@article{NawazKhanNoacketal.2020,
  author    = {Nawaz, Shiza and Khan, Muhammad Moman and Noack, Jonas and Awan, Asad Bashir and Schiebel, Juliane and Roggenbuck, Dirk and Schierack, Peter and Sarwar, Yasra and Ali, Aamir},
  title     = {Rapid detection of biofilm formation by zoonotic serovars of Salmonella enterica and avian pathogenic E. coli isolates from poultry},
  series = {Pakistan veterinary journal},
  volume    = {40},
  journal   = {Pakistan veterinary journal},
  number    = {4},
  publisher = {University of Agriculture, Faculty of Veterinary Science},
  address   = {Faisalabad},
  issn      = {0253-8318},
  doi       = {10.29261/pakvetj/2020.066},
  pages     = {527 -- 530},
  year      = {2020},
  abstract  = {Biofilms are complex, sessile microbial communities that are problematic in clinical settings due to their association with survival and pathogenicity of bacteria. The biofilm formation supporting conditions for zoonotic serovars of Salmonella and avian pathogenic E. coli (APEC) from poultry have not been well studied yet. Clinical isolates of zoonotic Salmonella and APEC from poultry were evaluated for biofilm formation in four media at 37 degrees C and 40 degrees C after incubation of 48 and 72 hrs. The biofilms formed in 96 well plates were visualized and quantified with a new module of Aklides system using fluorescence microscope coupled with automated VideoScan Technology. After 72 hrs, brain heart infusion at 40 degrees C and Rappaport-Vassiliadis Soya broth at 37 degrees C were found most suitable for APEC and Salmonella biofilm formations respectively. The new information will be useful for further biofilm associated studies particularly for evaluation of antibiofilm compounds and contribute in infection control. (C) 2020 PVJ. All rights reserved},
  language  = {en}
}
@article{TarazonaMachatschekLendlein2019,
  author    = {Tarazona, Natalia A. and Machatschek, Rainhard Gabriel and Lendlein, Andreas},
  title     = {Unraveling the interplay between abiotic hydrolytic degradation and crystallization of bacterial polyesters comprising short and medium side-chain-length Polyhydroxyalkanoates},
  series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  volume    = {21},
  journal   = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  number    = {2},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1525-7797},
  doi       = {10.1021/acs.biomac.9b01458},
  pages     = {761 -- 771},
  year      = {2019},
  abstract  = {Polyhydroxyalkanoates (PHAs) have attracted attention as degradable (co)polyesters which can be produced by microorganisms with variations in the side chain. This structural variation influences not only the thermomechanical properties of the material but also its degradation behavior. Here, we used Langmuir monolayers at the air-water (A-W) interface as suitable models for evaluating the abiotic degradation of two PHAs with different side-chain lengths and crystallinity. By controlling the polymer state (semi crystalline, amorphous), the packing density, the pH, and the degradation mechanism, we could draw several significant conclusions. (i) The maximum degree of crystallinity for a PHA film to be efficiently degraded up to pH = 12.3 is 40\%. (ii) PHA made of repeating units with shorter side-chain length are more easily hydrolyzed under alkaline conditions. The efficiency of alkaline hydrolysis decreased by about 65\% when the polymer was 40\% crystalline. (iii) In PHA films with a relatively high initial crystallinity, abiotic degradation initiated a chemicrystallization phenomenon, detected as an increase in the storage modulus (E'). This could translate into an increase in brittleness and reduction in the material degradability. Finally, we demonstrate the stability of the measurement system for long-term experiments, which allows degradation conditions for polymers that could closely simulate real-time degradation.},
  language  = {en}
}
@article{FujiharaZhangJacksonetal.2022,
  author    = {Fujihara, Kenji M. and Zhang, Bonnie Z. and Jackson, Thomas D. and Ogunkola, Moses and Nijagal, Brunda and Milne, Julia V. and Sallman, David A. and Ang, Ching-Seng and Nikolic, Iva and Kearney, Conor J. and Hogg, Simon J. and Cabalag, Carlos S. and Sutton, Vivien R. and Watt, Sally and Fujihara, Asuka T. and Trapani, Joseph A. and Simpson, Kaylene J. and Stojanovski, Diana and Leimk{\"u}hler, Silke and Haupt, Sue and Phillips, Wayne A. and Clemons, Nicholas J.},
