@article{ChapmanLantOhashietal.2019, author = {Chapman, Eric M. and Lant, Benjamin and Ohashi, Yota and Yu, Bin and Schertzberg, Michael and Go, Christopher and Dogra, Deepika and Koskimaki, Janne and Girard, Romuald and Li, Yan and Fraser, Andrew G. and Awad, Issam A. and Abdelilah-Seyfried, Salim and Gingras, Anne-Claude and Derry, William Brent}, title = {A conserved CCM complex promotes apoptosis non-autonomously by regulating zinc homeostasis}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-09829-z}, pages = {15}, year = {2019}, abstract = {Apoptotic death of cells damaged by genotoxic stress requires regulatory input from surrounding tissues. The C. elegans scaffold protein KRI-1, ortholog of mammalian KRIT1/CCM1, permits DNA damage-induced apoptosis of cells in the germline by an unknown cell non-autonomous mechanism. We reveal that KRI-1 exists in a complex with CCM-2 in the intestine to negatively regulate the ERK-5/MAPK pathway. This allows the KLF-3 transcription factor to facilitate expression of the SLC39 zinc transporter gene zipt-2.3, which functions to sequester zinc in the intestine. Ablation of KRI-1 results in reduced zinc sequestration in the intestine, inhibition of IR-induced MPK-1/ERK1 activation, and apoptosis in the germline. Zinc localization is also perturbed in the vasculature of krit1(-/-) zebrafish, and SLC39 zinc transporters are mis-expressed in Cerebral Cavernous Malformations (CCM) patient tissues. This study provides new insights into the regulation of apoptosis by cross-tissue communication, and suggests a link between zinc localization and CCM disease.}, language = {en} } @article{WolffGastEversetal.2021, author = {Wolff, Martin and Gast, Klaus and Evers, Andreas and Kurz, Michael and Pfeiffer-Marek, Stefania and Sch{\"u}ler, Anja and Seckler, Robert and Thalhammer, Anja}, title = {A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4}, series = {Biomolecules}, volume = {11}, journal = {Biomolecules}, number = {9}, publisher = {MDPI}, address = {Basel}, issn = {2218-273X}, doi = {10.3390/biom11091305}, pages = {20}, year = {2021}, abstract = {Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix-helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.}, language = {en} } @article{BuyinzaDereseNdakalaetal.2021, author = {Buyinza, Daniel and Derese, Solomon and Ndakala, Albert and Heydenreich, Matthias and Yenesew, Abiy and Koch, Andreas and Oriko, Richard}, title = {A coumestan and a coumaronochromone from Millettia lasiantha}, series = {Biochemical systematics and ecology}, volume = {97}, journal = {Biochemical systematics and ecology}, publisher = {Elsevier}, address = {Oxford}, issn = {0305-1978}, doi = {10.1016/j.bse.2021.104277}, pages = {5}, year = {2021}, abstract = {The manuscript describes the phytochemical investigation of the roots, leaves and stem bark of Millettia lasiantha resulting in the isolation of twelve compounds including two new isomeric isoflavones lascoumestan and las-coumaronochromone. The structures of the new compounds were determined using different spectroscopic techniques.}, language = {en} } @article{LuetkecosmannFaupelPorstmannetal.2019, author = {Luetkecosmann, Steffi and Faupel, Thomas and Porstmann, Silvia and Porstmann, Tomas and Micheel, Burkhard and Hanack, Katja}, title = {A cross-reactive monoclonal antibody as universal detection antibody in autoantibody diagnostic assays}, series = {Clinica chimica acta}, volume = {499}, journal = {Clinica chimica acta}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0009-8981}, doi = {10.1016/j.cca.2019.09.003}, pages = {87 -- 92}, year = {2019}, abstract = {Diagnostics of Autoimmune Diseases involve screening of patient samples for containing autoantibodies against various antigens. To ensure quality of diagnostic assays a calibrator is needed in each assay system. Different calibrators as recombinant human monoclonal antibodies as well as chimeric antibodies against the autoantigens of interest are described. A less cost-intensive and also more representative possibility covering different targets on the antigens is the utilization of polyclonal sera from other species. Nevertheless, the detection of human autoantibodies as well as the calibration reagent containing antibodies from other species in one assay constitutes a challenge in terms of assay calibration. We therefore developed a cross-reactive monoclonal antibody which binds human as well as rabbit sera with similar affinities in the nanomolar range. We tested our monoclonal antibody S38CD11B12 successfully in the commercial Serazym (R) Anti-Cardiolipin-beta 2-GPI IgG/IgM assay and could thereby prove the eligibility of S38CD11B12 as detection antibody in autoimmune diagnostic assays using rabbit derived sera as reference material.}, language = {en} } @article{DemalHeiseReizetal.2019, author = {Demal, Till Joscha and Heise, Melina and Reiz, Benedikt and Dogra, Deepika and Braenne, Ingrid and Reichenspurner, Hermann and M{\"a}nner, J{\"o}rg and Aherrahrou, Zouhair and Schunkert, Heribert and Erdmann, Jeanette and Abdelilah-Seyfried, Salim}, title = {A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A}, series = {Scientific reports}, volume = {9}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-39648-7}, pages = {12}, year = {2019}, abstract = {The genetics of many congenital heart diseases (CHDs) can only unsatisfactorily be explained by known chromosomal or Mendelian syndromes. Here, we present sequencing data of a family with a potentially multigenic origin of CHD. Twelve of nineteen family members carry a familial mutation [NM_004329.2:c.1328 G > A (p.R443H)] which encodes a predicted deleterious variant of BMPR1A. This mutation co-segregates with a linkage region on chromosome 1 that associates with the emergence of severe CHDs including Ebstein's anomaly, atrioventricular septal defect, and others. We show that the continuous overexpression of the zebrafish homologous mutation bmpr1aap.R438H within endocardium causes a reduced AV valve area, a downregulation of Wnt/ß-catenin signalling at the AV canal, and growth of additional tissue mass in adult zebrafish hearts. This finding opens the possibility of testing genetic interactions between BMPR1A and other candidate genes within linkage region 1 which may provide a first step towards unravelling more complex genetic patterns in cardiovascular disease aetiology.}, language = {en} } @article{XiaoLiuWangetal.2020, author = {Xiao, Shangbin and Liu, Liu and Wang, Wei and Lorke, Andreas and Woodhouse, Jason Nicholas and Grossart, Hans-Peter}, title = {A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water}, series = {Hydrology and earth system sciences : HESS}, volume = {24}, journal = {Hydrology and earth system sciences : HESS}, number = {7}, publisher = {European Geosciences Union (EGU) ; Copernicus}, address = {Munich}, issn = {1027-5606}, doi = {10.5194/hess-24-3871-2020}, pages = {3871 -- 3880}, year = {2020}, abstract = {Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95\%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6\% and a measurement accuracy of 0.5\% for CH4. A similar performance was observed for dissolved CO2 (t(95\%) = 10 s, equilibration ratio 67.1 \%). An equilibration ratio as high as 91.8\% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.}, language = {en} } @article{SharmaRuelensMaggenetal.2017, author = {Sharma, Neha and Ruelens, Philip and Maggen, Thomas and Dochy, Niklas and Torfs, Sanne and Kaufmann, Kerstin and Rohde, Antje and Geuten, Koen}, title = {A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {173}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.16.01161}, pages = {1301 -- 1315}, year = {2017}, abstract = {Winter cereals require prolonged cold to transition from vegetative to reproductive development. This process, referred to as vernalization, has been extensively studied in Arabidopsis (Arabidopsis thaliana). In Arabidopsis, a key flowering repressor called FLOWERING LOCUS C (FLC) quantitatively controls the vernalization requirement. By contrast, in cereals, the vernalization response is mainly regulated by the VERNALIZATION genes, VRN1 and VRN2. Here, we characterize ODDSOC2, a recently identified FLC ortholog in monocots, knowing that it belongs to the FLC lineage. By studying its expression in a diverse set of Brachypodium accessions, we find that it is a good predictor of the vernalization requirement. Analyses of transgenics demonstrated that BdODDSOC2 functions as a vernalization-regulated flowering repressor. In most Brachypodium accessions BdODDSOC2 is down-regulated by cold, and in one of the winter accessions in which this down-regulation was evident, BdODDSOC2 responded to cold before BdVRN1. When stably down-regulated, the mechanism is associated with spreading H3K27me3 modifications at the BdODDSOC2 chromatin. Finally, homoeolog-specific gene expression analyses identify TaAGL33 and its splice variant TaAGL22 as the FLC orthologs in wheat (Triticum aestivum) behaving most similar to Brachypodium ODDSOC2. Overall, our study suggests that ODDSOC2 is not only phylogenetically related to FLC in eudicots but also functions as a flowering repressor in the vernalization pathway of Brachypodium and likely other temperate grasses. These insights could prove useful in breeding efforts to refine the vernalization requirement of temperate cereals and adapt varieties to changing climates.}, language = {en} } @article{LahLoeberHsiangetal.2017, author = {Lah, Ljerka and L{\"o}ber, Ulrike and Hsiang, Tom and Hartmann, Stefanie}, title = {A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles}, series = {Fungal biology}, volume = {121}, journal = {Fungal biology}, publisher = {Elsevier}, address = {Oxford}, issn = {1878-6146}, doi = {10.1016/j.funbio.2016.12.002}, pages = {234 -- 252}, year = {2017}, abstract = {Ophiostomatoid fungi are vectored by their bark-beetle associates and colonize different host tree species. To survive and proliferate in the host, they have evolved mechanisms for detoxification and elimination of host defence compounds, efficient nutrient sequestration, and, in pathogenic species, virulence towards plants. Here, we assembled a draft genome of the spruce pathogen Ophiostoma bicolor. For our comparative and phylogenetic analyses, we mined the genomes of closely related species (Ophiostoma piceae, Ophiostoma ulmi, Ophiostoma novo-ulmi, and Grosmannia clavigera). Our aim was to acquire a genomic and evolutionary perspective of gene families important in host colonization. Genome comparisons showed that both the nuclear and mitochondrial genomes in our assembly were largely complete. Our O. bicolor 25.3 Mbp draft genome had 10 018 predicted genes, 6041 proteins with gene ontology (GO) annotation, 269 carbohydrate-active enzymes (CAZymes), 559 peptidases and inhibitors, and 1373 genes likely involved in pathogen-host interactions. Phylogenetic analyses of selected protein families revealed core sets of cytochrome P450 genes, ABC transporters and backbone genes involved in secondary metabolite (SM) biosynthesis (polyketide synthases (PKS) and non-ribosomal synthases), and species-specific gene losses and duplications. Phylogenetic analyses of protein families of interest provided insight into evolutionary adaptations to host biochemistry in ophiostomatoid fungi.}, language = {en} } @article{ZhangChenSiemiatkowskaetal.2020, author = {Zhang, Youjun and Chen, Moxian and Siemiatkowska, Beata and Toleco, Mitchell Rey and Jing, Yue and Strotmann, Vivien and Zhang, Jianghua and Stahl, Yvonne and Fernie, Alisdair R.}, title = {A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species}, series = {Plant Communications}, volume = {1}, journal = {Plant Communications}, number = {5}, publisher = {Science Direct}, address = {New York}, issn = {2590-3462}, pages = {12}, year = {2020}, abstract = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.}, language = {en} } @article{JantzenWozniakKappeletal.2019, author = {Jantzen, Friederike and Wozniak, Natalia Joanna and Kappel, Christian and Sicard, Adrien and Lenhard, Michael}, title = {A high‑throughput amplicon‑based method for estimating outcrossing rates}, series = {Plant Methods}, volume = {15}, journal = {Plant Methods}, number = {47}, publisher = {BioMed Central}, address = {London}, issn = {1746-4811}, doi = {10.1186/s13007-019-0433-9}, pages = {14}, year = {2019}, abstract = {Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming. Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd's Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons. Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.}, language = {en} } @article{WandtWinkelbeinerBornhorstetal.2021, author = {Wandt, Viktoria Klara Veronika and Winkelbeiner, Nicola Lisa and Bornhorst, Julia and Witt, Barbara and Raschke, Stefanie and Simon, Luise and Ebert, Franziska and Kipp, Anna Patricia and Schwerdtle, Tanja}, title = {A matter of concern}, series = {Redox Biology}, volume = {41}, journal = {Redox Biology}, publisher = {Elsevier}, address = {Amsterdam}, doi = {10.1016/j.redox.2021.101877}, pages = {13}, year = {2021}, abstract = {Neurons are post-mitotic cells in the brain and their integrity is of central importance to avoid neurodegeneration. Yet, the inability of self-replenishment of post-mitotic cells results in the need to withstand challenges from numerous stressors during life. Neurons are exposed to oxidative stress due to high oxygen consumption during metabolic activity in the brain. Accordingly, DNA damage can occur and accumulate, resulting in genome instability. In this context, imbalances in brain trace element homeostasis are a matter of concern, especially regarding iron, copper, manganese, zinc, and selenium. Although trace elements are essential for brain physiology, excess and deficient conditions are considered to impair neuronal maintenance. Besides increasing oxidative stress, DNA damage response and repair of oxidative DNA damage are affected by trace elements. Hence, a balanced trace element homeostasis is of particular importance to safeguard neuronal genome integrity and prevent neuronal loss. This review summarises the current state of knowledge on the impact of deficient, as well as excessive iron, copper, manganese, zinc, and selenium levels on neuronal genome stability}, language = {en} } @article{HartungBorghardt2020, author = {Hartung, Niklas and Borghardt, Jens Markus}, title = {A mechanistic framework for a priori pharmacokinetic predictions of orally inhaled drugs}, series = {PLoS Computational Biology : a new community journal}, volume = {16}, journal = {PLoS Computational Biology : a new community journal}, number = {12}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1008466}, pages = {24}, year = {2020}, abstract = {Author summary
The use of orally inhaled drugs for treating lung diseases is appealing since they have the potential for lung selectivity, i.e. high exposure at the site of action -the lung- without excessive side effects. However, the degree of lung selectivity depends on a large number of factors, including physiochemical properties of drug molecules, patient disease state, and inhalation devices. To predict the impact of these factors on drug exposure and thereby to understand the characteristics of an optimal drug for inhalation, we develop a predictive mathematical framework (a "pharmacokinetic model"). In contrast to previous approaches, our model allows combining knowledge from different sources appropriately and its predictions were able to adequately predict different sets of clinical data. Finally, we compare the impact of different factors and find that the most important factors are the size of the inhaled particles, the affinity of the drug to the lung tissue, as well as the rate of drug dissolution in the lung. In contrast to the common belief, the solubility of a drug in the lining fluids is not found to be relevant. These findings are important to understand how inhaled drugs should be designed to achieve best treatment results in patients.
