@article{AltattanUllrichMattigetal.2024, author = {Altattan, Basma and Ullrich, Jasmin and Mattig, Emily and Poppe, Aline and Ribeiro Martins, Renata Filipa and Bier, Frank Fabian}, title = {Direct TAMRA-dUTP labeling of M. tuberculosis genes using loop-mediated isothermal amplification (LAMP)}, series = {Scientific reports}, volume = {14}, journal = {Scientific reports}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-024-55289-x}, pages = {9}, year = {2024}, abstract = {Fluorescent molecule-based direct labeling of amplified DNA is a sensitive method employed across diverse DNA detection and diagnostics systems. However, using pre-labeled primers only allows for the attachment of a single fluorophore to each DNA strand and any modifications of the system are less flexible, requiring new sets of primers. As an alternative, direct labeling of amplified products with modified nucleotides is available, but still poorly characterized. To address these limitations, we sought a direct and adaptable approach to label amplicons produced through Loop-mediated isothermal amplification (LAMP), using labeled nucleotides (dUTPs) rather than primers. The focus of this study was the development and examination of a direct labeling technique of specific genes, including those associated with drug resistance in Mycobacterium tuberculosis. We used 5-(3-Aminoallyl)-2′-deoxyuridine-5′triphosphate, tagged with 5/6-TAMRA (TAMRA-dUTP) for labeling LAMP amplicons during the amplification process and characterized amplification and incorporation efficiency. The optimal TAMRA-dUTP concentration was first determined based on amplification efficiency (0.5\% to total dNTPs). Higher concentrations of modified nucleotides reduced or completely inhibited the amplification yield. Target size also showed to be determinant to the success of amplification, as longer sequences showed lower amplification rates, thus less TAMRA incorporated amplicons. Finally, we were able to successfully amplify all four M. tuberculosis target genes using LAMP and TAMRA-modified dUTPs.}, language = {en} } @article{ZhangWaffoYarmanetal.2022, author = {Zhang, Xiaorong and Waffo, Armel T. and Yarman, Aysu and Kovacs, Norbert and Bognar, Zsofia and Wollenberger, Ulla and El-Sherbiny, Ibrahim M. and Hassan, Rabeay Y. A. and Bier, Frank Fabian and Gyurcsanyi, Robert E. and Zebger, Ingo and Scheller, Frieder W.}, title = {How an ACE2 mimicking epitope-MIP nanofilm recognizes template-related peptides and the receptor binding domain of SARS-CoV-2}, series = {Nanoscale}, volume = {14}, journal = {Nanoscale}, number = {48}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {2040-3364}, doi = {10.1039/d2nr03898f}, pages = {18106 -- 18114}, year = {2022}, abstract = {Here we aim to gain a mechanistic understanding of the formation of epitope-imprinted polymer nanofilms using a non-terminal peptide sequence, i.e. the peptide GFNCYFP (G485 to P491) of the SARS-CoV-2 receptor binding domain (RBD). This epitope is chemisorbed on the gold surface through the central cysteine 488 followed by the electrosynthesis of a similar to 5 nm thick polyscopoletin film around the surface confined templates. The interaction of peptides and the parent RBD and spike protein with the imprinted polyscopoletin nanofilm was followed by electrochemical redox marker gating, surface enhanced infrared absorption spectroscopy and conductive AFM. Because the use of non-terminal epitopes is especially intricate, here we characterize the binding pockets through their interaction with 5 peptides rationally derived from the template sequence, i.e. implementing central single amino acid mismatch as well as elongations and truncations at its C- and N- termini. Already a single amino acid mismatch, i.e. the central Cys488 substituted by a serine, results in ca. 15-fold lower affinity. Further truncation of the peptides to tetrapeptide (EGFN) and hexapeptide (YFPLQS) results also in a significantly lower affinity. We concluded that the affinity towards the different peptides is mainly determined by the four amino acid motif CYFP present in the sequence of the template peptide. A higher affinity than that for the peptides is found for the parent proteins RBD and spike protein, which seems to be due to out of cavity effects caused by their larger footprint on the nanofilm surface.}, language = {en} } @article{PaetzigGeigerRascheetal.2020, author = {P{\"a}tzig, Marlene and Geiger, Frenze and Rasche, Daniel and Rauneker, Philipp and Eltner, Anette}, title = {Allometric relationships for selected macrophytes of kettle holes in northeast Germany as a basis for efficient biomass estimation using unmanned aerial systems (UAS)}, series = {Aquatic botany : an international scientific journal dealing with applied and fundamental research on submerged, floating and emergent plants in marine and freshwater ecosystems}, volume = {162}, journal = {Aquatic botany : an international scientific journal dealing with applied and fundamental research on submerged, floating and emergent plants in marine and freshwater ecosystems}, publisher = {Elsevier Science}, address = {Amsterdam}, issn = {0304-3770}, doi = {10.1016/j.aquabot.2020.103202}, pages = {8}, year = {2020}, abstract = {Quantifying plant biomass in ecosystems is an essential basis for many ecological questions. A direct estimation of macrophyte biomass proves to be difficult for the large number of kettle holes in Pleistocene landscapes, due to their strong heterogeneities. This study compared a classical non-destructive method for biomass estimation based on allometric relationships built from a larger selection of plant trait variables with regressions only based on plant height and cover of four macrophyte species typical for kettle holes in northeast Germany (i.e. Carex riparia, Phalaris arundinacea, Persicaria amphibia, Rorippa amphibia). Their predictive power and potential applicability for remotely sensed biomass estimation using unmanned aerial systems (UAS) was evaluated. The usage of several in-situ measured plant traits of individual plants revealed best macrophyte biomass predictions (R-2 = 0.84 to 0.95). Yet, using only plant height and cover to predict biomass still showed a moderate to good correlation (R-2 = 0.52 to 0.81). Using P. anmdinacea as an example, we demonstrated for one kettle hole the potential of calculating plant patch height from digital surface models (DSM) derived from UAS RGB images processed with structure-from-motion (SfM) photogrammetry. After applying a site-specific correction factor for discrepancies between reference field measurements of plant heights and DSM derived plant heights, we were able to calculate P. anmdinacea biomass of the entire kettle hole based on allometric relationships using plant height and cover. Finally, we briefly discuss how further methodological development can improve UAS-derived plant height as predictor variable for biomass estimation.}, language = {en} } @article{CuiLiuXuetal.2022, author = {Cui, Guojie and Liu, Zongbao and Xu, Wei and Gao, Yuanhao and Yang, Shuai and Grossart, Hans-Peter and Li, Meng and Luo, Zhuhua}, title = {Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China)}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {838}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, number = {Part 1}, publisher = {Elsevier Science}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2022.155784}, pages = {9}, year = {2022}, abstract = {In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7\% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4\% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.}, language = {en} } @article{PerezEscobarTussoPrzelomskaetal.2022, author = {P{\´e}rez-Escobar, Oscar A. and Tusso, Sergio and Przelomska, Natalia A. S. and Wu, Shan and Ryan, Philippa and Nesbitt, Mark and Silber, Martina and Preick, Michaela and Fei, Zhangjun and Hofreiter, Michael and Chomicki, Guillaume and Renner, Susanne S.}, title = {Genome sequencing of up to 6,000-year-old Citrullus seeds reveals use of a bitter-fleshed species prior to watermelon domestication}, series = {Molecular biology and evolution}, volume = {39}, journal = {Molecular biology and evolution}, number = {8}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msac168}, pages = {13}, year = {2022}, abstract = {Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions. Phylogenomic and population-genomic analyses reveal that (1) much of the nuclear genome of both ancient seeds is traceable to West African seed-use "egusi-type" watermelon (Citrullus mucosospermus) rather than domesticated pulp-use watermelon (Citrullus lanatus ssp. vulgaris); (2) the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh as today found in C. mucosospermus, given alleles in the bitterness regulators ClBT and in the red color marker LYCB; and (3) both ancient genomes showed admixture from C. mucosospermus, C. lanatus ssp. cordophanus, C. lanatus ssp. vulgaris, and even South African Citrullus amarus, and evident introgression between the Libyan seed (UMB-6) and populations of C. lanatus. An unexpected new insight is that Citrullus appears to have initially been collected or cultivated for its seeds, not its flesh, consistent with seed damage patterns induced by human teeth in the oldest Libyan material.}, language = {en} } @article{WuAharonovichRothRosenbergetal.2022, author = {Wu, Zhen and Aharonovich, Dikla and Roth-Rosenberg, Dalit and Weissberg, Osnat and Luzzatto-Knaan, Tal and Vogts, Angela and Zoccarato, Luca and Eigemann, Falk and Grossart, Hans-Peter and Voss, Maren and Follows, Michael J. and Sher, Daniel}, title = {Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus}, series = {Nature microbiology}, volume = {7}, journal = {Nature microbiology}, number = {12}, publisher = {Nature Publishing Group}, address = {London}, issn = {2058-5276}, doi = {10.1038/s41564-022-01250-5}, pages = {2068 -- 2077+6}, year = {2022}, abstract = {Marine phytoplankton are responsible for about half of the photosynthesis on Earth. Many are mixotrophs, combining photosynthesis with heterotrophic assimilation of organic carbon, but the relative contribution of these two lifestyles is unclear. Here single-cell measurements reveal that Prochlorococcus at the base of the photic zone in the Eastern Mediterranean Sea obtain only similar to 20\% of carbon required for growth by photosynthesis. This is supported by laboratory-calibrated calculations based on photo-physiology parameters and compared with in situ growth rates. Agent-based simulations show that mixotrophic cells could grow tens of metres deeper than obligate photo-autotrophs, deepening the nutricline by similar to 20 m. Time series from the North Atlantic and North Pacific indicate that, during thermal stratification, on average 8-10\% of the Prochlorococcus cells live without enough light to sustain obligate photo-autotrophic populations. Together, these results suggest that mixotrophy underpins the ecological success of a large fraction of the global Prochlorococcus population and its collective genetic diversity.}, language = {en} } @article{EliašovaLledoGrauetal.2022, author = {Eli{\´a}šov{\´a}, Krist{\´y}na and Lled{\´o}, J. Ignacio Lucas and Grau, Jos{\´e} Horacio and Loudov{\´a}, Miroslava and Bannikova, Anna A. and Zolotareva, Katerina and Beneš, Vladimir and Hulva, Pavel and Čern{\´a} Bolf{\´i}kov{\´a}, Barbora}, title = {Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data}, series = {Heredity : an official journal of the Genetical Society of Great Britain}, volume = {129}, journal = {Heredity : an official journal of the Genetical Society of Great Britain}, number = {5}, publisher = {Macmillan Publishers Limited, part of Springer Nature}, address = {London}, issn = {0018-067X}, doi = {10.1038/s41437-022-00567-5}, pages = {305 -- 315}, year = {2022}, abstract = {Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period, and detected a new refugial lineage of E. roumanicus outside the Mediterranean basin, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different age and thus of the different stage of evolution of reproductive isolating mechanisms in each hybrid zone.