  title     = {Eprenetapopt triggers ferroptosis, inhibits NFS1 cysteine desulfurase, and synergizes with serine and glycine dietary restriction},
  series = {Science Advances},
  volume    = {8},
  journal   = {Science Advances},
  number    = {37},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {2375-2548},
  doi       = {10.1126/sciadv.abm9427},
  pages     = {13},
  year      = {2022},
  abstract  = {The mechanism of action of eprenetapopt (APR-246, PRIMA-1MET) as an anticancer agent remains unresolved, al-though the clinical development of eprenetapopt focuses on its reported mechanism of action as a mutant-p53 reactivator. Using unbiased approaches, this study demonstrates that eprenetapopt depletes cellular antioxidant glutathione levels by increasing its turnover, triggering a nonapoptotic, iron-dependent form of cell death known as ferroptosis. Deficiency in genes responsible for supplying cancer cells with the substrates for de novo glutathione synthesis (SLC7A11, SHMT2, and MTHFD1L), as well as the enzymes required to synthesize glutathione (GCLC and GCLM), augments the activity of eprenetapopt. Eprenetapopt also inhibits iron-sulfur cluster biogenesis by limit-ing the cysteine desulfurase activity of NFS1, which potentiates ferroptosis and may restrict cellular proliferation. The combination of eprenetapopt with dietary serine and glycine restriction synergizes to inhibit esophageal xenograft tumor growth. These findings reframe the canonical view of eprenetapopt from a mutant-p53 reactivator to a ferroptosis inducer.},
  language  = {en}
}
@article{PremierFickelHeurichetal.2020,
  author    = {Premier, Joseph and Fickel, J{\"o}rns and Heurich, Marco and Kramer-Schadt, Stephanie},
  title     = {The boon and bane of boldness},
  series = {Movement Ecology},
  volume    = {8},
  journal   = {Movement Ecology},
  number    = {1},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {2051-3933},
  doi       = {10.1186/s40462-020-00204-y},
  pages     = {1 -- 17},
  year      = {2020},
  abstract  = {Background: Many felid species are of high conservation concern, and with increasing human disturbance the situation is worsening. Small isolated populations are at risk of genetic impoverishment decreasing within-species biodiversity. Movement is known to be a key behavioural trait that shapes both demographic and genetic dynamics and affects population survival. However, we have limited knowledge on how different manifestations of movement behaviour translate to population processes. In this study, we aimed to 1) understand the potential effects of movement behaviour on the genetic diversity of small felid populations in heterogeneous landscapes, while 2) presenting a simulation tool that can help inform conservation practitioners following, or considering, population management actions targeting the risk of genetic impoverishment. Methods: We developed a spatially explicit individual-based population model including neutral genetic markers for felids and applied this to the example of Eurasian lynx. Using a neutral landscape approach, we simulated reintroductions into a three-patch system, comprising two breeding patches separated by a larger patch of differing landscape heterogeneity, and tested for the effects of various behavioural movement syndromes and founder population sizes. We explored a range of movement syndromes by simulating populations with various movement model parametrisations that range from 'shy' to 'bold' movement behaviour. Results: We find that movement syndromes can lead to a higher loss of genetic diversity and an increase in between population genetic structure for both "bold" and "shy" movement behaviours, depending on landscape conditions, with larger decreases in genetic diversity and larger increases in genetic differentiation associated with bold movement syndromes, where the first colonisers quickly reproduce and subsequently dominate the gene pool. In addition, we underline the fact that a larger founder population can offset the genetic losses associated with subpopulation isolation and gene pool dominance. Conclusions We identified a movement syndrome