The fate of orally inhaled drugs is determined by pulmonary pharmacokinetic processes such as particle deposition, pulmonary drug dissolution, and mucociliary clearance. Even though each single process has been systematically investigated, a quantitative understanding on the interaction of processes remains limited and therefore identifying optimal drug and formulation characteristics for orally inhaled drugs is still challenging. To investigate this complex interplay, the pulmonary processes can be integrated into mathematical models. However, existing modeling attempts considerably simplify these processes or are not systematically evaluated against (clinical) data. In this work, we developed a mathematical framework based on physiologically-structured population equations to integrate all relevant pulmonary processes mechanistically. A tailored numerical resolution strategy was chosen and the mechanistic model was evaluated systematically against data from different clinical studies. Without adapting the mechanistic model or estimating kinetic parameters based on individual study data, the developed model was able to predict simultaneously (i) lung retention profiles of inhaled insoluble particles, (ii) particle size-dependent pharmacokinetics of inhaled monodisperse particles, (iii) pharmacokinetic differences between inhaled fluticasone propionate and budesonide, as well as (iv) pharmacokinetic differences between healthy volunteers and asthmatic patients. Finally, to identify the most impactful optimization criteria for orally inhaled drugs, the developed mechanistic model was applied to investigate the impact of input parameters on both the pulmonary and systemic exposure. Interestingly, the solubility of the inhaled drug did not have any relevant impact on the local and systemic pharmacokinetics. Instead, the pulmonary dissolution rate, the particle size, the tissue affinity, and the systemic clearance were the most impactful potential optimization parameters. In the future, the developed prediction framework should be considered a powerful tool for identifying optimal drug and formulation characteristics.}, language = {en} } @article{SchiroColangeliMueller2019, author = {Schiro, Gabriele and Colangeli, Pierluigi and M{\"u}ller, Marina E. H.}, title = {A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field}, series = {Frontiers in microbiology}, volume = {10}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2019.02095}, pages = {12}, year = {2019}, language = {en} } @article{WinkelbeinerWandtEbertetal.2020, author = {Winkelbeiner, Nicola Lisa and Wandt, Viktoria Klara Veronika and Ebert, Franziska and Lossow, Kristina and Bankoglu, Ezgi E. and Martin, Maximilian and Mangerich, Aswin and Stopper, Helga and Bornhorst, Julia and Kipp, Anna Patricia and Schwerdtle, Tanja}, title = {A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice}, series = {International Journal of Molecular Sciences}, volume = {21}, journal = {International Journal of Molecular Sciences}, number = {18}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms21186600}, pages = {19}, year = {2020}, abstract = {Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2'-deoxyguanosine (8-oxodG), 5-hydroxy-2'-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.}, language = {en} } @article{ObbardShiRobertsetal.2020, author = {Obbard, Darren J. and Shi, Mang and Roberts, Katherine E. and Longdon, Ben and Dennis, Alice B.}, title = {A new lineage of segmented RNA viruses infecting animals}, series = {Virus Evolution}, volume = {6}, journal = {Virus Evolution}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2057-1577}, doi = {10.1093/ve/vez061}, pages = {1 -- 10}, year = {2020}, abstract = {Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.}, language = {en} } @article{VandenWyngaertSetoRojasJimenezetal.2017, author = {Van den Wyngaert, Silke and Seto, Kensuke and Rojas-Jimenez, Keilor and Kagami, Maiko and Grossart, Hans-Peter}, title = {A New Parasitic Chytrid, Staurastromyces oculus (Rhizophydiales, Staurastromy-cetaceae fam. nov.), Infecting the Freshwater Desmid Staurastrum sp.}, series = {Protist}, volume = {168}, journal = {Protist}, publisher = {Elsevier}, address = {Jena}, issn = {1434-4610}, doi = {10.1016/j.protis.2017.05.001}, pages = {392 -- 407}, year = {2017}, abstract = {Chytrids are a diverse group of ubiquitous true zoosporic fungi. The recent molecular discovery of a large diversity of undescribed chytrids has raised awareness on their important, but so far understudied ecological role in aquatic ecosystems. In the pelagic zone, of both freshwater and marine ecosystems, many chytrid species have been morphologically described as parasites on almost all major groups of phytoplankton. However, the majority of these parasitic chytrids has rarely been isolated and lack DNA sequence data, resulting in a large proportion of "dark taxa" in databases. Here, we report on the isolation and in-depth morphological, molecular and host range characterization of a chytrid infecting the common freshwater desmid Staurastrum sp. We provide first insights on the metabolic activity of the different chytrid development stages by using the vital dye FUN (R)-1 (2-chloro-4-[2,3-dihydro-3-methyl-[benzo-1,3-thiazol-2-yl]-methylidene]-1-phenylquinolinium iodide). Cross infection experiments suggest that this chytrid is an obligate parasite and specific for the genus Staurastrum sp. Phylogenetic analysis, based on ITS1-5.8S-ITS2 and 28S rDNA sequences, placed it in the order Rhizophydiales. Based on the unique zoospore ultrastructure, combined with thallus morphology, and molecular phylogenetic placement, we describe this parasitic chytrid as a new genus and species Staurastromyces oculus, within a new family Staurastromycetaceae. (C) 2017 Elsevier GmbH. All rights reserved.}, language = {en} } @article{GoethelListekMesserschmidtetal.2021, author = {G{\"o}thel, Markus and Listek, Martin and Messerschmidt, Katrin and Schl{\"o}r, Anja and H{\"o}now, Anja and Hanack, Katja}, title = {A New Workflow to Generate Monoclonal Antibodies against Microorganisms}, series = {Applied Sciences}, volume = {11}, journal = {Applied Sciences}, number = {20}, publisher = {MDPI}, address = {Basel}, issn = {1454-5101}, doi = {10.3390/app11209359}, pages = {15}, year = {2021}, abstract = {Monoclonal antibodies are used worldwide as highly potent and efficient detection reagents for research and diagnostic applications. Nevertheless, the specific targeting of complex antigens such as whole microorganisms remains a challenge. To provide a comprehensive workflow, we combined bioinformatic analyses with novel immunization and selection tools to design monoclonal antibodies for the detection of whole microorganisms. In our initial study, we used the human pathogenic strain E. coli O157:H7 as a model target and identified 53 potential protein candidates by using reverse vaccinology methodology. Five different peptide epitopes were selected for immunization using epitope-engineered viral proteins. The identification of antibody-producing hybridomas was performed by using a novel screening technology based on transgenic fusion cell lines. Using an artificial cell surface receptor expressed by all hybridomas, the desired antigen-specific cells can be sorted fast and efficiently out of the fusion cell pool. Selected antibody candidates were characterized and showed strong binding to the target strain E. coli O157:H7 with minor or no cross-reactivity to other relevant microorganisms such as Legionella pneumophila and Bacillus ssp. This approach could be useful as a highly efficient workflow for the generation of antibodies against microorganisms.}, language = {en} } @article{HahnewaldLeimkuehlerVilasecaetal.2006, author = {Hahnewald, Rita and Leimk{\"u}hler, Silke and Vilaseca, Antonia and Acquaviva-Bourdain, Cecile and Lenz, Ulrike and Reiss, Jochen}, title = {A novel MOCS2 mutation reveals coordinated expression of the small and large subunit of molybdopterin synthase}, series = {Molecular genetics and metabolism}, volume = {89}, journal = {Molecular genetics and metabolism}, number = {3}, publisher = {Elsevier}, address = {San Diego}, issn = {1096-7192}, doi = {10.1016/j.ymgme.2006.04.008}, pages = {210 -- 213}, year = {2006}, abstract = {The small and large subunits of molybdopterin (MPT) synthase (MOCS2A and MOCS2B), are both encoded by the MOCS2 gene in overlapping and shifted open reading frames (ORFs), which is a highly unusual structure for eukaryotes. Theoretical analysis of genomic sequences suggested that the expression of these overlapping ORFs is facilitated by the use of alternate first exons leading to alternative transcripts. Here, we confirm the existence of these overlapping transcripts experimentally. Further, we identified a deletion in a molybdenum cofactor deficient patient, which removes the start codon for the small subunit (MOCS2A). We observed undisturbed production of both transcripts, while Western blot analysis demonstrated that MOCS2B, the large subunit, is unstable in the absence of MOCS2A. This reveals new insights into the expression of this evolutionary ancient anabolic system.}, language = {en} } @article{LuetkecosmannWarsinkeTschoepeetal.2017, author = {L{\"u}tkecosmann, Steffi and Warsinke, Axel and Tsch{\"o}pe, Winfried and Eichler, R{\"u}diger and Hanack, Katja}, title = {A novel monoclonal antibody suitable for the detection of leukotriene B4}, series = {Biochemical and biophysical research communications}, volume = {482}, journal = {Biochemical and biophysical research communications}, number = {4}, publisher = {Elsevier}, address = {San Diego}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2016.11.157}, pages = {1054 -- 1059}, year = {2017}, abstract = {Leukotriene B4 as an inflammatory mediator is an important biomarker for different respiratory diseases like asthma, chronic obstructive pulmonary disease or cystic lung fibrosis. Therefore the detection of LTB4 is helpful in the diagnosis of these pulmonary diseases. However, until now its determination in exhaled breath condensates suffers from problems of accuracy. Reasons for that could be improper sample collection and preparation methods of condensates and the lack of consistently assay specificity and reproducibility of the used immunoassay detection system. In this study we describe the development and the characterization of a specific monoclonal antibody (S27BC6) against LTB4, its use as molecular recognition element for the development of an enzyme-linked immunoassay to detect LTB4 and discuss possible future diagnostic applications.}, language = {en} } @article{KagelBierFrohmeetal.2019, author = {Kagel, Heike and Bier, Frank Fabian and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn F.}, title = {A Novel Optical Method To Reversibly Control Enzymatic Activity Based On Photoacids}, series = {Scientific reports}, volume = {9}, journal = {Scientific reports}, publisher = {Nature Publishing Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-50867-w}, pages = {6}, year = {2019}, abstract = {Most biochemical reactions depend on the pH value of the aqueous environment and some are strongly favoured to occur in an acidic environment. A non-invasive control of pH to tightly regulate such reactions with defined start and end points is a highly desirable feature in certain applications, but has proven difficult to achieve so far. We report a novel optical approach to reversibly control a typical biochemical reaction by changing the pH and using acid phosphatase as a model enzyme. The reversible photoacid G-acid functions as a proton donor, changing the pH rapidly and reversibly by using high power UV LEDs as an illumination source in our experimental setup. The reaction can be tightly controlled by simply switching the light on and off and should be applicable to a wide range of other enzymatic reactions, thus enabling miniaturization and parallelization through non-invasive optical means.}, language = {en} } @article{SpikesRodriguezSilvaBennettetal.2021, author = {Spikes, Montrai and Rodr{\´i}guez-Silva, Rodet and Bennett, Kerri-Ann and Br{\"a}ger, Stefan and Josaphat, James and Torres-Pineda, Patricia and Ernst, Anja and Havenstein, Katja and Schlupp, Ingo and Tiedemann, Ralph}, title = {A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario}, series = {BMC Research Notes}, volume = {14}, journal = {BMC Research Notes}, publisher = {BMC Research Notes / Biomed Central}, address = {London}, issn = {1756-0500}, doi = {10.1186/s13104-021-05843-x}, pages = {1 -- 8}, year = {2021}, abstract = {Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Mirago{\^a}ne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Mirago{\^a}ne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Mirago{\^a}ne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Mirago{\^a}ne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Mirago{\^a}ne clade.}, language = {en} } @article{KoppMuellerPohletal.2019, author = {Kopp, Johannes Florian and M{\"u}ller, Sandra Marie and Pohl, Gabriele and Lossow, Kristina and Kipp, Anna Patricia and Schwerdtle, Tanja}, title = {A quick and simple method for the determination of six trace elements in mammalian serum samples using ICP-MS/MS}, series = {Journal of trace elements in medicine and biology}, volume = {54}, journal = {Journal of trace elements in medicine and biology}, publisher = {Elsevier}, address = {M{\"u}nchen}, issn = {0946-672X}, doi = {10.1016/j.jtemb.2019.04.015}, pages = {221 -- 225}, year = {2019}, abstract = {In order to assess the individual trace element status of humans for either medical or scientific purposes, amongst others, blood serum levels are determined. Furthermore, animal models are used to study interactions of trace elements. Most published methods require larger amounts (500-1000 mu L) of serum to achieve a reliable determination of multiple trace elements. However, oftentimes, these amounts of serum cannot be dedicated to a single analysis and the amount available for TE-determination is much lower. Therefore, a published ICP-MS/MS method for trace element determination in serum was miniaturized, optimized and validated for the measurement of Mn, Fe, Cu Zn, I and Se in as little as 50 mu L of human and murine serum and is presented in this work. For validation, recoveries of multiple LOTs and levels from commercially available human reference serum samples were determined, infra- and inter-day variations were assessed and limits of detection and quantification determined. It is shown, that the method is capable of giving accurate and reproducible results for all six elements within the relevant concentration ranges for samples from humans living in central Europe as well as from laboratory mice. As a highlight, the achieved limits of detection and quantification for Mn were found to be at 0.02 mu g/L serum and 0.05 mu g/L serum, respectively, while using an alkaline diluent for the parallel determination of iodine.}, language = {en} } @article{PetrovićWendler2021, author = {Petrović, Saša and Wendler, Petra}, title = {A RADD approach to probing AAA plus protein function}, series = {Nature structural \& molecular biology}, volume = {28}, journal = {Nature structural \& molecular biology}, number = {4}, publisher = {Nature Publishing Group}, address = {Berlin}, issn = {1545-9993}, doi = {10.1038/s41594-021-00579-5}, pages = {329 -- 330}, year = {2021}, abstract = {AAA+ proteins (ATPases associated with various cellular activities) catalyze the energy-dependent movement or rearrangement of macromolecules. A new study addresses the important question of how to design a selective chemical inhibitor for specific proteins in this diverse superfamily. The powerful chemical genetics approach adds to a growing toolbox of applications that allow dissection of the functions of distinct AAA+ proteins in vivo, facilitating the first steps toward effective drug development.}, language = {en} } @article{FioriniDominguezReboredaetal.2022, author = {Fiorini, Vanina D. and Dom{\´i}nguez, Marisol and Reboreda, Juan C. and Swaddle, John P.}, title = {A recent invasive population of the European starling sturnus vulgaris has lower genetic diversity and higher fluctuating asymmetry than primary invasive and native populations}, series = {Biological invasions : unique international journal uniting scientists in the broad field of biological invasions}, volume = {24}, journal = {Biological invasions : unique international journal uniting scientists in the broad field of biological invasions}, number = {2}, publisher = {Springer}, address = {Dordrecht}, issn = {1387-3547}, doi = {10.1007/s10530-021-02653-x}, pages = {437 -- 448}, year = {2022}, abstract = {Fluctuating asymmetries (FA) are small stress-induced random deviations from perfect symmetry that arise during the development of bilaterally symmetrical traits. One of the factors that can reduce developmental stability of the individuals and cause FA at a population level is the loss of genetic variation. Populations of founding colonists frequently have lower genetic variation than their ancestral populations that could be reflected in a higher level of FA. The European starling (Sturnus vulgaris) is native to Eurasia and was introduced successfully in the USA in 1890 and Argentina in 1983. In this study, we documented the genetic diversity and FA of starlings from England (ancestral population), USA (primary introduction) and Argentina (secondary introduction). We predicted the Argentinean starlings would have the highest level of FA and lowest genetic diversity of the three populations. We captured wild adult European starlings in England, USA, and Argentina, measured their mtDNA diversity and allowed them to molt under standardized conditions to evaluate their FA of primary feathers. For genetic analyses, we extracted DNA from blood samples of individuals from Argentina and USA and from feather samples from individuals from England and sequenced the mitochondrial control region. Starlings in Argentina showed the highest composite FA and exhibited the lowest haplotype and nucleotide diversity. The USA population showed a level of FA and genetic diversity similar to the native population. Therefore, the level of asymmetry and genetic diversity found among these populations was consistent with our predictions based on their invasion history.}, language = {en} } @article{KerstingRauschBieretal.2018, author = {Kersting, Sebastian and Rausch, Valentina and Bier, Frank Fabian and von Nickisch-Rosenegk, Markus}, title = {A recombinase polymerase amplification assay for the diagnosis of atypical pneumonia}, series = {Analytical biochemistry : methods in the biological sciences}, volume = {550}, journal = {Analytical biochemistry : methods in the biological sciences}, publisher = {Elsevier}, address = {San Diego}, issn = {0003-2697}, doi = {10.1016/j.ab.2018.04.014}, pages = {54 -- 60}, year = {2018}, abstract = {Pneumonia is one of the most common and potentially lethal infectious conditions worldwide. Streptococcus pneumoniae is the pathogen most frequently associated with bacterial community-acquired pneumonia, while Legionella pneumophila is the major cause for local outbreaks of legionellosis. Both pathogens can be difficult to diagnose since signs and symptoms are nonspecific and do not differ from other causes of pneumonia. Therefore, a rapid diagnosis within a clinically relevant time is essential for a fast onset of the proper treatment. Although methods based on polymerase chain reaction significantly improved the identification of pathogens, they are difficult to conduct and need specialized equipment. We describe a rapid and sensitive test using isothermal recombinase polymerase amplification and detection on a disposable test strip. This method does not require any special instrumentation and can be performed in less than 20 min. The analytical sensitivity in the multiplex assay amplifying specific regions of S. pneumoniae and L. pneumophila simultaneously was 10 CFUs of genomic DNA per reaction. In cross detection studies with closely related strains and other bacterial agents the specificity of the RPA was confirmed. The presented method is applicable for near patient and field testing with a rather simple routine and the possibility for a read out with the naked eye.}, language = {en} } @article{SedaghatmehrThirumalaikumarKamranfaretal.2019, author = {Sedaghatmehr, Mastoureh and Thirumalaikumar, Venkatesh P. and Kamranfar, Iman and Marmagne, Anne and Masclaux-Daubresse, Celine and Balazadeh, Salma}, title = {A regulatory role of autophagy for resetting the memory of heat stress in plants}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {42}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/pce.13426}, pages = {1054 -- 1064}, year = {2019}, abstract = {As sessile life forms, plants are repeatedly confronted with adverse environmental conditions, which can impair development, growth, and reproduction. During evolution, plants have established mechanisms to orchestrate the delicate balance between growth and stress tolerance, to reset cellular biochemistry once stress vanishes, or to keep a molecular memory, which enables survival of a harsher stress that may arise later. Although there are several examples of memory in diverse plants species, the molecular machinery underlying the formation, duration, and resetting of stress memories is largely unknown so far. We report here that autophagy, a central self-degradative process, assists in resetting cellular memory of heat stress (HS) in Arabidopsis thaliana. Autophagy is induced by thermopriming (moderate HS) and, intriguingly, remains high long after stress termination. We demonstrate that autophagy mediates the specific degradation of heat shock proteins at later stages of the thermorecovery phase leading to the accumulation of protein aggregates after the second HS and a compromised heat tolerance. Autophagy mutants retain heat shock proteins longer than wild type and concomitantly display improved thermomemory. Our findings reveal a novel regulatory mechanism for HS memory in plants.