@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} } @article{DreymannSabrowskiDansoetal.2022, author = {Dreymann, Nico and Sabrowski, Wiebke and Danso, Jennifer and Menger, Marcus}, title = {Aptamer-based sandwich assay formats for detection and discrimination of human high- and low-molecular-weight uPA for cancer prognosis and diagnosis}, series = {Cancers / Molecular Diversity Preservation International (MDPI)}, volume = {14}, journal = {Cancers / Molecular Diversity Preservation International (MDPI)}, number = {21}, publisher = {MDPI}, address = {Basel}, issn = {2072-6694}, doi = {10.3390/cancers14215222}, pages = {17}, year = {2022}, abstract = {Simple Summary Urokinase-type plasminogen activator (urokinase, uPA) is a widely discussed biomarker for cancer prognosis and diagnosis. The gold standard for the determination of protein biomarkers in physiological samples is the enzyme-linked immunosorbent assay (ELISA). Here, antibodies are used to detect the specific protein. In our study, recently published urokinase aptamers were tested for their use in a sandwich assay format as alternative specific recognition elements. Different aptamer combinations were used for the detection of uPA in a sandwich-assay format and a combination of aptamers and antibodies additionally allowed the differentiation of human high and low molecular weight- (HMW- and LMW-) uPA. Hence, uPA aptamers offer a valuable alternative as specific recognition elements for analytical purposes. Since aptamers are easy to synthesize and modify, they can be used as a cost-effective alternative in sandwich assay formats for the detection of uPA in physiological samples. Abstract Urokinase-type plasminogen activator (urokinase, uPA) is a frequently discussed biomarker for prognosis, diagnosis, and recurrence of cancer. In a previous study, we developed ssDNA aptamers that bind to different forms of human urokinase, which are therefore assumed to have different binding regions. In this study, we demonstrate the development of aptamer-based sandwich assays that use different combinations of these aptamers to detect high molecular weight- (HMW-) uPA in a micro titer plate format. By combining aptamers and antibodies, it was possible to distinguish between HMW-uPA and low molecular weight- (LMW-) uPA. For the best performing aptamer combination, we calculated the limit of detection (LOD) and limit of quantification (LOQ) in spiked buffer and urine samples with an LOD up to 50 ng/mL and 138 ng/mL, respectively. To show the specificity and sequence dependence of the reporter aptamer uPAapt-02-FR, we have identified key nucleotides within the sequence that are important for specific folding and binding to uPA using a fluorescent dye-linked aptamer assay (FLAA). Since uPA is a much-discussed marker for prognosis and diagnosis in various types of cancers, these aptamers and their use in a micro titer plate assay format represent a novel, promising tool for the detection of uPA and for possible diagnostic applications.}, language = {en} } @article{ScholzKerestetzopoulouWiebachetal.2022, author = {Scholz, Stella and Kerestetzopoulou, Sofia and Wiebach, Vincent and Schnegotzki, Romina and Schmid, Bianca and Reyna-Gonzalez, Emmanuel and Ding, Ling and S{\"u}ssmuth, Roderich D. and Dittmann, Elke and Baunach, Martin}, title = {One-Pot chemoenzymatic synthesis of microviridin analogs containing functional tags}, series = {ChemBioChem : an official journal of the EFMC}, volume = {23}, journal = {ChemBioChem : an official journal of the EFMC}, number = {20}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1439-4227}, doi = {10.1002/cbic.202200345}, pages = {7}, year = {2022}, abstract = {Microviridins are a prominent family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) featuring characteristic lactone and lactam rings. Their unusual cage-like architecture renders them highly potent serine protease inhibitors of which individual variants specifically inhibit different types of proteases of pharmacological interest. While posttranslational modifications are key for the stability and bioactivity of RiPPs, additional attractive properties can be introduced by functional tags. To date - although highly desirable - no method has been reported to incorporate functional tags in microviridin scaffolds or the overarching class of graspetides. In this study, a chemoenzymatic in vitro platform is used to introduce functional tags in various microviridin variants yielding biotinylated, dansylated or propargylated congeners. This straightforward approach paves the way for customized protease inhibitors with built-in functionalities that can help to unravel the still elusive ecological roles and targets of this remarkable class of compounds and to foster applications based on protease inhibition.}, language = {en} } @article{HeinzeKrumpholzBlaumetal.2022, author = {Heinze, Johannes and Krumpholz, Laura and Blaum, Niels and Hoefgen, Rainer and Ogden, Michael}, title = {Shoot herbivory by grasshoppers has stronger effects on root morphology than clipping}, series = {Plant ecology : an international journal}, volume = {223}, journal = {Plant ecology : an international journal}, number = {9}, publisher = {Springer Science + Business Media B.V.}, address = {Dordrecht}, issn = {1385-0237}, doi = {10.1007/s11258-022-01259-0}, pages = {1069 -- 1078}, year = {2022}, abstract = {Studies investigating the effect of aboveground herbivory on plants often use clipping to simulate the effects of herbivores, for practical reasons. However, herbivore movements and transfer of oral secretions during herbivory may cause a different response in plant physiology and morphology compared to clipping. While studies have compared effects of real herbivory vs. clipping on biomass production, plant physiology, and shoot morphology, no study has compared such effects on root morphology. Therefore, we investigated the effect of herbivory by grasshoppers, herbivory simulated by clipping, and no herbivory on root morphological traits of ten grassland plant species. Root morphological traits were differently affected by the two herbivory treatments. Grasshopper herbivory significantly changed root morphology toward thinner roots with increased specific root length and root area, and decreased root tissue density compared to untreated control plants. Clipping had mostly similar, but weaker effects on root morphology than grasshopper herbivory. On the species level, grasshopper herbivory led to strongest changes in root morphology in almost all cases. In contrast, depending on the species, clipping resulted in varying root morphological trait values similar to grasshopper-damaged plants, or in some cases, more closely aligned with control plants. Though clipping was partly able to mimic the effects of herbivory by grasshoppers, results also indicate that, depending on the species, grasshopper herbivory had different but mostly stronger effects. We, therefore, recommend that future studies apply herbivory with real herbivores to better reflect natural responses in plants and related processes that root morphological traits mediate.}, language = {en} } @article{SchoedlOdemerBecheretal.2022, author = {Sch{\"o}dl, Isabel and Odemer, Richard and Becher, Matthias A. and Berg, Stefan and Otten, Christoph and Grimm, Volker and Groeneveld, J{\"u}rgen}, title = {Simulation of Varroa mite control in honey bee colonies without synthetic acaricides: demonstration of Good Beekeeping Practice for Germany in the BEEHAVE model}, series = {Ecology and evolution}, volume = {12}, journal = {Ecology and evolution}, number = {11}, publisher = {John Wiley \& Sons, Inc.}, issn = {2045-7758}, doi = {10.1002/ece3.9456}, pages = {14}, year = {2022}, abstract = {The BEEHAVE model simulates the population dynamics and foraging activity of a single honey bee colony (Apis mellifera) in great detail. Although it still makes numerous simplifying assumptions, it appears to capture a wide range of empirical observations. It could, therefore, in principle, also be used as a tool in beekeeper education, as it allows the implementation and comparison of different management options. Here, we focus on treatments aimed at controlling the mite Varroa destructor. However, since BEEHAVE was developed in the UK, mite treatment includes the use of a synthetic acaricide, which is not part of Good Beekeeping Practice in Germany. A practice that consists of drone brood removal from April to June, treatment with formic acid in August/September, and treatment with oxalic acid in November/December. We implemented these measures, focusing on the timing, frequency, and spacing between drone brood removals. The effect of drone brood removal and acid treatment, individually or in combination, on a mite-infested colony was examined. We quantify the efficacy of Varroa mite control as the reduction of mites in treated bee colonies compared to untreated bee colonies. We found that drone brood removal was very effective, reducing mites by 90\% at the end of the first simulation year after the introduction of mites. This value was significantly higher than the 50-67\% reduction expected by bee experts and confirmed by empirical studies. However, literature reports varying percent reductions in mite numbers from 10 to 85\% after drone brood removal. The discrepancy between model results, empirical data, and expert estimates indicate that these three sources should be reviewed and refined, as all are based on simplifying assumptions. These results and the adaptation of BEEHAVE to the Good Beekeeping Practice are a decisive step forward for the future use of BEEHAVE in beekeeper education in Germany and anywhere where organic acids and drone brood removal are utilized.}, language = {en} } @article{MeyerCherstvySeckleretal.2023, author = {Meyer, Philipp and Cherstvy, Andrey G. and Seckler, Henrik and Hering, Robert and Blaum, Niels and Jeltsch, Florian and Metzler, Ralf}, title = {Directedeness, correlations, and daily cycles in springbok motion}, series = {Physical review research}, volume = {5}, journal = {Physical review research}, number = {4}, publisher = {APS}, address = {College Park}, issn = {2643-1564}, doi = {10.1103/PhysRevResearch.5.043129}, pages = {17}, year = {2023}, abstract = {How predictable is the next move of an animal? Specifically, which factors govern the short- and long-term motion patterns and the overall dynamics of land-bound, plant-eating animals in general and ruminants in particular? To answer this question, we here study the movement dynamics of springbok antelopes Antidorcas marsupialis. We propose several complementary statistical-analysis techniques combined with machine-learning approaches to analyze—across multiple time scales—the springbok motion recorded in long-term GPS tracking of collared springboks at a private wildlife reserve in Namibia. As a result, we are able to predict the springbok movement within the next hour with a certainty of about 20\%. The remaining about 80\% are stochastic in nature and are induced by unaccounted factors in the modeling algorithm and by individual behavioral features of springboks. We find that directedness of motion contributes approximately 17\% to this predicted fraction. We find that the measure for directedeness is strongly dependent on the daily cycle of springbok activity. The previously known daily affinity of springboks to their water points, as predicted from our machine-learning algorithm, overall accounts for only about 3\% of this predicted deterministic component of springbok motion. Moreover, the resting points are found to affect the motion of springboks at least as much as the formally studied effects of water points. The generality of these statements for the motion patterns and their underlying behavioral reasons for other ruminants can be examined on the basis of our statistical-analysis tools in the future.