}, language = {en} } @article{BussmannHornHoppertetal.2021, author = {Bussmann, Ingeborg and Horn, Fabian and Hoppert, Michael and Klings, Karl-Walter and Saborowski, Anke and Warnstedt, Julia and Liebner, Susanne}, title = {Methylomonas albis sp. nov. and Methylomonas fluvii sp. nov.}, series = {Systematic and applied microbiology}, volume = {44}, journal = {Systematic and applied microbiology}, number = {6}, publisher = {Elsevier}, address = {M{\"u}nchen}, issn = {0723-2020}, doi = {10.1016/j.syapm.2021.126248}, pages = {10}, year = {2021}, abstract = {Three strains of methanotrophic bacteria (EbA(T), EbB(T) and Eb1) were isolated from the River Elbe, Germany. These Gram-negative, rod-shaped or coccoid cells contain intracytoplasmic membranes perpendicular to the cell surface. Colonies and liquid cultures appeared bright-pink. The major cellular fatty acids were 12:0 and 14:0, in addition in Eb1 the FA 16:1 omega 5(t) was also dominant. Methane and methanol were utilized as sole carbon sources by EbB(T) and Eb1, while EbA(T) could not use methanol. All strains oxidize methane using the particulate methane monooxygenase. Both strains contain an additional soluble methane monooxygenase. The strains grew optimally at 15-25 degrees C and at pH 6 and 8. Based on 16S rRNA gene analysis recovered from the full genome, the phylogenetic position of EbA(T) is robustly outside any species clade with its closest relatives being Methylomonas sp. MK1 (98.24\%) and Methylomonas sp. 11b (98.11\%). Its closest type strain is Methylomonas methanica NCIMB11130 (97.91\%). The 16S rRNA genes of EbB(T) are highly similar to Methylomonas methanica strains with Methylomonas methanica R-45371 as the closest relative (99.87\% sequence identity). However, average nucleotide identity (ANI) and digital DNA DNA-hybridization (dDDH) values reveal it as distinct species. The DNA G + C contents were 51.07 mol\% and 51.5 mol\% for EbA(T) and EbB(T), and 50.7 mol\% for Eb1, respectively. Strains EbA(T) and EbB(T) are representing two novel species within the genus Methylomonas. For strain EbA(T) we propose the name Methylomonas albis sp. nov (LMG 29958, JCM 32282) and for EbB(T), we propose the name Methylomonas fluvii sp. nov (LMG 29959, JCM 32283). Eco-physiological descriptions for both strains are provided. Strain Eb1 (LMG 30323, JCM 32281) is a member of the species Methylovulum psychrotolerans. This genus is so far only represented by two isolates but Eb1 is the first isolate from a temperate environment; so, an emended description of the species is given.}, language = {en} } @article{Singh2024, author = {Singh, Aakanksha}, title = {Deducing the role of starch-related proteins in transitory starch metabolism through biochemical studies in Arabidopsis thaliana}, pages = {131}, year = {2024}, language = {en} } @article{GoreckiHolmDziurzynskietal.2021, author = {Gorecki, Adrian and Holm, Stine and Dziurzynski, Mikolaj and Winkel, Matthias and Yang, Sizhong and Liebner, Susanne and Wagner, Dirk and Dziewit, Lukasz and Horn, Fabian}, title = {Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils}, series = {The ISME journal : multidisciplinary journal of microbial ecology}, volume = {15}, journal = {The ISME journal : multidisciplinary journal of microbial ecology}, number = {11}, publisher = {Nature Publishing Group}, address = {Basingstoke}, issn = {1751-7362}, doi = {10.1038/s41396-021-01003-y}, pages = {3258 -- 3270}, year = {2021}, abstract = {Plasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil-an environment with a relatively low biomass and seasonal freeze-thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged to Moraxellaceae, Pseudomonadaceae, Enterobacteriaceae, Pectobacteriaceae, Burkholderiaceae, and Firmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold.}, language = {en} } @article{LiStoofLeichsenringLiuetal.2021, author = {Li, Kai and Stoof-Leichsenring, Kathleen R. and Liu, Sisi and Jia, Weihan and Liao, Mengna and Liu, Xingqi and Ni, Jian and Herzschuh, Ulrike}, title = {Plant sedimentary DNA as a proxy for vegetation reconstruction in eastern and northern Asia}, series = {Ecological indicators : integrating monitoring, assessment and management}, volume = {132}, journal = {Ecological indicators : integrating monitoring, assessment and management}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1470-160X}, doi = {10.1016/j.ecolind.2021.108303}, pages = {10}, year = {2021}, abstract = {Plant DNA from sediments (sedDNA) are increasingly used to reconstruct the past vegetation composition, which contrasts with the few investigations on the relationship between the plant sedDNA signal and modern vegetation. Here, we applied broad-scale terrestrial plant sedDNA metabarcoding on surface sediments from 201 lakes in eastern and northern Asia to discuss the applicability as well as the limitations of using plant sedDNA metabarcoding for palaeovegetation studies. In total, 381 terrestrial plant taxa were determined with the universal plant primers of trnL g and h. Overall, plant sedDNA approach is able to retrieve major vegetation signals. The composition of plant sedDNA reflect well the vegetation types and related climate characteristics, and it also signals which are the dominant taxa in the vegetation. Our results indicate that plant sedDNA metabarcoding could be a reliable proxy of vegetation composition at a sub-continental scale and along large environmental gradients. But certain drawbacks such as limited taxonomic resolution, biases in the relative abundance of taxa, and a generally high variability of samples from similar vegetation types need to be solved before it can be widely applied to reconstruct palaeofloras.}, language = {en} } @article{IsantaNavarroArnottKlauschiesetal.2021, author = {Isanta-Navarro, Jana and Arnott, Shelley E. and Klauschies, Toni and Martin-Creuzburg, Dominik}, title = {Dietary lipid quality mediates salt tolerance of a freshwater keystone herbivore}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {769}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2020.144657}, pages = {9}, year = {2021}, abstract = {Salinization of freshwater ecosystems is a growing hazard for organisms and ecosystem functioning worldwide. In northern latitudes, road salt that is being transported into water bodies can cause year-round increases in lake salinity levels. Exploring the environmental factors driving the susceptibility of freshwater zooplankton to road salt is crucial for assessing the impact of salinization on food web processes. We studied the role of essential lipids, i.e., sterols and long-chain polyunsaturated fatty acids (PUFAs), in mediating salt tolerance of the freshwater keystone herbivore Daphnia. Sterols and PUFAs are involved in regulating ion permeability of biological membranes and thus we hypothesized that the susceptibility to salt is affected by the dietary sterol and PUFA supply. Life history experiments revealed opposing effects of sterol and PUFA supplementation on salt tolerance, i.e., tolerance increased upon sterol supplementation but decreased upon PUFA supplementation, which is consistent with their proposed impact on membrane permeability. Our results suggest that the susceptibility of freshwater zooplankton to salinization strongly depends on the dietary lipid supply and thus the phytoplankton community composition. Hence, trophic state related differences in the phytoplankton community composition need to be considered when assessing the consequences of salinization for freshwater ecosystem functioning.}, language = {en} } @article{YangXuZhangetal.2022, author = {Yang, Shuai and Xu, Wei and Zhang, Kai and Hu, Jiege and Gao, Yuanhao and Cui, Guojie and Grossart, Hans-Peter and Luo, Zhuhua}, title = {Fungal communities differ with microplastic types in deep sea sediment enrichments of the Eastern Pacific}, series = {International biodeterioration \& biodegradation}, volume = {173}, journal = {International biodeterioration \& biodegradation}, publisher = {Elsevier}, address = {Barling}, issn = {0964-8305}, doi = {10.1016/j.ibiod.2022.105461}, pages = {9}, year = {2022}, abstract = {In this study, we used three plastic powders (polystyrene (PS), polyethylene terephthalate (PET) and poly-urethane (PU)) to conduct micro-enrichments with deep-sea sediments from the Eastern Pacific. High-throughput sequencing of the ITS marker gene was performed during the enrichment process. The results showed that in comparison to culture time, plastic type significantly influenced the richness and diversity of the associated fungal community. The fungal community structures in PS and PET enrichments were similar, and there was no significant difference in fungal beta diversity. Culture time, however, did not have any significant impact on the fungal community. On the other hand, based on FUNGuild analysis, we revealed that the fungal community compositions in PS and PET samples were highly similar, whereas PU enrichment was very different. The OTU network indicated more interactions between the different OTUs in the PU-enriched samples, demonstrating a highly complex interaction network. Fungal abundance, however, was not significantly affected by plastic type or culture time. In conclusion, compared to the original deep-sea sediments, addition of microplastics results in changes of the fungal community structure. Furthermore, different plastic types lead to different fungal com-munities, and compared with PS and PET, the enrichment effect of PU was stronger. Finally, rather than culture time, plastic type has a significant impact on fungal diversity and community composition.}, language = {en} } @article{KraftRezaeiBreueretal.2021, author = {Kraft, Philipp and Rezaei, Ehsan Eyshi and Breuer, Lutz and Ewert, Frank and Große-Stoltenberg, Andr{\´e} and Kleinebecker, Till and Seserman, Diana-Maria and Nendel, Claas}, title = {Modelling agroforestry's contributions to people}, series = {Agronomy / Molecular Diversity Preservation International (MDPI)}, volume = {11}, journal = {Agronomy / Molecular Diversity Preservation International (MDPI)}, number = {11}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {2073-4395}, doi = {10.3390/agronomy11112106}, pages = {25}, year = {2021}, abstract = {Climate change, increasing environmental pollution, continuous loss of biodiversity, and a growing human population with increasing food demand, threaten the functioning of agro-ecosystems and their contribution to people and society. Agroforestry systems promise a number of benefits to enhance nature's contributions to people. There are a wide range of agroforestry systems implemented representing different levels of establishment across the globe. This range and the long time periods for the establishment of these systems make empirical assessments of impacts on ecosystem functions difficult. In this study we investigate how simulation models can help to assess and predict the role of agroforestry in nature's contributions. The review of existing models to simulate agroforestry systems reveals that most models predict mainly biomass production and yield. Regulating ecosystem services are mostly considered as a means for the assessment of yield only. Generic agroecosystem models with agroforestry extensions provide a broader scope, but the interaction between trees and crops is often addressed in a simplistic way. The application of existing models for agroforestry systems is particularly hindered by issues related to code structure, licences or availability. Therefore, we call for a community effort to connect existing agroforestry models with ecosystem effect models towards an open-source, multi-effect agroforestry modelling framework.