}, language = {en} } @article{AlbersUestuenWitzeletal.2019, author = {Albers, Philip and {\"U}st{\"u}n, Suayib and Witzel, Katja and Kraner, Max Erdmund and B{\"o}rnke, Frederik}, title = {A Remorin from Nicotiana benthamiana Interacts with the Pseudomonas Type-III Effector Protein HopZ1a and is Phosphorylated by the Immune-Related Kinase PBS1}, series = {Molecular Plant-Microbe Interactions}, volume = {32}, journal = {Molecular Plant-Microbe Interactions}, number = {9}, publisher = {Amer phytopathological SOC}, address = {ST Paul}, issn = {0894-0282}, doi = {10.1094/MPMI-04-19-0105-R}, pages = {1229 -- 1242}, year = {2019}, abstract = {The plasma membrane (PM) is at the interface of plant-pathogen interactions and, thus, many bacterial type-III effector (T3E) proteins target membrane-associated processes to interfere with immunity. The Pseudomonas syringae T3E HopZ1a is a host cell PM-localized effector protein that has several immunity-associated host targets but also activates effector-triggered immunity in resistant backgrounds. Although HopZ1a has been shown to interfere with early defense signaling at the PM, no dedicated PM-associated HopZ1a target protein has been identified until now. Here, we show that HopZ1a interacts with the PM-associated remorin protein NbREM4 from Nicotiana benthamiana in several independent assays. NbREM4 relocalizes to membrane nanodomains after treatment with the bacterial elicitor flg22 and transient overexpression of NbREM4 in N. benthamiana induces the expression of a subset of defense-related genes. We can further show that NbREM4 interacts with the immune-related receptor-like cytoplasmic kinase avrPphB-susceptible 1 (PBS1) and is phosphorylated by PBS1 on several residues in vitro. Thus, we conclude that NbREM4 is associated with early defense signaling at the PM. The possible relevance of the HopZ1a-NbREM4 interaction for HopZ1a virulence and avirulence functions is discussed.}, language = {en} } @article{RojasJimenezRieckWurzbacheretal.2019, author = {Rojas-Jimenez, Keilor and Rieck, Angelika and Wurzbacher, Christian and J{\"u}rgens, Klaus and Labrenz, Matthias and Grossart, Hans-Peter}, title = {A Salinity Threshold Separating Fungal Communities in the Baltic Sea}, series = {Frontiers in Microbiology}, volume = {10}, journal = {Frontiers in Microbiology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2019.00680}, pages = {9}, year = {2019}, abstract = {Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world's largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales, and Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm.}, language = {en} } @article{Trindade2020, author = {Trindade, Ines}, title = {A shelter for the future}, series = {Molecular plant}, volume = {13}, journal = {Molecular plant}, number = {12}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1016/j.molp.2020.11.009}, pages = {1675 -- 1675}, year = {2020}, abstract = {Plant development in its majority occurs post-embryonically through the activity of local meristems that provide daughter cells for the development of new organs. It has long been acknowledged that the shoot apical meristem (SAM), which holds the stem cells that will form above-ground organs, is recalcitrant to infection by multiple pathogens, a crucial strategy to safeguard normal devel- opment and subsequent generations. However, the molecular mechanisms underlying SAM immunity remain largely unknown.}, language = {en} } @article{GrimmBergerBastiansenetal.2006, author = {Grimm, Volker and Berger, Uta and Bastiansen, Finn and Eliassen, Sigrunn and Ginot, Vincent and Giske, Jarl and Goss-Custard, John and Grand, Tamara and Heinz, Simone K. and Huse, Geir and Huth, Andreas and Jepsen, Jane U. and Jorgensen, Christian and Mooij, Wolf M. and Mueller, Birgit and Piou, Cyril and Railsback, Steven Floyd and Robbins, Andrew M. and Robbins, Martha M. and Rossmanith, Eva and Rueger, Nadja and Strand, Espen and Souissi, Sami and Stillman, Richard A. and Vabo, Rune and Visser, Ute and DeAngelis, Donald L.}, title = {A standard protocol for describing individual-based and agent-based models}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {198}, 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.2006.04.023}, pages = {115 -- 126}, year = {2006}, abstract = {Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers. (c) 2006 Elsevier B.V. All rights reserved.}, language = {en} } @article{CaoTianAndreevetal.2020, author = {Cao, Xianyong and Tian, Fang and Andreev, Andrei and Anderson, Patricia M. and Lozhkin, Anatoly V. and Bezrukova, Elena and Ni, Jian and Rudaya, Natalia and Stobbe, Astrid and Wieczorek, Mareike and Herzschuh, Ulrike}, title = {A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr}, series = {Earth System Science Data}, volume = {12}, journal = {Earth System Science Data}, number = {1}, publisher = {Copernics Publications}, address = {Katlenburg-Lindau}, issn = {1866-3508}, doi = {10.5194/essd-12-119-2020}, pages = {119 -- 135}, year = {2020}, abstract = {Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 \% of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 \% were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 \%) and lake sediments (33 \%). Most of the records (83 \%) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa.}, language = {en} } @article{SchellerSchmid2020, author = {Scheller, Frieder W. and Schmid, Rolf}, title = {A tribute to Isao Karube (1942-2020) and his influence on sensor science}, series = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica}, volume = {412}, journal = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica}, number = {28}, publisher = {Springer}, address = {Berlin}, issn = {1618-2642}, doi = {10.1007/s00216-020-02946-5}, pages = {7709 -- 7711}, year = {2020}, language = {en} } @article{GonzalezFortesTassiTrucchietal.2019, author = {Gonzalez-Fortes, Gloria M. and Tassi, F. and Trucchi, E. and Henneberger, K. and Paijmans, Johanna L. A. and Diez-del-Molino, D. and Schroeder, H. and Susca, R. R. and Barroso-Ruiz, C. and Bermudez, F. J. and Barroso-Medina, C. and Bettencourt, A. M. S. and Sampaio, H. A. and Salas, A. and de Lombera-Hermida, A. and Fabregas Valcarce, Ram{\´o}n and Vaquero, M. and Alonso, S. and Lozano, Marina and Rodriguez-Alvarez, Xose Pedro and Fernandez-Rodriguez, C. and Manica, Andrea and Hofreiter, Michael and Barbujani, Guido}, title = {A western route of prehistoric human migration from Africa into the Iberian Peninsula}, series = {Proceedings of the Royal Society of London : B, Biological sciences}, volume = {286}, journal = {Proceedings of the Royal Society of London : B, Biological sciences}, number = {1895}, publisher = {Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2018.2288}, pages = {10}, year = {2019}, abstract = {Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from northern Portugal and southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequivocal sub-Saharan mitogenome of most probably West or West-Central African origin, to our knowledge never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. We interpret this result as evidence of an early migration process from Africa into the Iberian Peninsula through a western route, possibly across the Strait of Gibraltar.}, language = {en} } @article{AlkerSchwerdtleSchomburgetal.2019, author = {Alker, Wiebke and Schwerdtle, Tanja and Schomburg, Lutz and Haase, Hajo}, title = {A Zinpyr-1-based Fluorimetric Microassay for Free Zinc in Human Serum}, series = {International journal of molecular sciences}, volume = {20}, journal = {International journal of molecular sciences}, number = {16}, publisher = {MDPI}, address = {Basel}, issn = {1661-6596}, doi = {10.3390/ijms20164006}, pages = {13}, year = {2019}, abstract = {Zinc is an essential trace element, making it crucial to have a reliable biomarker for evaluating an individual's zinc status. The total serum zinc concentration, which is presently the most commonly used biomarker, is not ideal for this purpose, but a superior alternative is still missing. The free zinc concentration, which describes the fraction of zinc that is only loosely bound and easily exchangeable, has been proposed for this purpose, as it reflects the highly bioavailable part of serum zinc. This report presents a fluorescence-based method for determining the free zinc concentration in human serum samples, using the fluorescent probe Zinpyr-1. The assay has been applied on 154 commercially obtained human serum samples. Measured free zinc concentrations ranged from 0.09 to 0.42 nM with a mean of 0.22 ± 0.05 nM. It did not correlate with age or the total serum concentrations of zinc, manganese, iron or selenium. A negative correlation between the concentration of free zinc and total copper has been seen for sera from females. In addition, the free zinc concentration in sera from females (0.21 ± 0.05 nM) was significantly lower than in males (0.23 ± 0.06 nM). The assay uses a sample volume of less than 10 µL, is rapid and cost-effective and allows us to address questions regarding factors influencing the free serum zinc concentration, its connection with the body's zinc status, and its suitability as a future biomarker for an individual's zinc status.}, language = {en} } @article{HasnatZupokOlasApeltetal.2021, author = {Hasnat, Muhammad Abrar and Zupok, Arkadiusz and Olas-Apelt, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Leimk{\"u}hler, Silke}, title = {A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical S-adenosylmethionine protein MoaA for the synthesis of active molybdoenzymes}, series = {Journal of bacteriology}, volume = {203}, journal = {Journal of bacteriology}, number = {12}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {1098-5530}, doi = {10.1128/JB.00086-21}, pages = {20}, year = {2021}, abstract = {Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression, and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them have been characterized in detail in Escherichia coli, namely, IscA, SufA, and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster-dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli. Our studies include the identification of the A-type carrier proteins ErpA and IscA, involved in [4Fe-4S] cluster insertion into the radical Sadenosyl-methionine (SAM) enzyme MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not appear to have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth employing nitrate respiration, based on the low level of gene expression.
IMPORTANCE Understanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics, and gene regulation. Remaining critical gaps in our knowledge include how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SufA, and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions.}, language = {en} } @article{BoekstegersMarcelainBarahonaPonceetal.2020, author = {Boekstegers, Felix and Marcelain, Katherine and Barahona Ponce, Carol and Baez Benavides, Pablo F. and M{\"u}ller, Bettina and de Toro, Gonzalo and Retamales, Javier and Barajas, Olga and Ahumada, Monica and Aleksandrova, Krasimira and Bermejo, Justo Lorenzo}, title = {ABCB1/4 gallbladder cancer risk variants identified in India also show strong effects in Chileans}, series = {Cancer Epidemiology}, volume = {65}, journal = {Cancer Epidemiology}, publisher = {Elsevier}, address = {Amsterdam}, pages = {5}, year = {2020}, abstract = {Background: The first large-scale genome-wide association study of gallbladder cancer (GBC) recently identified and validated three susceptibility variants in the ABCB1 and ABCB4 genes for individuals of Indian descent. We investigated whether these variants were also associated with GBC risk in Chileans, who show the highest incidence of GBC worldwide, and in Europeans with a low GBC incidence. Methods: This population-based study analysed genotype data from retrospective Chilean case-control (255 cases, 2042 controls) and prospective European cohort (108 cases, 181 controls) samples consistently with the original publication. Results: Our results confirmed the reported associations for Chileans with similar risk effects. Particularly strong associations (per-allele odds ratios close to 2) were observed for Chileans with high Native American (=Mapuche) ancestry. No associations were noticed for Europeans, but the statistical power was low. Conclusion: Taking full advantage of genetic and ethnic differences in GBC risk may improve the efficiency of current prevention programs.}, language = {en} } @article{LauxWengerBieretal.2020, author = {Laux, Eva-Maria and Wenger, Christian and Bier, Frank Fabian and Hoelzel, Ralph}, title = {AC electrokinetic immobilization of organic dye molecules}, series = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry and Analusis}, volume = {412}, journal = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry and Analusis}, number = {16}, publisher = {Springer}, address = {Berlin}, issn = {1618-2642}, doi = {10.1007/s00216-020-02480-4}, pages = {3859 -- 3870}, year = {2020}, abstract = {The application of inhomogeneous AC electric fields for molecular immobilization is a very fast and simple method that does not require any adaptions to the molecule's functional groups or charges. Here, the method is applied to a completely new category of molecules: small organic fluorescence dyes, whose dimensions amount to only 1 nm or even less. The presented setup and the electric field parameters used allow immobilization of dye molecules on the whole electrode surface as opposed to pure dielectrophoretic applications, where molecules are attracted only to regions of high electric field gradients, i.e., to the electrode tips and edges. In addition to dielectrophoresis and AC electrokinetic flow, molecular scale interactions and electrophoresis at short time scales are discussed as further mechanisms leading to migration and immobilization of the molecules.}, language = {en} } @article{LangBohnBhatetal.2020, author = {Lang, Judith and Bohn, Patrick and Bhat, Hilal and Jastrow, Holger and Walkenfort, Bernd and Cansiz, Feyza and Fink, Julian and Bauer, Michael and Schumacher, Fabian and Kleuser, Burkhard and Lang, Karl S.}, title = {Acid ceramidase of macrophages traps herpes simplex virus in multivesicular bodies and protects from severe disease}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group UK}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-020-15072-8}, pages = {1 -- 15}, year = {2020}, abstract = {Macrophages have important protective functions during infection with herpes simplex virus type 1 (HSV-1). However, molecular mechanisms that restrict viral propagation and protect from severe disease are unclear. Here we show that macrophages take up HSV-1 via endocytosis and transport the virions into multivesicular bodies (MVBs). In MVBs, acid ceramidase (aCDase) converts ceramide into sphingosine and increases the formation of sphingosine-rich intraluminal vesicles (ILVs). Once HSV-1 particles reach MVBs, sphingosine-rich ILVs bind to HSV-1 particles, which restricts fusion with the limiting endosomal membrane and prevents cellular infection. Lack of aCDase in macrophage cultures or in Asah1(-/-) mice results in replication of HSV-1 and Asah1(-/-) mice die soon after systemic or intravaginal inoculation. The treatment of macrophages with sphingosine enhancing compounds blocks HSV-1 propagation, suggesting a therapeutic potential of this pathway. In conclusion, aCDase loads ILVs with sphingosine, which prevents HSV-1 capsids from penetrating into the cytosol.}, language = {en} } @article{ZeitlerYeAndreyevaetal.2019, author = {Zeitler, Stefanie and Ye, Lian and Andreyeva, Aksana and Schumacher, Fabian and Monti, Juliana and N{\"u}rnberg, Bernd and Nowak, Gabriel and Kleuser, Burkhard and Reichel, Martin and Fejtova, Anna and Kornhuber, Johannes and Rhein, Cosima and Friedland, Kristina}, title = {Acid sphingomyelinase - a regulator of canonical transient receptor potential channel 6 (TRPC6) activity}, series = {Journal of neurochemistry}, volume = {150}, journal = {Journal of neurochemistry}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {0022-3042}, doi = {10.1111/jnc.14823}, pages = {678 -- 690}, year = {2019}, abstract = {Recent investigations propose the acid sphingomyelinase (ASM)/ceramide system as a novel target for antidepressant action. ASM catalyzes the breakdown of the abundant membrane lipid sphingomyelin to the lipid messenger ceramide. This ASM-induced lipid modification induces a local shift in membrane properties, which influences receptor clustering and downstream signaling. Canonical transient receptor potential channels 6 (TRPC6) are non-selective cation channels located in the cell membrane that play an important role in dendritic growth, synaptic plasticity and cognition in the brain. They can be activated by hyperforin, an ingredient of the herbal remedy St. John's wort for treatment of depression disorders. Because of their role in the context of major depression, we investigated the crosstalk between the ASM/ceramide system and TRPC6 ion channels in a pheochromocytoma cell line 12 neuronal cell model (PC12 rat pheochromocytoma cell line). Ca2+ imaging experiments indicated that hyperforin-induced Ca2+ influx through TRPC6 channels is modulated by ASM activity. While antidepressants, known as functional inhibitors of ASM activity, reduced TRPC6-mediated Ca2+ influx, extracellular application of bacterial sphingomyelinase rebalanced TRPC6 activity in a concentration-related way. This effect was confirmed in whole-cell patch clamp electrophysiology recordings. Lipidomic analyses revealed a decrease in very long chain ceramide/sphingomyelin molar ratio after ASM inhibition, which was connected with changes in the abundance of TRPC6 channels in flotillin-1-positive lipid rafts as visualized by western blotting. Our data provide evidence that the ASM/ceramide system regulates TRPC6 channels likely by controlling their recruitment to specific lipid subdomains and thereby fine-tuning their physical properties.}, language = {en} } @article{BeckmannBeckerKadowetal.2019, author = {Beckmann, Nadine and Becker, Katrin Anne and Kadow, Stephanie and Schumacher, Fabian and Kramer, Melanie and Kuehn, Claudine and Schulz-Schaeffer, Walter J. and Edwards, Michael J. and Kleuser, Burkhard and Gulbins, Erich and Carpinteiro, Alexander}, title = {Acid Sphingomyelinase Deficiency Ameliorates Farber Disease}, series = {International journal of molecular sciences}, volume = {20}, journal = {International journal of molecular sciences}, number = {24}, publisher = {MDPI}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms20246253}, pages = {18}, year = {2019}, abstract = {Farber disease is a rare lysosomal storage disorder resulting from acid ceramidase deficiency and subsequent ceramide accumulation. No treatments for Farber disease are clinically available, and affected patients have a severely shortened lifespan. We have recently reported a novel acid ceramidase deficiency model that mirrors the human disease closely. Acid sphingomyelinase is the enzyme that generates ceramide upstream of acid ceramidase in the lysosomes. Using our acid ceramidase deficiency model, we tested if acid sphingomyelinase could be a potential novel therapeutic target for the treatment of Farber disease. A number of functional acid sphingomyelinase inhibitors are clinically available and have been used for decades to treat major depression. Using these as a therapeutic for Farber disease, thus, has the potential to improve central nervous symptoms of the disease as well, something all other treatment options for Farber disease can't achieve so far. As a proof-of-concept study, we first cross-bred acid ceramidase deficient mice with acid sphingomyelinase deficient mice in order to prevent ceramide accumulation. Double-deficient mice had reduced ceramide accumulation, fewer disease manifestations, and prolonged survival. We next targeted acid sphingomyelinase pharmacologically, to test if these findings would translate to a setting with clinical applicability. Surprisingly, the treatment of acid ceramidase deficient mice with the acid sphingomyelinase inhibitor amitriptyline was toxic to acid ceramidase deficient mice and killed them within a few days of treatment. In conclusion, our study provides the first proof-of-concept that acid sphingomyelinase could be a potential new therapeutic target for Farber disease to reduce disease manifestations and prolong survival. However, we also identified previously unknown toxicity of the functional acid sphingomyelinase inhibitor amitriptyline in the context of Farber disease, strongly cautioning against the use of this substance class for Farber disease patients.