trade-off for population genetic variation, whereby bold-explorers could be saviours - by connecting populations and promoting panmixia, or sinks - by increasing genetic losses via a 'founder takes all' effect, whereas shy-stayers maintain a more gradual genetic drift due to their more cautious behaviour. Simulations should incorporate movement behaviour to provide better projections of long-term population viability and within-species biodiversity, which includes genetic diversity. Simulations incorporating demographics and genetics have great potential for informing conservation management actions, such as population reintroductions or reinforcements. Here, we present such a simulation tool for solitary felids.},
  language  = {en}
}
@article{DeSousaMotaDinizCoelhoetal.2021,
  author    = {De Sousa Mota, Cristiano and Diniz, Ana and Coelho, Catarina and Santos-Silva, Teresa and Esmaeeli Moghaddam Tabalvandani, Mariam and Leimk{\"u}hler, Silke and Cabrita, Eurico J. and Marcelo, Filipa and Rom{\~a}o, Maria Jo{\~a}o},
  title     = {Interrogating the inhibition mechanisms of human aldehyde oxidase by X-ray crystallography and NMR spectroscopy},
  series = {Journal of medicinal chemistry / American Chemical Society},
  volume    = {64},
  journal   = {Journal of medicinal chemistry / American Chemical Society},
  number    = {17},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0022-2623},
  doi       = {10.1021/acs.jmedchem.1c01125},
  pages     = {13025 -- 13037},
  year      = {2021},
  abstract  = {Human aldehyde oxidase (hAOX1) is mainly present in the liver and has an emerging role in drug metabolism, since it accepts a wide range of molecules as substrates and inhibitors. Herein, we employed an integrative approach by combining NMR, X-ray crystallography, and enzyme inhibition kinetics to understand the inhibition modes of three hAOX1 inhibitors-thioridazine, benzamidine, and raloxifene. These integrative data indicate that thioridazine is a noncompetitive inhibitor, while benzamidine presents a mixed type of inhibition. Additionally, we describe the first crystal structure of hAOX1 in complex with raloxifene. Raloxifene binds tightly at the entrance of the substrate tunnel, stabilizing the flexible entrance gates and elucidating an unusual substrate-dependent mechanism of inhibition with potential impact on drug-drug interactions. This study can be considered as a proof-of-concept for an efficient experimental screening of prospective substrates and inhibitors of hAOX1 relevant in drug discovery.},
  language  = {en}
}
@article{BrandesSicksBerger2021,
  author    = {Brandes, Stefanie and Sicks, Florian and Berger, Anne},
  title     = {Behaviour classification on giraffes (Giraffa camelopardalis) using machine learning algorithms on triaxial acceleration data of two commonly used GPS devices and its possible application for their management and conservation},
  series = {Sensors},
  volume    = {21},
  journal   = {Sensors},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1424-8220},
  doi       = {10.3390/s21062229},
  pages     = {22},
  year      = {2021},
  abstract  = {Averting today's loss of biodiversity and ecosystem services can be achieved through conservation efforts, especially of keystone species. Giraffes (Giraffa camelopardalis) play an important role in sustaining Africa's ecosystems, but are 'vulnerable' according to the IUCN Red List since 2016. Monitoring an animal's behavior in the wild helps to develop and assess their conservation management. One mechanism for remote tracking of wildlife behavior is to attach accelerometers to animals to record their body movement. We tested two different commercially available high-resolution accelerometers, e-obs and Africa Wildlife Tracking (AWT), attached to the top of the heads of three captive giraffes and analyzed the accuracy of automatic behavior classifications, focused on the Random Forests algorithm. For both accelerometers, behaviors of lower variety in head and neck movements could be better predicted (i.e., feeding above eye level, mean prediction accuracy e-obs/AWT: 97.6\%/99.7\%; drinking: 96.7\%/97.0\%) than those with a higher variety of body postures (such as standing: 90.7-91.0\%/75.2-76.7\%; rumination: 89.6-91.6\%/53.5-86.5\%). Nonetheless both devices come with limitations and especially the AWT needs technological adaptations before applying it on animals in the wild. Nevertheless, looking at the prediction results, both are promising accelerometers for behavioral classification of giraffes. Therefore, these devices when applied to free-ranging animals, in combination with GPS tracking, can contribute greatly to the conservation of giraffes.},