}, language = {en} } @article{GuillenLindgrenMuffetal.2023, author = {Guillen, Rafael Arce and Lindgren, Finn and Muff, Stefanie and Glass, Thomas W. and Breed, Greg A. and Schl{\"a}gel, Ulrike}, title = {Accounting for unobserved spatial variation in step selection analyses of animal movement via spatial random effects}, series = {Methods in ecology and evolution : MEE}, volume = {14}, journal = {Methods in ecology and evolution : MEE}, number = {10}, publisher = {Wiley}, address = {Oxford}, issn = {2041-210X}, doi = {10.1111/2041-210X.14208}, pages = {2639 -- 2653}, year = {2023}, abstract = {Step selection analysis (SSA) is a common framework for understanding animal movement and resource selection using telemetry data. Such data are, however, inherently autocorrelated in space, a complication that could impact SSA-based inference if left unaddressed. Accounting for spatial correlation is standard statistical practice when analysing spatial data, and its importance is increasingly recognized in ecological models (e.g. species distribution models). Nonetheless, no framework yet exists to account for such correlation when analysing animal movement using SSA. Here, we extend the popular method integrated step selection analysis (iSSA) by including a Gaussian field (GF) in the linear predictor to account for spatial correlation. For this, we use the Bayesian framework R-INLA and the stochastic partial differential equations (SPDE) technique. We show through a simulation study that our method provides accurate fixed effects estimates, quantifies their uncertainty well and improves the predictions. In addition, we demonstrate the practical utility of our method by applying it to three wolverine (Gulo gulo) tracks. Our method solves the problems of assuming spatially independent residuals in the SSA framework. In addition, it offers new possibilities for making long-term predictions of habitat usage.}, language = {en} } @article{VillalbaKasadaZoccaratoetal.2022, author = {Villalba, Luis Alberto and Kasada, Minoru and Zoccarato, Luca and Wollrab, Sabine and Grossart, Hans Peter}, title = {Differing escape responses of the marine bacterium Marinobacter adhaerens in the presence of planktonic vs. surface-associated protist grazers}, series = {International journal of molecular sciences}, volume = {23}, journal = {International journal of molecular sciences}, number = {17}, publisher = {MDPI}, address = {Basel}, issn = {1661-6596}, doi = {10.3390/ijms231710082}, pages = {13}, year = {2022}, abstract = {Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.}, 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{MachinPiontekTodheetal.2022, author = {Machin, Laura and Piontek, Martin and Todhe, Sara and Staniek, Katrin and Monzote, Lianet and Fudickar, Werner and Linker, Torsten and Gille, Lars}, title = {Antileishmanial anthracene endoperoxides: efficacy in vitro, mechanisms and structure-activity relationships}, series = {Molecules : a journal of synthetic chemistry and natural product chemistry}, volume = {27}, journal = {Molecules : a journal of synthetic chemistry and natural product chemistry}, number = {20}, publisher = {MDPI}, address = {Basel}, issn = {1420-3049}, doi = {10.3390/molecules27206846}, pages = {22}, year = {2022}, abstract = {Leishmaniasis is a vector-borne disease caused by protozoal Leishmania parasites. Previous studies have shown that endoperoxides (EP) can selectively kill Leishmania in host cells. Therefore, we studied in this work a set of new anthracene-derived EP (AcEP) together with their non-endoperoxidic analogs in model systems of Leishmania tarentolae promastigotes (LtP) and J774 macrophages for their antileishmanial activity and selectivity. The mechanism of effective compounds was explored by studying their reaction with iron (II) in chemical systems and in Leishmania. The correlation of structural parameters with activity demonstrated that in this compound set, active compounds had a LogP(OW) larger than 3.5 and a polar surface area smaller than 100 angstrom(2). The most effective compounds (IC50 in LtP < 2 mu M) with the highest selectivity (SI > 30) were pyridyl-/tert-butyl-substituted AcEP. Interestingly, also their analogs demonstrated activity and selectivity. In mechanistic studies, it was shown that EP were activated by iron in chemical systems and in LtP due to their EP group. However, the molecular structure beyond the EP group significantly contributed to their differential mitochondrial inhibition in Leishmania. The identified compound pairs are a good starting point for subsequent experiments in pathogenic Leishmania in vitro and in animal models.}, language = {en} } @article{HermanussenDammhahnScheffleretal.2023, author = {Hermanussen, Michael and Dammhahn, Melanie and Scheffler, Christiane and Groth, Detlef}, title = {Winner-loser effects improve social network efficiency between competitors with equal resource holding power}, series = {Scientific reports}, volume = {13}, journal = {Scientific reports}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-023-41225-y}, pages = {9}, year = {2023}, abstract = {Animal societies are structured of dominance hierarchy (DH). DH can be viewed as networks and analyzed by graph theory. We study the impact of state-dependent feedback (winner-loser effect) on the emergence of local dominance structures after pairwise contests between initially equal-ranking members (equal resource-holding-power, RHP) of small and large social groups. We simulated pairwise agonistic contests between individuals with and without a priori higher RHP by Monte-Carlo-method. Random pairwise contests between equal-ranking competitors result in random dominance structures ('Null variant') that are low in transitive triads and high in pass along triads; whereas state-dependent feedback ('Winner-loser variant') yields centralized 'star' structured DH that evolve from competitors with initially equal RHP and correspond to hierarchies that evolve from keystone individuals. Monte-Carlo simulated DH following state-dependent feedback show motif patterns very similar to those of a variety of natural DH, suggesting that state-dependent feedback plays a pivotal role in robust self-organizing phenomena that transcend the specifics of the individual. Self-organization based on state-dependent feedback leads to social structures that correspond to those resulting from pre-existing keystone individuals. As the efficiency of centralized social networks benefits both, the individual and the group, centralization of social networks appears to be an important evolutionary goal.}, language = {en} } @article{BergholzBalthasarWeissetal.2023, author = {Bergholz, Kolja and Balthasar, Cathrina and Weiss, Anne-Marie and Brunkhardt, Jennifer and Ristow, Michael and Weiß, Lina}, title = {Niche differentiation of arthropods and plants along small-scale gradients in temporary wetlands (kettle holes)}, series = {Basic and applied ecology : journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {73}, journal = {Basic and applied ecology : journal of the Gesellschaft f{\"u}r {\"O}kologie}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1439-1791}, doi = {10.1016/j.baae.2023.10.003}, pages = {10 -- 17}, year = {2023}, abstract = {Small temporary wetlands, like kettle holes, provide many valuable ecosystem functions and serve as refuge habitats in otherwise monotonous agricultural landscapes. However, the mechanisms that maintain biodiversity in these habitats are still poorly understood. In this study, we investigate how three taxa (vascular plants, ground beetles and spiders) respond to small-scale flooding and disturbance gradients in kettle holes as well as kettle hole area. For this purpose, we determined total, hygrophilic and red list species richness for all taxa and activity density for arthropods along transects extending from the edge towards the center of kettle holes. Furthermore, we calculated the community-weighted mean body size for arthropods and seed mass for plants as surrogates for the ability to respond to disturbance. Our analyses revealed that in particular plants and ground beetles showed strong responses along the small-scale spatial gradient. Total plant species richness decreased towards the center, while hygrophilic plant species increased. In contrast, both total and hygrophilic species richness of ground beetles increased towards the center. Spiders showed similar responses as ground beetles, but less pronounced. We found no evidence that disturbance at the edge of kettle holes leads to smaller body sizes or seed masses. However, arthropods in adjacent arable fields (one meter from the kettle hole edge) were particularly small. Kettle hole area had only weak effects on plants, but not on arthropods. Our study indicates that differences in the depth at the drier edge and the moist, regularly flooded center have a large and taxon-dependent influence on the species composition. Therefore, small-scale heterogeneity seems to be an important predictor for the maintenance of species diversity.}, language = {en} } @article{KumarLeimkuehler2023, author = {Kumar, Hemant and Leimk{\"u}hler, Silke}, title = {Changing the electron acceptor specificity of rhodobacter capsulatus formate dehydrogenase from NAD+ to NADP+}, series = {International journal of molecular sciences}, volume = {24}, journal = {International journal of molecular sciences}, number = {22}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms242216067}, pages = {13}, year = {2023}, abstract = {Formate dehydrogenases catalyze the reversible oxidation of formate to carbon dioxide. These enzymes play an important role in CO2 reduction and serve as nicotinamide cofactor recycling enzymes. More recently, the CO2-reducing activity of formate dehydrogenases, especially metal-containing formate dehydrogenases, has been further explored for efficient atmospheric CO2 capture. Here, we investigate the nicotinamide binding site of formate dehydrogenase from Rhodobacter capsulatus for its specificity toward NAD+ vs. NADP+ reduction. Starting from the NAD+-specific wild-type RcFDH, key residues were exchanged to enable NADP+ binding on the basis of the NAD+-bound cryo-EM structure (PDB-ID: 6TG9). It has been observed that the lysine at position 157 (Lys157) in the β-subunit of the enzyme is essential for the binding of NAD+. RcFDH variants that had Glu259 exchanged for either a positively charged or uncharged amino acid had additional activity with NADP+. The FdsBL279R and FdsBK276A variants also showed activity with NADP+. Kinetic parameters for all the variants were determined and tested for activity in CO2 reduction. The variants were able to reduce CO2 using NADPH as an electron donor in a coupled assay with phosphite dehydrogenase (PTDH), which regenerates NADPH. This makes the enzyme suitable for applications where it can be coupled with other enzymes that use NADPH.