}, language = {en} } @article{HoehnJerniganJaptoketal.2017, author = {Hoehn, Richard S. and Jernigan, Peter L. and Japtok, Lukasz and Chang, Alex L. and Midura, Emily F. and Caldwell, Charles C. and Kleuser, Burkhard and Lentsch, Alex B. and Edwards, Michael J. and Gulbins, Erich and Pritts, Timothy A.}, title = {Acid sphingomyelinase inhibition in stored erythrocytes reduces transfusion-associated lung inflammation}, series = {Annals of surgery : a monthly review of surgical science and practice}, volume = {265}, journal = {Annals of surgery : a monthly review of surgical science and practice}, number = {1}, publisher = {Lippincott Williams \& Wilkins}, address = {Philadelphia}, issn = {0003-4932}, doi = {10.1097/SLA.0000000000001648}, pages = {218 -- 226}, year = {2017}, abstract = {Objective: We aimed to identify the role of the enzyme acid sphingomyelinase in the aging of stored units of packed red blood cells (pRBCs) and subsequent lung inflammation after transfusion. Summary Background Data: Large volume pRBC transfusions are associated with multiple adverse clinical sequelae, including lung inflammation. Microparticles are formed in stored pRBCs over time and have been shown to contribute to lung inflammation after transfusion. Methods: Human and murine pRBCs were stored with or without amitriptyline, a functional inhibitor of acid sphingomyelinase, or obtained from acid sphingomyelinase-deficient mice, and lung inflammation was studied in mice receiving transfusions of pRBCs and microparticles isolated from these units. Results: Acid sphingomyelinase activity in pRBCs was associated with the formation of ceramide and the release of microparticles. Treatment of pRBCs with amitriptyline inhibited acid sphingomyelinase activity, ceramide accumulation, and microparticle production during pRBC storage. Transfusion of aged pRBCs or microparticles isolated from aged blood into mice caused lung inflammation. This was attenuated after transfusion of pRBCs treated with amitriptyline or from acid sphingomyelinase-deficient mice. Conclusions: Acid sphingomyelinase inhibition in stored pRBCs offers a novel mechanism for improving the quality of stored blood.}, language = {en} } @article{McVeyKimTabuchietal.2017, author = {McVey, Mark J. and Kim, Michael and Tabuchi, Arata and Srbely, Victoria and Japtok, Lukasz and Arenz, Christoph and Rotstein, Ori and Kleuser, Burkhard and Semple, John W. and Kuebler, Wolfgang M.}, title = {Acid sphingomyelinase mediates murine acute lung injury following transfusion of aged platelets}, series = {American journal of physiology : Lung cellular and molecular physiology}, volume = {312}, journal = {American journal of physiology : Lung cellular and molecular physiology}, number = {5}, publisher = {American Physiological Society}, address = {Bethesda}, issn = {1040-0605}, doi = {10.1152/ajplung.00317.2016}, pages = {625 -- 637}, year = {2017}, abstract = {Pulmonary complications from stored blood products are the leading cause of mortality related to transfusion. Transfusion-related acute lung injury is mediated by antibodies or bioactive mediators, yet underlying mechanisms are incompletely understood. Sphingolipids such as ceramide regulate lung injury, and their composition changes as a function of time in stored blood. Here, we tested the hypothesis that aged platelets may induce lung injury via a sphingolipid-mediated mechanism. To assess this hypothesis, a two-hit mouse model was devised. Recipient mice were treated with 2 mg/kg intraperitoneal lipopolysaccharide (priming) 2 h before transfusion of 10 ml/kg stored (1-5 days) platelets treated with or without addition of acid sphingomyelinase inhibitor ARC39 or platelets from acid sphingomyelinase-deficient mice, which both reduce ceramide formation. Transfused mice were examined for signs of pulmonary neutrophil accumulation, endothelial barrier dysfunction, and histological evidence of lung injury. Sphingolipid profiles in stored platelets were analyzed by mass spectrophotometry. Transfusion of aged platelets into primed mice induced characteristic features of lung injury, which increased in severity as a function of storage time. Ceramide accumulated in platelets during storage, but this was attenuated by ARC39 or in acid sphingomyelinase-deficient platelets. Compared with wild-type platelets, transfusion of ARC39-treated or acid sphingomyelinase-deficient aged platelets alleviated lung injury. Aged platelets elicit lung injury in primed recipient mice, which can be alleviated by pharmacological inhibition or genetic deletion of acid sphingomyelinase. Interventions targeting sphingolipid formation represent a promising strategy to increase the safety and longevity of stored blood products.}, language = {en} } @article{AndresDelgadoErnstGalardiCastillaetal.2019, author = {Andr{\´e}s-Delgado, Laura and Ernst, Alexander and Galardi-Castilla, Mar{\´i}a and Bazaga, David and Peralta, Marina and M{\"u}nch, Juliane and Gonzalez-Rosa, Juan M. and Marques, In{\^e}s and Tessadori, Federico and de la Pompa, Jos{\´e} Luis and Vermot, Julien and Mercader, Nadia}, title = {Actin dynamics and the Bmp pathway drive apical extrusion of proepicardial cells}, series = {Development : Company of Biologists}, volume = {146}, journal = {Development : Company of Biologists}, number = {13}, publisher = {The Company of Biologists Ltd}, address = {Cambridge}, issn = {0950-1991}, doi = {10.1242/dev.174961}, pages = {15}, year = {2019}, abstract = {The epicardium, the outer mesothelial layer enclosing the myocardium, plays key roles in heart development and regeneration. During embryogenesis, the epicardium arises from the proepicardium (PE), a cell cluster that appears in the dorsal pericardium (DP) close to the venous pole of the heart. Little is known about how the PE emerges from the pericardial mesothelium. Using a zebrafish model and a combination of genetic tools, pharmacological agents and quantitative in vivo imaging, we reveal that a coordinated collective movement of DP cells drives PE formation. We found that Bmp signaling and the actomyosin cytoskeleton promote constriction of the DP, which enables PE cells to extrude apically. We provide evidence that cell extrusion, which has been described in the elimination of unfit cells from epithelia and the emergence of hematopoietic stem cells, is also a mechanism for PE cells to exit an organized mesothelium and fulfil their developmental fate to form a new tissue layer, the epicardium.}, language = {en} } @article{PrueferWengerBieretal.2022, author = {Pr{\"u}fer, Mareike and Wenger, Christian and Bier, Frank Fabian and Laux, Eva-Maria and H{\"o}lzel, Ralph}, title = {Activity of AC electrokinetically immobilized horseradish peroxidase}, series = {Electrophoresis : microfluidics, nanoanalysis \& proteomics}, journal = {Electrophoresis : microfluidics, nanoanalysis \& proteomics}, publisher = {Wiley}, address = {Hoboken}, issn = {0173-0835}, doi = {10.1002/elps.202200073}, pages = {1920 -- 1933}, year = {2022}, abstract = {Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H2O2 to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45\% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.}, language = {en} } @article{WronskiApioPlath2006, author = {Wronski, Torsten and Apio, Ann and Plath, Martin}, title = {Activity patterns of bushbuck (Tragelaphus scriptus) in Queen Elizabeth National Park}, series = {Behavioural processes}, volume = {73}, journal = {Behavioural processes}, number = {3}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0376-6357}, doi = {10.1016/j.beproc.2006.08.003}, pages = {333 -- 341}, year = {2006}, abstract = {Activity patterns and time budgets of bushbuck (Tragelaphus scriptus) were studied in a free-ranging population in Queen Elizabeth National Park, Uganda from August 2000 to January 2002. We investigated differences in activity patterns in relation to daytime, season, sun radiation, moonlight, age and sex. Bushbuck were found to show peak activities around sunrise and at dawn. No difference in the mean activity rates was found between the dry and wet season. Daytime activity was not predicted by differences in sun radiation, nor was nighttime activity predicted by the presence or absence of moonlight. We found the activity of adult territorial males to be strongly positively correlated with that of females, whereas the activity of young-adult non-territorial males was not significantly correlated with the activity of females. This suggests that young-adult males shift their peak activity to phases when adult territorial males are less active.}, language = {en} } @article{RomeroMujalliRochowKahletal.2021, author = {Romero-Mujalli, Daniel and Rochow, Markus and Kahl, Sandra M. and Paraskevopoulou, Sofia and Folkertsma, Remco and Jeltsch, Florian and Tiedemann, Ralph}, title = {Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies}, series = {Ecology and Evolution}, volume = {11}, journal = {Ecology and Evolution}, number = {11}, publisher = {John Wiley \& Sons, Inc.}, address = {New Jersey}, issn = {2045-7758}, pages = {17}, year = {2021}, abstract = {Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype-phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.}, language = {en} } @article{RadchukReedTeplitskyetal.2019, author = {Radchuk, Viktoriia and Reed, Thomas and Teplitsky, Celine and van de Pol, Martijn and Charmantier, Anne and Hassall, Christopher and Adamik, Peter and Adriaensen, Frank and Ahola, Markus P. and Arcese, Peter and Miguel Aviles, Jesus and Balbontin, Javier and Berg, Karl S. and Borras, Antoni and Burthe, Sarah and Clobert, Jean and Dehnhard, Nina and de Lope, Florentino and Dhondt, Andre A. and Dingemanse, Niels J. and Doi, Hideyuki and Eeva, Tapio and Fickel, J{\"o}rns and Filella, Iolanda and Fossoy, Frode and Goodenough, Anne E. and Hall, Stephen J. G. and Hansson, Bengt and Harris, Michael and Hasselquist, Dennis and Hickler, Thomas and Jasmin Radha, Jasmin and Kharouba, Heather and Gabriel Martinez, Juan and Mihoub, Jean-Baptiste and Mills, James A. and Molina-Morales, Mercedes and Moksnes, Arne and Ozgul, Arpat and Parejo, Deseada and Pilard, Philippe and Poisbleau, Maud and Rousset, Francois and R{\"o}del, Mark-Oliver and Scott, David and Carlos Senar, Juan and Stefanescu, Constanti and Stokke, Bard G. and Kusano, Tamotsu and Tarka, Maja and Tarwater, Corey E. and Thonicke, Kirsten and Thorley, Jack and Wilting, Andreas and Tryjanowski, Piotr and Merila, Juha and Sheldon, Ben C. and Moller, Anders Pape and Matthysen, Erik and Janzen, Fredric and Dobson, F. Stephen and Visser, Marcel E. and Beissinger, Steven R. and Courtiol, Alexandre and Kramer-Schadt, Stephanie}, title = {Adaptive responses of animals to climate change are most likely insufficient}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-10924-4}, pages = {14}, year = {2019}, abstract = {Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.}, language = {en} } @article{ZouWangNeffeetal.2017, author = {Zou, Jie and Wang, Weiwei and Neffe, Axel T. and Xu, Xun and Li, Zhengdong and Deng, Zijun and Sun, Xianlei and Ma, Nan and Lendlein, Andreas}, title = {Adipogenic differentiation of human adipose derived mesenchymal stem cells in 3D architectured gelatin based hydrogels (ArcGel)}, series = {Clinical hemorheology and microcirculation : blood flow and vessels}, volume = {67}, journal = {Clinical hemorheology and microcirculation : blood flow and vessels}, number = {3-4}, publisher = {IOS Press}, address = {Amsterdam}, issn = {1386-0291}, doi = {10.3233/CH-179210}, pages = {297 -- 307}, year = {2017}, abstract = {Polymeric matrices mimicking multiple functions of the ECM are expected to enable a material induced regeneration of tissues. Here, we investigated the adipogenic differentiation of human adipose derived mesenchymal stem cells (hADSCs) in a 3D architectured gelatin based hydrogel (ArcGel) prepared from gelatin and L-lysine diisocyanate ethyl ester (LDI) in an one-step process, in which the formation of an open porous morphology and the chemical network formation were integrated. The ArcGel was designed to support adipose tissue regeneration with its 3D porous structure, high cell biocompatibility, and mechanical properties compatible with human subcutaneous adipose tissue. The ArcGel could support initial cell adhesion and survival of hADSCs. Under static culture condition, the cells could migrate into the inner part of the scaffold with a depth of 840 +/- 120 mu m after 4 days, and distributed in the whole scaffold (2mm in thickness) within 14 days. The cells proliferated in the scaffold and the fold increase of cell number after 7 days of culture was 2.55 +/- 0.08. The apoptotic rate of hADSCs in the scaffold was similar to that of cells maintained on tissue culture plates. When cultured in adipogenic induction medium, the hADSCs in the scaffold differentiated into adipocytes with a high efficiency (93 +/- 1\%). Conclusively, this gelatin based 3D scaffold presented high cell compatibility for hADSC cultivation and differentiation, which could serve as a potential implant material in clinical applications for adipose tissue reparation and regeneration.}, language = {en} } @article{HeunischChaykovskavonEinemetal.2017, author = {Heunisch, Fabian and Chaykovska, Lyubov and von Einem, Gina and Alter, Markus and Dschietzig, Thomas and Kretschmer, Axel and Kellner, Karl-Heinz and Hocher, Berthold}, title = {ADMA predicts major adverse renal events in patients with mild renal impairment and/or diabetes mellitus undergoing coronary angiography}, series = {Medicine}, volume = {96}, journal = {Medicine}, number = {6}, publisher = {Lippincott Williams \& Wilkins}, address = {Philadelphia}, issn = {0025-7974}, doi = {10.1097/MD.0000000000006065}, pages = {7}, year = {2017}, abstract = {Asymmetric dimethylarginine (ADMA) is a competitive inhibitor of the nitric oxide (NO)-synthase and a biomarker of endothelial dysfunction (ED). ED plays an important role in the pathogenesis of contrast-induced nephropathy (CIN). The aim of our study was to evaluate serum ADMA concentration as a biomarker of an acute renal damage during the follow-up of 90 days after contrast medium (CM) application. Blood samples were obtained from 330 consecutive patients with diabetes mellitus or mild renal impairment immediately before, 24 and 48 hours after the CM application for coronary angiography. The patients were followed for 90 days. The composite endpoints were major adverse renal events (MARE) defined as occurrence of death, initiation of dialysis, or a doubling of serum creatinine concentration. Overall, ADMA concentration in plasma increased after CM application, although, there was no differences between ADMA levels in patients with and without CIN. ADMA concentration 24 hours after the CM application was predictive for dialysis with a specificity of 0.889 and sensitivity of 0.653 at values higher than 0.71 mu mol/L (area under the curve: 0.854, 95\% confidential interval: 0.767-0.941, P<0.001). This association remained significant in multivariate Cox regression models adjusted for relevant factors of long-term renal outcome. 24 hours after the CM application, ADMA concentration in plasma was predictive for MARE with a specificity of 0.833 and sensitivity of 0.636 at a value of more than 0.70 mu mol/L (area under the curve: 0.750, 95\% confidence interval: 0.602-0.897, P=0.004). Multivariate logistic regression analysis confirmed that ADMA and anemia were significant predictors of MARE. Further analysis revealed that increased ADMA concentration in plasma was highly significant predictor of MARE in patients with CIN. Moreover, patients with CIN and MARE had the highest plasma ADMA levels 24 hours after CM exposure in our study cohort. The impact of ADMA on MARE was independent of such known CIN risk factors as anemia, pre-existing renal failure, pre-existing heart failure, and diabetes. ADMA concentration in plasma is a promising novel biomarker of major contrast-induced nephropathy-associated events 90 days after contrast media exposure.}, language = {en} } @article{OezerScheffler2018, author = {{\"O}zer, Aydan and Scheffler, Christiane}, title = {Affinity to host population stimulates physical growth in adult offspring of Turkish migrants in Germany}, series = {Journal of biological and clinical anthropology}, volume = {74}, journal = {Journal of biological and clinical anthropology}, number = {5}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2018/0825}, pages = {359 -- 364}, year = {2018}, abstract = {Because of political conflicts and climate change, migration will be increased worldwide and integration in host societies is a challenge also for migrants. We hypothesize that migrants, who take up the challenge in a new social environment are taller than migrants who do not pose this challenge. We analyze by a questionnaire possible social, nutritional and ethnic influencing factors to body height (BH) of adult offspring of Turkish migrants (n = 82, 39 males) aged from 18 to 34 years (mean age 24.6 years). The results of multiple regression (downward selection) show that the more a male adult offspring of Turkish migrants feels like belonging to the Turkish culture, the smaller he is (95\% CI, -3.79, -0.323). Further, the more a male adult offspring of Turkish migrants feels like belonging to the German culture, the taller he is (95\% CI, -0.152, 1.738). We discussed it comparable to primates taking up their challenge in dominance, where as a result their body size increase is associated with higher IGF-1 level. IGF-1 is associated with emotional belonging and has a fundamental role in the regulation of metabolism and growth of the human body. With all pilot characteristics of our study results show that the successful challenge of integration in a new society is strongly associated with the emotional integration and identification in the sense of a personal sense of belonging to society. We discuss taller BH as a signal of social growth adjustment. In this sense, a secular trend of BH adaptation of migrants to hosts is a sign of integration.}, language = {en} } @article{ReegStriglJeltsch2022, author = {Reeg, Jette and Strigl, Lea and Jeltsch, Florian}, title = {Agricultural buffer zone thresholds to safeguard functional bee diversity}, series = {Ecology and Evolution}, volume = {12}, journal = {Ecology and Evolution}, edition = {3}, publisher = {Wiley Online Library}, address = {Hoboken, New Jersey, USA}, issn = {2045-7758}, doi = {10.1002/ece3.8748}, pages = {1 -- 17}, year = {2022}, abstract = {Wild bee species are important pollinators in agricultural landscapes. However, population decline was reported over the last decades and is still ongoing. While agricultural intensification is a major driver of the rapid loss of pollinating species, transition zones between arable fields and forest or grassland patches, i.e., agricultural buffer zones, are frequently mentioned as suitable mitigation measures to support wild bee populations and other pollinator species. Despite the reported general positive effect, it remains unclear which amount of buffer zones is needed to ensure a sustainable and permanent impact for enhancing bee diversity and abundance. To address this question at a pollinator community level, we implemented a process-based, spatially explicit simulation model of functional bee diversity dynamics in an agricultural landscape. More specifically, we introduced a variable amount of agricultural buffer zones (ABZs) at the transition of arable to grassland, or arable to forest patches to analyze the impact on bee functional diversity and functional richness. We focused our study on solitary bees in a typical agricultural area in the Northeast of Germany. Our results showed positive effects with at least 25\% of virtually implemented agricultural buffer zones. However, higher amounts of ABZs of at least 75\% should be considered to ensure a sufficient increase in Shannon diversity and decrease in quasi-extinction risks. These high amounts of ABZs represent effective conservation measures to safeguard the stability of pollination services provided by solitary bee species. As the model structure can be easily adapted to other mobile species in agricultural landscapes, our community approach offers the chance to compare the effectiveness of conservation measures also for other pollinator communities in future.}, language = {en} } @article{FischbachLohBieretal.2017, author = {Fischbach, Jens and Loh, Qiuting and Bier, Frank Fabian and Lim, Theam Soon and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn}, title = {Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method}, series = {Scientific reports}, volume = {7}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep45085}, pages = {9}, year = {2017}, abstract = {We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate.