@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 = {G{\"o}ttingen}, 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} }