}, language = {en} } @article{LaunDuffusKumaretal.2022, author = {Laun, Konstantin and Duffus, Benjamin R. and Kumar, Hemant and Oudsen, Jean-Pierre H. and Karafoulidi-Retsou, Chara and Waffo, Armel Tadjoung and Hildebrandt, Peter and Ly, Khoa Hoang and Leimk{\"u}hler, Silke and Katz, Sagie and Zebger, Ingo}, title = {A minimal light-driven system to study the enzymatic CO2 reduction of formate dehydrogenase}, series = {ChemCatChem : the European Society Journal for Catalysis}, volume = {14}, journal = {ChemCatChem : the European Society Journal for Catalysis}, number = {24}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1867-3880}, doi = {10.1002/cctc.202201067}, pages = {7}, year = {2022}, abstract = {A minimal light-driven approach was established for studying enzymatic CO2 conversion spectroscopically. The system consists of a photosensitizer Eosin Y, EDTA as a sacrificial electron donor and substrate source, and formate dehydrogenase from Rhodobacter capsulatus (RcFDH) as a biocatalyst. This simplified three-component system provides a photo-triggered control for in situ characterization of the entire catalytic reaction. Direct reduction of RcFDH by the photosensitizer without additional electron carriers was confirmed via UV-Vis spectroscopy, while GC-MS and IR spectroscopy were used to follow photoinduced CO2 generation from EDTA and its subsequent enzymatic reduction, yielding the product formate. Photo-driven and in vitro, dye-based CO2 reduction was inhibited by azide under a mixed (competitive-non-competitive) inhibition mode. IR spectroscopy reveals displacement of the competitively-bound azide by CO2, reflecting an interaction of both with the active site cofactor. This work comprises a proof-of-concept for a new approach to employ light for regulating the reaction of formate dehydrogenases and other CO2 reductases.}, language = {en} } @article{BoginHermanussenScheffler2022, author = {Bogin, Barry and Hermanussen, Michael and Scheffler, Christiane}, title = {Bergmann's rule is a "just-so" story of human body size}, series = {Journal of physiological anthropology}, volume = {41}, journal = {Journal of physiological anthropology}, number = {1}, publisher = {BMC}, address = {London}, issn = {1880-6805}, doi = {10.1186/s40101-022-00287-z}, pages = {13}, year = {2022}, abstract = {Carl Bergmann was an astute naturalist and physiologist. His ideas about animal size and shape were important advances in the pre-Darwinian nineteenth century. Bergmann's rule claims that that in cold climates, large body mass increases the ratio of volume-to-surface area and provides for maximum metabolic heat retention in mammals and birds. Conversely, in warmer temperatures, smaller body mass increases surface area relative to volume and allows for greater heat loss. For humans, we now know that body size and shape are regulated more by social-economic-political-emotional (SEPE) factors as well as nutrition-infection interactions. Temperature has virtually no effect. Bergmann's rule is a "just-so" story and should be relegated to teaching and scholarship about the history of science. That "rule" is no longer acceptable science and has nothing to tell us about physiological anthropology.}, language = {en} } @article{YarmanKurbanoglu2022, author = {Yarman, Aysu and Kurbanoglu, Sevinc}, title = {Molecularly imprinted polymer-based sensors for SARS-CoV-2}, series = {Biomimetics}, volume = {7}, journal = {Biomimetics}, number = {2}, publisher = {MDPI}, address = {Basel}, issn = {2313-7673}, doi = {10.3390/biomimetics7020058}, pages = {17}, year = {2022}, abstract = {Since the first reported case of COVID-19 in 2019 in China and the official declaration from the World Health Organization in March 2021 as a pandemic, fast and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has played a major role worldwide. For this reason, various methods have been developed, comprising reverse transcriptase-polymerase chain reaction (RT-PCR), immunoassays, clustered regularly interspaced short palindromic repeats (CRISPR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and bio(mimetic)sensors. Among the developed methods, RT-PCR is so far the gold standard. Herein, we give an overview of the MIP-based sensors utilized since the beginning of the pandemic.}, language = {en} } @article{MitzscherlingMacLeanLipusetal.2022, author = {Mitzscherling, Julia and MacLean, Joana and Lipus, Daniel and Bartholom{\"a}us, Alexander and Mangelsdorf, Kai and Lipski, Andre and Roddatis, Vladimir and Liebner, Susanne and Wagner, Dirk}, title = {Paenalcaligenes niemegkensis sp. nov., a novel species of the family Alcaligenaceae isolated from plastic waste}, series = {International journal of systematic and evolutionary microbiology}, volume = {72}, journal = {International journal of systematic and evolutionary microbiology}, number = {4}, publisher = {Microbiology Society}, address = {London}, issn = {1466-5026}, doi = {10.1099/ijsem.0.005333}, pages = {9}, year = {2022}, abstract = {Strain NGK35T is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 mu m long and 0.6-0.8 mu m wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 degrees C (optimum, 28 degrees C), in 0-10 \% NaCl (optimum, 1 \%) and at pH 6.0-9.5 (optimum, pH 7.5-8.5). It was positive for cytochrome c oxidase, catalase as well as H2S production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate. The predominant membrane fatty acids were C-16:1 cis9 and C-16:0, followed by C-17:0 cyclo and C-18:1 cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35(T) belongs to the genus Paenalcaligenes (family Alcaligenaceae), appearing most closely related to Paenalcaligenes hominis CCUG 53761A(T) (96.90 \%) and Paenalcaligenes suwonensis ABC02-12(T) (96.94 \%). The genomic DNA G+C content of strain NGK35(T) was 52.1 mol\%. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Paenalcaligenes. Based on phenotypic and molecular characterization, strain NGK35(T) can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name Paenalcaligenes niemegkensis sp. nov. is proposed. The type strain is NGK35T (=DSM 113270(T)=NCCB 100854(T)).}, language = {en} } @article{CheshmehElahiGhayyemetal.2022, author = {Cheshmeh, Sahar and Elahi, Negin and Ghayyem, Maysa and Mosaieby, Elaheh and Moradi, Shima and Pasdar, Yahya and Tahmasebi, Susan and Moradinazar, Mehdi}, title = {Effect of green cardamom on the expression of genes implicated in obesity and diabetes among obese women with polycystic ovary syndrome}, series = {Genes \& nutrition}, volume = {17}, journal = {Genes \& nutrition}, number = {1}, publisher = {Springer}, address = {Berlin}, issn = {1865-3499}, doi = {10.1186/s12263-022-00719-6}, pages = {11}, year = {2022}, abstract = {Background: Polycystic ovary syndrome (PCOS) is an endocrine disease in which related to obesity, metabolic disorders and is considered as one of the main causes of infertility in women. This trial was investigated the effects of green cardamom on the expression of genes implicated in obesity and diabetes among obese women with PCOS. Methods: One hundred ninety-four PCOS women were randomly divided two groups: intervention (n = 99; 3 g/day green cardamom) and control groups (n = 95). All of them were given low calorie diet. Anthropometric, glycemic and androgen hormones were assessed before and after 16-week intervention. The reverse transcription-polymerase chain reaction (RT-PCR) method was used to measure fat mass and obesity-associated (FTO), peroxisome proliferative activating receptor- (PPAR-), carnitine palmitoyltransferase 1A (CPT1A), acetyl-CoA carboxylase beta (ACAB), leptin receptor (LEPR), ghrelin, and lamin A/C (LAMIN) genes expression in each group. Results: Anthropometric indices were significantly decreased after intervention in both two studied groups. Glycemic indices and androgen hormones were significantly improved in the intervention group compared to the control group. The expression levels of FTO, CPT1A, LEPR, and LAMIN were significantly downregulated compared to control group (P < 0.001), as well as, PPAR-y was significantly upregulated in the intervention group after intervention with green cardamom compared to control group (P < 0.001). Conclusion: This current study showed that the administration of green cardamom is a beneficial approach for improving anthropometric, glycemic, and androgen hormones, as well as obesity and diabetes genes expression in PCOS women under the low-calorie diet.}, language = {en} } @article{GrzesiukPietrzakWackeretal.2022, author = {Grzesiuk, Malgorzata and Pietrzak, Barbara and Wacker, Alexander and Pijanowska, Joanna}, title = {Photosynthetic activity in both algae and cyanobacteria changes in response to cues of predation}, series = {Frontiers in plant science}, volume = {13}, journal = {Frontiers in plant science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2022.907174}, pages = {8}, year = {2022}, abstract = {A plethora of adaptive responses to predation has been described in microscopic aquatic producers. Although the energetic costs of these responses are expected, with their consequences going far beyond an individual, their underlying molecular and metabolic mechanisms are not fully known. One, so far hardly considered, is if and how the photosynthetic efficiency of phytoplankton might change in response to the predation cues. Our main aim was to identify such responses in phytoplankton and to detect if they are taxon-specific. We exposed seven algae and seven cyanobacteria species to the chemical cues of an efficient consumer, Daphnia magna, which was fed either a green alga, Acutodesmus obliquus, or a cyanobacterium, Synechococcus elongatus (kairomone and alarm cues), or was not fed (kairomone alone). In most algal and cyanobacterial species studied, the quantum yield of photosystem II increased in response to predator fed cyanobacterium, whereas in most of these species the yield did not change in response to predator fed alga. Also, cyanobacteria tended not to respond to a non-feeding predator. The modal qualitative responses of the electron transport rate were similar to those of the quantum yield. To our best knowledge, the results presented here are the broadest scan of photosystem II responses in the predation context so far.