}, language = {en} } @article{WangDanielsConnellyetal.2021, author = {Wang, Ningzhen and Daniels, Robert and Connelly, Liam and Sotzing, Michael and Wu, Chao and Gerhard, Reimund and Sotzing, Gregory A. and Cao, Yang}, title = {All-organic flexible ferroelectret nanogenerator with fabric-based electrodes for self-powered body area networks}, series = {Small : nano micro}, volume = {17}, journal = {Small : nano micro}, number = {33}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1613-6810}, doi = {10.1002/smll.202103161}, pages = {11}, year = {2021}, abstract = {Due to their electrically polarized air-filled internal pores, optimized ferroelectrets exhibit a remarkable piezoelectric response, making them suitable for energy harvesting. Expanded polytetrafluoroethylene (ePTFE) ferroelectret films are laminated with two fluorinated-ethylene-propylene (FEP) copolymer films and internally polarized by corona discharge. Poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS)-coated spandex fabric is employed for the electrodes to assemble an all-organic ferroelectret nanogenerator (FENG). The outer electret-plus-electrode double layers form active device layers with deformable electric dipoles that strongly contribute to the overall piezoelectric response in the proposed concept of wearable nanogenerators. Thus, the FENG with spandex electrodes generates a short-circuit current which is twice as high as that with aluminum electrodes. The stacking sequence spandex/FEP/ePTFE/FEP/ePTFE/FEP/spandex with an average pore size of 3 mu m in the ePTFE films yields the best overall performance, which is also demonstrated by the displacement-versus-electric-field loop results. The all-organic FENGs are stable up to 90 degrees C and still perform well 9 months after being polarized. An optimized FENG makes three light emitting diodes (LEDs) blink twice with the energy generated during a single footstep. The new all-organic FENG can thus continuously power wearable electronic devices and is easily integrated, for example, with clothing, other textiles, or shoe insoles.}, language = {en} } @article{SharmaDangSinghetal.2018, author = {Sharma, Niharika and Dang, Trang Minh and Singh, Namrata and Ruzicic, Slobodan and M{\"u}ller-R{\"o}ber, Bernd and Baumann, Ute and Heuer, Sigrid}, title = {Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice}, series = {Rice}, volume = {11}, journal = {Rice}, number = {2}, publisher = {Springer Open}, address = {London}, issn = {1939-8425}, doi = {10.1186/s12284-017-0192-z}, pages = {19}, year = {2018}, abstract = {Background: Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. Results: Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression. Conclusion: This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance.}, language = {en} } @article{SchroeterNeugartSchreineretal.2019, author = {Schr{\"o}ter, David and Neugart, Susanne and Schreiner, Monika and Grune, Tilman and Rohn, Sascha and Ott, Christiane}, title = {Amaranth's 2-Caffeoylisocitric Acid—An Anti-Inflammatory Caffeic Acid Derivative That Impairs NF-κB Signaling in LPS-Challenged RAW 264.7 Macrophages}, series = {Nutrients}, volume = {11}, journal = {Nutrients}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {2072-6643}, doi = {10.3390/nu11030571}, pages = {14}, year = {2019}, abstract = {For centuries, Amaranthus sp. were used as food, ornamentals, and medication. Molecular mechanisms, explaining the health beneficial properties of amaranth, are not yet understood, but have been attributed to secondary metabolites, such as phenolic compounds. One of the most abundant phenolic compounds in amaranth leaves is 2-caffeoylisocitric acid (C-IA) and regarding food occurrence, C-IA is exclusively found in various amaranth species. In the present study, the anti-inflammatory activity of C-IA, chlorogenic acid, and caffeic acid in LPS-challenged macrophages (RAW 264.7) has been investigated and cellular contents of the caffeic acid derivatives (CADs) were quantified in the cells and media. The CADs were quantified in the cell lysates in nanomolar concentrations, indicating a cellular uptake. Treatment of LPS-challenged RAW 264.7 cells with 10 µM of CADs counteracted the LPS effects and led to significantly lower mRNA and protein levels of inducible nitric oxide synthase, tumor necrosis factor alpha, and interleukin 6, by directly decreasing the translocation of the nuclear factor κB/Rel-like containing protein 65 into the nucleus. This work provides new insights into the molecular mechanisms that attribute to amaranth's anti-inflammatory properties and highlights C-IA's potential as a health-beneficial compound for future research.}, language = {en} } @article{EccardLiesenjohannDammhahn2020, author = {Eccard, Jana and Liesenjohann, Thilo and Dammhahn, Melanie}, title = {Among-individual differences in foraging modulate resource exploitation under perceived predation risk}, series = {Oecologia}, volume = {194}, journal = {Oecologia}, number = {4}, publisher = {Springer}, address = {Berlin}, issn = {0029-8549}, doi = {10.1007/s00442-020-04773-y}, pages = {621 -- 634}, year = {2020}, abstract = {Foraging is risky and involves balancing the benefits of resource acquisition with costs of predation. Optimal foraging theory predicts where, when and how long to forage in a given spatiotemporal distribution of risks and resources. However, significant variation in foraging behaviour and resource exploitation remain unexplained. Using single foragers in artificial landscapes of perceived risks and resources with diminishing returns, we aimed to test whether foraging behaviour and resource exploitation are adjusted to risk level, vary with risk during different components of foraging, and (co)vary among individuals. We quantified foraging behaviour and resource exploitation for 21 common voles (Microtus arvalis). By manipulating ground cover, we created simple landscapes of two food patches varying in perceived risk during feeding in a patch and/or while travelling between patches. Foraging of individuals was variable and adjusted to risk level and type. High risk during feeding reduced feeding duration and food consumption more strongly than risk while travelling. Risk during travelling modified the risk effects of feeding for changes between patches and resulting evenness of resource exploitation. Across risk conditions individuals differed consistently in when and how long they exploited resources and exposed themselves to risk. These among-individual differences in foraging behaviour were associated with consistent patterns of resource exploitation. Thus, different strategies in foraging-under-risk ultimately lead to unequal payoffs and might affect lower trophic levels in food webs. Inter-individual differences in foraging behaviour, i.e. foraging personalities, are an integral part of foraging behaviour and need to be fully integrated into optimal foraging theory.}, language = {en} } @article{SallehRamosMadrigalPenalozaetal.2017, author = {Salleh, Faezah Mohd and Ramos-Madrigal, Jazmin and Penaloza, Fernando and Liu, Shanlin and Sinding, Mikkel-Holger S. and Patel, Riddhi P. and Martins, Renata and Lenz, Dorina and Fickel, J{\"o}rns and Roos, Christian and Shamsir, Mohd Shahir and Azman, Mohammad Shahfiz and Lim, Burton K. and Rossiter, Stephen J. and Wilting, Andreas and Gilbert, M. Thomas P.}, title = {An expanded mammal mitogenome dataset from Southeast Asia}, series = {Gigascience}, volume = {6}, journal = {Gigascience}, number = {8}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2047-217X}, pages = {1 -- 19}, year = {2017}, abstract = {Background: Findings: Approximately 55 gigabases of raw sequence were generated. From this data we assembled 72 complete mitogenome sequences, with an average depth of coverage of 102.9x and 55.2x for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Conclusion:}, language = {en} } @article{WarschburgerWortmannGischetal.2022, author = {Warschburger, Petra and Wortmann, Hanna Rosalie and Gisch, Ulrike Alexandra and Baer, Nadja-Raphaela and Schenk, Liane and Anton, Verena and Bergmann, Manuela M.}, title = {An experimental approach to training interoceptive sensitivity}, series = {Nutrition Journal}, volume = {21}, journal = {Nutrition Journal}, publisher = {Springer Nature}, address = {London}, issn = {1475-2891}, doi = {10.1186/s12937-022-00827-4}, pages = {16}, year = {2022}, abstract = {Background Eating in absence of hunger is quite common and often associated with an increased energy intake co-existent with a poorer food choice. Intuitive eating (IE), i.e., eating in accordance with internal hunger and satiety cues, may protect from overeating. IE, however, requires accurate perception and processing of one's own bodily signals, also referred to as interoceptive sensitivity. Training interoceptive sensitivity might therefore be an effective method to promote IE and prevent overeating. As most studies on eating behavior are conducted in younger adults and close social relationships influence health-related behavior, this study focuses on middle-aged and older couples. Methods The present pilot randomized intervention study aims at investigating the feasibility and effectiveness of a 21-day mindfulness-based training program designed to increase interoceptive sensitivity. A total of N = 60 couples participating in the NutriAct Family Study, aged 50-80 years, will be recruited. This randomized-controlled intervention study comprises three measurement points (pre-intervention, post-intervention, 4-week follow-up) and a 21-day training that consists of daily mindfulness-based guided audio exercises (e.g., body scan). A three-arm intervention study design is applied to compare two intervention groups (training together as a couple vs. training alone) with a control group (no training). Each measurement point includes the assessment of self-reported and objective indicators of interoceptive sensitivity (primary outcome), self-reported indicators of intuitive and maladaptive eating (secondary outcomes), and additional variables. A training evaluation applying focus group discussions will be conducted to assess participants' overall acceptance of the training and its feasibility. Discussion By investigating the feasibility and effectiveness of a mindfulness-based training program to increase interoceptive sensitivity, the present study will contribute to a deeper understanding of how to promote healthy eating in older age.}, language = {en} } @article{LiuFengGuetal.2019, author = {Liu, Junzhong and Feng, Lili and Gu, Xueting and Deng, Xian and Qiu, Qi and Li, Qun and Zhang, Yingying and Wang, Muyang and Deng, Yiwen and Wang, Ertao and He, Yuke and B{\"a}urle, Isabel and Li, Jianming and Cao, Xiaofeng and He, Zuhua}, title = {An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis}, series = {Cell research}, volume = {29}, journal = {Cell research}, number = {5}, publisher = {Nature Publ. Group}, address = {London}, issn = {1001-0602}, doi = {10.1038/s41422-019-0145-8}, pages = {379 -- 390}, year = {2019}, abstract = {Global warming has profound effects on plant growth and fitness. Plants have evolved sophisticated epigenetic machinery to respond quickly to heat, and exhibit transgenerational memory of the heat-induced release of post-transcriptional gene silencing (PTGS). However, how thermomemory is transmitted to progeny and the physiological relevance are elusive. Here we show that heat-induced HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2) directly activates the H3K27me3 demethylase RELATIVE OF EARLY FLOWERING 6 (REF6), which in turn derepresses HSFA2. REF6 and HSFA2 establish a heritable feedback loop, and activate an E3 ubiquitin ligase, SUPPRESSOR OF GENE SILENCING 3 (SGS3)-INTERACTING PROTEIN 1 (SGIP1). SGIP1-mediated SGS3 degradation leads to inhibited biosynthesis of trans-acting siRNA (tasiRNA). The REF6-HSFA2 loop and reduced tasiRNA converge to release HEAT-INDUCED TAS1 TARGET 5 (HTT5), which drives early flowering but attenuates immunity. Thus, heat induces transmitted phenotypes via a coordinated epigenetic network involving histone demethylases, transcription factors, and tasiRNAs, ensuring reproductive success and transgenerational stress adaptation.}, language = {en} } @article{BrauneGuetschowBlaut2019, author = {Braune, Annett and G{\"u}tschow, Michael and Blaut, Michael}, title = {An NADH-Dependent Reductase from Eubacterium ramulus Catalyzes the Stereospecific Heteroring Cleavage of Flavanones and Flavanonols}, series = {Applied and environmental microbiology}, volume = {85}, journal = {Applied and environmental microbiology}, number = {19}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0099-2240}, doi = {10.1128/AEM.01233-19}, pages = {15}, year = {2019}, abstract = {The human intestinal anaerobe Eubacterium ramulus is known for its ability to degrade various dietary flavonoids. In the present study, we demonstrate the cleavage of the heterocyclic C-ring of flavanones and flavanonols by an oxygen-sensitive NADH-dependent reductase, previously described as enoate reductase, from E. ramulus. This flavanone- and flavanonol-cleaving reductase (Fcr) was purified following its heterologous expression in Escherichia coli and further characterized. Fcr cleaved the flavanones naringenin, eriodictyol, liquiritigenin, and homoeriodictyol. Moreover, the flavanonols taxifolin and dihydrokaempferol served as substrates. The catalyzed reactions were stereospecific for the (2R)-enantiomers of the flavanone substrates and for the (25,35)-configured flavanonols. The enantioenrichment of the nonconverted stereoisomers allowed for the determination of hitherto unknown flavanone racemization rates. Fcr formed the corresponding dihydrochalcones and hydroxydihydrochalcones in the course of an unusual reductive cleavage of cyclic ether bonds. Fcr did not convert members of other flavonoid subclasses, including flavones, flavonols, and chalcones, the latter indicating that the reaction does not involve a chalcone intermediate. This view is strongly supported by the observed enantiospecificity of Fcr. Cinnamic acids, which are typical substrates of bacterial enoate reductases, were also not reduced by Fcr. Based on the presence of binding motifs for dinucleotide cofactors and a 4Fe-4S cluster in the amino acid sequence of Fcr, a cofactor-mediated hydride transfer from NADH onto C-2 of the respective substrate is proposed. IMPORTANCE Gut bacteria play a crucial role in the metabolism of dietary flavonoids, thereby contributing to their activation or inactivation after ingestion by the human host. Thus, bacterial activities in the intestine may influence the beneficial health effects of these polyphenolic plant compounds. While an increasing number of flavonoid-converting gut bacterial species have been identified, knowledge of the responsible enzymes is still limited. Here, we characterized Fcr as a key enzyme involved in the conversion of flavonoids of several subclasses by Eubacterium ramulus, a prevalent human gut bacterium. Sequence similarity of this enzyme to hypothetical proteins from other flavonoid-degrading intestinal bacteria in databases suggests a more widespread occurrence of this enzyme. Functional characterization of gene products of human intestinal microbiota enables the assignment of metagenomic sequences to specific bacteria and, more importantly, to certain activities, which is a prerequisite for targeted modulation of gut microbial functionality.}, language = {en} } @article{HeHoeperDodenhoeftetal.2020, author = {He, Hai and H{\"o}per, Rune and Dodenh{\"o}ft, Moritz and Marli{\`e}re, Philippe and Bar-Even, Arren}, title = {An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli}, series = {Metabolic Engineering}, volume = {60}, journal = {Metabolic Engineering}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, issn = {1096-7176}, doi = {10.1016/j.ymben.2020.03.002}, pages = {1 -- 13}, year = {2020}, abstract = {Engineering biotechnological microorganisms to use methanol as a feedstock for bioproduction is a major goal for the synthetic metabolism community. Here, we aim to redesign the natural serine cycle for implementation in E. coli. We propose the homoserine cycle, relying on two promiscuous formaldehyde aldolase reactions, as a superior pathway design. The homoserine cycle is expected to outperform the serine cycle and its variants with respect to biomass yield, thermodynamic favorability, and integration with host endogenous metabolism. Even as compared to the RuMP cycle, the most efficient naturally occurring methanol assimilation route, the homoserine cycle is expected to support higher yields of a wide array of products. We test the in vivo feasibility of the homoserine cycle by constructing several E. coli gene deletion strains whose growth is coupled to the activity of different pathway segments. Using this approach, we demonstrate that all required promiscuous enzymes are active enough to enable growth of the auxotrophic strains. Our findings thus identify a novel metabolic solution that opens the way to an optimized methylotrophic platform.}, language = {en} } @article{ThomasCarvalhoHaileetal.2017, author = {Thomas, Jessica E. and Carvalho, Gary R. and Haile, James and Martin, Michael D. and Castruita, Jose A. Samaniego and Niemann, Jonas and Sinding, Mikkel-Holger S. and Sandoval-Velasco, Marcela and Rawlence, Nicolas J. and Fuller, Errol and Fjeldsa, Jon and Hofreiter, Michael and Stewart, John R. and Gilbert, M. Thomas P. and Knapp, Michael}, title = {An ‛Aukward' tale}, series = {Genes}, volume = {8}, journal = {Genes}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes8060164}, pages = {164}, year = {2017}, abstract = {One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller's candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars' minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.}, language = {en} } @article{CzernitzkiPospisilMusaleketal.2017, author = {Czernitzki, Anna-Franziska and Pospisil, Christina and Musalek, Martin and Mumm, Rebekka and Scheffler, Christiane}, title = {Analysis of longitudinal data of height z-scores in kindergarten children}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {74}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {2}, publisher = {Schweizerbart science publishers}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2017/0708}, pages = {109 -- 112}, year = {2017}, abstract = {Changes in body height throughout extended historic periods are very complex and dynamic processes. Thispilot study aimed to investigate the pattern of longitudinal height z-scores changes in children before and after entering kindergarten. In summer 2016, we measured height and weight of 32 children from 4 groups of two kindergartens aged 3-6 years. All ages were centered according to the age of entry into the kindergarten. For each child we determined mean z-scores for height before and after entering the kindergarten, and assessed the variances for each kindergarten group. Twenty-two children targeted in height z-scores towards average height of their respective kindergarten group, 10 children did not. Due to the small numbers, the convergence in height variance however, remained insignificant (chi-squared independence test, p = 0.127). Additional studies with larger sample sizes are needed to confirm this pilot study.}, language = {en} } @article{SchindlerMoldenhawerStangeetal.2021, author = {Schindler, Daniel and Moldenhawer, Ted and Stange, Maike and Lepro, Valentino and Beta, Carsten and Holschneider, Matthias and Huisinga, Wilhelm}, title = {Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows}, series = {PLoS Computational Biology : a new community journal}, volume = {17}, journal = {PLoS Computational Biology : a new community journal}, number = {8}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1009268}, pages = {33}, year = {2021}, abstract = {Amoeboid cell motility is essential for a wide range of biological processes including wound healing, embryonic morphogenesis, and cancer metastasis. It relies on complex dynamical patterns of cell shape changes that pose long-standing challenges to mathematical modeling and raise a need for automated and reproducible approaches to extract quantitative morphological features from image sequences. Here, we introduce a theoretical framework and a computational method for obtaining smooth representations of the spatiotemporal contour dynamics from stacks of segmented microscopy images. Based on a Gaussian process regression we propose a one-parameter family of regularized contour flows that allows us to continuously track reference points (virtual markers) between successive cell contours. We use this approach to define a coordinate system on the moving cell boundary and to represent different local geometric quantities in this frame of reference. In particular, we introduce the local marker dispersion as a measure to identify localized membrane expansions and provide a fully automated way to extract the properties of such expansions, including their area and growth time. The methods are available as an open-source software package called AmoePy, a Python-based toolbox for analyzing amoeboid cell motility (based on time-lapse microscopy data), including a graphical user interface and detailed documentation. Due to the mathematical rigor of our framework, we envision it to be of use for the development of novel cell motility models. We mainly use experimental data of the social amoeba Dictyostelium discoideum to illustrate and validate our approach.