}, language = {en} } @article{IrmscherRoskeGayketal.2021, author = {Irmscher, Tobias and Roske, Yvette and Gayk, Igor and Dunsing, Valentin and Chiantia, Salvatore and Heinemann, Udo and Barbirz, Stefanie}, title = {Pantoea stewartii WceF is a glycan biofilm-modifying enzyme with a bacteriophage tailspike-like fold}, series = {The journal of biological chemistry : JBC / publ. by the American Society for Biochemistry and Molecular Biology}, volume = {296}, journal = {The journal of biological chemistry : JBC / publ. by the American Society for Biochemistry and Molecular Biology}, publisher = {ASBMB Publications}, address = {Bethesda, Md.}, issn = {1083-351X}, doi = {10.1016/j.jbc.2021.100286}, pages = {10}, year = {2021}, abstract = {Pathogenic microorganisms often reside in glycan-based biofilms. Concentration and chain length distribution of these mostly anionic exopolysaccharides (EPS) determine the overall biophysical properties of a biofilm and result in a highly viscous environment. Bacterial communities regulate this biofilm state via intracellular small-molecule signaling to initiate EPS synthesis. Reorganization or degradation of this glycan matrix, however, requires the action of extracellular glycosidases. So far, these were mainly described for bacteriophages that must degrade biofilms for gaining access to host bacteria. The plant pathogen Pantoea stewartii (P. stewartii) encodes the protein WceF within its EPS synthesis cluster. WceF has homologs in various biofilm forming plant pathogens of the Erwinia family. In this work, we show that WceF is a glycosidase active on stewartan, the main P. stewartii EPS biofilm component. WceF has remarkable structural similarity with bacteriophage tailspike proteins (TSPs). Crystal structure analysis showed a native trimer of right-handed parallel beta-helices. Despite its similar fold, WceF lacks the high stability found in bacteriophage TSPs. WceF is a stewartan hydrolase and produces oligosaccharides, corresponding to single stewartan repeat units. However, compared with a stewartan-specific glycan hydrolase of bacteriophage origin, WceF showed lectin-like autoagglutination with stewartan, resulting in notably slower EPS cleavage velocities. This emphasizes that the bacterial enzyme WceF has a role in P. stewartii biofilm glycan matrix reorganization clearly different from that of a bacteriophage exopolysaccharide depolymerase.}, language = {en} } @article{HuWestburyYuanetal.2021, author = {Hu, Jiaming and Westbury, Michael V. and Yuan, Junxia and Zhang, Zhen and Chen, Shungang and Xiao, Bo and Hou, Xindong and Ji, Hailong and Lai, Xulong and Hofreiter, Michael and Sheng, Guilian}, title = {Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta}, series = {Proceedings of the Royal Society of London. Series B, Biological sciences}, volume = {288}, journal = {Proceedings of the Royal Society of London. Series B, Biological sciences}, number = {1943}, publisher = {Royal Society of London}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2020.2934}, pages = {9}, year = {2021}, abstract = {Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95\% CI 1.62-2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.}, language = {en} } @article{HernandezSanchezMaruriLopezMartinezMartinezetal.2022, author = {Hernandez-Sanchez, Itzell E. and Maruri-Lopez, Israel and Martinez-Martinez, Coral and Janis, Brett and Juan Francisco, Jimenez-Bremont and Covarrubias, Alejandra A. and Menze, Michael A. and Graether, Steffen P. and Thalhammer, Anja}, title = {LEAfing through literature}, series = {Journal of experimental botany}, volume = {73}, journal = {Journal of experimental botany}, number = {19}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/erac293}, pages = {6525 -- 6546}, year = {2022}, abstract = {To deal with increasingly severe periods of dehydration related to global climate change, it becomes increasingly important to understand the complex strategies many organisms have developed to cope with dehydration and desiccation. While it is undisputed that late embryogenesis abundant (LEA) proteins play a key role in the tolerance of plants and many anhydrobiotic organisms to water limitation, the molecular mechanisms are not well understood. In this review, we summarize current knowledge of the physiological roles of LEA proteins and discuss their potential molecular functions. As these are ultimately linked to conformational changes in the presence of binding partners, post-translational modifications, or water deprivation, we provide a detailed summary of current knowledge on the structure-function relationship of LEA proteins, including their disordered state in solution, coil to helix transitions, self-assembly, and their recently discovered ability to undergo liquid-liquid phase separation. We point out the promising potential of LEA proteins in biotechnological and agronomic applications, and summarize recent advances. We identify the most relevant open questions and discuss major challenges in establishing a solid understanding of how these intriguing molecules accomplish their tasks as cellular sentinels at the limits of surviving water scarcity. LEA proteins are vital players in tolerance to water deficit. We explore our current understanding of their physiological roles, emphasize exciting future directions, and highlight their potential for biotechnological applications.}, language = {en} } @article{YangZhuChenetal.2022, author = {Yang, Ming-Kang and Zhu, Xiao-Jie and Chen, Chu-Min and Guo, Xu and Xu, Shu-Xuan and Xu, Ya-Rou and Du, Shen-Xiu and Xiao, Shi and M{\"u}ller-R{\"o}ber, Bernd and Huang, Wei and Chen, Liang}, title = {The plant circadian clock regulates autophagy rhythm through transcription factor LUX ARRHYTHMO}, series = {Journal of integrative plant biology}, volume = {64}, journal = {Journal of integrative plant biology}, number = {11}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {1672-9072}, doi = {10.1111/jipb.13343}, pages = {2135 -- 2149}, year = {2022}, abstract = {Autophagy is an evolutionarily conserved degradation pathway in eukaryotes; it plays a critical role in nutritional stress tolerance. The circadian clock is an endogenous timekeeping system that generates biological rhythms to adapt to daily changes in the environment. Accumulating evidence indicates that the circadian clock and autophagy are intimately interwoven in animals. However, the role of the circadian clock in regulating autophagy has been poorly elucidated in plants. Here, we show that autophagy exhibits a robust circadian rhythm in both light/dark cycle (LD) and in constant light (LL) in Arabidopsis. However, autophagy rhythm showed a different pattern with a phase-advance shift and a lower amplitude in LL compared to LD. Moreover, mutation of the transcription factor LUX ARRHYTHMO (LUX) removed autophagy rhythm in LL and led to an enhanced amplitude in LD. LUX represses expression of the core autophagy genes ATG2, ATG8a, and ATG11 by directly binding to their promoters. Phenotypic analysis revealed that LUX is responsible for improved resistance of plants to carbon starvation, which is dependent on moderate autophagy activity. Comprehensive transcriptomic analysis revealed that the autophagy rhythm is ubiquitous in plants. Taken together, our findings demonstrate that the LUX-mediated circadian clock regulates plant autophagy rhythms.}, language = {en} } @article{HeinzDoellingerMausetal.2022, author = {Heinz, Jacob and D{\"o}llinger, J{\"o}rg and Maus, Deborah and Schneider, Andy and Lasch, Peter and Grossart, Hans-Peter and Schulze-Makuch, Dirk}, title = {Perchlorate-specific proteomic stress responses of Debaryomyces hansenii could enable microbial survival in Martian brines}, series = {Environmental microbiology}, volume = {24}, journal = {Environmental microbiology}, number = {11}, publisher = {Blackwell}, address = {Oxford [u.a.]}, issn = {1462-2912}, doi = {10.1111/1462-2920.16152}, pages = {5051 -- 5065}, year = {2022}, abstract = {If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganisms on the cellular level. Here, we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO4-induced stresses share many common metabolic features, for example, signalling pathways, elevated energy metabolism, or osmolyte biosynthesis. Nevertheless, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for putative life on Mars, which-given the environmental conditions-likely developed chaotropic defence strategies such as stabilized confirmations of biomacromolecules or the formation of cell clusters.}, language = {en} } @article{BandekarMonikhKekalainenetal.2022, author = {Bandekar, Mandar and Monikh, Fazel Abdolahpur and Kekalainen, Jukka and Tahvanainen, Teemu and Kortet, Raine and Zhang, Peng and Guo, Zhiling and Akkanen, Jarkko and Leskinen, Jari T. T. and Gomez-Gonzalez, Miguel A. and Darbha, Gopala Krishna and Grossart, Hans-Peter and Valsami-Jones, Eugenia and Kukkonen, Jussi V. K.}, title = {Submicron plastic adsorption by peat, accumulation in Sphagnum Mosses and influence on bacterial communities in peatland ecosystems}, series = {Environmental science \& technology}, volume = {56}, journal = {Environmental science \& technology}, number = {22}, publisher = {American Chemical Society}, address = {Columbus, Ohio}, issn = {0013-936X}, doi = {10.1021/acs.est.2c04892}, pages = {15661 -- 15671}, year = {2022}, abstract = {The smallest fraction of plastic pollution, submicron plastics (SMPs <1 mu m) are expected to be ubiquitous in the environment. No information is available about SMPs in peatlands, which have a key role in sequestering carbon in terrestrial ecosystems. It is unknown how these plastic particles might behave and interact with (micro)organisms in these ecosystems. Here, we show that the chemical composition of polystyrene (PS) and poly(vinyl diloride) (PVC)-SMPs influenced their adsorption to peat. Consequently, this influenced the accumualtion of SMPs by Sphagnum moss and the composition and diversity of the microbial communities in peatland. Natural organic matter (NOM), which adsorbs from the surrounding water to the surface of SMPs, decreased the adsorption of the particles to peat and their accumulation by Sphagnum moss. However, the presence of NOM on SMPs significantly altered the bacterial community structure compared to SMPs without NOM. Our findings show that peatland ecosystems can potentially adsorb plastic particles. This can not only impact mosses themselves but also change the local microbial communities.}, language = {en} } @article{KoziolOdriozolaNyholmetal.2022, author = {Koziol, Adam and Odriozola, I{\~n}aki and Nyholm, Lasse and Leonard, Aoife and San Jos{\´e}, Carlos and Pauperio, Joana and Mendes Ferreira, Clara and Hansen, Anders J. and Aizpurua, Ostaizka and Gilbert, M. Thomas P. and Alberdi, Antton}, title = {Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals}, series = {MicrobiologyOpen}, volume = {11}, journal = {MicrobiologyOpen}, number = {5}, publisher = {Wiley}, address = {Malden, Mass.}, issn = {2045-8827}, doi = {10.1002/mbo3.1318}, pages = {19}, year = {2022}, abstract = {As continued growth in gut microbiota studies in captive and model animals elucidates the importance of their role in host biology, further pursuit of how to retain a wild-like microbial community is becoming increasingly important to obtain representative results from captive animals. In this study, we assessed how the gut microbiota of two wild-caught small mammals, namely Crocidura russula (Eulipotyphla, insectivore) and Apodemus sylvaticus (Rodentia, omnivore), changed when bringing them into captivity. We analyzed fecal samples of 15 A. sylvaticus and 21 C. russula, immediately after bringing them into captivity and 5 weeks later, spread over two housing treatments: a "natural" setup enriched with elements freshly collected from nature and a "laboratory" setup with sterile artificial elements. Through sequencing of the V3-V4 region of the 16S recombinant RNA gene, we found that the initial microbial diversity dropped during captivity in both species, regardless of treatment. Community composition underwent a change of similar magnitude in both species and under both treatments. However, we did observe that the temporal development of the gut microbiome took different trajectories (i.e., changed in different directions) under different treatments, particularly in C. russula, suggesting that C. russula may be more susceptible to environmental change. The results of this experiment do not support the use of microbially enriched environments to retain wild-like microbial diversities and compositions, yet show that specific housing conditions can significantly affect the drift of microbial communities under captivity.