  language  = {en}
}
@article{FioriniDominguezReboredaetal.2022,
  author    = {Fiorini, Vanina D. and Dom{\´i}nguez, Marisol and Reboreda, Juan C. and Swaddle, John P.},
  title     = {A recent invasive population of the European starling sturnus vulgaris has lower genetic diversity and higher fluctuating asymmetry than primary invasive and native populations},
  series = {Biological invasions : unique international journal uniting scientists in the broad field of biological invasions},
  volume    = {24},
  journal   = {Biological invasions : unique international journal uniting scientists in the broad field of biological invasions},
  number    = {2},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1387-3547},
  doi       = {10.1007/s10530-021-02653-x},
  pages     = {437 -- 448},
  year      = {2022},
  abstract  = {Fluctuating asymmetries (FA) are small stress-induced random deviations from perfect symmetry that arise during the development of bilaterally symmetrical traits. One of the factors that can reduce developmental stability of the individuals and cause FA at a population level is the loss of genetic variation. Populations of founding colonists frequently have lower genetic variation than their ancestral populations that could be reflected in a higher level of FA. The European starling (Sturnus vulgaris) is native to Eurasia and was introduced successfully in the USA in 1890 and Argentina in 1983. In this study, we documented the genetic diversity and FA of starlings from England (ancestral population), USA (primary introduction) and Argentina (secondary introduction). We predicted the Argentinean starlings would have the highest level of FA and lowest genetic diversity of the three populations. We captured wild adult European starlings in England, USA, and Argentina, measured their mtDNA diversity and allowed them to molt under standardized conditions to evaluate their FA of primary feathers. For genetic analyses, we extracted DNA from blood samples of individuals from Argentina and USA and from feather samples from individuals from England and sequenced the mitochondrial control region. Starlings in Argentina showed the highest composite FA and exhibited the lowest haplotype and nucleotide diversity. The USA population showed a level of FA and genetic diversity similar to the native population. Therefore, the level of asymmetry and genetic diversity found among these populations was consistent with our predictions based on their invasion history.},
  language  = {en}
}
@article{SchellenbergReichertHardtetal.2020,
  author    = {Schellenberg, Johannes and Reichert, Jessica and Hardt, Martin and Klingelh{\"o}fer, Ines and Morlock, Gertrud and Schubert, Patrick and Bižić, Mina and Grossart, Hans-Peter and K{\"a}mpfer, Peter and Wilke, Thomas and Glaeser, Stefanie P.},
  title     = {The bacterial microbiome of the long-term aquarium cultured high-microbial abundance sponge Haliclona cnidata},
  series = {Frontiers in Marine Science},
  volume    = {7},
  journal   = {Frontiers in Marine Science},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-7745},
  doi       = {10.3389/fmars.2020.00266},
  pages     = {20},
  year      = {2020},
  abstract  = {Marine sponges host highly diverse but specific bacterial communities that provide essential functions for the sponge holobiont, including antimicrobial defense. Here, we characterized the bacterial microbiome of the marine sponge Haliclona cnidata that has been in culture in an artificial marine aquarium system. We tested the hypotheses (1) that the long-term aquarium cultured sponge H. cnidata is tightly associated with a typical sponge bacterial microbiota and (2) that the symbiotic Bacteria sustain bioactivity under harmful environmental conditions to facilitate holobiont survival by preventing pathogen invasion. Microscopic and phylogenetic analyses of the bacterial microbiota revealed that H. cnidata