}, 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{HashemiRazaghiMoghadamLaitinenetal.2022, author = {Hashemi, Seirana and Razaghi-Moghadam, Zahra and Laitinen, Roosa A. E. and Nikoloski, Zoran}, title = {Relative flux trade-offs and optimization of metabolic network functionalities}, series = {Computational and structural biotechnology journal}, volume = {20}, 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.2022.07.038}, pages = {3963 -- 3971}, year = {2022}, abstract = {Trade-offs between traits are present across different levels of biological systems and ultimately reflect constraints imposed by physicochemical laws and the structure of underlying biochemical networks. Yet, mechanistic explanation of how trade-offs between molecular traits arise and how they relate to optimization of fitness-related traits remains elusive. Here, we introduce the concept of relative flux trade-offs and propose a constraint-based approach, termed FluTOr, to identify metabolic reactions whose fluxes are in relative trade-off with respect to an optimized fitness-related cellular task, like growth. We then employed FluTOr to identify relative flux trade-offs in the genome-scale metabolic networks of Escherichia coli, Saccharomyces cerevisiae, and Arabidopsis thaliana. For the metabolic models of E. coli and S. cerevisiae we showed that: (i) the identified relative flux trade-offs depend on the carbon source used and that (ii) reactions that participated in relative trade-offs in both species were implicated in cofactor biosynthesis. In contrast to the two microorganisms, the relative flux trade-offs for the metabolic model of A. thaliana did not depend on the available nitrogen sources, reflecting the differences in the underlying metabolic network as well as the considered environments. Lastly, the established connection between relative flux trade-offs allowed us to identify overexpression targets that can be used to optimize fitness-related traits. Altogether, our computational approach and findings demonstrate how relative flux trade-offs can shape optimization of metabolic tasks, important in biotechnological applications.}, language = {en} } @article{WassermannAbdelfattahCernavaetal.2022, author = {Wassermann, Birgit and Abdelfattah, Ahmed and Cernava, Tomislav and Wicaksono, Wisnu and Berg, Gabriele}, title = {Microbiome-based biotechnology for reducing food loss post harvest}, series = {Current opinion in biotechnology}, volume = {78}, journal = {Current opinion in biotechnology}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0958-1669}, doi = {10.1016/j.copbio.2022.102808}, pages = {9}, year = {2022}, abstract = {Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50\% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety.}, language = {en} } @article{ArnoldHagemannGilissenetal.2022, author = {Arnold, Patrick and Hagemann, Justus and Gilissen, Emmanuel and Hofreiter, Michael}, title = {Otter shrew mitogenomes (Afrotheria, Potamogalidae) reconstructed from historical museum skins}, series = {Mitochondrial DNA. Part B}, volume = {7}, journal = {Mitochondrial DNA. Part B}, number = {9}, publisher = {Taylor \& Francis Group}, address = {London}, issn = {2380-2359}, doi = {10.1080/23802359.2022.2122747}, pages = {1699 -- 1701}, year = {2022}, abstract = {African otter shrews (Potamogalidae) are Afrotherian mammals adapted to a semi-aquatic lifestyle. Given their rareness, genetic data on otter shrews are limited. By applying laboratory methods tuned for the recovery of archival DNA and an iterative mapping approach, we reconstructed whole mitochondrial genomes of the Giant (Potamogale velox) and Ruwenzori pygmy otter shrew (Micropotamogale ruwenzorii) from historical museum skins. Phylogenetic analyses are consistent with previous reports in recovering a sister relationship between African otter shrews and Malagasy tenrecs. The long branches separating both lineages, however, support their recognition as separate families.}, language = {en} } @article{ThongthaisongKasadaGrossartetal.2022, author = {Thongthaisong, Patch and Kasada, Minoru and Grossart, Hans-Peter and Wollrab, Sabine}, title = {Critical role of parasite-mediated energy pathway on community response to nutrient enrichment}, series = {Ecology and evolution}, volume = {12}, journal = {Ecology and evolution}, number = {12}, publisher = {John Wiley \& Sons, Inc.}, address = {[Hoboken]}, issn = {2045-7758}, doi = {10.1002/ece3.9622}, pages = {12}, year = {2022}, abstract = {Parasites form an integral part of food webs, however, they are often ignored in classic food web theory or limited to the investigation of trophic transmission pathways. Specifically, direct consumption of parasites by nonhost predators is rarely considered, while it can contribute substantially to energy flow in food webs. In aquatic systems, chytrids constitute a major group of fungal parasites whose free-living infective stages (zoospores) form a highly nutritional food source to zooplankton. Thereby, the consumption of zoospores can create an energy pathway from otherwise inedible phytoplankton to zooplankton ( "mycoloop "). This parasite-mediated energy pathway might be of special importance during phytoplankton blooms dominated by inedible or toxic primary producers like cyanobacteria, which are on the rise with eutrophication and global warming. We theoretically investigated community dynamics and energy transfer in a food web consisting of an edible nonhost and an inedible host phytoplankton species, a parasitic fungus, and a zooplankton species grazing on edible phytoplankton and fungi. Food web dynamics were investigated along a nutrient gradient contrasting nonadaptive zooplankton species representative for filter feeders like cladocerans and zooplankton with the ability to actively adapt their feeding preferences like many copepod species. Overall, the importance of the mycoloop for zooplankton increases with nutrient availability. This increase is smooth for nonadaptive consumers. For adaptive consumers, we observe an abrupt shift from an almost exclusive preference for edible phytoplankton at low nutrient levels to a strong preference for parasitic fungi at high nutrient levels. The model predicts that parasitic fungi could contribute up to 50\% of the zooplankton diet in nutrient-rich environments, which agrees with empirical observations on zooplankton gut content from eutrophic systems during blooms of inedible diatoms or cyanobacteria. Our findings highlight the role of parasite-mediated energy pathways for predictions of energy flow and community composition under current and future environmental change.}, language = {en} } @article{WicaksonoErschenKrauseetal.2022, author = {Wicaksono, Wisnu Adi and Erschen, Sabine and Krause, Robert and M{\"u}ller, Henry and Cernava, Tomislav and Berg, Gabriele}, title = {Enhanced survival of multi-species biofilms under stress is promoted by low-abundant but antimicrobial-resistant keystone species}, series = {Journal of hazardous materials : environmental control, risk assessment, impact and management}, volume = {422}, journal = {Journal of hazardous materials : environmental control, risk assessment, impact and management}, publisher = {Science Direct}, address = {New York, NY [u.a.]}, issn = {0304-3894}, doi = {10.1016/j.jhazmat.2021.126836}, pages = {10}, year = {2022}, abstract = {Multi-species biofilms are more resistant against stress compared to single-species biofilms. However, the mechanisms underlying this common observation remain elusive. Therefore, we studied biofilm formation of well-known opportunistic pathogens (Acinetobacter baumanii, Enterococcus faecium, Escherichia coli, Staphylococcus haemolyticus and Stenotrophomonas maltophilia) in various approaches. Synergistic effects in their multi species biofilms were observed. Using metatranscriptomics, changes in the gene expression of the involved members became evident, and provided explanations for the improved survivability under nutrient limitation and exposure to disinfectants. Genes encoding proteins for vitamin B6 synthesis and iron uptake were linked to synergism in the multi-species biofilm under nutrient-limited conditions. Our study indicates that sub-lethal concentrations of an alcohol-based disinfectant enhance biofilm yields in multi-species assemblages. A reduction of the dominant taxa in the multi-species biofilm under disinfectant pressure allowed minor taxa to bloom. The findings underline the importance of minor but antimicrobial-resistant species that serve as "protectors" for the whole assemblage due to upregulation of genes involved in defence mechanisms and biofilm formation. This ultimately results in an increase in the total yield of the multi-species biofilm. We conclude that inter-species interactions may be crucial for the survival of opportunistic pathogens; especially under conditions that are typically found under hospital settings.}, language = {en} } @article{OlimiBickelWicaksonoetal.2022, author = {Olimi, Expedito and Bickel, Samuel and Wicaksono, Wisnu Adi and Kusstatscher, Peter and Matzer, Robert and Cernava, Tomislav and Berg, Gabriele}, title = {Deciphering the microbial composition of biodynamic preparations and their effects on the apple rhizosphere microbiome}, series = {Frontiers in soil science}, volume = {2}, journal = {Frontiers in soil science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2673-8619}, doi = {10.3389/fsoil.2022.1020869}, pages = {18}, year = {2022}, abstract = {Soil microbial communities are crucial for plant growth and are already depleted by anthropogenic activities. The application of microbial transplants provides a strategy to restore beneficial soil traits, but less is known about the microbiota of traditional inoculants used in biodynamic agriculture. In this study, we used amplicon sequencing and quantitative PCR to decipher microbial communities of composts, biodynamic manures, and plant preparations from Austria and France. In addition, we investigated the effect of extracts derived from biodynamic manure and compost on the rhizosphere microbiome of apple trees. Microbiota abundance, composition, and diversity of biodynamic manures, plant preparations, and composts were distinct. Microbial abundances ranged between 1010-1011 (bacterial 16S rRNA genes) and 109-1011 (fungal ITS genes). The bacterial diversity was significantly higher in biodynamic manures compared to compost without discernible differences in abundance. Fungal diversity was not significantly different while abundance was increased in biodynamic manures. The microbial communities of biodynamic manures and plant preparations were specific for each production site, but all contain potentially plant-beneficial bacterial genera. When applied in apple orchards, biodynamic preparations (extracts) had the non-significant effect of reducing bacterial and fungal abundance in apple rhizosphere (4 months post-application), while increasing fungal and lowering bacterial Shannon diversity. One to four months after inoculation, individual taxa indicated differential abundance. We observed the reduction of the pathogenic fungus Alternaria, and the enrichment of potentially beneficial bacterial genera such as Pseudomonas. Our study paves way for the science-based adaptation of empirically developed biodynamic formulations under different farming practices to restore the vitality of agricultural soils.