}, language = {en} } @article{MuroLinstaedterMagdonetal.2022, author = {Muro, Javier and Linst{\"a}dter, Anja and Magdon, Paul and Woellauer, Stephan and M{\"a}nner, Florian A. and Schwarz, Lisa-Maricia and Ghazaryan, Gohar and Schultz, Johannes and Malenovsky, Zbynek and Dubovyk, Olena}, title = {Predicting plant biomass and species richness in temperate grasslands across regions, time, and land management with remote sensing and deep learning}, series = {Remote sensing of environment : an interdisciplinary journal}, volume = {282}, journal = {Remote sensing of environment : an interdisciplinary journal}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0034-4257}, doi = {10.1016/j.rse.2022.113262}, pages = {18}, year = {2022}, abstract = {Spatial predictions of biomass production and biodiversity at regional scale in grasslands are critical to evaluate the effects of management practices across environmental gradients. New generations of remote sensing sensors and machine learning approaches can predict these grassland characteristics with varying accuracy. However, such studies frequently fail to cover a sufficiently broad range of environmental conditions, and their prediction models are often case-specific. To address this gap, we have modelled above-ground biomass and species richness in 150 spatially independent grassland plots of three geographical regions in Germany. These regions follow a North-South climate gradient and differ in soil types, topography, elevation, climatic conditions, historical contexts, and management intensities. The predictors tested in this study are Sentinel-1 backscatter, Sentinel-2 time series of surface reflectance along with derived vegetation indices and Rao's Q, and a set of topoedaphic variables. We compared the performance of a feed-forward deep neural network (DNN) with a random forest (RF) regression algorithm. The DNN achieved the best estimations of biomass (r2 = 0.45) when trained with Sentinel-2 surface reflectance only. Moreover, the DNN showed a higher generalizability than RF during spatial cross-validations (i.e., calibrating and validating in different regions, r2 = 0.38 vs. 0.26). Species richness pre-dictions by both algorithms improved when the full time series of Sentinel-2 surface reflectance values were used (highest r2 = 0.42 achieved by the DNN), but both performed poorly during spatial cross-validations. Overall, the DNN-based models were more robust than RF models, showed a lower bias and lower systematic error, and required fewer inputs. Explainability analysis indicated that red-edge and near infrared information from May and October was the most relevant to predict species richness. This study presents an important step forward in generating robust spatially explicit predictions of grassland attributes and biodiversity variables across large areas, environmental gradients, and phenological stages.}, language = {en} } @article{FlemerGulatiBergnaetal.2022, author = {Flemer, Burkhardt and Gulati, Sneha and Bergna, Alessandro and R{\"a}ndler, Manuela and Cernava, Tomislav and Witzel, Katja and Berg, Gabriele and Grosch, Rita}, title = {Biotic and abiotic stress factors induce microbiome shifts and enrichment of distinct beneficial bacteria in tomato roots}, series = {Phytobiomes journal}, volume = {6}, journal = {Phytobiomes journal}, number = {4}, publisher = {American Phytopathological Society}, address = {St. Paul}, issn = {2471-2906}, doi = {10.1094/PBIOMES-10-21-0067-R}, pages = {276 -- 289}, year = {2022}, abstract = {Crops are often simultaneously threatened by abiotic and biotic stress factors but the stress response of the plant holobiont is not well understood, despite the high importance of this response to ensure future plant production. Therefore, the aim of this study was to assess the impact of individual and combined abiotic (ionic and osmotic) and biotic ( Verticillium dahliae and Fusarium oxysporum) stress factors on plant performance and on the bacterial composition of the root endosphere in tomato. Structure and function of the microbiota was analyzed by 16S ribosomal RNA gene amplicon sequencing and a complementary cultivation approach, including in vitro and in vivo assays. Under all stress conditions, tomato growth and photosynthetic activity was reduced. Combined abiotic stressors with F. oxysporum but not with V. dahliae infection led to an additive negative effect on plant performance. All stress conditions induced a microbiome shift, and changed the relative abundance of phyla such as Firmicutes and classes of Proteobacteria. Endophytes identified as Bacillus, Paenibacillus, and Microbacterium spp. showed tolerance to abiotic stress conditions and plant beneficial effects. Stressor-specific enrichments of beneficial bacteria in the root were discovered (e.g., Paenibacillus in roots infected with F. oxysporum and Microbacterium in roots infected with V. dahliae). Interestingly, endophytes that were able to promote plant growth were obtained only from roots exposed to individual biotic and combined abiotic and biotic stress conditions but not individual abiotic stressors. Our study revealed stressor-specific enrichment of beneficial bacteria in tomato roots, which has implications for novel plant protection strategies.}, language = {en} } @article{RoelekeSchlaegelGallagheretal.2022, author = {Roeleke, Manuel and Schl{\"a}gel, Ulrike E. and Gallagher, Cara and Pufelski, Jan and Blohm, Torsten and Nathan, Ran and Toledo, Sivan and Jeltsch, Florian and Voigt, Christian C.}, title = {Insectivorous bats form mobile sensory networks to optimize prey localization: The case of the common noctule bat}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {33}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.2203663119}, pages = {10}, year = {2022}, abstract = {Animals that depend on ephemeral, patchily distributed prey often use public information to locate resource patches. The use of public information can lead to the aggregation of foragers at prey patches, a mechanism known as local enhancement. However, when ephemeral resources are distributed over large areas, foragers may also need to increase search efficiency, and thus apply social strategies when sampling the landscape. While sensory networks of visually oriented animals have already been confirmed, we lack an understanding of how acoustic eavesdropping adds to the formation of sensory networks. Here we radio-tracked a total of 81 aerial-hawking bats at very high spatiotemporal resolution during five sessions over 3 y, recording up to 19 individuals simultaneously. Analyses of interactive flight behavior provide conclusive evidence that bats form temporary mobile sensory networks by adjusting their movements to neighboring conspecifics while probing the airspace for prey. Complementary agent-based simulations confirmed that the observed movement patterns can lead to the formation of mobile sensory networks, and that bats located prey faster when networking than when relying only on local enhancement or searching solitarily. However, the benefit of networking diminished with decreasing group size. The combination of empirical analyses and simulations elucidates how animal groups use acoustic information to efficiently locate unpredictable and ephemeral food patches. Our results highlight that declining local populations of social foragers may thus suffer from Allee effects that increase the risk of collapses under global change scenarios, like insect decline and habitat degradation.}, language = {en} } @article{OrfTenenboimOmranianetal.2022, author = {Orf, Isabel and Tenenboim, Hezi and Omranian, Nooshin and Nikoloski, Zoran and Fernie, Alisdair R. and Lisec, Jan and Brotman, Yariv and Bromke, Mariusz A.}, title = {Transcriptomic and metabolomic analysis of a Pseudomonas-resistant versus a susceptible Arabidopsis accession}, series = {International journal of molecular sciences}, volume = {23}, journal = {International journal of molecular sciences}, number = {20}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms232012087}, pages = {27}, year = {2022}, abstract = {Accessions of one plant species may show significantly different levels of susceptibility to stresses. The Arabidopsis thaliana accessions Col-0 and C24 differ significantly in their resistance to the pathogen Pseudomonas syringae pv. tomato (Pst). To help unravel the underlying mechanisms contributing to this naturally occurring variance in resistance to Pst, we analyzed changes in transcripts and compounds from primary and secondary metabolism of Col-0 and C24 at different time points after infection with Pst. Our results show that the differences in the resistance of Col-0 and C24 mainly involve mechanisms of salicylic-acid-dependent systemic acquired resistance, while responses of jasmonic-acid-dependent mechanisms are shared between the two accessions. In addition, arginine metabolism and differential activity of the biosynthesis pathways of aliphatic glucosinolates and indole glucosinolates may also contribute to the resistance. Thus, this study highlights the difference in the defense response strategies utilized by different genotypes.}, language = {en} } @article{WangChenHouetal.2022, author = {Wang, Jun and Chen, Xiaowen and Hou, Xin and Wang, Jingan and Yue, Wucheng and Huang, Shu and Xu, Gangchun and Yan, Jizhou and Lu, Guoqing and Hofreiter, Michael and Li, Chenhong and Wang, Chenghui}, title = {"Omics" data unveil early molecular response underlying limb regeneration in the Chinese mitten crab, Eriocheir sinensis}, series = {Science Advances}, volume = {8}, journal = {Science Advances}, number = {37}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington, DC [u.a.]}, issn = {2375-2548}, doi = {10.1126/sciadv.abl4642}, pages = {15}, year = {2022}, abstract = {Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely allowed it to become a worldwide invasive species. Here, we report a chromosome-level genome of E. sinensis as well as large-scale transcriptome data during the limb regeneration process. Our results reveal that arthropod -specific genes involved in signal transduction, immune response, histone methylation, and cuticle development all play fundamental roles during the regeneration process. Particularly, Innexin2-mediated signal transduction likely facilitates the early stage of the regeneration process, while an effective crustacean-specific prophenoloxidase system (ProPo-AS) plays crucial roles in the initial immune response. Collectively, our findings uncover novel genetic pathways pertaining to arthropod limb regeneration and provide valuable resources for studies on regeneration from a comparative perspective.