represents a high microbial abundance (HMA) sponge with a temporally stable bacterial community that significantly shifts with changing aquarium conditions. A 4-week incubation experiment was performed in small closed aquarium systems with antibiotic and/or light exclusion treatments to reduce the total bacterial and photosynthetically active sponge-associated microbiota to a treatment-specific resilient community. While the holobiont was severely affected by the experimental treatment (i.e., bleaching of the sponge, reduced bacterial abundance, shifted bacterial community composition), the biological defense and bacterial community interactions (i.e., quorum sensing activity) remained intact. 16S rRNA gene amplicon sequencing revealed a resilient community of 105 bacterial taxa, which remained in the treated sponges. These 105 taxa accounted for a relative abundance of 72-83\% of the bacterial sponge microbiota of non-treated sponge fragments that have been cultured under the same conditions. We conclude that a sponge-specific resilient community stays biologically active under harmful environmental conditions, facilitating the resilience of the holobiont. In H. cnidata, bacteria are located in bacteriocytes, which may have contributed to the observed phenomenon.},
  language  = {en}
}
@article{KappelIllingHuuetal.2020,
  author    = {Kappel, Christian and Illing, Nicola and Huu, Cuong Nguyen and Barger, Nichole N. and Cramer, Michael D. and Lenhard, Michael and Midgley, Jeremy J.},
  title     = {Fairy circles in Namibia are assembled from genetically distinct grasses},
  series = {Communications biology},
  volume    = {3},
  journal   = {Communications biology},
  number    = {1},
  publisher = {Springer Nature},
  address   = {London},
  issn      = {2399-3642},
  doi       = {10.1038/s42003-020-01431-0},
  pages     = {8},
  year      = {2020},
  abstract  = {Fairy circles are striking regularly sized and spaced, bare circles surrounded by Stipagrostis grasses that occur over thousands of square kilometres in Namibia. The mechanisms explaining their origin, shape, persistence and regularity remain controversial. One hypothesis for the formation of vegetation rings is based on the centrifugal expansion of a single individual grass plant, via clonal growth and die-back in the centre. Clonality could explain FC origin, shape and long-term persistence as well as their regularity, if one clone competes with adjacent clones. Here, we show that for virtually all tested fairy circles the periphery is not exclusively made up of genetically identical grasses, but these peripheral grasses belong to more than one unrelated genet. These results do not support a clonal explanation for fairy circles. Lack of clonality implies that a biological reason for their origin, shape and regularity must emerge from competition between near neighbor individuals within each fairy circle. Such lack of clonality also suggests a mismatch between longevity of fairy circles versus their constituent plants. Furthermore, our findings of lack of clonality have implications for some models of spatial patterning of fairy circles that are based on self-organization. Christian Kappel et al. examine the genetic composition of fairy circles, regular circular patterns of grasses in the Namib Desert, using ddRAD-seq. They find that these grasses are made up of multiple unrelated genets rather than genetically identical grasses, suggesting non-clonality.},
  language  = {en}
}
@article{desAulnoisReveillonRobertetal.2020,
  author    = {des Aulnois, Maxime Georges and R{\´e}veillon, Damien and Robert, Elise and Caruana, Amandine and Briand, Enora and Guljamow, Arthur and Dittmann, Elke and Amzil, Zouher and Bormans, Myriam},
  title     = {Salt shock responses of Microcystis revealed through physiological, transcript, and metabolomic analyses},
  series = {Toxins},
  volume    = {12},
  journal   = {Toxins},
  number    = {3},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2072-6651},
  doi       = {10.3390/toxins12030192},
  pages     = {18},
  year      = {2020},