Author summary Amoeboid motion is a crawling-like cell migration that plays an important key role in multiple biological processes such as wound healing and cancer metastasis. This type of cell motility results from expanding and simultaneously contracting parts of the cell membrane. From fluorescence images, we obtain a sequence of points, representing the cell membrane, for each time step. By using regression analysis on these sequences, we derive smooth representations, so-called contours, of the membrane. Since the number of measurements is discrete and often limited, the question is raised of how to link consecutive contours with each other. In this work, we present a novel mathematical framework in which these links are described by regularized flows allowing a certain degree of concentration or stretching of neighboring reference points on the same contour. This stretching rate, the so-called local dispersion, is used to identify expansions and contractions of the cell membrane providing a fully automated way of extracting properties of these cell shape changes. We applied our methods to time-lapse microscopy data of the social amoeba Dictyostelium discoideum.}, language = {en} } @article{NeukranzKotterBeilschmidtetal.2019, author = {Neukranz, Yannika and Kotter, Annika and Beilschmidt, Lena and Marelja, Zvonimir and Helm, Mark and Graf, Ralph and Leimk{\"u}hler, Silke}, title = {Analysis of the Cellular Roles of MOCS3 Identifies a MOCS3-Independent Localization of NFS1 at the Tips of the Centrosome}, series = {Biochemistry}, volume = {58}, journal = {Biochemistry}, number = {13}, publisher = {American Chemical Society}, address = {Washington}, issn = {0006-2960}, doi = {10.1021/acs.biochem.8b01160}, pages = {1786 -- 1798}, year = {2019}, abstract = {The deficiency of the molybdenum cofactor (Moco) is an autosomal recessive disease, which leads to the loss of activity of all molybdoenzymes in humans with sulfite oxidase being the essential protein. Moco deficiency generally results in death in early childhood. Moco is a sulfur-containing cofactor synthesized in the cytosol with the sulfur being provided by a sulfur relay system composed of the L-cysteine desulfurase NFS1, MOCS3, and MOCS2A. Human MOCS3 is a dual-function protein that was shown to play an important role in Moco biosynthesis and in the mcm(5)s(2) U thio modifications of nucleosides in cytosolic tRNAs for Lys, Gln, and Glu. In this study, we constructed a homozygous MOCS3 knockout in HEK293T cells using the CRISPR/Cas9 system. The effects caused by the absence of MOCS3 were analyzed in detail. We show that sulfite oxidase activity was almost completely abolished, on the basis of the absence of Moco in these cells. In addition, mcm(5)s(2)U thio-modified tRNAs were not detectable. Because the L-cysteine desulfurase NFS1 was shown to act as a sulfur donor for MOCS3 in the cytosol, we additionally investigated the impact of a MOCS3 knockout on the cellular localization of NFS1. By different methods, we identified a MOCS3-independent novel localization of NFS1 at the centrosome.}, language = {en} } @article{LucenaPerezBazzicalupoPaijmansetal.2022, author = {Lucena-Perez, Mar{\´i}a and Bazzicalupo, Enrico and Paijmans, Johanna and Kleinman-Ruiz, Daniel and Dal{\´e}n, Love and Hofreiter, Michael and Delibes, Miguel and Clavero, Miguel and Godoy, Jos{\´e} A.}, title = {Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe}, series = {Quaternary science reviews : the international multidisciplinary research and review journal}, volume = {285}, journal = {Quaternary science reviews : the international multidisciplinary research and review journal}, publisher = {Elsevier}, address = {Oxford}, issn = {0277-3791}, doi = {10.1016/j.quascirev.2022.107518}, pages = {9}, year = {2022}, abstract = {The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past.}, language = {en} } @article{DuffusSchrapersSchuthetal.2020, author = {Duffus, Benjamin R. and Schrapers, Peer and Schuth, Nils and Mebs, Stefan and Dau, Holger and Leimk{\"u}hler, Silke and Haumann, Michael}, title = {Anion binding and oxidative modification at the molybdenum cofactor of formate dehydrogenase from Rhodobacter capsulatus studied by X-ray absorption spectroscopy}, series = {Inorganic chemistry}, volume = {59}, journal = {Inorganic chemistry}, number = {1}, publisher = {American Chemical Society}, address = {Washington, DC}, issn = {0020-1669}, doi = {10.1021/acs.inorgchem.9b01613}, pages = {214 -- 225}, year = {2020}, abstract = {Formate dehydrogenase (FDH) enzymes are versatile catalysts for CO2 conversion. The FDH from Rhodobacter capsulatus contains a molybdenum cofactor with the dithiolene functions of two pyranopterin guanine dinucleotide molecules, a conserved cysteine, and a sulfido group bound at Mo(VI). In this study, we focused on metal oxidation state and coordination changes in response to exposure to O-2, inhibitory anions, and redox agents using X-ray absorption spectroscopy (XAS) at the Mo K-edge. Differences in the oxidative modification of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor relative to samples prepared aerobically without inhibitor, such as variations in the relative numbers of sulfido (Mo=S) and oxo (Mo=O) bonds, were observed in the presence of azide (N-3(-)) or cyanate (OCN-). Azide provided best protection against O-2, resulting in a quantitatively sulfurated cofactor with a displaced cysteine ligand and optimized formate oxidation activity. Replacement of the cysteine ligand by a formate (HCO2-) ligand at the molybdenum in active enzyme is compatible with our XAS data. Cyanide (CN-) inactivated the enzyme by replacing the sulfido ligand at Mo(VI) with an oxo ligand. Evidence that the sulfido group may become protonated upon molybdenum reduction was obtained. Our results emphasize the role of coordination flexibility at the molybdenum center during inhibitory and catalytic processes of FDH enzymes.}, language = {en} } @article{HartmannPreickAbeltetal.2020, author = {Hartmann, Stefanie and Preick, Michaela and Abelt, Silke and Scheffel, Andr{\´e} and Hofreiter, Michael}, title = {Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea}, series = {BMC Research Notes}, volume = {13}, journal = {BMC Research Notes}, publisher = {Biomed Central}, address = {London}, issn = {1756-0500}, doi = {10.1186/s13104-020-05254-4}, pages = {6}, year = {2020}, abstract = {Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira's lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales. Results Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2\% and 89.5\%, respectively. We used their predicted genes together with publicly available data from other Ericales' genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies.}, language = {en} } @article{IlicicWoodhouseKarstenetal.2022, author = {Ilicic, Doris and Woodhouse, Jason and Karsten, Ulf and Zimmermann, Jonas and Wichard, Thomas and Quartino, Maria Liliana and Campana, Gabriela Laura and Livenets, Alexandra and Van den Wyngaert, Silke and Grossart, Hans-Peter}, title = {Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones}, series = {Frontiers in microbiology}, journal = {Frontiers in microbiology}, number = {13}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2022.805694}, pages = {12}, year = {2022}, abstract = {Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota.}, language = {en} } @article{KangLimOhetal.2017, author = {Kang, Mi-Sun and Lim, Hae-Soon and Oh, Jong-Suk and Lim, You-jin and Wuertz-Kozak, Karin and Harro, Janette M. and Shirtliff, Mark E. and Achermann, Yvonne}, title = {Antimicrobial activity of Lactobacillus salivarius and Lactobacillus fermentum against Staphylococcus aureus}, series = {Pathogens and disease / Federation of European Microbiology Societies}, volume = {75}, journal = {Pathogens and disease / Federation of European Microbiology Societies}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2049-632X}, doi = {10.1093/femspd/ftx009}, pages = {10}, year = {2017}, abstract = {The increasing prevalence of methicillin-resistant Staphylococcus aureus has become a major public health threat. While lactobacilli were recently found useful in combating various pathogens, limited data exist on their therapeutic potential for S. aureus infections. The aim of this study was to determine whether Lactobacillus salivarius was able to produce bactericidal activities against S. aureus and to determine whether the inhibition was due to a generalized reduction in pH or due to secreted Lactobacillus product(s). We found an 8.6-log10 reduction of planktonic and a 6.3-log10 reduction of biofilm S. aureus. In contrast, the previously described anti-staphylococcal effects of L. fermentum only caused a 4.0-log10 reduction in planktonic S. aureus cells, with no effect on biofilm S. aureus cells. Killing of S. aureus was partially pH dependent, but independent of nutrient depletion. Cell-free supernatant that was pH neutralized and heat inactivated or proteinase K treated had significantly reduced killing of L. salivarius than with pH-neutralized supernatant alone. Proteomic analysis of the L. salivarius secretome identified a total of five secreted proteins including a LysM-containing peptidoglycan binding protein and a protein peptidase M23B. These proteins may represent potential novel anti-staphylococcal agents that could be effective against S. aureus biofilms.}, language = {en} } @article{KieferClaesNzayisengaetal.2015, author = {Kiefer, Christian S. and Claes, Andrea R. and Nzayisenga, Jean-Claude and Pietra, Stefano and Stanislas, Thomas and Ikeda, Yoshihisa and Grebe, Markus}, title = {Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity}, series = {Development}, journal = {Development}, number = {142}, doi = {doi: 10.1242/dev.111013}, pages = {151 -- 161}, year = {2015}, abstract = {The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity.}, language = {en} } @article{ShahnejatBushehriAlluMehterovetal.2017, author = {Shahnejat-Bushehri, Sara and Allu, Annapurna Devi and Mehterov, Nikolay and Thirumalaikumar, Venkatesh P. and Alseekh, Saleh and Fernie, Alisdair R. and Mueller-Roeber, Bernd and Balazadeh, Salma}, title = {Arabidopsis NAC Transcription Factor JUNGBRUNNEN1 Exerts Conserved Control Over Gibberellin and Brassinosteroid Metabolism and Signaling Genes in Tomato}, series = {Frontiers in plant science}, volume = {8}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2017.00214}, pages = {13}, year = {2017}, abstract = {The Arabidopsis thaliana NAC transcription factor JUNGBRUNNEN1 (AtJUB1) regulates growth by directly repressing GA3ox1 and DWF4, two key genes involved in gibberellin (GA) and brassinosteroid (BR) biosynthesis, respectively, leading to GA and BR deficiency phenotypes. AtJUB1 also reduces the expression of PIF4, a bHLH transcription factor that positively controls cell elongation, while it stimulates the expression of DELLA genes, which are important repressors of growth. Here, we extend our previous findings by demonstrating that AtJUB1 induces similar GA and BR deficiency phenotypes and changes in gene expression when overexpressed in tomato (Solanum lycopersicum). Importantly, and in accordance with the growth phenotypes observed, AtJUB1 inhibits the expression of growth-supporting genes, namely the tomato orthologs of GA3ox1, DWF4 and PIF4, but activates the expression of DELLA orthologs, by directly binding to their promoters. Overexpression of AtJUB1 in tomato delays fruit ripening, which is accompanied by reduced expression of several ripeningrelated genes, and leads to an increase in the levels of various amino acids (mostly proline, beta-alanine, and phenylalanine), gamma-aminobutyric acid (GABA), and major organic acids including glutamic acid and aspartic acid. The fact that AtJUB1 exerts an inhibitory effect on the GA/BR biosynthesis and PIF4 genes but acts as a direct activator of DELLA genes in both, Arabidopsis and tomato, strongly supports the model that the molecular constituents of the JUNGBRUNNEN1 growth control module are considerably conserved across species.}, language = {en} } @article{MuellerFinkeEbertetal.2018, author = {M{\"u}ller, S. M. and Finke, Hannah and Ebert, Franziska and Kopp, Johannes Florian and Schumacher, Fabian and Kleuser, Burkhard and Francesconi, Kevin A. and Raber, G. and Schwerdtle, Tanja}, title = {Arsenic-containing hydrocarbons}, series = {Archives of toxicology : official journal of EUROTOX}, volume = {92}, journal = {Archives of toxicology : official journal of EUROTOX}, number = {5}, publisher = {Springer}, address = {Heidelberg}, issn = {0340-5761}, doi = {10.1007/s00204-018-2194-z}, pages = {1751 -- 1765}, year = {2018}, abstract = {Arsenic-containing hydrocarbons (AsHCs), a subgroup of arsenolipids found in fish and algae, elicit substantial toxic effects in various human cell lines and have a considerable impact on cellular energy levels. The underlying mode of action, however, is still unknown. The present study analyzes the effects of two AsHCs (AsHC 332 and AsHC 360) on the expression of 44 genes covering DNA repair, stress response, cell death, autophagy, and epigenetics via RT-qPCR in human liver (HepG2) cells. Both AsHCs affected the gene expression, but to different extents. After treatment with AsHC 360, flap structure-specific endonuclease 1 (FEN1) as well as xeroderma pigmentosum group A complementing protein (XPA) and (cytosine-5)-methyltransferase 3A (DNMT3A) showed time- and concentration-dependent alterations in gene expression, thereby indicating an impact on genomic stability. In the subsequent analysis of epigenetic markers, within 72 h, neither AsHC 332 nor AsHC 360 showed an impact on the global DNA methylation level, whereas incubation with AsHC 360 increased the global DNA hydroxymethylation level. Analysis of cell extracts and cell media by HPLC-mass spectrometry revealed that both AsHCs were considerably biotransformed. The identified metabolites include not only the respective thioxo-analogs of the two AsHCs, but also several arsenic-containing fatty acids and fatty alcohols, contributing to our knowledge of biotransformation mechanisms of arsenolipids.}, language = {en} } @article{BoginHermanussenScheffler2018, author = {Bogin, Barry and Hermanussen, Michael and Scheffler, Christiane}, title = {As tall as my peers}, series = {Journal of biological and clinical anthropology}, volume = {74}, journal = {Journal of biological and clinical anthropology}, number = {5}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2018/0828}, pages = {365 -- 376}, year = {2018}, abstract = {Background: We define migrants as people who move from their place of birth to a new place of residence. Migration usually is directed by "Push-Pull" factors, for example to escape from poor living conditions or to find more prosperous socio-economic conditions. Migrant children tend to assimilate quickly, and soon perceive themselves as peers within their new social networks. Differences exist between growth of first generation and second generation migrants. Methods: We review body heights and height distributions of historic and modern migrant populations to test two hypotheses: 1) that migrant and adopted children coming from lower social status localities to higher status localities adjust their height growth toward the mean of the dominant recipient social network, and 2) social dominant colonial and military migrants display growth that significantly surpasses the median height of both the conquered population and the population of origin. Our analytical framework also considered social networks. Recent publications indicate that spatial connectedness (community effects) and social competitiveness can affect human growth. Results: Migrant children and adolescents of lower social status rapidly adjust in height towards average height of their hosts, but tend to mature earlier, and are prone to overweight. The mean height of colonial/military migrants does surpass that of the conquered and origin population. Conclusion: Observations on human social networks, non-human animal strategic growth adjustments, and competitive growth processes strengthen the concept of social connectedness being involved in the regulation of human migrant growth.}, language = {en} } @article{GasparatosSchefflerHermanussen2023, author = {Gasparatos, Nikolaos and Scheffler, Christiane and Hermanussen, Michael}, title = {Assessing the applicability of changepoint analysis to analyse short-term growth}, series = {Human biology and public health}, volume = {1}, journal = {Human biology and public health}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, issn = {2748-9957}, doi = {10.52905/hbph2023.1.62}, pages = {15}, year = {2023}, abstract = {Background: Assessing short-term growth in humans is still fraught with difficulties. Especially when looking for small variations and increments, such as mini growth spurts, high precision instruments or frequent measurements are necessary. Daily measurements however require a lot of effort, both for anthropologists and for the subjects. Therefore, new sophisticated approaches are needed that reduce fluctuations and reveal underlying patterns. Objectives: Changepoints are abrupt variations in the properties of time series data. In the context of growth, such variations could be variation in mean height. By adjusting the variance and using different growth models, we assessed the ability of changepoint analysis to analyse short-term growth and detect mini growth spurts. Sample and Methods: We performed Bayesian changepoint analysis on simulated growth data using the bcp package in R. Simulated growth patterns included stasis, linear growth, catch-up growth, and mini growth spurts. Specificity and a normalised variant of the Matthews correlation coefficient (MCC) were used to assess the algorithm's performance. Welch's t-test was used to compare differences of the mean. Results: First results show that changepoint analysis can detect mini growth spurts. However, the ability to detect mini growth spurts is highly dependent on measurement error. Data preparation, such as ranking and rotating time series data, showed negligible improvements. Missing data was an issue and may affect the prediction quality of the classification metrics. Conclusion: Changepoint analysis is a promising tool to analyse short-term growth. However, further optimisation and analysis of real growth data is needed to make broader generalisations.}, language = {en} } @article{CavaelDiehlLentzsch2020, author = {Cavael, Ulrike and Diehl, Katharina and Lentzsch, Peter}, title = {Assessment of growth suppression in apple production with replant soils}, series = {Ecological indicators : integrating monitoring, assessment and management}, volume = {109}, journal = {Ecological indicators : integrating monitoring, assessment and management}, publisher = {Elsevier Science}, address = {Amsterdam}, issn = {1470-160X}, doi = {10.1016/j.ecolind.2019.105846}, pages = {9}, year = {2020}, abstract = {Apple replant disease (ARD) is a specific apple-related form of soil fertility loss due to unidentified causes and is also known as soil fatigue. The effect typically appears in monoculture production sites and leads to production decreases of up to 50\%, even though the cultivation practice remains the same. However, an indication of replant disease is challenged by the lack of specification of the particular microbial group responsible for ARD. The objective of this study was to establish an algorithm for estimating growth suppression in orchards irrespective of the unknowns in the complex causal relationship by assessing plant-soil interaction in the orchard several years after planting. Based on a comparison between no-replant and replant soils, the Alternaria group (Ag) was identified as a soil-fungal population responding to replant with abundance. The trunk cross-sectional area (CSA) was found to be a practical and robust parameter representing below-ground and above-ground tree performance. Suppression of tree vigour was therefore calculated by dividing the two inversely related parameters, Q = ln(Ag)/CSA, as a function of soil-fungal proportions and plant responses at the single-tree level. On this basis, five clusters of tree vigour suppression (Q) were defined: (1) no tree vigour suppression/vital (0\%), (2) escalating (- 38\%), (3) strong (- 53\%), (4) very strong (- 62\%), and (5) critical (- 74\%). By calculating Q at the level of the single tree, trees were clustered according to tree vigour suppression. The weighted frequency of clusters in the field allowed replant impact to be quantified at field level. Applied to a case study on sandy brown, dry diluvial soils in Brandenburg, Germany, the calculated tree vigour suppression was 46\% compared to the potential tree vigour on no-replant soil in the same field. It is highly likely that the calculated growth suppression corresponds to ARD-impact This result is relevant for identifying functional changes in soil and for monitoring the economic effects of soil fatigue in apple orchards, particularly where long-period crop rotation or plot exchange are improbable.