@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{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{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{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{BocediPalmerMalchowetal.2021, author = {Bocedi, Greta and Palmer, Stephen C. F. and Malchow, Anne-Kathleen and Zurell, Damaris and Watts, Kevin and Travis, Justin M. J.}, title = {RangeShifter 2.0}, series = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos}, volume = {44}, journal = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos}, number = {10}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {0906-7590}, doi = {10.1111/ecog.05687}, pages = {1453 -- 1462}, year = {2021}, abstract = {Process-based models are becoming increasingly used tools for understanding how species are likely to respond to environmental changes and to potential management options. RangeShifter is one such modelling platform, which has been used to address a range of questions including identifying effective reintroduction strategies, understanding patterns of range expansion and assessing population viability of species across complex landscapes. Here we introduce a new version, RangeShifter 2.0, which incorporates important new functionality. It is now possible to simulate dynamics over user-specified, temporally changing landscapes. Additionally, we integrated a new genetic module, notably introducing an explicit genetic modelling architecture, which allows for simulation of neutral and adaptive genetic processes. Furthermore, emigration, transfer and settlement traits can now all evolve, allowing for sophisticated simulation of the evolution of dispersal. We illustrate the potential application of RangeShifter 2.0's new functionality by two examples. The first illustrates the range expansion of a virtual species across a dynamically changing UK landscape. The second demonstrates how the software can be used to explore the concept of evolving connectivity in response to land-use modification, by examining how movement rules come under selection over landscapes of different structure and composition. RangeShifter 2.0 is built using object-oriented C++ providing computationally efficient simulation of complex individual-based, eco-evolutionary models. The code has been redeveloped to enable use across operating systems, including on high performance computing clusters, and the Windows graphical user interface has been enhanced. RangeShifter 2.0 will facilitate the development of in-silico assessments of how species will respond to environmental changes and to potential management options for conserving or controlling them. By making the code available open source, we hope to inspire further collaborations and extensions by the ecological community.}, language = {en} } @article{FernerLinstaedterRogassetal.2021, author = {Ferner, Jessica and Linst{\"a}dter, Anja and Rogass, Christian and S{\"u}dekum, Karl-Heinz and Schmidtlein, Sebastian}, title = {Towards forage resource monitoring in subtropical savanna grasslands}, series = {European journal of remote sensing}, volume = {54}, journal = {European journal of remote sensing}, number = {1}, publisher = {geoLAB, Laboratory of Geomatics}, address = {Florence}, issn = {2279-7254}, doi = {10.1080/22797254.2021.1934556}, pages = {364 -- 384}, year = {2021}, abstract = {Forage supply of savanna grasslands plays a crucial role for local food security and consequently, a reliable monitoring system could help to better manage vital forage resources. To help installing such a monitoring system, we investigated whether in-situ hyperspectral data could be resampled to match the spectral resolution of multi- and hyperspectral satellites; if the type of sensor affected model transfer; and if spatio-temporal patterns of forage characteristics could be related to environmental drivers. We established models for forage quantity (green biomass) and five forage quality proxies (metabolisable energy, acid/neutral detergent fibre, ash, phosphorus). Hyperspectral resolution of the Hyperion satellite mostly resulted in higher accuracies (i.e. higher R-2, lower RMSE). When applied to satellite data, though, the greater quality of the multispectral Sentinel-2 satellite data leads to more realistic forage maps. By analysing a three-year time series, we found plant phenology and cumulated precipitation to be the most important environmental drivers of forage supply. We conclude that none of the investigated satellites provide optimal conditions for monitoring purposes. Future hyperspectral satellite missions like EnMAP, combining the high information level of Hyperion with the good data quality and resolution of Sentinel-2, will provide the prerequisites for installing a regular monitoring service.}, language = {en} } @article{YangLiebnerSvenningetal.2021, author = {Yang, Sizhong and Liebner, Susanne and Svenning, Mette Marianne and Tveit, Alexander T{\o}sdal}, title = {Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming}, series = {Molecular ecology}, volume = {30}, journal = {Molecular ecology}, number = {20}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {0962-1083}, doi = {10.1111/mec.16118}, pages = {5094 -- 5104}, year = {2021}, abstract = {Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507-E2516). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1-30 degrees C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomic-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures.}, language = {en} } @article{EgliMehrabiSeppelt2021, author = {Egli, Lukas and Mehrabi, Zia and Seppelt, Ralf}, title = {More farms, less specialized landscapes, and higher crop diversity stabilize food supplies}, series = {Environmental research letters}, volume = {16}, journal = {Environmental research letters}, number = {5}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1748-9326}, doi = {10.1088/1748-9326/abf529}, pages = {10}, year = {2021}, abstract = {Theoretical and empirical studies show increased diversity in crops, supply chains, and markets helps stabilize food systems. At the same time global commodity markets and industrial agriculture have driven homogenization of local and regional production systems, and consolidated power in fewer larger specialized farms and distributers. This is a global challenge, with no obvious global solutions. An important question therefore, is how individual countries can build their own resilience through maintaining or increasing diversity within their borders. Here we show, using farm level data from Germany, that spreading production risk by growing the same crops across different farms carries stabilizing benefits by allowing for increased spatiotemporal asynchrony within crops. We also find that increasing asynchrony between the year-to-year production of different crops has stabilizing effects on food supply. Importantly, the benefits of increasing crop diversity are lower in specialized landscapes growing the same crop on large patches. Our results illustrate clear benefits of diversified crops, producers, and agricultural landscapes to buffer supply side shocks, and for incorporation in subsidies and other regulatory measures aimed at stabilizing food systems.}, language = {en} } @article{ShikangalahMapaniMapaureetal.2021, author = {Shikangalah, Rosemary and Mapani, Benjamin and Mapaure, Isaac and Herzschuh, Ulrike}, title = {Responsiveness of Dichrostachys cinerea to seasonal variations in temperature and rainfall in central Namibia}, series = {Flora}, volume = {286}, journal = {Flora}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0367-2530}, doi = {10.1016/j.flora.2021.151974}, pages = {7}, year = {2021}, abstract = {Woody plants provide natural archives of climatic variation which can be investigated by applying dendroclimatological methods. Such studies are limited in Southern Africa but have great potential of improving our understanding of past climates and plant functional adaptations in the region. This study therefore investigated the responsiveness of Dichrostachys cinerea to seasonal variations in temperature and rainfall at two sites in central Namibia, Waterberg and Kuzikus. Dichrostachys cinerea is one of the encroacher species thriving well in Namibia. A moving correlation and response function analysis were used to test its responsiveness to seasonal climatic variations over time. Dichrostachys cinerea growth rings showed relationships to late summer warming, lasting up to half of the rainy season. The results also revealed that past temperatures had been fluctuating and their influence on growth rings had been intensifying over the years, but to varying extents between the two sites. Temperature was a more important determinant of ring growth at the drier site (Kuzikus), while rainfall was more important at the wetter site (Waterberg). Growth ring responsiveness to rainfall was not immediate but showed a rather lagged pattern. We conclude that D. cinerea differentially responds to variations in rainfall and temperature across short climatic gradients. This study showed that the species, due to its somewhat wide ecological amplitude, has great potential for dendroclimatological studies in tropical regions.}, language = {en} }