}, language = {en} } @article{GaoMaWangetal.2022, author = {Gao, Qiancheng and Ma, Xiaowan and Wang, Zhichao and Chen, Haisheng and Luo, Yu and Wu, Bi and Qi, Shanni and Lin, Miaozhen and Tian, Jing and Qiao, Ying and Grossart, Hans-Peter and Xu, Wei and Huang, Lixing}, title = {Seasonal variation, virulence gene and antibiotic resistance of Vibrio in a semi-enclosed bay with mariculture (Dongshan Bay, Southern China)}, series = {Marine pollution bulletin : the international journal for marine environmental scientists, engineers, administrators, politicians and lawyers}, volume = {184}, journal = {Marine pollution bulletin : the international journal for marine environmental scientists, engineers, administrators, politicians and lawyers}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0025-326X}, doi = {10.1016/j.marpolbul.2022.114112}, pages = {9}, year = {2022}, abstract = {In this study, the virulence genes, antibiotic resistance of culturable Vibrio and the environmental factors affecting Vibrio abundance were analyzed in four seasons in DongShan Bay with different intensity of aquaculture practice. A total of 253 bacteria isolates were obtained, of which 177 Vibrio strains belonged to 26 species. Annual Vibrio abundance in this region ranged from 20 to 11,600 CFU mL(-1) and the most significant positive correlation occurred with temperature. Detection of 9 different Vibrio virulence genes revealed that most isolates contained atypical virulence genes in addition to the typical ones. In particular, virulence genes of hemolysin such as tdh, trh, and hlyA (6.32 \%, 15.52 \%, and 11.30 \%) showed different degrees of horizontal gene transfer (HGT). In our antibiotic resistance test, the multiple antibiotic resistance (MAR) index of the isolates ranged from 0.01 to 0.03 in different seasons, and three MAR Vibrio strains were detected. Overall, our study sheds new light on the spatial distribution patterns and the occurrence of virulence genes and antibiotics resistance Vibrio iso-lated from a subtropical bay with intensive aquaculture. Our study provides a suitable microbial quality sur-veillance in a mariculture impacted coastal environment. It will help to establish effective disease prevention measures in this area and provide useful guidance and support for formulating local antibiotics use policies.}, language = {en} } @article{ZhouWangXuetal.2022, author = {Zhou, Yaqi and Wang, Hongkai and Xu, Sunde and Liu, Kai and Qi, Hao and Wang, Mengcen and Chen, Xiaoyulong and Berg, Gabriele and Ma, Zhonghua and Cernava, Tomislav and Chen, Yun}, title = {Bacterial-fungal interactions under agricultural settings: from physical to chemical interactions}, series = {Stress biology}, volume = {2}, journal = {Stress biology}, number = {1}, publisher = {Springer Nature, Northwest A\&F University}, address = {Singapore, Yangling}, issn = {2731-0450}, doi = {10.1007/s44154-022-00046-1}, pages = {17}, year = {2022}, abstract = {Bacteria and fungi are dominant members of environmental microbiomes. Various bacterial-fungal interactions (BFIs) and their mutual regulation are important factors for ecosystem functioning and health. Such interactions can be highly dynamic, and often require spatiotemporally resolved assessments to understand the interplay which ranges from antagonism to mutualism. Many of these interactions are still poorly understood, especially in terms of the underlying chemical and molecular interplay, which is crucial for inter-kingdom communication and interference. BFIs are highly relevant under agricultural settings; they can be determinative for crop health. Advancing our knowledge related to mechanisms underpinning the interactions between bacteria and fungi will provide an extended basis for biological control of pests and pathogens in agriculture. Moreover, it will facilitate a better understanding of complex microbial community networks that commonly occur in nature. This will allow us to determine factors that are crucial for community assembly under different environmental conditions and pave the way for constructing synthetic communities for various biotechnological applications. Here, we summarize the current advances in the field of BFIs with an emphasis on agriculture.}, language = {en} } @article{HoefsHuelagueBennetetal.2021, author = {H{\"o}fs, Soraya and Huelague, Deniz and Bennet, Francesca and Carl, Peter and Flemig, Sabine and Schmid, Thomas and Schenk, Jorg A. and Hodoroaba, Vasile-Dan and Schneider, Rudolf J.}, title = {Electrochemical immunomagnetic Ochratoxin A sensing}, series = {ChemElectroChem}, volume = {8}, journal = {ChemElectroChem}, number = {13}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {2196-0216}, doi = {10.1002/celc.202100446}, pages = {2597 -- 2606}, year = {2021}, abstract = {Electrochemical methods offer great promise in meeting the demand for user-friendly on-site devices for monitoring important parameters. The food industry often runs own lab procedures, for example, for mycotoxin analysis, but it is a major goal to simplify analysis, linking analytical methods with smart technologies. Enzyme-linked immunosorbent assays, with photometric detection of 3,3',5,5'-tetramethylbenzidine (TMB), form a good basis for sensitive detection. To provide a straightforward approach for the miniaturization of the detection step, we have studied the pitfalls of the electrochemical TMB detection. By cyclic voltammetry it was found that the TMB electrochemistry is strongly dependent on the pH and the electrode material. A stable electrode response to TMB could be achieved at pH 1 on gold electrodes. We created a smartphone-based, electrochemical, immunomagnetic assay for the detection of ochratoxin A in real samples, providing a solid basis for sensing of further analytes.}, language = {en} } @article{RazaghiMoghadamSokolowskaSowaetal.2021, author = {Razaghi-Moghadam, Zahra and Sokolowska, Ewelina and Sowa, Marcin A. and Skirycz, Aleksandra and Nikoloski, Zoran}, title = {Combination of network and molecule structure accurately predicts competitive inhibitory interactions}, series = {Computational and structural biotechnology journal}, volume = {19}, journal = {Computational and structural biotechnology journal}, publisher = {Research Network of Computational and Structural Biotechnology (RNCSB)}, address = {Gotenburg}, issn = {2001-0370}, doi = {10.1016/j.csbj.2021.04.012}, pages = {2170 -- 2178}, year = {2021}, abstract = {Mining of metabolite-protein interaction networks facilitates the identification of design principles underlying the regulation of different cellular processes. However, identification and characterization of the regulatory role that metabolites play in interactions with proteins on a genome-scale level remains a pressing task. Based on availability of high-quality metabolite-protein interaction networks and genome-scale metabolic networks, here we propose a supervised machine learning approach, called CIRI that determines whether or not a metabolite is involved in a competitive inhibitory regulatory interaction with an enzyme. First, we show that CIRI outperforms the naive approach based on a structural similarity threshold for a putative competitive inhibitor and the substrates of a metabolic reaction. We also validate the performance of CIRI on several unseen data sets and databases of metabolite-protein interactions not used in the training, and demonstrate that the classifier can be effectively used to predict competitive inhibitory interactions. Finally, we show that CIRI can be employed to refine predictions about metabolite-protein interactions from a recently proposed PROMIS approach that employs metabolomics and proteomics profiles from size exclusion chromatography in E. coli to predict metaboliteprotein interactions. Altogether, CIRI fills a gap in cataloguing metabolite-protein interactions and can be used in directing future machine learning efforts to categorize the regulatory type of these interactions.}, language = {en} } @article{HabelSchmittGrosetal.2022, author = {Habel, Jan Christian and Schmitt, Thomas and Gros, Patrick and Ulrich, Werner}, title = {Breakpoints in butterfly decline in Central Europe over the last century}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {851}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, number = {Part 2}, publisher = {Elsevier Science}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2022.158315}, pages = {9}, year = {2022}, abstract = {Recent studies indicated severe decline of insect diversity and abundance across major parts of Central Europe. Theoretical studies showed that the drivers behind biodiversity loss vary considerably over time. However, these scenarios so far have been insufficiently approved by long-term and large-scale data. In this study we analysed the temporal trends of butterflies and Zygaenid moths across the federal state of Salzburg, northern Austria, from 1920 to 2019. Our study area covers a large variety of habitats and altitudes. Various changes of land use and intensification occurred during and shortly before our studied period, with a first wave of habitat destruction starting in the late 19th century, followed by the deterioration of habitat quality since the mid-20th century. We used 59,870 presence-only data of 168 butterfly and burnet moth species. Each of these species was classified according to ecological characteristics. Break point analyses for non-linear temporal trends in the community composition returned two major time windows. These time windows coincide with periods characterized by severe habitat destruction and the deterioration of habitat quality due to agricultural intensification. We found significant reductions of the proportion of species requiring specific habitats since 1920 and until today. We identified additional break points for species requiring high habitat qualities, endangered butterfly species, and sedentary species, particularly after a main break point in the 1960s. Our findings underline that, apart from habitat destruction, the deterioration of habitat quality is a main driver of biodiversity loss in general. Therefore, nature conservation should focus on maintaining the highest possible habitat quality.}, language = {en} } @article{GlawKohlerHawlitscheketal.2021, author = {Glaw, Frank and Kohler, Jorn and Hawlitschek, Oliver and Ratsoavina, Fanomezana M. and Rakotoarison, Andolalao and Scherz, Mark D. and Vences, Miguel}, title = {Extreme miniaturization of a new amniote vertebrate and insights into the evolution of genital size in chameleons}, series = {Scientific reports}, volume = {11}, journal = {Scientific reports}, number = {1}, publisher = {Springer Nature}, address = {Berlin}, issn = {2045-2322}, doi = {10.1038/s41598-020-80955-1}, pages = {14}, year = {2021}, abstract = {Evolutionary reduction of adult body size (miniaturization) has profound consequences for organismal biology and is an important subject of evolutionary research. Based on two individuals we describe a new, extremely miniaturized chameleon, which may be the world's smallest reptile species. The male holotype of Brookesia nana sp. nov. has a snout-vent length of 13.5 mm (total length 21.6 mm) and has large, apparently fully developed hemipenes, making it apparently the smallest mature male amniote ever recorded. The female paratype measures 19.2 mm snout-vent length (total length 28.9 mm) and a micro-CT scan revealed developing eggs in the body cavity, likewise indicating sexual maturity. The new chameleon is only known from a degraded montane rainforest in northern Madagascar and might be threatened by extinction. Molecular phylogenetic analyses place it as sister to B. karchei, the largest species in the clade of miniaturized Brookesia species, for which we resurrect Evoluticauda Angel, 1942 as subgenus name. The genetic divergence of B. nana sp. nov. is rather strong (9.914.9\% to all other Evoluticauda species in the 16S rRNA gene). A comparative study of genital length in Malagasy chameleons revealed a tendency for the smallest chameleons to have the relatively largest hemipenes, which might be a consequence of a reversed sexual size dimorphism with males substantially smaller than females in the smallest species. The miniaturized males may need larger hemipenes to enable a better mechanical fit with female genitals during copulation. Comprehensive studies of female genitalia are needed to test this hypothesis and to better understand the evolution of genitalia in reptiles.