}, language = {en} } @article{KhozroughiKrohSchlueteretal.2018, author = {Khozroughi, Amin Ghadiri and Kroh, Lothar W. and Schlueter, Oliver and Rawel, Harshadrai Manilal}, title = {Assessment of the bacterial impact on the post-mortem formation of zinc protoporphyrin IX in pork meat}, series = {Food chemistry}, volume = {256}, journal = {Food chemistry}, publisher = {Elsevier}, address = {Oxford}, issn = {0308-8146}, doi = {10.1016/j.foodchem.2018.01.045}, pages = {25 -- 30}, year = {2018}, abstract = {The post-mortem accumulation of the heme biosynthesis metabolite zinc protoporphyrin IX (ZnPP) in porcine muscle is associated with both a meat-inherent and a bacterial enzymatic reaction during meat storage. To estimate the bacterial impact on ZnPP formation, meat and meat-like media were investigated by HPLC-FLD (and MALDI-TOF-MS) after inoculation with a representative microorganism (P. fluorescens). Results indicate the principal ability of meat-inherent bacteria to form ZnPP in meat extracts and meat-like media, but not on the meat muscle. Thus it was concluded that the ZnPP formation in meat is due to a meat-inherent enzymatic reaction induced by porcine ferrochelatase (FECH), while the bacterial (FECH) induced reaction seems to be not significant.}, language = {en} } @article{AwanSchiebelBoehmetal.2019, author = {Awan, Asad Bashir and Schiebel, Juliane and Boehm, Alexander and Nitschke, Joerg and Sarwar, Yasra and Schierack, Peter and Ali, Aamir}, title = {Association of biofilm formation and cytotoxic potential with multidrug resistance in clinical isolates of pseudomonas aeruginosa}, series = {EXCLI Journal}, volume = {18}, journal = {EXCLI Journal}, publisher = {Leibniz Research Centre for Working Environment and Human Factors}, address = {Dortmund}, issn = {1611-2156}, doi = {10.17179/excli2018-1948}, pages = {79 -- 90}, year = {2019}, abstract = {Multidrug resistant (MDR) Pseudomonas aeruginosa having strong biofilm potential and virulence factors are a serious threat for hospitalized patients having compromised immunity In this study, 34 P. aeruginosa isolates of human origin (17 MDR and 17 non-MDR clinical isolates) were checked for biofilm formation potential in enriched and minimal media. The biofilms were detected using crystal violet method and a modified software package of the automated VideoScan screening method. Cytotoxic potential of the isolates was also investigated on HepG2, LoVo and T24 cell lines using automated VideoScan technology. Pulse field gel electrophoresis revealed 10 PFGE types in MDR and 8 in non-MDR isolates. Although all isolates showed biofilm formation potential, strong biofilm formation was found more in enriched media than in minimal media. Eight MDR isolates showed strong biofilm potential in both enriched and minimal media by both detection methods. Strong direct correlation between crystal violet and VideoScan methods was observed in identifying strong biofilm forming isolates. High cytotoxic effect was observed by 4 isolates in all cell lines used while 6 other isolates showed high cytotoxic effect on T24 cell line only. Strong association of multidrug resistance was found with biofilm formation as strong biofilms were observed significantly higher in MDR isolates (p-value < 0.05) than non-MDR isolates. No significant association of cytotoxic potential with multidrug resistance or biofilm formation was found (p-value > 0.05). The MDR isolates showing significant cytotoxic effects and strong biofilm formation impose a serious threat for hospitalized patients with weak immune system.}, language = {en} } @article{EichelmannSchulzeWittenbecheretal.2019, author = {Eichelmann, Fabian and Schulze, Matthias Bernd and Wittenbecher, Clemens and Menzel, Juliane and Weikert, Cornelia and di Giuseppe, Romina and Biemann, Ronald and Isermann, Berend and Fritsche, Andreas and Boeing, Heiner and Aleksandrova, Krasimira}, title = {Association of Chemerin Plasma Concentration With Risk of Colorectal Cancer}, series = {JAMA network open}, volume = {2}, journal = {JAMA network open}, number = {3}, publisher = {American Veterinary Medical Association}, address = {Chicago}, issn = {2574-3805}, doi = {10.1001/jamanetworkopen.2019.0896}, pages = {14}, year = {2019}, abstract = {IMPORTANCE Inflammatory processes have been suggested to have an important role in colorectal cancer (CRC) etiology. Chemerin is a recently discovered inflammatory biomarker thought to exert chemotactic, adipogenic, and angiogenic functions. However, its potential link with CRC has not been sufficiently explored. OBJECTIVE To evaluate the prospective association of circulating plasma chemerin concentrations with incident CRC. DESIGN, SETTING, AND PARTICIPANTS Prospective case-cohort study based on 27 548 initially healthy participants from the European Prospective Investigation Into Cancer and Nutrition (EPIC)-Potsdam cohort who were followed for up to 16 years. Baseline study information and samples were collected between August 23, 1994, and September 25, 1998. Recruitment was according to random registry sampling from the geographical area of Potsdam, Germany, and surrounding municipalities. The last date of study follow-up was May 10, 2010. Statistical analysis was conducted in 2018. MAIN OUTCOMES AND MEASURES Incident CRC, colon cancer, and rectal cancer. Baseline chemerin plasma concentrations were measured by enzyme-linked immunosorbent assay. CONCLUSIONS AND RELEVANCE This study found that the association between chemerin concentration and the risk of incident CRC was linear and independent of established CRC risk factors. Further studies are warranted to evaluate chemerin as a novel immune-inflammatory agent in colorectal carcinogenesis.}, language = {en} } @article{WittenbecherKuxhausBoeingetal.2019, author = {Wittenbecher, Clemens and Kuxhaus, Olga and Boeing, Heiner and Stefan, Norbert and Schulze, Matthias Bernd}, title = {Associations of short stature and components of height with incidence of type 2 diabetes}, series = {Diabetologia : journal of the European Association for the Study of Diabetes (EASD)}, volume = {62}, journal = {Diabetologia : journal of the European Association for the Study of Diabetes (EASD)}, number = {12}, publisher = {Springer}, address = {New York}, issn = {0012-186X}, doi = {10.1007/s00125-019-04978-8}, pages = {2211 -- 2221}, year = {2019}, abstract = {Aims/hypothesis This study aimed to evaluate associations of height as well as components of height (sitting height and leg length) with risk of type 2 diabetes and to explore to what extent associations are explainable by liver fat and cardiometabolic risk markers. Methods A case-cohort study within the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam study comprising 26,437 participants who provided blood samples was designed. We randomly selected a subcohort of 2500 individuals (2029 diabetes-free at baseline and with anamnestic, anthropometrical and metabolic data for analysis). Of the 820 incident diabetes cases identified in the full cohort during 7 years of follow-up, 698 remained for analyses after similar exclusions. Results After adjustment for age, potential lifestyle confounders, education and waist circumference, greater height was related to lower diabetes risk (HR per 10 cm, men 0.59 [95\% CI 0.47, 0.75] and women 0.67 [0.51, 0.88], respectively). Leg length was related to lower risk among men and women, but only among men if adjusted for total height. Adjustment for liver fat and triacylglycerols, adiponectin and C-reactive protein substantially attenuated associations between height and diabetes risk, particularly among women. Conclusions/interpretation We observed inverse associations between height and risk of type 2 diabetes, which was largely related to leg length among men. The inverse associations may be partly driven by lower liver fat content and a more favourable cardiometabolic profile.}, language = {en} } @article{HornychEkrtRiedeletal.2019, author = {Hornych, Ondrej and Ekrt, Libor and Riedel, Felix and Koutecky, Petr and Košnar, Jiř{\´i}}, title = {Asymmetric hybridization in Central European populations of the Dryopteris carthusiana group}, series = {America Journal of Botany}, volume = {106}, journal = {America Journal of Botany}, number = {11}, publisher = {Wiley}, address = {Hoboken}, issn = {0002-9122}, doi = {10.1002/ajb2.1369}, pages = {1477 -- 1486}, year = {2019}, abstract = {Premise Hybridization is a key process in plant speciation. Despite its importance, there is no detailed study of hybridization rates in fern populations. A proper estimate of hybridization rates is needed to understand factors regulating hybridization. Methods We studied hybridization in the European Dryopteris carthusiana group, represented by one diploid and two tetraploid species and their hybrids. We sampled 100 individuals per population in 40 mixed populations of the D. carthusiana group across Europe. All plants were identified by measuring genome size (DAPI staining) using flow cytometry. To determine the maternal parentage of hybrids, we sequenced the chloroplast region trnL-trnF of all taxa involved. Results We found hybrids in 85\% of populations. Triploid D. xambroseae occurred in every population that included both parent species and is most abundant when the parent species are equally abundant. By contrast, tetraploid D. xdeweveri was rare (15 individuals total) and triploid D. xsarvelae was absent. The parentage of hybrid taxa is asymmetric. Despite expectations from previous studies, tetraploid D. dilatata is the predominant male parent of its triploid hybrid. Conclusions This is a thorough investigation of hybridization rates in natural populations of ferns. Hybridization rates differ greatly even among closely related fern taxa. In contrast to angiosperms, our data suggest that hybridization rates are highest in balanced parent populations and support the notion that some ferns possess very weak barriers to hybridization. Our results from sequencing cpDNA challenge established notions about the correlation of ploidy level and mating tendencies.}, language = {en} } @article{Omel'chenkoOcampoEspindolaKiss2021, author = {Omel'chenko, Oleh and Ocampo-Espindola, Jorge Luis and Kiss, Istv{\´a}n Z.}, title = {Asymmetry-induced isolated fully synchronized state in coupled oscillator populations}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {104}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {2}, publisher = {American Physical Society}, address = {Melville, NY}, issn = {2470-0045}, doi = {10.1103/PhysRevE.104.L022202}, pages = {6}, year = {2021}, abstract = {A symmetry-breaking mechanism is investigated that creates bistability between fully and partially synchronized states in oscillator networks. Two populations of oscillators with unimodal frequency distribution and different amplitudes, in the presence of weak global coupling, are shown to simplify to a modular network with asymmetrical coupling. With increasing the coupling strength, a synchronization transition is observed with an isolated fully synchronized state. The results are interpreted theoretically in the thermodynamic limit and confirmed in experiments with chemical oscillators.}, language = {en} } @article{BollierSicardLeblondetal.2018, author = {Bollier, Norbert and Sicard, Adrien and Leblond, Julie and Latrasse, David and Gonzalez, Nathalie and Gevaudant, Frederic and Benhamed, Moussa and Raynaud, Cecile and Lenhard, Michael and Chevalier, Christian and Hernould, Michel and Delmas, Frederic}, title = {At-MINI ZINC FINGER2 and Sl-INHIBITOR OF MERISTEM ACTIVITY, a Conserved Missing Link in the Regulation of Floral Meristem Termination in Arabidopsis and Tomato}, series = {The plant cell}, volume = {30}, journal = {The plant cell}, number = {1}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.17.00653}, pages = {83 -- 100}, year = {2018}, abstract = {In angiosperms, the gynoecium is the last structure to develop within the flower due to the determinate fate of floral meristem (FM) stem cells. The maintenance of stem cell activity before its arrest at the stage called FM termination affects the number of carpels that develop. The necessary inhibition at this stage of WUSCHEL (WUS), which is responsible for stem cell maintenance, involves a two-step mechanism. Direct repression mediated by the MADS domain transcription factor AGAMOUS (AG), followed by indirect repression requiring the C2H2 zinc-finger protein KNUCKLES (KNU), allow for the complete termination of floral stem cell activity. Here, we show that Arabidopsis thaliana MINI ZINC FINGER2 (AtMIF2) and its homolog in tomato (Solanum lycopersicum), INHIBITOR OF MERISTEM ACTIVITY (SlIMA), participate in the FM termination process by functioning as adaptor proteins. AtMIF2 and SlIMA recruit AtKNU and SlKNU, respectively, to form a transcriptional repressor complex together with TOPLESS and HISTONE DEACETYLASE19. AtMIF2 and SlIMA bind to the WUS and SIWUS loci in the respective plants, leading to their repression. These results provide important insights into the molecular mechanisms governing (FM) termination and highlight the essential role of AtMIF2/SlIMA during this developmental step, which determines carpel number and therefore fruit size.}, language = {en} } @article{BatsiosIshikawaAnkerholdRothetal.2019, author = {Batsios, Petros and Ishikawa-Ankerhold, Hellen Christina and Roth, Heike and Schleicher, Michael and Wong, Catherine C. L. and M{\"u}ller-Taubenberger, Annette}, title = {Ate1-mediated posttranslational arginylation affects substrate adhesion and cell migration in Dictyostelium discoideum}, series = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, volume = {30}, journal = {Molecular biology of the cell : the official publication of the American Society for Cell Biology}, number = {4}, publisher = {American Society for Cell Biology}, address = {Bethesda}, issn = {1059-1524}, doi = {10.1091/mbc.E18-02-0132}, pages = {453 -- 466}, year = {2019}, abstract = {The highly conserved enzyme arginyl-tRNA-protein transferase (Ate1) mediates arginylation, a posttranslational modification that is only incompletely understood at its molecular level. To investigate whether arginylation affects actin-dependent processes in a simple model organism, Dictyostelium discoideum, we knocked out the gene encoding Ate1 and characterized the phenotype of ate1-null cells. Visualization of actin cytoskeleton dynamics by live-cell microscopy indicated significant changes in comparison to wild-type cells. Ate1-null cells were almost completely lacking focal actin adhesion sites at the substrate-attached surface and were only weakly adhesive. In two-dimensional chemotaxis assays toward folate or cAMP, the motility of ate1-null cells was increased. However, in three-dimensional chemotaxis involving more confined conditions, the motility of ate1-null cells was significantly reduced. Live-cell imaging showed that GFP-tagged Ate1 rapidly relocates to sites of newly formed actin-rich protrusions. By mass spectrometric analysis, we identified four arginylation sites in the most abundant actin isoform of Dictyostelium, in addition to arginylation sites in other actin isoforms and several actin-binding proteins. In vitro polymerization assays with actin purified from ate1-null cells revealed a diminished polymerization capacity in comparison to wild-type actin. Our data indicate that arginylation plays a crucial role in the regulation of cytoskeletal activities.}, language = {en} } @article{DeFrenneBlondeelBrunetetal.2018, author = {De Frenne, Pieter and Blondeel, H. and Brunet, J. and Caron, M. M. and Chabrerie, O. and Cougnon, M. and Cousins, S. A. O. and Decocq, G. and Diekmann, M. and Graae, B. J. and Hanley, M. E. and Heinken, Thilo and Hermy, M. and Kolb, A. and Lenoir, J. and Liira, J. and Orczewska, A. and Shevtsova, A. and Vanneste, T. and Verheyen, K.}, title = {Atmospheric nitrogen deposition on petals enhances seed quality of the forest herb Anemone nemorosa}, series = {Plant biology}, volume = {20}, journal = {Plant biology}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {1435-8603}, doi = {10.1111/plb.12688}, pages = {619 -- 626}, year = {2018}, abstract = {Elevated atmospheric input of nitrogen (N) is currently affecting plant biodiversity and ecosystem functioning. The growth and survival of numerous plant species is known to respond strongly to N fertilisation. Yet, few studies have assessed the effects of N deposition on seed quality and reproductive performance, which is an important life-history stage of plants. Here we address this knowledge gap by assessing the effects of atmospheric N deposition on seed quality of the ancient forest herb Anemone nemorosa using two complementary approaches. By taking advantage of the wide spatiotemporal variation in N deposition rates in pan-European temperate and boreal forests over 2years, we detected positive effects of N deposition on the N concentration (percentage N per unit seed mass, increased from 2.8\% to 4.1\%) and N content (total N mass per seed more than doubled) of A.nemorosa seeds. In a complementary experiment, we applied ammonium nitrate to aboveground plant tissues and the soil surface to determine whether dissolved N sources in precipitation could be incorporated into seeds. Although the addition of N to leaves and the soil surface had no effect, a concentrated N solution applied to petals during anthesis resulted in increased seed mass, seed N concentration and N content. Our results demonstrate that N deposition on the petals enhances bioaccumulation of N in the seeds of A.nemorosa. Enhanced atmospheric inputs of N can thus not only affect growth and population dynamics via root or canopy uptake, but can also influence seed quality and reproduction via intake through the inflorescences.}, language = {en} } @article{OzcelikayKurbanogluYarmanetal.2020, author = {Ozcelikay, Goksu and Kurbanoglu, Sevinc and Yarman, Aysu and Scheller, Frieder W. and Ozkan, Sibel A.}, title = {Au-Pt nanoparticles based molecularly imprinted nanosensor for electrochemical detection of the lipopeptide antibiotic drug Daptomycin}, series = {Sensors and actuators : B, Chemical}, volume = {320}, journal = {Sensors and actuators : B, Chemical}, publisher = {Elsevier Science}, address = {Amsterdam}, issn = {0925-4005}, doi = {10.1016/j.snb.2020.128285}, pages = {7}, year = {2020}, abstract = {In this work, a novel electrochemical molecularly imprinted polymer (MIP) sensor for the detection of the lipopeptide antibiotic Daptomycin (DAP) is presented which integrates gold decorated platinum nanoparticles (Au-Pt NPs) into the nanocomposite film. The sensor was prepared by electropolymerization of o-phenylenediamine (o-PD) in the presence of DAP using cyclic voltammetry. Cyclic voltammetry and differential pulse voltammetry were applied to follow the changes in the MIP-layer related to rebinding and removal of the target DAP by using the redox marker [Fe(CN)(6)](3-/4-). Under optimized operational conditions, the MIP/Au-Pt NPs/ GCE nanosensor exhibits a linear response in the range of 1-20 pM towards DAP. The limit of detection and limit of quantification were determined to be 0.161pM +/- 0.012 and 0.489pM +/- 0.012, respectively. The sensitivity towards the antibiotics Vancomycin and Erythromycin and the amino acids glycine and tryptophan was below 7 percent as compared with DAP. Moreover, the nanosensor was also successfully used for the detection of DAP in deproteinated human serum samples.}, language = {en} } @article{DeutschmannRoggenbuckSchieracketal.2020, author = {Deutschmann, Claudia and Roggenbuck, Dirk and Schierack, Peter and R{\"o}diger, Stefan}, title = {Autoantibody testing by enzyme-linked immunosorbent assay-a case in which the solid phase decides on success and failure}, series = {Heliyon}, volume = {6}, journal = {Heliyon}, number = {1}, publisher = {Elsevier}, address = {London [u.a.]}, issn = {2405-8440}, doi = {10.1016/j.heliyon.2020.e03270}, pages = {6}, year = {2020}, abstract = {Background: The enzyme-linked immunosorbent assay (ELISA) is an indispensable tool for clinical diagnostics to identify or differentiate diseases such as autoimmune illnesses, but also to monitor their progression or control the efficacy of drugs. One use case of ELISA is to differentiate between different states (e.g. healthy vs. diseased). Another goal is to quantitatively assess the biomarker in question, like autoantibodies. Thus, the ELISA technology is used for the discovery and verification of new autoantibodies, too. Of key interest, however, is the development of immunoassays for the sensitive and specific detection of such biomarkers at early disease stages. Therefore, users have to deal with many parameters, such as buffer systems or antigen-autoantibody interactions, to successfully establish an ELISA. Often, fine-tuning like testing of several blocking substances is performed to yield high signal-to-noise ratios.
Methods: We developed an ELISA to detect IgA and IgG autoantibodies against chitinase-3-like protein 1 (CHI3L1), a newly identified autoantigen in inflammatory bowel disease (IBD), in the serum of control and disease groups (n = 23, respectively). Microwell plates with different surface modifications (PolySorp and MaxiSorp coating) were tested to detect reproducibility problems.
Results: We found a significant impact of the surface properties of the microwell plates. IgA antibody reactivity was significantly lower, since it was in the range of background noise, when measured on MaxiSorp coated plates (p < 0.0001). The IgG antibody reactivity did not differ on the diverse plates, but the plate surface had a significant influence on the test result (p = 0.0005).