  abstract  = {The transfer of Microcystis aeruginosa from freshwater to estuaries has been described worldwide and salinity is reported as the main factor controlling the expansion of M. aeruginosa to coastal environments. Analyzing the expression levels of targeted genes and employing both targeted and non-targeted metabolomic approaches, this study investigated the effect of a sudden salt increase on the physiological and metabolic responses of two toxic M. aeruginosa strains separately isolated from fresh and brackish waters, respectively, PCC 7820 and 7806. Supported by differences in gene expressions and metabolic profiles, salt tolerance was found to be strain specific. An increase in salinity decreased the growth of M. aeruginosa with a lesser impact on the brackish strain. The production of intracellular microcystin variants in response to salt stress correlated well to the growth rate for both strains. Furthermore, the release of microcystins into the surrounding medium only occurred at the highest salinity treatment when cell lysis occurred. This study suggests that the physiological responses of M. aeruginosa involve the accumulation of common metabolites but that the intraspecific salt tolerance is based on the accumulation of specific metabolites. While one of these was determined to be sucrose, many others remain to be identified. Taken together, these results provide evidence that M. aeruginosa is relatively salt tolerant in the mesohaline zone and microcystin (MC) release only occurs when the capacity of the cells to deal with salt increase is exceeded.},
  language  = {en}
}
@article{BaralRoenschRichteretal.2022,
  author    = {Baral, Hans Otto and R{\"o}nsch, Peter and Richter, Udo and Urban, Alexander and Kruse, Julia and Bemmann, Martin and Kummer, Volker and Javier Valencia, Francisco and Huth, Wolfgang},
  title     = {Schroeteria decaisneana, S. poeltii, and Ciboria ploettneriana (Sclerotiniaceae, Helotiales, Ascomycota), three parasites on Veronica seeds},
  series = {Mycological progress : international journal of the German Mycological Society},
  volume    = {21},
  journal   = {Mycological progress : international journal of the German Mycological Society},
  number    = {1},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg},
  issn      = {1617-416X},
  doi       = {10.1007/s11557-021-01742-4},
  pages     = {359 -- 407},
  year      = {2022},
  abstract  = {Ciboria ploettneriana, Schroeteria decaisneana, and S. poeltii produce morphologically very similar apothecia emerging from fallen stromatized seeds of Veronica spp., the former two on V. hederifolia agg. in temperate central Europe and S. poeltii on V. cymbalaria in mediterranean southern Europe. They are described and illustrated in detail based on fresh collections or moist chamber cultures of infected seeds. A key is provided to differentiate the three species from their teleomorphs. For the first time, connections between two teleomorphs and two Schroeteria anamorphs are reported. Members of the anamorph-typified genus Schroeteria are known as host-specific plant parasites that infect seeds of different Veronica spp. In earlier times, they were classified in the Ustilaginales (Basidiomycota), but since more than 30 years, they are referred to as false smut fungi producing smut-like chlamydospores, based on light microscopic and ultrastructural studies which referred them to the Sclerotiniaceae (Helotiales). During the present study, rDNA sequences were obtained for the first time from chlamydospores of Schroeteria bornmuelleri (on V. rubrifolia), S. decaisneana (on V. hederifolia), S. delastrina (generic type, on V. arvensis), and S. poeltii (on V. cymbalaria) and from apothecia of C. ploettneriana, S. decaisneana, and S. poeltii. As a result, the anamorph-teleomorph connection could be established for S. decaisneana and S. poeltii by a 100\% ITS similarity, whereas C. ploettneriana could not be connected to a smut-like anamorph. Ciboria ploettneriana in the here-redefined sense clustered in our combined phylogenetic analyses of ITS and LSU in relationship of Sclerotinia s.l., Botrytis, and Myriosclerotinia rather than Ciboria, but its placement was not supported. Its affiliation in Ciboria was retained until a better solution is found. Also Schroeteria poeltii clustered unresolved in this relationship but with a much higher molecular distance. The remaining three Schroeteria spp. formed a strongly supported monophyletic group, here referred to as "Schroeteria core clade", which