}, language = {en} } @article{WicaksonoEgamberdievaBergetal.2022, author = {Wicaksono, Wisnu Adi and Egamberdieva, Dilfuza and Berg, Christian and Mora, Maximilian and Kusstatscher, Peter and Cernava, Tomislav and Berg, Gabriele}, title = {Function-based rhizosphere assembly along a gradient of desiccation in the former Aral Sea}, series = {mSystems}, volume = {7}, journal = {mSystems}, number = {6}, publisher = {American Society for Microbiology}, address = {Washington, DC}, issn = {2379-5077}, doi = {10.1128/msystems.00739-22}, pages = {16}, year = {2022}, abstract = {The desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches.IMPORTANCE The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. Here, we investigated bacterial and archaeal communities in the rhizosphere of pioneer plants by combining classic molecular methods with amplicon sequencing as well as metagenomics for functional insights. By implementing a desiccation gradient, we observed (i) remarkable differences in the archaeon-bacterium ratio of plant rhizosphere samples, (ii) replacement of archaeal indicator taxa during succession, and (iii) the presence of specific, potentially plant-beneficial biosynthetic pathways in archaea present during the early stages. In addition, our results provide hitherto-undescribed insights into the functional redundancy between plant-associated archaea and bacteria. The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin.}, language = {en} } @article{VyseHerzschuhPfalzetal.2021, author = {Vyse, Stuart A. and Herzschuh, Ulrike and Pfalz, Gregor and Pestryakova, Lyudmila A. and Diekmann, Bernhard and Nowaczyk, Norbert and Biskaborn, Boris K.}, title = {Sediment and carbon accumulation in a glacial lake in Chukotka (Arctic Siberia) during the Late Pleistocene and Holocene}, series = {Biogeosciences}, volume = {18}, journal = {Biogeosciences}, number = {16}, publisher = {Copernicus}, address = {Katlenburg-Lindau}, issn = {1726-4170}, doi = {10.5194/bg-18-4791-2021}, pages = {4791 -- 4816}, year = {2021}, abstract = {Lakes act as important sinks for inorganic and organic sediment components. However, investigations of sedimentary carbon budgets within glacial lakes are currently absent from Arctic Siberia. The aim of this paper is to provide the first reconstruction of accumulation rates, sediment and carbon budgets from a lacustrine sediment core from Lake Rauchuagytgyn, Chukotka (Arctic Siberia). We combined multiple sediment biogeochemical and sedimentological parameters from a radiocarbon-dated 6.5m sediment core with lake basin hydroacoustic data to derive sediment stratigraphy, sediment volumes and infill budgets. Our results distinguished three principal sediment and carbon accumulation regimes that could be identified across all measured environmental proxies including early Marine Isotope Stage 2 (MIS2) (ca. 29-23.4 ka cal BP), mid-MIS2-early MIS1 (ca. 23.4-11.69 ka cal BP) and the Holocene (ca. 11.69-present). Estimated organic carbon accumulation rates (OCARs) were higher within Holocene sediments (average 3.53 gOCm(-2) a(-1)) than Pleistocene sediments (average 1.08 gOCm(-2) a(-1)) and are similar to those calculated for boreal lakes from Quebec and Finland and Lake Baikal but significantly lower than Siberian thermokarst lakes and Alberta glacial lakes. Using a bootstrapping approach, we estimated the total organic carbon pool to be 0.26 +/- 0.02 Mt and a total sediment pool of 25.7 +/- 1.71 Mt within a hydroacoustically derived sediment volume of ca. 32 990 557m(3). The total organic carbon pool is substantially smaller than Alaskan yedoma, thermokarst lake sediments and Alberta glacial lakes but shares similarities with Finnish boreal lakes. Temporal variability in sediment and carbon accumulation dynamics at Lake Rauchuagytgyn is controlled predominantly by palaeoclimate variation that regulates lake ice-cover dynamics and catchment glacial, fluvial and permafrost processes through time. These processes, in turn, affect catchment and within-lake primary productivity as well as catchment soil development. Spatial differences compared to other lake systems at a trans-regional scale likely relate to the high-latitude, mountainous location of Lake Rauchuagytgyn.}, language = {en} } @article{SedaghatmehrStueweMuellerRoeberetal.2022, author = {Sedaghatmehr, Mastoureh and St{\"u}we, Benno and M{\"u}ller-R{\"o}ber, Bernd and Balazadeh, Salma}, title = {Heat shock factor HSFA2 fine-tunes resetting of thermomemory via plastidic metalloprotease FtsH6}, series = {Journal of experimental botany}, volume = {73}, journal = {Journal of experimental botany}, number = {18}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/erac257}, pages = {6394 -- 6404}, year = {2022}, abstract = {The transcription factor HSFA2 fine-tunes a balance between prolongation and resetting of thermomemory in Arabidopsis via the regulation of both memory-supporting and memory-resetting genes. Plants 'memorize' stressful events and protect themselves from future, often more severe, stresses. To maximize growth after stress, plants 'reset' or 'forget' memories of stressful situations, which requires an intricate balance between stress memory formation and the degree of forgetfulness. HEAT SHOCK PROTEIN 21 (HSP21) encodes a small heat shock protein in plastids of Arabidopsis thaliana. HSP21 functions as a key component of thermomemory, which requires a sustained elevated level of HSP21 during recovery from heat stress. A heat-induced metalloprotease, filamentation temperature-sensitive H6 (FtsH6), degrades HSP21 to its pre-stress abundance, thereby resetting memory during the recovery phase. The transcription factor heat shock factor A2 (HSFA2) activates downstream genes essential for mounting thermomemory, acting as a positive regulator in the process. Here, using a yeast one-hybrid screen, we identify HSFA2 as an upstream transactivator of the resetting element FtsH6. Constitutive and inducible overexpression of HSFA2 increases expression of FtsH6, whereas it is drastically reduced in the hsfa2 knockout mutant. Chromatin immunoprecipitation reveals in planta binding of HSFA2 to the FtsH6 promoter. Importantly, overexpression of HSFA2 improves thermomemory more profoundly in ftsh6 than wild-type plants. Thus, by activating both memory-supporting and memory-resetting genes, HSFA2 acts as a cellular homeostasis factor during thermomemory.}, language = {en} } @article{BaumasLeMoigneGareletal.2021, author = {Baumas, Chloe M. J. and Le Moigne, Fr{\´e}d{\´e}ric A. C. and Garel, Marc and Bhairy, Nagib and Guasco, Sophie and Riou, Virginie and Armougom, Fabrice and Grossart, Hans-Peter and Tamburini, Christian}, title = {Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions}, series = {The ISME journal : multidisciplinary journal of microbial ecology}, volume = {15}, journal = {The ISME journal : multidisciplinary journal of microbial ecology}, number = {6}, publisher = {Nature Publishing Group}, address = {Basingstoke}, issn = {1751-7362}, doi = {10.1038/s41396-020-00880-z}, pages = {1695 -- 1708}, year = {2021}, abstract = {The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.}, language = {en} } @article{HirschbergBauerKamhiehMilzetal.2022, author = {Hirschberg, Stefan and Bauer, Hannes and Kamhieh-Milz, Julian and Ringel, Frauke and Harms, Christoph and Eddin, Omar Kamal and Pruss, Axel and Hanack, Katja and Schulze-Forster, Kai}, title = {SARS-CoV-2 virus-like particles (VLPs) specifically detect humoral immune reactions in an ELISA-Based Platform}, series = {Antibodies}, volume = {11}, journal = {Antibodies}, number = {4}, publisher = {MDPI}, address = {Basel}, issn = {2073-4468}, doi = {10.3390/antib11040076}, pages = {10}, year = {2022}, abstract = {A key in controlling the SARS-CoV-2 pandemic is the assessment of the immune status of the population. We explored the utility of SARS-CoV-2 virus-like particles (VLPs) as antigens to detect specific humoral immune reactions in an enzyme-linked immunosorbent assay (ELISA). For this purpose, SARS-CoV-2 VLPs were produced from an engineered cell line and characterized by Western blot, ELISA, and nanoparticle tracking analysis. Subsequently, we collected 42 serum samples from before the pandemic (2014), 89 samples from healthy subjects, and 38 samples from vaccinated subjects. Seventeen samples were collected less than three weeks after infection, and forty-four samples more than three weeks after infection. All serum samples were characterized for their reactivity with VLPs and the SARS-CoV-2 N- and S-protein. Finally, we compared the performance of the VLP-based ELISA with a certified in vitro diagnostic device (IVD). In the applied set of samples, we determined a sensitivity of 95.5\% and a specificity of 100\% for the certified IVD. There were seven samples with an uncertain outcome. Our VLP-ELISA demonstrated a superior performance, with a sensitivity of 97.5\%, a specificity of 100\%, and only three uncertain outcomes. This result warrants further research to develop a certified IVD based on SARS-CoV-2 VLPs as an antigen.}, language = {en} } @article{DreymannSabrowskiDansoetal.2022, author = {Dreymann, Nico and Sabrowski, Wiebke and Danso, Jennifer and Menger, Marcus}, title = {Aptamer-based sandwich assay formats for detection and discrimination of human high- and low-molecular-weight uPA for cancer prognosis and diagnosis}, series = {Cancers / Molecular Diversity Preservation International (MDPI)}, volume = {14}, journal = {Cancers / Molecular Diversity Preservation International (MDPI)}, number = {21}, publisher = {MDPI}, address = {Basel}, issn = {2072-6694}, doi = {10.3390/cancers14215222}, pages = {17}, year = {2022}, abstract = {Simple Summary Urokinase-type plasminogen activator (urokinase, uPA) is a widely discussed biomarker for cancer prognosis and diagnosis. The gold standard for the determination of protein biomarkers in physiological samples is the enzyme-linked immunosorbent assay (ELISA). Here, antibodies are used to detect the specific protein. In our study, recently published urokinase aptamers were tested for their use in a sandwich assay format as alternative specific recognition elements. Different aptamer combinations were used for the detection of uPA in a sandwich-assay format and a combination of aptamers and antibodies additionally allowed the differentiation of human high and low molecular weight- (HMW- and LMW-) uPA. Hence, uPA aptamers offer a valuable alternative as specific recognition elements for analytical purposes. Since aptamers are easy to synthesize and modify, they can be used as a cost-effective alternative in sandwich assay formats for the detection of uPA in physiological samples. Abstract Urokinase-type plasminogen activator (urokinase, uPA) is a frequently discussed biomarker for prognosis, diagnosis, and recurrence of cancer. In a previous study, we developed ssDNA aptamers that bind to different forms of human urokinase, which are therefore assumed to have different binding regions. In this study, we demonstrate the development of aptamer-based sandwich assays that use different combinations of these aptamers to detect high molecular weight- (HMW-) uPA in a micro titer plate format. By combining aptamers and antibodies, it was possible to distinguish between HMW-uPA and low molecular weight- (LMW-) uPA. For the best performing aptamer combination, we calculated the limit of detection (LOD) and limit of quantification (LOQ) in spiked buffer and urine samples with an LOD up to 50 ng/mL and 138 ng/mL, respectively. To show the specificity and sequence dependence of the reporter aptamer uPAapt-02-FR, we have identified key nucleotides within the sequence that are important for specific folding and binding to uPA using a fluorescent dye-linked aptamer assay (FLAA). Since uPA is a much-discussed marker for prognosis and diagnosis in various types of cancers, these aptamers and their use in a micro titer plate assay format represent a novel, promising tool for the detection of uPA and for possible diagnostic applications.