}, language = {en} } @article{UllrichGoehmannZemellaetal.2022, author = {Ullrich, Jessica and G{\"o}hmann, Philip Jonas and Zemella, Anne and Kubick, Stefan}, title = {Oligomerization of the heteromeric γ-aminobutyric acid receptor GABAB in a eukaryotic cell-free system}, series = {Scientific reports}, volume = {12}, journal = {Scientific reports}, number = {1}, publisher = {Springer Nature}, address = {[London]}, issn = {2045-2322}, doi = {10.1038/s41598-022-24885-0}, pages = {10}, year = {2022}, abstract = {Understanding the assembly mechanism and function of membrane proteins is a fundamental problem in biochemical research. Among the membrane proteins, G protein-coupled receptors (GPCRs) represent the largest class in the human body and have long been considered to function as monomers. Nowadays, the oligomeric assembly of GPCRs is widely accepted, although the functional importance and therapeutic intervention remain largely unexplored. This is partly due to difficulties in the heterologous production of membrane proteins. Cell-free protein synthesis (CFPS) with its endogenous endoplasmic reticulum-derived structures has proven as a technique to address this issue. In this study, we investigate for the first time the conceptual CFPS of a heteromeric GPCR, the gamma-aminobutyric acid receptor type B (GABA(B)), from its protomers BR1 and BR2 using a eukaryotic cell-free lysate. Using a fluorescence-based proximity ligation assay, we provide evidence for colocalization and thus suggesting heterodimerization. We prove the heterodimeric assembly by a bioluminescence resonance energy transfer saturation assay providing the manufacturability of a heterodimeric GPCR by CFPS. Additionally, we show the binding of a fluorescent orthosteric antagonist, demonstrating the feasibility of combining the CFPS of GPCRs with pharmacological applications. These results provide a simple and powerful experimental platform for the synthesis of heteromeric GPCRs and open new perspectives for the modelling of protein-protein interactions. Accordingly, the presented technology enables the targeting of protein assemblies as a new interface for pharmacological intervention in disease-relevant dimers.}, 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{MeierBraunsGrimmetal.2022, author = {Meier, Laura and Brauns, Mario and Grimm, Volker and Weitere, Markus and Frank, Karin}, title = {MASTIFF: a mechanistic model for cross-scale analyses of the functioning of multiple stressed riverine ecosystems}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {470}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2022.110007}, pages = {15}, year = {2022}, abstract = {Riverine ecosystems provide various ecosystem services. One of these services is the biological control of eutrophication by grazing macroinvertebrates. However, riverine ecosystems are subject to numerous stressors that affect community structure, functions, and stability properties. To manage rivers in response to these stressors, a better understanding of the ecological functions underlying services is needed. This requires consideration of local and regional processes, which requires a metacommunity approach that links local food webs through drift and dispersal. This takes into account long-distance interactions that can compensate for local effects of stressors. Our modular model MASTIFF (Multiple Aquatic STressors In Flowing Food webs) is stage-structured, spatially explicit, and includes coupled food webs consisting of benthic resource-consumer interactions between biofilm and three competing macroinvertebrate functional types. River segments are unidirectionally connected through organismal drift and bidirectionally connected through dispersal. Climate and land use stressors along the river can be accounted for. Biocontrol of biofilm eutrophication is used as an exemplary functional indicator. We present the model and the underlying considerations, and show in an exemplary application that explicit consideration of drift and dispersal is essential for understanding the spatiotemporal biocontrol of eutrophication. The combination of drift and dispersal reduced eutrophication events. While dispersal events were linked to specific periods in the species life cycles and therefore had limited potential to control, drift was ubiquitous and thus responded more readily to changing habitat conditions. This indicates that drift is an important factor for coping with stress situations. Finally, we outline and discuss the potential and possibilities of MASTIFF as a tool for mechanistic, cross-scale analyses of multiple stressors to advance knowledge of riverine ecosystem functioning.}, language = {en} } @article{HouZhaoZhangetal.2022, author = {Hou, Xindong and Zhao, Jian and Zhang, Hucai and Preick, Michaela and Hu, Jiaming and Xiao, Bo and Wang, Linying and Deng, Miaoxuan and Liu, Sizhao and Chang, Fengqin and Sheng, Guilian and Lai, Xulong and Hofreiter, Michael and Yuan, Junxia}, title = {Paleogenomes reveal a complex evolutionary history of late Pleistocene bison in Northeastern China}, series = {Genes}, volume = {13}, journal = {Genes}, number = {10}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes13101684}, pages = {16}, year = {2022}, abstract = {Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95\% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.}, language = {en} } @article{JacobsSchneiderMolenaaretal.2022, author = {Jacobs, Bas and Schneider, Ren{\´e} and Molenaar, Jaap and Filion, Laura and Deinum, Eva E.}, title = {Microtubule nucleation complex behavior is critical for cortical array homogeneity and xylem wall patterning}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {50}, publisher = {National Acad. of Sciences}, address = {Washington, DC}, issn = {0027-8424}, doi = {10.1073/pnas.2203900119}, pages = {10}, year = {2022}, abstract = {Plant cell walls are versatile materials that can adopt a wide range of mechanical properties through controlled deposition of cellulose fibrils. Wall integrity requires a sufficiently homogeneous fibril distribution to cope effectively with wall stresses. Additionally, specific conditions, such as the negative pressure in water transporting xylem vessels, may require more complex wall patterns, e.g., bands in protoxylem. The orientation and patterning of cellulose fibrils are guided by dynamic cortical microtubules. New microtubules are predominantly nucleated from parent microtubules causing positive feedback on local microtubule density with the potential to yield highly inhomogeneous patterns. Inhomogeneity indeed appears in all current cortical array simulations that include microtubule-based nucleation, suggesting that plant cells must possess an as-yet unknown balancing mechanism to prevent it. Here, in a combined simulation and experimental approach, we show that a limited local recruitment of nucleation complexes to microtubules can counter the positive feedback, whereas local tubulin depletion cannot. We observe that nucleation complexes preferentially appear at the plasma membrane near microtubules. By incorporating our experimental findings in stochastic simulations, we find that the spatial behavior of nucleation complexes delicately balances the positive feedback, such that differences in local microtubule dynamics-as in developing protoxylem-can quickly turn a homogeneous array into a banded one. Our results provide insight into how the plant cytoskeleton has evolved to meet diverse mechanical requirements and greatly increase the predictive power of computational cell biology studies.}, language = {en} } @article{MasigolRezakhaniPourmoghaddametal.2022, author = {Masigol, Hossein and Rezakhani, Forough and Pourmoghaddam, Mohammad Javad and Khodaparast, Seyed Akbar and Grossart, Hans-Peter}, title = {The introduction of two new species of aquatic fungi from Anzali Lagoon, Northern Iran}, series = {Diversity}, volume = {14}, journal = {Diversity}, number = {10}, publisher = {MDPI}, address = {Basel}, issn = {1424-2818}, doi = {10.3390/d14100889}, pages = {12}, year = {2022}, abstract = {During a survey of aquatic fungi from Anzali Lagoon in Iran, several fungal specimens were isolated from freshwater habitats. Morphological evidence and comparing sequencing based on rDNA (ITS and LSU) and protein-coding genes (TEF1 and TUB2) showed that some isolates belong to undescribed fungal species. These isolates belong to Arthrobotrys and Sarocladium, two ascomycetes genera. Arthrobotrys hyrcanus, sp. nov., differs from closely related species such as A. dianchiensis by its larger conidia and septation of primary conidia. Sarocladium pseudokiliense, sp. nov., was similar to S. kiliense, but distinguished by its conidial shape and the absence of adelophialides and chlamydospores. Morphological descriptions, illustrations and multilocus phylogenetic analysis for both new species are provided.}, language = {en} } @article{LiebchenWeineltScharfetal.2022, author = {Liebchen, Uwe and Weinelt, Ferdinand and Scharf, Christina and Schr{\"o}der, Ines and Paal, Michael and Zoller, Michael and Kloft, Charlotte and Jung, Jette and Michelet, Robin}, title = {Combination of pharmacokinetic and pathogen susceptibility information to optimize meropenem treatment of Gram-negative infections in critically iII patients}, series = {Antimicrobial Agents and Chemotherapy}, volume = {66}, journal = {Antimicrobial Agents and Chemotherapy}, number = {2}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0066-4804}, doi = {10.1128/aac.01831-21}, pages = {12}, year = {2022}, abstract = {Meropenem is one of the most frequently used antibiotics to treat life-threatening infections in critically ill patients. This study aimed to develop a meropenem dosing algorithm for the treatment of Gram-negative infections based on intensive care unit (ICU)-specific resistance data. Antimicrobial susceptibility testing of Gram-negative bacteria obtained from critically ill patients was carried out from 2016 to 2020 at a tertiary care hospital. Based on the observed MIC distribution, stochastic simulations (n = 1,000) of an evaluated pharmacokinetic meropenem model, and a defined pharmacokinetic/pharmacodynamic target (100\%T->4xMIC while minimum concentrations were <44.5 mg/L), dosing recommendations for patients with varying renal function were derived. Pathogen-specific MIC distributions were used to calculate the cumulative fraction of response (CFR), and the overall MIC distribution was used to calculate the local pathogen-independent mean fraction of response (LPIFR) for the investigated dosing regimens. A CFR/LPIFR of >90\% was considered adequate. The observed MIC distribution significantly differed from the EUCAST database. Based on the 6,520 MIC values included, a three-level dosing algorithm was developed. If the pathogen causing the infection is unknown (level 1), known (level 2), known to be neither Pseudomonas aeruginosa nor Acinetobacrer baumannii, or classified as susceptible (level 3), a continuous infusion of 1.5 g daily reached sufficient target attainment independent of renal function. In all other cases, dosing needs to be adjusted based on renal function. ICU-specific susceptibility data should be assessed regularly and integrated into dosing decisions. The presented workflow may serve as a blueprint for other antimicrobial settings.