plastidic metalloprotease FtsH6}, series = {Journal of experimental botany}, volume = {73}, journal = {Journal of experimental botany}, number = {18}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/erac257}, pages = {6394 -- 6404}, year = {2022}, abstract = {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.}, language = {en} } @article{BaumasLeMoigneGareletal.2021, author = {Baumas, Chloe M. J. and Le Moigne, Fr{\´e}d{\´e}ric A. C. and Garel, Marc and Bhairy, Nagib and Guasco, Sophie and Riou, Virginie and Armougom, Fabrice and Grossart, Hans-Peter and Tamburini, Christian}, title = {Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions}, series = {The ISME journal : multidisciplinary journal of microbial ecology}, volume = {15}, journal = {The ISME journal : multidisciplinary journal of microbial ecology}, number = {6}, publisher = {Nature Publishing Group}, address = {Basingstoke}, issn = {1751-7362}, doi = {10.1038/s41396-020-00880-z}, pages = {1695 -- 1708}, year = {2021}, abstract = {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.}, language = {en} } @article{HirschbergBauerKamhiehMilzetal.2022, author = {Hirschberg, Stefan and Bauer, Hannes and Kamhieh-Milz, Julian and Ringel, Frauke and Harms, Christoph and Eddin, Omar Kamal and Pruss, Axel and Hanack, Katja and Schulze-Forster, Kai}, title = {SARS-CoV-2 virus-like particles (VLPs) specifically detect humoral immune reactions in an ELISA-Based Platform}, series = {Antibodies}, volume = {11}, journal = {Antibodies}, number = {4}, publisher = {MDPI}, address = {Basel}, issn = {2073-4468}, doi = {10.3390/antib11040076}, pages = {10}, year = {2022}, abstract = {A key in controlling the SARS-CoV-2 pandemic is the assessment of the immune status of the population. We explored the utility of SARS-CoV-2 virus-like particles (VLPs) as antigens to detect specific humoral immune reactions in an enzyme-linked immunosorbent assay (ELISA). For this purpose, SARS-CoV-2 VLPs were produced from an engineered cell line and characterized by Western blot, ELISA, and nanoparticle tracking analysis. Subsequently, we collected 42 serum samples from before the pandemic (2014), 89 samples from healthy subjects, and 38 samples from vaccinated subjects. Seventeen samples were collected less than three weeks after infection, and forty-four samples more than three weeks after infection. All serum samples were characterized for their reactivity with VLPs and the SARS-CoV-2 N- and S-protein. Finally, we compared the performance of the VLP-based ELISA with a certified in vitro diagnostic device (IVD). In the applied set of samples, we determined a sensitivity of 95.5\% and a specificity of 100\% for the certified IVD. There were seven samples with an uncertain outcome. Our VLP-ELISA demonstrated a superior performance, with a sensitivity of 97.5\%, a specificity of 100\%, and only three uncertain outcomes. This result warrants further research to develop a certified IVD based on SARS-CoV-2 VLPs as an antigen.}, language = {en} } @misc{VicenteAnnunziataSantelia2022, author = {Vicente, Ruben and Annunziata, Maria Grazia and Santelia, Diana}, title = {Editorial: Insights and regulation of plant carbon metabolism}, series = {Frontiers in plant science}, volume = {13}, journal = {Frontiers in plant science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2022.1011224}, pages = {3}, year = {2022}, language = {en} }