clustered with medium to high support as a sister clade of Monilinia jezoensis, a member of the Monilinia alpina group of section Disjunctoriae. We observed ITS distances of 5-6.3\% among members of the Schroeteria core clade, but 13.8-14.7\% between this clade and S. poeltii, which appears to be correlated with the deviating chlamydospore morphology of S. poeltii. Despite its apparent paraphyly, Schroeteria is accepted here in a wide sense as a genus distinct from Monilinia, particularly because of its very special anamorphs. A comparable heterogeneity in rDNA analyses was observed in Monilinia and other genera of Sclerotiniaceae. Such apparent heterogeneity should be met with skepticism, however, because the inclusion of protein-coding genes in phylogenetic analyses resulted in a monophyletic genus Monilinia. More sclerotiniaceous taxa should be analysed for protein-coding genes in the future, including Schroeteria. Four syntype specimens of Ciboria ploettneriana in B were reexamined in the present study, revealing a mixture of the two species growing on V. hederifolia agg. Based on its larger ascospores in comparison with S. decaisneana, a lectotype is proposed for C. ploettneriana.},
  language  = {en}
}
@article{HermanussenErofeevScheffler2022,
  author    = {Hermanussen, Michael and Erofeev, Sergei and Scheffler, Christiane},
  title     = {The socio-endocrine regulation of human growth},
  series = {Acta paediatrica : nurturing the child},
  journal   = {Acta paediatrica : nurturing the child},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0803-5253},
  doi       = {10.1111/apa.16504},
  pages     = {5},
  year      = {2022},
  abstract  = {Aim Growth is a multifarious phenomenon that has been studied by nutritionists, economists, paediatric endocrinologists; archaeologists, child psychologists and other experts. Yet, a unifying theory of understanding growth regulation is still lacking. Method Critical review of the literature. Results We summarise evidence linking social competition and its effect on hierarchies in social structures, with the neuronal networks of the ventromedial hypothalamus and body size. The endocrine signalling system regulating growth hormone, Insulin-like-Growth-Factor1 and skeletal growth, is well conserved in the evolution of vertebrata for some 400 million years. The link between size and status permits adaptive plasticity, competitive growth and strategic growth adjustments also in humans. Humans perceive size as a signal of dominance with tallness being favoured and particularly prevalent in the upper social classes. Conclusion Westernised societies are competitive. People are tall, and "open to change." Social values include striving for status and prestige implying socio-economic domination. We consider the transition of political and social values following revolutions and civil wars, as key elements that interact with the evolutionarily conserved neuroendocrine competence for adaptive developmental plasticity, overstimulate the hypothalamic growth regulation and finally lead to the recent historic increases in average height.},
  language  = {en}
}
@article{ApriyantoCompartZimmermannetal.2022,
  author    = {Apriyanto, Ardha and Compart, Julia and Zimmermann, Vincent and Alseekh, Saleh and Fernie, Alisdair and Fettke, J{\"o}rg},
  title     = {Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.)},
  series = {Food chemistry},
  volume    = {393},
  journal   = {Food chemistry},
  publisher = {Elsevier},
  address   = {New York, NY [u.a.]},
  issn      = {0308-8146},
  doi       = {10.1016/j.foodchem.2022.133361},
  pages     = {11},
  year      = {2022},
  abstract  = {Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield.},
  language  = {en}
}
@article{GutschmannSimoesSchieweetal.2022,
  author    = {Gutschmann, Bj{\"o}rn and Sim{\~o}es, Matilde Maldonado and Schiewe, Thomas and Schr{\"o}ter, Edith S. and M{\"u}nzberg, Marvin and Neubauer, Peter and Bockisch, Anika and Riedel, Sebastian Lothar Stefan},
  title     = {Continuous feeding strategy for polyhydroxyalkanoate production from solid waste animal fat at laboratory- and pilot-scale},
  series = {Microbial biotechnology / Society for Applied Microbiology},
  journal   = {Microbial biotechnology / Society for Applied Microbiology},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1751-7915},