}, language = {en} } @article{HuthSchwarzGorb2022, author = {Huth, Steven and Schwarz, Lisa-Maricia and Gorb, Stanislav N.}, title = {Quantifying the influence of pollen aging on the adhesive properties of Hypochaeris radicata pollen}, series = {Insects}, volume = {13}, journal = {Insects}, number = {9}, publisher = {MDPI}, address = {Basel}, issn = {2075-4450}, doi = {10.3390/insects13090811}, pages = {13}, year = {2022}, abstract = {Simple Summary Pollination is the transfer of pollen from a plant's male part (anther) to the corresponding female part (stigma). It is a fundamental biological process that ensures plant reproduction. Most studies investigate pollination from a biological perspective, but the underlying physical processes are poorly understood. Many plants rely on insects to transport pollen and the forces with which pollen adhere to insects and floral surfaces are fundamental for successful pollination. We quantified pollen adhesion by measuring the forces necessary to detach Hypochaeris radicata (catsear, a common insect-pollinated plant) pollen from glass and studied for the first time how the adhesion forces change with pollen aging. Our results show that newly formed adhesion bonds between H. radicata pollen and glass are stronger for fresh pollen than for old ones. On the other hand, when H. radicata pollen age in contact with glass, the adhesion between pollen and glass strengthens over time. These effects are probably caused by the viscous liquid covering most pollen (pollenkitt) changing its viscoelastic properties as it dries. Although pollination is one of the most crucial biological processes that ensures plant reproduction, its mechanisms are poorly understood. Especially in insect-mediated pollination, a pollen undergoes several attachment and detachment cycles when being transferred from anther to insect and from insect to stigma. The influence of the properties of pollen, insect and floral surfaces on the adhesion forces that mediate pollen transfer have been poorly studied. Here, we investigate the adhesive properties of Hypochaeris radicata pollen and their dependence on pollen aging by quantifying the pull-off forces from glass slides using centrifugation and atomic force microscopy. We found that the properties of the pollenkitt-the viscous, lipid liquid on the surface of most pollen grains-influences the forces necessary to detach a pollen from hydrophilic surfaces. Our results show that aged H. radicata pollen form weaker adhesions to hydrophilic glass than fresh ones. On the other hand, when a pollen grain ages in contact with glass, the adhesion between the two surfaces increases over time. This study shows for the first time the pollen aging effect on the pollination mechanism.}, language = {en} } @article{RybakovaMuellerOlimietal.2022, author = {Rybakova, Daria and M{\"u}ller, Henry and Olimi, Expedito and Sch{\"a}fer, Angelika and Cernava, Tomislav and Berg, Gabriele}, title = {To defend or to attack? Antagonistic interactions between Serratia plymuthica and fungal plant pathogens, a species-specific volatile dialogue}, series = {Frontiers in sustainable food systems}, volume = {6}, journal = {Frontiers in sustainable food systems}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2571-581X}, doi = {10.3389/fsufs.2022.1020634}, pages = {14}, year = {2022}, abstract = {Volatile organic compounds (VOCs) are involved in microbial interspecies communication and in the mode of action of various antagonistic interactions. They are important for balancing host-microbe interactions and provide the basis for developing biological control strategies to control plant pathogens. We studied the interactions between the bacterial antagonist Serratia plymuthica HRO-C48 and three fungal plant pathogens Rhizoctonia solani, Leptosphaeria maculans and Verticillium longisporum. Significant differences in fungal growth inhibition by the Serratia-emitted VOCs in pairwise dual culture assays and changes in the transcriptome of the bacterium and in the volatilomes of both interacting partners were observed. Even though the rate of fungal growth inhibition by Serratia was variable, the confrontation of the bacterium with the VOCs of all three fungi changed the levels of expression of the genes involved in stress response, biofilm formation, and the production of antimicrobial VOCs. Pairwise interacting microorganisms switched between defense (downregulation of gene expression) and attack (upregulation of gene expression and metabolism followed by growth inhibition of the interacting partner) modes, subject to the combinations of microorganisms that were interacting. In the attack mode HRO-C48 significantly inhibited the growth of R. solani while simultaneously boosting its own metabolism; by contrast, its metabolism was downregulated when HRO-C48 went into a defense mode that was induced by the L. maculans and V. longisporum VOCs. L. maculans growth was slightly reduced by the one bacterial VOC methyl acetate that induced a strong downregulation of expression of genes involved in almost all metabolic functions in S. plymuthica. Similarly, the interaction between S. plymuthica and V. longisporum resulted in an insignificant growth reduction of the fungus and repressed the rate of bacterial metabolism on the transcriptional level, accompanied by an intense volatile dialogue. Overall, our results indicate that VOCs substantially contribute to the highly break species-specific interactions between pathogens and their natural antagonists and thus deserving of increased consideration for pathogen control.}, language = {en} } @article{KathThomasGaedke2022, author = {Kath, Nadja J. and Thomas, Mridul K. and Gaedke, Ursula}, title = {Mysterious ciliates: seasonally recurrent and yet hard to predict}, series = {Journal of plankton research}, volume = {44}, journal = {Journal of plankton research}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0142-7873}, doi = {10.1093/plankt/fbac043}, pages = {903 -- 922}, year = {2022}, abstract = {Ciliates represent a crucial link between phytoplankton and bacteria and mesozooplankton in pelagic food webs, but little is known about the processes influencing the dynamics of individual species. Using long-term, high-frequency observations, we compared the diversity and the temporal variability in biomass and species composition of the ciliate community in large, deep, mesotrophic Lake Constance to that of the phytoplankton and rotifer communities in the same lake. Furthermore, we used boosted regression trees to evaluate possible environmental predictors (temperature, three prey groups, four predator/competitor groups) influencing ciliate net growth. The biomass of all ciliate species showed a common, recurrent seasonal pattern, often with peaks in spring and summer. The ciliate community was more diverse than the rotifer community, exhibited highly synchronous dynamics and its species were regularly encountered during the season. The top-down control by copepods likely contributes to the ciliates' synchronized decline prior to the clear-water phase when food concentration is still high. The high temporal autocorrelation of the ciliate biomasses together with the inter-annual recurrent seasonal patterns and the low explanatory power of the environmental predictors suggest that the dynamics of individual ciliate species are strictly controlled, yet it remains difficult to determine the responsible factors.}, language = {en} } @article{KarwinkelWinklhoferJanneretal.2022, author = {Karwinkel, Thiemo and Winklhofer, Michael and Janner, Lars Erik and Brust, Vera and H{\"u}ppop, Ommo and Bairlein, Franz and Schmaljohann, Heiko}, title = {A magnetic pulse does not affect free-flight navigation behaviour of a medium-distance songbird migrant in spring}, series = {The journal of experimental biology}, volume = {225}, journal = {The journal of experimental biology}, number = {19}, publisher = {Company of Biologists}, address = {Cambridge}, issn = {0022-0949}, doi = {10.1242/jeb.244473}, pages = {7}, year = {2022}, abstract = {Current evidence suggests that migratory animals extract map information from the geomagnetic field for true navigation. The sensory basis underlying this feat is elusive, but presumably involves magnetic particles. A common experimental manipulation procedure consists of pre-treating animals with a magnetic pulse, with the aim of re-magnetising particles to alter the internal representation of the external field prior to a navigation task. Although pulsing provoked deflected bearings in caged songbirds, analogous studies with free-flying songbirds yielded inconsistent results. Here, we pulsed European robins (Erithacus rubecula) at an offshore stopover site during spring migration and monitored their free-flight behaviour with a regional-scale network of radio-receiving stations. We found no pulse effect on departure probability, nocturnal departure timing departure direction or consistency of flight direction. This suggests either no use of the geomagnetic map by our birds, or that magnetic pulses do not affect the sensory system underlying geomagnetic map detection.}, language = {en} } @article{SandhageHofmannAngombeKindermannetal.2022, author = {Sandhage-Hofmann, Alexandra and Angombe, Simon and Kindermann, Liana and Linst{\"a}dter, Anja and M{\"o}rchen, Ramona}, title = {Conservation with elephants and agricultural intensification}, series = {Geoderma : an international journal of soil science}, volume = {425}, journal = {Geoderma : an international journal of soil science}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0016-7061}, doi = {10.1016/j.geoderma.2022.116009}, pages = {15}, year = {2022}, abstract = {Nature conservation is currently shaping many terrestrial ecosystems in Africa. This is particularly evident in Sub-Saharan Africa (SSA), where conservation is intended to recover wildlife populations, with special focus on elephants. Rising numbers of elephants induce woody biomass losses but increase soil organic carbon (SOC) stocks from decaying wood and dung. We hypothesized that these increases under wildlife conservation in SSA go along with rising contents of plant residues in SOC, traceable by the molecular markers lignin and n-alkanes. In contrast, agricultural intensification would reduce them due to lower C input and faster SOC turnover through tillage. To test this, we analyzed lignin by the CuO oxidation method and n-alkanes by fast pressurized solvent extraction in topsoils (0-10 cm) of Arenosols and corresponding plant samples (trees, grasses and crops). Sampling sites followed conservation gradients with low, medium and high elephant densities and intensification gradients with rangeland and cropland in the woodland savanna of the Namibian Zambezi Region. Patterns of lignin-derived phenols were retained in the soil, whereas n-alkanes showed shifts in chain lengths. n-Alkanes also showed no clear increase or decrease under conservation or intensification, respectively. Differently, lignin-derived phenols showed lower values under intensification than under conservation. Confirming our hypothesis, rising SOC contents with rising elephant densities (from 4.4 at low to 5.7 g kg(-1) SOC at high elephant densities) went along with an increasing accumulation of lignin-derived phenols (24.4-34.8 g kg(-1) VSCOC). This increase is associated with the input of woody debris to the soil, as indicated by V-units and carbon isotopes, modulated by clay and woody biomass. We conclude, that increasing input of woody residues into soil by browsing behaviour of elephants is an important mechanism for controlling SOC supply in the context of wildlife conservation and is traceable with lignin-derived phenols, but not with n-alkanes.