Conclusion: With this report, we want to draw readers' attention to the properties of solid phases and their effects on the detection of autoantibodies by ELISA. We want to sensitize the reader to the fact that the choice of the wrong plate can lead to a false negative test result, which in turn has serious consequences for the discovery of autoantibodies.}, language = {en} } @article{NakamuraClaesGrebeetal.2017, author = {Nakamura, Moritaka and Claes, Andrea R. and Grebe, Tobias and Hermkes, Rebecca and Viotti, Corrado and Ikeda, Yoshihisa and Grebe, Markus}, title = {Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {176}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {1}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.17.00713}, pages = {378 -- 391}, year = {2017}, abstract = {Polar nuclear migration is crucial during the development of diverse eukaryotes. In plants, root hair growth requires polar nuclear migration into the outgrowing hair. However, knowledge about the dynamics and the regulatory mechanisms underlying nuclear movements in root epidermal cells remains limited. Here, we show that both auxin and Rho-of-Plant (ROP) signaling modulate polar nuclear position at the inner epidermal plasma membrane domain oriented to the cortical cells during cell elongation as well as subsequent polar nuclear movement to the outer domain into the emerging hair bulge in Arabidopsis (Arabidopsis thaliana). Auxin signaling via the nuclear AUXIN RESPONSE FACTOR7 (ARF7)/ARF19 and INDOLE ACETIC ACID7 pathway ensures correct nuclear placement toward the inner membrane domain. Moreover, precise inner nuclear placement relies on SPIKE1 Rho-GEF, SUPERCENTIPEDE1 Rho-GDI, and ACTIN7 (ACT7) function and to a lesser extent on VTI11 vacuolar SNARE activity. Strikingly, the directionality and/or velocity of outer polar nuclear migration into the hair outgrowth along actin strands also are ACT7 dependent, auxin sensitive, and regulated by ROP signaling. Thus, our findings provide a founding framework revealing auxin and ROP signaling of inner polar nuclear position with some contribution by vacuolar morphology and of actin-dependent outer polar nuclear migration in root epidermal hair cells.}, language = {en} } @article{BatistaFigueiredoSantosGonzalezetal.2019, author = {Batista, Rita A. and Figueiredo, Duarte Dionisio and Santos-Gonzalez, Juan and K{\"o}hler, Claudia}, title = {Auxin regulates endosperm cellularization in Arabidopsis}, series = {Genes \& Development}, volume = {33}, journal = {Genes \& Development}, number = {7-8}, publisher = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, NY}, issn = {0890-9369}, doi = {10.1101/gad.316554.118}, pages = {466 -- 476}, year = {2019}, abstract = {The endosperm is an ephemeral tissue that nourishes the developing embryo, similar to the placenta in mammals. In most angiosperms, endosperm development starts as a syncytium, in which nuclear divisions are not followed by cytokinesis. The timing of endosperm cellularization largely varies between species, and the event triggering this transition remains unknown. Here we show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest. Auxin-overproducing seeds phenocopy paternal-excess triploid seeds derived from hybridizations of diploid maternal plants with tetraploid fathers. Concurrently, auxin-related genes are strongly overexpressed in triploid seeds, correlating with increased auxin activity. Reducing auxin biosynthesis and signaling reestablishes endosperm cellularization in triploid seeds and restores their viability, highlighting a causal role of increased auxin in preventing endosperm cellularization. We propose that auxin determines the time of endosperm cellularization, and thereby uncovered a central role of auxin in establishing hybridization barriers in plants.}, language = {en} } @article{LechthalerColangeliGazzabinetal.2019, author = {Lechthaler, Silvia and Colangeli, Pierluigi and Gazzabin, Moira and Anfodillo, Tommaso}, title = {Axial anatomy of the leaf midrib provides new insights into the hydraulic architecture and cavitation patterns of Acer pseudoplatanus leaves}, series = {Journal of experimental botany}, volume = {70}, journal = {Journal of experimental botany}, number = {21}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/erz347}, pages = {6195 -- 6201}, year = {2019}, abstract = {The structure of leaf veins is typically described by a hierarchical scheme (e.g. midrib, 1(st) order, 2nd order), which is used to predict variation in conduit diameter from one order to another whilst overlooking possible variation within the same order. We examined whether xylem conduit diameter changes within the same vein order, with resulting consequences for resistance to embolism. We measured the hydraulic diameter (D-h), and number of vessels (V-N) along the midrib and petioles of leaves of Acer pseudoplatanus, and estimated the leaf area supplied (A(leaf-sup)) at different points of the midrib and how variation in anatomical traits affected embolism resistance. We found that D-h scales with distance from the midrib tip (path length, L) with a power of 0.42, and that V-N scales with A(leaf-sup) with a power of 0.66. Total conductive area scales isometrically with A(leaf-sup). Embolism events along the midrib occurred first in the basipetal part and then at the leaf tip where vessels are narrower. The distance from the midrib tip is a good predictor of the variation in vessel diameter along the 1st order veins in A. pseudoplatanus leaves and this anatomical pattern seems to have an effect on hydraulic integrity since wider vessels at the leaf base embolize first.}, language = {en} } @article{LeimkuehlerLemaireIobbiNivol2017, author = {Leimk{\"u}hler, Silke and Lemaire, Olivier N. and Iobbi-Nivol, Chantal}, title = {Bacterial Molybdoenzymes}, series = {Molybdenum and tungsten enzymes : biochemistry}, volume = {5}, journal = {Molybdenum and tungsten enzymes : biochemistry}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, isbn = {978-1-78262-391-5}, doi = {10.1039/9781782623915-00117}, pages = {117 -- 142}, year = {2017}, abstract = {The biogenesis of molybdoenzymes is a cytoplasmic event requiring both the folded apoenzymes and the matured molybdenum cofactor. The structure and the complexity of the molybdenum cofactor varies in each molybdoenzyme family and consequently different accessory proteins are required for the maturation of the respective enzymes. Thus, for enzymes of both the DMSO reductase and xanthine oxidase families, specific chaperones exist which are dedicated to increase the stability and the folding of specific members of each family. In this review, we describe the role of these chaperones for molybdoenzyme maturation. We present a model which describes step by step the mechanism of the maturation of representative molybdoenzymes from each family.}, language = {en} } @article{SchmidtRabschBroekeretal.2016, author = {Schmidt, Andreas and Rabsch, Wolfgang and Broeker, Nina K. and Barbirz, Stefanie}, title = {Bacteriophage tailspike protein based assay to monitor phase variable glucosylations in Salmonella O-antigens}, series = {BMC microbiology}, volume = {16}, journal = {BMC microbiology}, publisher = {BioMed Central}, address = {London}, issn = {1471-2180}, doi = {10.1186/s12866-016-0826-0}, pages = {11}, year = {2016}, abstract = {Background Non-typhoid Salmonella Typhimurium (S. Typhimurium) accounts for a high number of registered salmonellosis cases, and O-serotyping is one important tool for monitoring epidemiology and spread of the disease. Moreover, variations in glucosylated O-antigens are related to immunogenicity and spread in the host. However, classical autoagglutination tests combined with the analysis of specific genetic markers cannot always reliably register phase variable glucose modifications expressed on Salmonella O-antigens and additional tools to monitor O-antigen glucosylation phenotypes of S. Typhimurium would be desirable. Results We developed a test for the phase variable O-antigen glucosylation state of S. Typhimurium using the tailspike proteins (TSP) of Salmonella phages 9NA and P22. We used this ELISA like tailspike adsorption (ELITA) assay to analyze a library of 44 Salmonella strains. ELITA was successful in discriminating strains that carried glucose 1-6 linked to the galactose of O-polysaccharide backbone (serotype O1) from non-glucosylated strains. This was shown by O-antigen compositional analyses of the respective strains with mass spectrometry and capillary electrophoresis. The ELITA test worked rapidly in a microtiter plate format and was highly O-antigen specific. Moreover, TSP as probes could also detect glucosylated strains in flow cytometry and distinguish multiphasic cultures differing in their glucosylation state. Conclusions Tailspike proteins contain large binding sites with precisely defined specificities and are therefore promising tools to be included in serotyping procedures as rapid serotyping agents in addition to antibodies. In this study, 9NA and P22TSP as probes could specifically distinguish glucosylation phenotypes of Salmonella on microtiter plate assays and in flow cytometry. This opens the possibility for flow sorting of cell populations for subsequent genetic analyses or for monitoring phase variations during large scale O-antigen preparations necessary for vaccine production.}, language = {en} } @article{HaberlandHampeAutenriethetal.2019, author = {Haberland, Christian and Hampe, Oliver and Autenrieth, Marijke and Voss, Manja}, title = {Balaenoptera borealis Lesson, 1828}, series = {Mammalia}, volume = {83}, journal = {Mammalia}, number = {4}, publisher = {De Gruyter}, address = {Berlin}, issn = {0025-1461}, doi = {10.1515/mammalia-2017-0149}, pages = {343 -- 351}, year = {2019}, abstract = {The whereabouts of the Balaenoptera borealis holotype, the skeleton of a 1819 stranded specimen, have been unknown since the World War II (WWII). Due to nomenclatural confusion, deficient documentation, and finally WWII bombing, which destroyed predominantly cetacean material in the Museum fib Naturkunde Berlin (MfN), the type skeleton of the sei whale sank into oblivion. Construction activities enabled a recent search and study on the remaining whale material. Here, we provide evidence that the type specimen was not destroyed. On the basis of species-wide and individual characters of the type material such as the shape of cranial elements and the pattern of the maxillary foramina, we show that the skull and mandibles, the vertebral column (except the atlas), and the ribs of the holotype remain intact. Further evidence that these skeletal remains belong to the previously missing holotype is provided by the characteristics of the spine. In addition, we analyzed ancient DNA from bone samples and confirm they are B. borealis, and the occurrence of same mitochondrial haplotypes indicate that the bones belong to the same individual. Additionally, a blue inscription was discovered at the caudal epiphysis of a thoracic vertebra; historical research matched this inscription with the material belonging to the former Anatomical-Zootomical Museum, from which the holotype was once bought.}, language = {en} } @article{IlicicGrossart2022, author = {Ilicic, Doris and Grossart, Hans-Peter}, title = {Basal parasitic fungi in marine food webs-a mystery yet to unravel}, series = {Journal of Fungi}, volume = {8}, journal = {Journal of Fungi}, number = {2}, publisher = {MDPI}, address = {Basel}, issn = {2309-608X}, doi = {10.3390/jof8020114}, pages = {16}, year = {2022}, abstract = {Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.}, language = {en} } @article{BendjeddouLoumassineScheffleretal.2017, author = {Bendjeddou, Mohammed Lamine and Loumassine, Hibat Allah and Scheffler, Ingo and Bouslama, Zihad and Amr, Zuhair}, title = {Bat ectoparasites (Nycteribiidae, Streblidae, Siphonaptera, Heteroptera, Mesostigmata, Argasidae, and Ixodidae) from Algeria}, series = {Journal of Vector Ecology}, volume = {42}, journal = {Journal of Vector Ecology}, publisher = {Wiley Interscience}, address = {Hoboken, NJ}, issn = {1948-7134}, doi = {10.1111/jvec.12235}, pages = {13 -- 23}, year = {2017}, abstract = {Twenty two species of ectoparasites (Family Nycteribiidae: Nycteribia (Listropoda) schmidlii schmidlii, Nycteribia (Nycteribia) latreillii, Nycteribia (Nycteribia) pedicularia, Penicillidia (Penicillidia) dufourii, and Phthiridium biarticulatum; Family Streblidae: Brachytarsina (Brachytarsina) flavipennis and Raymondia huberi; Order Siphonaptera: Rhinolophopsylla unipectinata arabs, Nycteridopsylla longiceps, Araeopsylla gestroi, Ischnopsyllus intermedius, and Ischnopsyllus octactenus; Order Heteroptera: Cimex pipistrelli, Cimex lectularius, and Cacodmus vicinus; Class Arachnida: Order Mesostigmata: Spinturnix myoti and Eyndhovenia euryalis; Order Ixodida: Family Argasidae: Argas transgariepinus and Argas vespertilionis; Family Ixodidae: Hyalomma dromedarii, Ixodes ricinus, and Ixodes vespertilionis) were recovered from 19 bat species in Algeria. New host records for bats are recorded for the first time: N. schmidlii from Rh. clivosus and R. cystops; N. latreillii from Rh. blasii and P. gaisleri; R. huberi from Rh. clivosus; C. pipistrelli from E. isabellinus and H. savii; C. vicinus from E. isabellinus; S. myoti from P. gaisleri; E. euryalis from P. gaisleri and Rh. blasii; A. vespertilionis from P. gaisleri; I. ricinus from T. teniotis and Rh. hipposideros and H. dromedarii from P. kuhlii. Raymondia huberi is recorded for the first time from Algeria.}, language = {en} } @article{ParrySchlaegelTiedemannetal.2022, author = {Parry, Victor and Schl{\"a}gel, Ulrike E. and Tiedemann, Ralph and Weithoff, Guntram}, title = {Behavioural Responses of Defended and Undefended Prey to Their Predator}, series = {Biology}, volume = {11}, journal = {Biology}, number = {8}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {2079-7737}, doi = {10.3390/biology11081217}, pages = {14}, year = {2022}, abstract = {Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status.}, language = {en} } @article{ParrySchlaegelTiedemannetal.2022, author = {Parry, Victor and Schl{\"a}gel, Ulrike E. and Tiedemann, Ralph and Weithoff, Guntram}, title = {Behavioural responses of defended and undefended prey to their predator}, series = {Biology : open access journal}, volume = {11}, journal = {Biology : open access journal}, number = {8}, publisher = {MDPI}, address = {Basel}, issn = {2079-7737}, doi = {10.3390/biology11081217}, pages = {14}, year = {2022}, abstract = {Many animals that have to cope with predation have evolved mechanisms to reduce their predation risk. One of these mechanisms is change in morphology, for example, the development of spines. These spines are induced, when mothers receive chemical signals of a predator (kairomones) and their daughters are then equipped with defensive spines. We studied the behaviour of a prey and its predator when the prey is either defended or undefended. We used common aquatic micro-invertebrates, the rotifers Brachionus calyciflorus (prey) and Asplanchna brightwellii (predator) as experimental animals. We found that undefended prey increased its swimming speed in the presence of the predator. The striking result was that the defended prey did not respond to the predator's presence. This suggests that defended prey has a different response behaviour to a predator than undefended conspecifics. Our study provides further insights into complex zooplankton predator-prey interactions. Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status.}, language = {en} } @article{DwiPutraReichetzederHasanetal.2020, author = {Dwi Putra, Sulistyo Emantoko and Reichetzeder, Christoph and Hasan, Ahmed Abdallah Abdalrahman Mohamed and Slowinski, Torsten and Chu, Chang and Kr{\"a}mer, Bernhard K. and Kleuser, Burkhard and Hocher, Berthold}, title = {Being born large for gestational age is associated with increased global placental DNA methylation}, series = {Scientific Reports}, volume = {10}, journal = {Scientific Reports}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-020-57725-0}, pages = {1 -- 10}, year = {2020}, abstract = {Being born small (SGA) or large for gestational age (LGA) is associated with adverse birth outcomes and metabolic diseases in later life of the offspring. It is known that aberrations in growth during gestation are related to altered placental function. Placental function is regulated by epigenetic mechanisms such as DNA methylation. Several studies in recent years have demonstrated associations between altered patterns of DNA methylation and adverse birth outcomes. However, larger studies that reliably investigated global DNA methylation are lacking. The aim of this study was to characterize global placental DNA methylation in relationship to size for gestational age. Global DNA methylation was assessed in 1023 placental samples by LC-MS/MS. LGA offspring displayed significantly higher global placental DNA methylation compared to appropriate for gestational age (AGA; p<0.001). ANCOVA analyses adjusted for known factors impacting on DNA methylation demonstrated an independent association between placental global DNA methylation and LGA births (p<0.001). Tertile stratification according to global placental DNA methylation levels revealed a significantly higher frequency of LGA births in the third tertile. Furthermore, a multiple logistic regression analysis corrected for known factors influencing birth weight highlighted an independent positive association between global placental DNA methylation and the frequency of LGA births (p=0.001).}, language = {en} } @article{EscalanteDominguezGomezRuizetal.2022, author = {Escalante, Ignacio and Dominguez, Marisol and Gomez-Ruiz, Daisy Alejandra and Machado, Glauco}, title = {Benefits and costs of mixed-species aggregations in Harvestmen (Arachnida: Opiliones)}, series = {Frontiers in ecology and evolution}, volume = {9}, journal = {Frontiers in ecology and evolution}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-701X}, doi = {10.3389/fevo.2021.766323}, pages = {24}, year = {2022}, abstract = {Many animals form aggregations with individuals of the same species (single-species aggregations, SSA). Less frequently, individuals may also aggregate with individuals of other species (mixed-species aggregations, MSA). Although the benefits and costs of SSA have been intensively studied, the same is not true for MSA. Here, we first review the cases of MSA in harvestmen, an arachnid order in which the records of MSA are more frequent than other arthropod orders. We then propose several benefits and costs of MSA in harvestmen, and contrast them with those of SSA. Second, using field-gathered data we describe gregariousness in seven species of Prionostemma harvestmen from Costa Rica. These species form MSA, but individuals are also found solitarily or in SSA. We tested one possible benefit and one possible cost of gregariousness in Prionostemma harvestmen. Regarding the benefit, we hypothesized that individuals missing legs would be more exposed to predation than eight-legged individuals and thus they should be found preferentially in aggregations, where they would be more protected from predators. Our data, however, do not support this hypothesis. Regarding the cost, we hypothesized that gregariousness increases the chances of parasitism. We found no support for this hypothesis either because both mite prevalence and infestation intensity did not differ between solitary or aggregated individuals. Additionally, the type of aggregation (SSA or MSA) was not associated with the benefit or the cost we explored. This lack of effect may be explained by the fluid membership of the aggregations, as we found high turnover over time in the number of individuals and species composition of the aggregations. In conclusion, we hope our review and empirical data stimulate further studies on MSA, which remains one of the most elusive forms of group living in animals.}, language = {en} } @article{ZhangHuYangetal.2022, author = {Zhang, Kai and Hu, Jiege and Yang, Shuai and Xu, Wei and Wang, Zhichao and Zhuang, Peiwen and Grossart, Hans-Peter and Luo, Zhuhua}, title = {Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1}, series = {Journal of hazardous materials}, volume = {437}, journal = {Journal of hazardous materials}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3894}, doi = {10.1016/j.jhazmat.2022.129406}, pages = {10}, year = {2022}, abstract = {Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80\% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.}, language = {en} }