}, language = {en} } @article{ScholzKerestetzopoulouWiebachetal.2022, author = {Scholz, Stella and Kerestetzopoulou, Sofia and Wiebach, Vincent and Schnegotzki, Romina and Schmid, Bianca and Reyna-Gonzalez, Emmanuel and Ding, Ling and S{\"u}ssmuth, Roderich D. and Dittmann, Elke and Baunach, Martin}, title = {One-Pot chemoenzymatic synthesis of microviridin analogs containing functional tags}, series = {ChemBioChem : an official journal of the EFMC}, volume = {23}, journal = {ChemBioChem : an official journal of the EFMC}, number = {20}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1439-4227}, doi = {10.1002/cbic.202200345}, pages = {7}, year = {2022}, abstract = {Microviridins are a prominent family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) featuring characteristic lactone and lactam rings. Their unusual cage-like architecture renders them highly potent serine protease inhibitors of which individual variants specifically inhibit different types of proteases of pharmacological interest. While posttranslational modifications are key for the stability and bioactivity of RiPPs, additional attractive properties can be introduced by functional tags. To date - although highly desirable - no method has been reported to incorporate functional tags in microviridin scaffolds or the overarching class of graspetides. In this study, a chemoenzymatic in vitro platform is used to introduce functional tags in various microviridin variants yielding biotinylated, dansylated or propargylated congeners. This straightforward approach paves the way for customized protease inhibitors with built-in functionalities that can help to unravel the still elusive ecological roles and targets of this remarkable class of compounds and to foster applications based on protease inhibition.}, language = {en} } @article{HeinzeKrumpholzBlaumetal.2022, author = {Heinze, Johannes and Krumpholz, Laura and Blaum, Niels and Hoefgen, Rainer and Ogden, Michael}, title = {Shoot herbivory by grasshoppers has stronger effects on root morphology than clipping}, series = {Plant ecology : an international journal}, volume = {223}, journal = {Plant ecology : an international journal}, number = {9}, publisher = {Springer Science + Business Media B.V.}, address = {Dordrecht}, issn = {1385-0237}, doi = {10.1007/s11258-022-01259-0}, pages = {1069 -- 1078}, year = {2022}, abstract = {Studies investigating the effect of aboveground herbivory on plants often use clipping to simulate the effects of herbivores, for practical reasons. However, herbivore movements and transfer of oral secretions during herbivory may cause a different response in plant physiology and morphology compared to clipping. While studies have compared effects of real herbivory vs. clipping on biomass production, plant physiology, and shoot morphology, no study has compared such effects on root morphology. Therefore, we investigated the effect of herbivory by grasshoppers, herbivory simulated by clipping, and no herbivory on root morphological traits of ten grassland plant species. Root morphological traits were differently affected by the two herbivory treatments. Grasshopper herbivory significantly changed root morphology toward thinner roots with increased specific root length and root area, and decreased root tissue density compared to untreated control plants. Clipping had mostly similar, but weaker effects on root morphology than grasshopper herbivory. On the species level, grasshopper herbivory led to strongest changes in root morphology in almost all cases. In contrast, depending on the species, clipping resulted in varying root morphological trait values similar to grasshopper-damaged plants, or in some cases, more closely aligned with control plants. Though clipping was partly able to mimic the effects of herbivory by grasshoppers, results also indicate that, depending on the species, grasshopper herbivory had different but mostly stronger effects. We, therefore, recommend that future studies apply herbivory with real herbivores to better reflect natural responses in plants and related processes that root morphological traits mediate.}, language = {en} } @article{SchoedlOdemerBecheretal.2022, author = {Sch{\"o}dl, Isabel and Odemer, Richard and Becher, Matthias A. and Berg, Stefan and Otten, Christoph and Grimm, Volker and Groeneveld, J{\"u}rgen}, title = {Simulation of Varroa mite control in honey bee colonies without synthetic acaricides: demonstration of Good Beekeeping Practice for Germany in the BEEHAVE model}, series = {Ecology and evolution}, volume = {12}, journal = {Ecology and evolution}, number = {11}, publisher = {John Wiley \& Sons, Inc.}, issn = {2045-7758}, doi = {10.1002/ece3.9456}, pages = {14}, year = {2022}, abstract = {The BEEHAVE model simulates the population dynamics and foraging activity of a single honey bee colony (Apis mellifera) in great detail. Although it still makes numerous simplifying assumptions, it appears to capture a wide range of empirical observations. It could, therefore, in principle, also be used as a tool in beekeeper education, as it allows the implementation and comparison of different management options. Here, we focus on treatments aimed at controlling the mite Varroa destructor. However, since BEEHAVE was developed in the UK, mite treatment includes the use of a synthetic acaricide, which is not part of Good Beekeeping Practice in Germany. A practice that consists of drone brood removal from April to June, treatment with formic acid in August/September, and treatment with oxalic acid in November/December. We implemented these measures, focusing on the timing, frequency, and spacing between drone brood removals. The effect of drone brood removal and acid treatment, individually or in combination, on a mite-infested colony was examined. We quantify the efficacy of Varroa mite control as the reduction of mites in treated bee colonies compared to untreated bee colonies. We found that drone brood removal was very effective, reducing mites by 90\% at the end of the first simulation year after the introduction of mites. This value was significantly higher than the 50-67\% reduction expected by bee experts and confirmed by empirical studies. However, literature reports varying percent reductions in mite numbers from 10 to 85\% after drone brood removal. The discrepancy between model results, empirical data, and expert estimates indicate that these three sources should be reviewed and refined, as all are based on simplifying assumptions. These results and the adaptation of BEEHAVE to the Good Beekeeping Practice are a decisive step forward for the future use of BEEHAVE in beekeeper education in Germany and anywhere where organic acids and drone brood removal are utilized.}, language = {en} } @article{MeyerCherstvySeckleretal.2023, author = {Meyer, Philipp and Cherstvy, Andrey G. and Seckler, Henrik and Hering, Robert and Blaum, Niels and Jeltsch, Florian and Metzler, Ralf}, title = {Directedeness, correlations, and daily cycles in springbok motion}, series = {Physical review research}, volume = {5}, journal = {Physical review research}, number = {4}, publisher = {APS}, address = {College Park}, issn = {2643-1564}, doi = {10.1103/PhysRevResearch.5.043129}, pages = {17}, year = {2023}, abstract = {How predictable is the next move of an animal? Specifically, which factors govern the short- and long-term motion patterns and the overall dynamics of land-bound, plant-eating animals in general and ruminants in particular? To answer this question, we here study the movement dynamics of springbok antelopes Antidorcas marsupialis. We propose several complementary statistical-analysis techniques combined with machine-learning approaches to analyze—across multiple time scales—the springbok motion recorded in long-term GPS tracking of collared springboks at a private wildlife reserve in Namibia. As a result, we are able to predict the springbok movement within the next hour with a certainty of about 20\%. The remaining about 80\% are stochastic in nature and are induced by unaccounted factors in the modeling algorithm and by individual behavioral features of springboks. We find that directedness of motion contributes approximately 17\% to this predicted fraction. We find that the measure for directedeness is strongly dependent on the daily cycle of springbok activity. The previously known daily affinity of springboks to their water points, as predicted from our machine-learning algorithm, overall accounts for only about 3\% of this predicted deterministic component of springbok motion. Moreover, the resting points are found to affect the motion of springboks at least as much as the formally studied effects of water points. The generality of these statements for the motion patterns and their underlying behavioral reasons for other ruminants can be examined on the basis of our statistical-analysis tools in the future.}, language = {en} } @article{GuillenLindgrenMuffetal.2023, author = {Guillen, Rafael Arce and Lindgren, Finn and Muff, Stefanie and Glass, Thomas W. and Breed, Greg A. and Schl{\"a}gel, Ulrike}, title = {Accounting for unobserved spatial variation in step selection analyses of animal movement via spatial random effects}, series = {Methods in ecology and evolution : MEE}, volume = {14}, journal = {Methods in ecology and evolution : MEE}, number = {10}, publisher = {Wiley}, address = {Oxford}, issn = {2041-210X}, doi = {10.1111/2041-210X.14208}, pages = {2639 -- 2653}, year = {2023}, abstract = {Step selection analysis (SSA) is a common framework for understanding animal movement and resource selection using telemetry data. Such data are, however, inherently autocorrelated in space, a complication that could impact SSA-based inference if left unaddressed. Accounting for spatial correlation is standard statistical practice when analysing spatial data, and its importance is increasingly recognized in ecological models (e.g. species distribution models). Nonetheless, no framework yet exists to account for such correlation when analysing animal movement using SSA. Here, we extend the popular method integrated step selection analysis (iSSA) by including a Gaussian field (GF) in the linear predictor to account for spatial correlation. For this, we use the Bayesian framework R-INLA and the stochastic partial differential equations (SPDE) technique. We show through a simulation study that our method provides accurate fixed effects estimates, quantifies their uncertainty well and improves the predictions. In addition, we demonstrate the practical utility of our method by applying it to three wolverine (Gulo gulo) tracks. Our method solves the problems of assuming spatially independent residuals in the SSA framework. In addition, it offers new possibilities for making long-term predictions of habitat usage.}, language = {en} } @article{VillalbaKasadaZoccaratoetal.2022, author = {Villalba, Luis Alberto and Kasada, Minoru and Zoccarato, Luca and Wollrab, Sabine and Grossart, Hans Peter}, title = {Differing escape responses of the marine bacterium Marinobacter adhaerens in the presence of planktonic vs. surface-associated protist grazers}, series = {International journal of molecular sciences}, volume = {23}, journal = {International journal of molecular sciences}, number = {17}, publisher = {MDPI}, address = {Basel}, issn = {1661-6596}, doi = {10.3390/ijms231710082}, pages = {13}, year = {2022}, abstract = {Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.