}, language = {en} } @article{WenderingNikoloski2022, author = {Wendering, Philipp and Nikoloski, Zoran}, title = {Genome-scale modeling specifies the metabolic capabilities of Rhizophagus irregularis}, series = {mSystems}, volume = {7}, journal = {mSystems}, number = {1}, publisher = {American Society for Microbiology}, address = {Washington, DC}, issn = {2379-5077}, doi = {10.1128/msystems.01216-21}, pages = {17}, year = {2022}, abstract = {Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R. irregularis renders it challenging to investigate molecular mechanisms that shape the physiology and interactions of this AMF with plants. Here, we used all published genomics, transcriptomics, and metabolomics resources to gain insights into the metabolic functionalities of R. irregularis by reconstructing its high-quality genome-scale metabolic network that considers enzyme constraints. Extensive validation tests with the enzyme-constrained metabolic model demonstrated that it can be used to (i) accurately predict increased growth of R. irregularis on myristate with minimal medium; (ii) integrate enzyme abundances and carbon source concentrations that yield growth predictions with high and significant Spearman correlation (rS = 0.74) to measured hyphal dry weight; and (iii) simulate growth rate increases with tighter association of this AMF with the host plant across three fungal structures. Based on the validated model and system-level analyses that integrate data from transcriptomics studies, we predicted that differences in flux distributions between intraradical mycelium and arbuscles are linked to changes in amino acid and cofactor biosynthesis. Therefore, our results demonstrated that the enzyme-constrained metabolic model can be employed to pinpoint mechanisms driving developmental and physiological responses of R. irregularis to different environmental cues. In conclusion, this model can serve as a template for other AMF and paves the way to identify metabolic engineering strategies to modulate fungal metabolic traits that directly affect plant performance. IMPORTANCE Mounting evidence points to the benefits of the symbiotic interactions between the arbuscular mycorrhiza fungus Rhizophagus irregularis and crops; however, the molecular mechanisms underlying the physiological responses of this fungus to different host plants and environments remain largely unknown. We present a manually curated, enzyme-constrained, genome-scale metabolic model of R. irregularis that can accurately predict experimentally observed phenotypes. We show that this high-quality model provides an entry point into better understanding the metabolic and physiological responses of this fungus to changing environments due to the availability of different nutrients. The model can be used to design metabolic engineering strategies to tailor R. irregularis metabolism toward improving the performance of host plants.}, language = {en} } @article{MatzWangKulshreshthaetal.2022, author = {Matz, Timon W. and Wang, Yang and Kulshreshtha, Ritika and Sampathkumar, Arun and Nikoloski, Zoran}, title = {Topological properties accurately predict cell division events and organization of shoot apical meristem in Arabidopsis thaliana}, series = {Development : Company of Biologists}, volume = {149}, journal = {Development : Company of Biologists}, number = {16}, publisher = {Company of Biologists}, address = {Cambridge}, issn = {0950-1991}, doi = {10.1242/dev.201024}, pages = {11}, year = {2022}, abstract = {Cell division and the resulting changes to the cell organization affect the shape and functionality of all tissues. Thus, understanding the determinants of the tissue-wide changes imposed by cell division is a key question in developmental biology. Here, we use a network representation of live cell imaging data from shoot apical meristems (SAMs) in Arabidopsis thaliana to predict cell division events and their consequences at the tissue level. We show that a support vector machine classifier based on the SAM network properties is predictive of cell division events, with test accuracy of 76\%, which matches that based on cell size alone. Furthermore, we demonstrate that the combination of topological and biological properties, including cell size, perimeter, distance and shared cell wall between cells, can further boost the prediction accuracy of resulting changes in topology triggered by cell division. Using our classifiers, we demonstrate the importance of microtubule-mediated cell-to-cell growth coordination in influencing tissue-level topology. Together, the results from our network-based analysis demonstrate a feedback mechanism between tissue topology and cell division in A. thaliana SAMs.}, language = {en} } @article{MollavaliBoernke2022, author = {Mollavali, Mohanna and B{\"o}rnke, Frederik}, title = {Characterization of trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase genes of tomato (Solanum lycopersicum L.) and analysis of their differential expression in response to temperature}, series = {International journal of molecular sciences}, volume = {23}, journal = {International journal of molecular sciences}, number = {19}, publisher = {MDPI}, address = {Basel}, issn = {1661-6596}, doi = {10.3390/ijms231911436}, pages = {17}, year = {2022}, abstract = {In plants, the trehalose biosynthetic pathway plays key roles in the regulation of carbon allocation and stress adaptation. Engineering of the pathway holds great promise to increase the stress resilience of crop plants. The synthesis of trehalose proceeds by a two-step pathway in which a trehalose-phosphate synthase (TPS) uses UDP-glucose and glucose-6-phosphate to produce trehalose-6 phosphate (T6P) that is subsequently dephosphorylated by trehalose-6 phosphate phosphatase (TPP). While plants usually do not accumulate high amounts of trehalose, their genome encodes large families of putative trehalose biosynthesis genes, with many members lacking obvious enzymatic activity. Thus, the function of putative trehalose biosynthetic proteins in plants is only vaguely understood. To gain a deeper insight into the role of trehalose biosynthetic proteins in crops, we assessed the enzymatic activity of the TPS/TPP family from tomato (Solanum lycopersicum L.) and investigated their expression pattern in different tissues as well as in response to temperature shifts. From the 10 TPS isoforms tested, only the 2 proteins belonging to class I showed enzymatic activity, while all 5 TPP isoforms investigated were catalytically active. Most of the TPS/TPP family members showed the highest expression in mature leaves, and promoter-reporter gene studies suggest that the two class I TPS genes have largely overlapping expression patterns within the vasculature, with only subtle differences in expression in fruits and flowers. The majority of tomato TPS/TPP genes were induced by heat stress, and individual family members also responded to cold. This suggests that trehalose biosynthetic pathway genes could play an important role during temperature stress adaptation. In summary, our study represents a further step toward the exploitation of the TPS and TPP gene families for the improvement of tomato stress resistance.}, language = {en} } @article{GaetjenWieczorekListeketal.2022, author = {G{\"a}tjen, Dominic and Wieczorek, Marek and Listek, Martin and Tomszak, Florian and N{\"o}lle, Volker and Hanack, Katja and Droste, Miriam Susanna}, title = {A switchable secrete-and-capture system enables efficient selection of Pichia pastoris clones producing high yields of Fab fragments}, series = {Journal of immunological methods}, volume = {511}, journal = {Journal of immunological methods}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0022-1759}, doi = {10.1016/j.jim.2022.113383}, pages = {14}, year = {2022}, abstract = {Pichia pastoris (syn. Komagataella phaffii) represents a commonly used expression system in the biotech industry. High clonal variation of transformants, however, typically results in a broad range of specific productivities for secreted proteins. To isolate rare clones with exceedingly high product titers, an extensive number of clones need to be screened. In contrast to high-throughput screenings of P. pastoris clones in microtiter plates, secrete-and -capture methodologies have the potential to efficiently isolate high-producer clones among millions of cells through fluorescence-activated cell sorting (FACS).Here, we describe a novel approach for the non-covalent binding of fragment antigen-binding (Fab) proteins to the cell surface for the isolation of high-producing clones. Eight different single-chain variable fragment (scFv)-based capture matrices specific for the constant part of the Fabs were fused to the Saccharomyces cerevisiae alpha -agglutinin (SAG1) anchor protein for surface display in P. pastoris. By encoding the capture matrix on an episomal plasmid harboring inherently unstable autonomously replicating sequences (ARS), this secrete-and -capture system offers a switchable scFv display. Efficient plasmid clearance upon removal of selective pres-sure enabled the direct use of isolated clones for subsequent Fab production. Flow-sorted clones (n = 276) displaying high amounts of Fabs showed a significant increase in median Fab titers detected in the cell-free supernatant (CFS) compared to unsorted clones (n = 276) when cells were cultivated in microtiter plates (fac-tor in the range of-21-49). Fab titers of clones exhibiting the highest product titer observed for each of the two approaches were increased by up to 8-fold for the sorted clone. Improved Fab yields of sorted cells vs. unsorted cells were confirmed in an upscaled shake flask cultivation of selected candidates (factor in the range of-2-3). Hence, the developed display-based selection method proved to be a valuable tool for efficient clone screening in the early stages of our bioprocess development.}, language = {en} } @article{BanerjeeSilvaLipowskyetal.2022, author = {Banerjee, Pallavi and Silva, Daniel Varon and Lipowsky, Reinhard and Santer, Mark}, title = {The importance of side branches of glycosylphosphatidylinositol anchors}, series = {Glycobiology}, volume = {32}, journal = {Glycobiology}, number = {11}, publisher = {Oxford Univ. Press}, address = {Cary}, issn = {1460-2423}, doi = {10.1093/glycob/cwac037}, pages = {933 -- 948}, year = {2022}, abstract = {Many proteins are anchored to the cell surface of eukaryotes using a unique family of glycolipids called glycosylphosphatidylinositol (GPI) anchors. These glycolipids also exist without a covalently bound protein, in particular on the cell surfaces of protozoan parasites where they are densely populated. GPIs and GPI-anchored proteins participate in multiple cellular processes such as signal transduction, cell adhesion, protein trafficking and pathogenesis of Malaria, Toxoplasmosis, Trypanosomiasis and prion diseases, among others. All GPIs share a common conserved glycan core modified in a cell-dependent manner with additional side glycans or phosphoethanolamine residues. Here, we use atomistic molecular dynamic simulations and perform a systematic study to evaluate the structural properties of GPIs with different side chains inserted in lipid bilayers. Our results show a flop-down orientation of GPIs with respect to the membrane surface and the presentation of the side chain residues to the solvent. This finding agrees well with experiments showing the role of the side residues as active epitopes for recognition of GPIs by macrophages and induction of GPI-glycan-specific immune responses. Protein-GPI interactions were investigated by attaching parasitic GPIs to Green Fluorescent Protein. GPIs are observed to recline on the membrane surface and pull down the attached protein close to the membrane facilitating mutual contacts between protein, GPI and the lipid bilayer. This model is efficient in evaluating the interaction of GPIs and GPI-anchored proteins with membranes and can be extended to study other parasitic GPIs and proteins and develop GPI-based immunoprophylaxis to treat infectious diseases.}, language = {en} } @article{SzangoliesRohwaederJeltsch2022, author = {Szangolies, Leonna and Rohw{\"a}der, Marie-Sophie and Jeltsch, Florian}, title = {Single large AND several small habitat patches}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {65}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, publisher = {Elsevier}, address = {M{\"u}nchen}, issn = {1439-1791}, doi = {10.1016/j.baae.2022.09.004}, pages = {16 -- 27}, year = {2022}, abstract = {The debate whether single large or several small (SLOSS) patches benefit biodiversity has existed for decades, but recent literature provides increasing evidence for the importance of small habitats. Possible beneficial mechanisms include reduced presence of preda-tors and competitors in small habitat areas or specific functions such as stepping stones for dispersal. Given the increasing amount of studies highlighting individual behavioral differences that may influence these functions, we hypothesize that the advantage of small versus large habitat patches not only depends on patch functionality but also on the presence of animal personalities (i.e., risk-tolerant vs. risk-averse). Using an individual-based, spatially-explicit community model, we analyzed the diversity of mammal communities in landscapes consisting of a few large habitat islands interspersed with different amounts and sizes of small habitat patches. Within these heterogeneous environments, individuals compete for resources and form home-ranges, with only risk-tolerant individuals using habitat edges. Results show that when risk-tolerant individuals exist, small patches increase species diversity. A strong peak occurs at approximately 20\% habitat cover in small patches when those small habitats are only used for foraging but not for breeding and home-range core position. Additional usage as stepping stones for juvenile dispersal further increases species persistence. Over-all, our results reveal that a combination of a few large and several small habitat patches promotes biodiversity by enhancing land-scape heterogeneity. Here, heterogeneity is created by pronounced differences in habitat functionality, increasing edge density, and variability in habitat use by different behavioral types. The finding that a combination of single large AND several small (SLASS) patches is needed for effective biodiversity preservation has implications for advancing landscape conservation. Particularly in struc-turally poor agricultural areas, modern technology enables precise management with the opportunity to create small foraging habitats by excluding less profitable agricultural land from cultivation.}, language = {en} } @article{LangaryKuekenNikoloski2023, author = {Langary, Damoun and K{\"u}ken, Anika and Nikoloski, Zoran}, title = {The effective deficiency of biochemical networks}, series = {Scientific reports}, volume = {13}, journal = {Scientific reports}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-023-41767-1}, pages = {12}, year = {2023}, abstract = {The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of a network to permit variations of the complex formation rate vector at steady state, irrespective of the network kinetics. However, the deficiency is by definition completely insensitive to the fine details of the directionality of reactions as well as bounds on reaction fluxes. While the classical definition of deficiency can be readily applied in the analysis of unconstrained, weakly reversible networks, it only provides an upper bound in the cases where relevant constraints on reaction fluxes are imposed. Here we propose the concept of effective deficiency, which provides a more accurate assessment of the network's capacity to permit steady state variations at the complex level for constrained networks of any reversibility patterns. The effective deficiency relies on the concept of nonstoichiometric balanced complexes, which we have already shown to be present in real-world biochemical networks operating under flux constraints. Our results demonstrate that the effective deficiency of real-world biochemical networks is smaller than the classical deficiency, indicating the effects of reaction directionality and flux bounds on the variation of the complex formation rate vector at steady state.}, language = {en} } @article{KuekenTrevesNikoloski2023, author = {K{\"u}ken, Anika and Treves, Haim and Nikoloski, Zoran}, title = {A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae}, series = {Frontiers in plant science : FPLS}, volume = {14}, journal = {Frontiers in plant science : FPLS}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2023.1140829}, pages = {12}, year = {2023}, abstract = {Introduction Flux phenotypes from different organisms and growth conditions allow better understanding of differential metabolic networks functions. Fluxes of metabolic reactions represent the integrated outcome of transcription, translation, and post-translational modifications, and directly affect growth and fitness. However, fluxes of intracellular metabolic reactions cannot be directly measured, but are estimated via metabolic flux analysis (MFA) that integrates data on isotope labeling patterns of metabolites with metabolic models. While the application of metabolomics technologies in photosynthetic organisms have resulted in unprecedented data from 13CO2-labeling experiments, the bottleneck in flux estimation remains the application of isotopically nonstationary MFA (INST-MFA). INST-MFA entails fitting a (large) system of coupled ordinary differential equations, with metabolite pools and reaction fluxes as parameters. Here, we focus on the Calvin-Benson cycle (CBC) as a key pathway for carbon fixation in photosynthesizing organisms and ask if approaches other than classical INST-MFA can provide reliable estimation of fluxes for reactions comprising this pathway. Methods First, we show that flux estimation with the labeling patterns of all CBC intermediates can be formulated as a single constrained regression problem, avoiding the need for repeated simulation of time-resolved labeling patterns. Results We then compare the flux estimates of the simulation-free constrained regression approach with those obtained from the classical INST-MFA based on labeling patterns of metabolites from the microalgae Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii under different growth conditions. Discussion Our findings indicate that, in data-rich scenarios, simulation-free regression-based approaches provide a suitable alternative for flux estimation from classical INST-MFA since we observe a high qualitative agreement (rs=0.89) to predictions obtained from INCA, a state-of-the-art tool for INST-MFA.}, language = {en} } @article{NendelRecklingDebaekeetal.2023, author = {Nendel, Claas and Reckling, Moritz and Debaeke, Philippe and Schulz, Susanne and Berg-Mohnicke, Michael and Constantin, Julie and Fronzek, Stefan and Hoffmann, Munir and Jakšić, Snežana and Kersebaum, Kurt-Christian and Klimek-Kopyra, Agnieszka and Raynal, H{\´e}l{\`e}ne and Schoving, C{\´e}line and Stella, Tommaso and Battisti, Rafael}, title = {Future area expansion outweighs increasing drought risk for soybean in Europe}, series = {Global change biology}, volume = {29}, journal = {Global change biology}, number = {5}, publisher = {Wiley-Blackwell}, address = {Ocford [u.a]}, issn = {1354-1013}, doi = {10.1111/gcb.16562}, pages = {1340 -- 1358}, year = {2023}, abstract = {The European Union is highly dependent on soybean imports from overseas to meet its protein demands. Individual Member States have been quick to declare self-sufficiency targets for plant-based proteins, but detailed strategies are still lacking. Rising global temperatures have painted an image of a bright future for soybean production in Europe, but emerging climatic risks such as drought have so far not been included in any of those outlooks. Here, we present simulations of future soybean production and the most prominent risk factors across Europe using an ensemble of climate and soybean growth models. Projections suggest a substantial increase in potential soybean production area and productivity in Central Europe, while southern European production would become increasingly dependent on supplementary irrigation. Average productivity would rise by 8.3\% (RCP 4.5) to 8.7\% (RCP 8.5) as a result of improved growing conditions (plant physiology benefiting from rising temperature and CO2 levels) and farmers adapting to them by using cultivars with longer phenological cycles. Suitable production area would rise by 31.4\% (RCP 4.5) to 37.7\% (RCP 8.5) by the mid-century, contributing considerably more than productivity increase to the production potential for closing the protein gap in Europe. While wet conditions at harvest and incidental cold spells are the current key challenges for extending soybean production, the models and climate data analysis anticipate that drought and heat will become the dominant limitations in the future. Breeding for heat-tolerant and water-efficient genotypes is needed to further improve soybean adaptation to changing climatic conditions.}, 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} }