}, language = {en} } @article{PetrichChiantia2023, author = {Petrich, Annett and Chiantia, Salvatore}, title = {Influenza a virus infection alters lipid packing and surface electrostatic potential of the host plasma membrane}, series = {Viruses}, volume = {15}, journal = {Viruses}, number = {9}, publisher = {MDPI}, address = {Basel}, issn = {1999-4915}, doi = {10.3390/v15091830}, pages = {17}, year = {2023}, abstract = {The pathogenesis of influenza A viruses (IAVs) is influenced by several factors, including IAV strain origin and reassortment, tissue tropism and host type. While such factors were mostly investigated in the context of virus entry, fusion and replication, little is known about the viral-induced changes to the host lipid membranes which might be relevant in the context of virion assembly. In this work, we applied several biophysical fluorescence microscope techniques (i.e., F{\"o}rster energy resonance transfer, generalized polarization imaging and scanning fluorescence correlation spectroscopy) to quantify the effect of infection by two IAV strains of different origin on the plasma membrane (PM) of avian and human cell lines. We found that IAV infection affects the membrane charge of the inner leaflet of the PM. Moreover, we showed that IAV infection impacts lipid-lipid interactions by decreasing membrane fluidity and increasing lipid packing. Because of such alterations, diffusive dynamics of membrane-associated proteins are hindered. Taken together, our results indicate that the infection of avian and human cell lines with IAV strains of different origins had similar effects on the biophysical properties of the PM.}, language = {en} } @article{BocediPalmerMalchowetal.2021, author = {Bocedi, Greta and Palmer, Stephen C. F. and Malchow, Anne-Kathleen and Zurell, Damaris and Watts, Kevin and Travis, Justin M. J.}, title = {RangeShifter 2.0}, series = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos}, volume = {44}, journal = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos}, number = {10}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {0906-7590}, doi = {10.1111/ecog.05687}, pages = {1453 -- 1462}, year = {2021}, abstract = {Process-based models are becoming increasingly used tools for understanding how species are likely to respond to environmental changes and to potential management options. RangeShifter is one such modelling platform, which has been used to address a range of questions including identifying effective reintroduction strategies, understanding patterns of range expansion and assessing population viability of species across complex landscapes. Here we introduce a new version, RangeShifter 2.0, which incorporates important new functionality. It is now possible to simulate dynamics over user-specified, temporally changing landscapes. Additionally, we integrated a new genetic module, notably introducing an explicit genetic modelling architecture, which allows for simulation of neutral and adaptive genetic processes. Furthermore, emigration, transfer and settlement traits can now all evolve, allowing for sophisticated simulation of the evolution of dispersal. We illustrate the potential application of RangeShifter 2.0's new functionality by two examples. The first illustrates the range expansion of a virtual species across a dynamically changing UK landscape. The second demonstrates how the software can be used to explore the concept of evolving connectivity in response to land-use modification, by examining how movement rules come under selection over landscapes of different structure and composition. RangeShifter 2.0 is built using object-oriented C++ providing computationally efficient simulation of complex individual-based, eco-evolutionary models. The code has been redeveloped to enable use across operating systems, including on high performance computing clusters, and the Windows graphical user interface has been enhanced. RangeShifter 2.0 will facilitate the development of in-silico assessments of how species will respond to environmental changes and to potential management options for conserving or controlling them. By making the code available open source, we hope to inspire further collaborations and extensions by the ecological community.}, language = {en} } @article{MachinPiontekTodheetal.2022, author = {Machin, Laura and Piontek, Martin and Todhe, Sara and Staniek, Katrin and Monzote, Lianet and Fudickar, Werner and Linker, Torsten and Gille, Lars}, title = {Antileishmanial anthracene endoperoxides: efficacy in vitro, mechanisms and structure-activity relationships}, series = {Molecules : a journal of synthetic chemistry and natural product chemistry}, volume = {27}, journal = {Molecules : a journal of synthetic chemistry and natural product chemistry}, number = {20}, publisher = {MDPI}, address = {Basel}, issn = {1420-3049}, doi = {10.3390/molecules27206846}, pages = {22}, year = {2022}, abstract = {Leishmaniasis is a vector-borne disease caused by protozoal Leishmania parasites. Previous studies have shown that endoperoxides (EP) can selectively kill Leishmania in host cells. Therefore, we studied in this work a set of new anthracene-derived EP (AcEP) together with their non-endoperoxidic analogs in model systems of Leishmania tarentolae promastigotes (LtP) and J774 macrophages for their antileishmanial activity and selectivity. The mechanism of effective compounds was explored by studying their reaction with iron (II) in chemical systems and in Leishmania. The correlation of structural parameters with activity demonstrated that in this compound set, active compounds had a LogP(OW) larger than 3.5 and a polar surface area smaller than 100 angstrom(2). The most effective compounds (IC50 in LtP < 2 mu M) with the highest selectivity (SI > 30) were pyridyl-/tert-butyl-substituted AcEP. Interestingly, also their analogs demonstrated activity and selectivity. In mechanistic studies, it was shown that EP were activated by iron in chemical systems and in LtP due to their EP group. However, the molecular structure beyond the EP group significantly contributed to their differential mitochondrial inhibition in Leishmania. The identified compound pairs are a good starting point for subsequent experiments in pathogenic Leishmania in vitro and in animal models.}, language = {en} } @article{HermanussenDammhahnScheffleretal.2023, author = {Hermanussen, Michael and Dammhahn, Melanie and Scheffler, Christiane and Groth, Detlef}, title = {Winner-loser effects improve social network efficiency between competitors with equal resource holding power}, series = {Scientific reports}, volume = {13}, journal = {Scientific reports}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-023-41225-y}, pages = {9}, year = {2023}, abstract = {Animal societies are structured of dominance hierarchy (DH). DH can be viewed as networks and analyzed by graph theory. We study the impact of state-dependent feedback (winner-loser effect) on the emergence of local dominance structures after pairwise contests between initially equal-ranking members (equal resource-holding-power, RHP) of small and large social groups. We simulated pairwise agonistic contests between individuals with and without a priori higher RHP by Monte-Carlo-method. Random pairwise contests between equal-ranking competitors result in random dominance structures ('Null variant') that are low in transitive triads and high in pass along triads; whereas state-dependent feedback ('Winner-loser variant') yields centralized 'star' structured DH that evolve from competitors with initially equal RHP and correspond to hierarchies that evolve from keystone individuals. Monte-Carlo simulated DH following state-dependent feedback show motif patterns very similar to those of a variety of natural DH, suggesting that state-dependent feedback plays a pivotal role in robust self-organizing phenomena that transcend the specifics of the individual. Self-organization based on state-dependent feedback leads to social structures that correspond to those resulting from pre-existing keystone individuals. As the efficiency of centralized social networks benefits both, the individual and the group, centralization of social networks appears to be an important evolutionary goal.}, language = {en} } @article{BergholzBalthasarWeissetal.2023, author = {Bergholz, Kolja and Balthasar, Cathrina and Weiss, Anne-Marie and Brunkhardt, Jennifer and Ristow, Michael and Weiß, Lina}, title = {Niche differentiation of arthropods and plants along small-scale gradients in temporary wetlands (kettle holes)}, series = {Basic and applied ecology : journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {73}, journal = {Basic and applied ecology : journal of the Gesellschaft f{\"u}r {\"O}kologie}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1439-1791}, doi = {10.1016/j.baae.2023.10.003}, pages = {10 -- 17}, year = {2023}, abstract = {Small temporary wetlands, like kettle holes, provide many valuable ecosystem functions and serve as refuge habitats in otherwise monotonous agricultural landscapes. However, the mechanisms that maintain biodiversity in these habitats are still poorly understood. In this study, we investigate how three taxa (vascular plants, ground beetles and spiders) respond to small-scale flooding and disturbance gradients in kettle holes as well as kettle hole area. For this purpose, we determined total, hygrophilic and red list species richness for all taxa and activity density for arthropods along transects extending from the edge towards the center of kettle holes. Furthermore, we calculated the community-weighted mean body size for arthropods and seed mass for plants as surrogates for the ability to respond to disturbance. Our analyses revealed that in particular plants and ground beetles showed strong responses along the small-scale spatial gradient. Total plant species richness decreased towards the center, while hygrophilic plant species increased. In contrast, both total and hygrophilic species richness of ground beetles increased towards the center. Spiders showed similar responses as ground beetles, but less pronounced. We found no evidence that disturbance at the edge of kettle holes leads to smaller body sizes or seed masses. However, arthropods in adjacent arable fields (one meter from the kettle hole edge) were particularly small. Kettle hole area had only weak effects on plants, but not on arthropods. Our study indicates that differences in the depth at the drier edge and the moist, regularly flooded center have a large and taxon-dependent influence on the species composition. Therefore, small-scale heterogeneity seems to be an important predictor for the maintenance of species diversity.}, language = {en} } @article{KumarLeimkuehler2023, author = {Kumar, Hemant and Leimk{\"u}hler, Silke}, title = {Changing the electron acceptor specificity of rhodobacter capsulatus formate dehydrogenase from NAD+ to NADP+}, series = {International journal of molecular sciences}, volume = {24}, journal = {International journal of molecular sciences}, number = {22}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms242216067}, pages = {13}, year = {2023}, abstract = {Formate dehydrogenases catalyze the reversible oxidation of formate to carbon dioxide. These enzymes play an important role in CO2 reduction and serve as nicotinamide cofactor recycling enzymes. More recently, the CO2-reducing activity of formate dehydrogenases, especially metal-containing formate dehydrogenases, has been further explored for efficient atmospheric CO2 capture. Here, we investigate the nicotinamide binding site of formate dehydrogenase from Rhodobacter capsulatus for its specificity toward NAD+ vs. NADP+ reduction. Starting from the NAD+-specific wild-type RcFDH, key residues were exchanged to enable NADP+ binding on the basis of the NAD+-bound cryo-EM structure (PDB-ID: 6TG9). It has been observed that the lysine at position 157 (Lys157) in the β-subunit of the enzyme is essential for the binding of NAD+. RcFDH variants that had Glu259 exchanged for either a positively charged or uncharged amino acid had additional activity with NADP+. The FdsBL279R and FdsBK276A variants also showed activity with NADP+. Kinetic parameters for all the variants were determined and tested for activity in CO2 reduction. The variants were able to reduce CO2 using NADPH as an electron donor in a coupled assay with phosphite dehydrogenase (PTDH), which regenerates NADPH. This makes the enzyme suitable for applications where it can be coupled with other enzymes that use NADPH.}, language = {en} }