  doi       = {10.1111/1751-7915.14104},
  pages     = {12},
  year      = {2022},
  abstract  = {Bioconversion of waste animal fat (WAF) to polyhydroxyalkanoates (PHAs) is an approach to lower the production costs of these plastic alternatives. However, the solid nature of WAF requires a tailor-made process development. In this study, a double-jacket feeding system was built to thermally liquefy the WAF to employ a continuous feeding strategy. During laboratory-scale cultivations with Ralstonia eutropha Re2058/pCB113, 70\% more PHA (45 g(PHA) L-1) and a 75\% higher space-time yield (0.63 g(PHA) L-1 h(-1)) were achieved compared to previously reported fermentations with solid WAF. During the development process, growth and PHA formation were monitored in real-time by in-line photon density wave spectroscopy. The process robustness was further evaluated during scale-down fermentations employing an oscillating aeration, which did not alter the PHA yield although cells encountered periods of oxygen limitation. Flow cytometry with propidium iodide staining showed that more than two-thirds of the cells were viable at the end of the cultivation and viability was even little higher in the scale-down cultivations. Application of this feeding system at 150-L pilot-scale cultivation yielded in 31.5 g(PHA) L-1, which is a promising result for the further scale-up to industrial scale.},
  language  = {en}
}
@article{SauterKratzFarhanetal.2022,
  author    = {Sauter, Tilman and Kratz, Karl and Farhan, Muhammad and Heuchel, Matthias and Lendlein, Andreas},
  title     = {Design and fabrication of fiber mesh actuators},
  series = {Applied materials today},
  volume    = {29},
  journal   = {Applied materials today},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {2352-9407},
  doi       = {10.1016/j.apmt.2022.101562},
  pages     = {13},
  year      = {2022},
  abstract  = {Soft actuator performance can be tuned by chemistry or mechanical manipulation, but this adjustability is limited especially in view of their growing technological relevance. Inspired from textile engineering, we designed and fabricated fiber mesh actuators and introduced new features like anisotropic behavior and soft-tissue like elastic deformability. Design criteria for the meshes are the formation of fiber bundles, the angle between fiber bundles in different stacked layers and covalent crosslinks forming within and between fibers at their interfacial contact areas. Through crosslinking the interfiber bond strength increased from a bond transmitting neither axial nor rotational loads (pin joint) to a bond strength capable of both (welded joint). For non-linear elastic stiffening, stacked fiber bundles with four embracing fibers were created forming microstructural rhombus shapes. Loading the rhombus diagonally allowed generation of "soft tissue"-like mechanics. By adjustment of stacking angles, the point of strong increase in stress is tuned. While the highest stresses are observed in aligned and crosslinked fiber mats along the direction of the fiber, the strongest shape-memory actuation behavior is found in randomly oriented fiber mats. Fiber mesh actuators controlled by temperature are of high significance as soft robot skins and as for active patches supporting tissue regeneration.},
  language  = {en}
}
@article{MarzetzWacker2021,
  author    = {Marzetz, Vanessa and Wacker, Alexander},
  title     = {Evaluating the relevance of species sorting and physiological plasticity of phytoplankton communities grown in a multifactor environment},
  series = {Freshwater biology / Freshwater Biological Association},
  volume    = {66},
  journal   = {Freshwater biology / Freshwater Biological Association},
  number    = {10},
  publisher = {Wiley-Blackwell},
  address   = {Oxford},
  issn      = {0046-5070},
  doi       = {10.1111/fwb.13810},
  pages     = {1992 -- 2003},
  year      = {2021},
  abstract  = {The two important mechanisms influencing the response of phytoplankton communities to alterations of abiotic factors in their environment are difficult to distinguish: species sorting resulting from a change in interspecific competitive pressure, and phenotypic plasticity (here explicitly physiological plasticity i.e. species-specific physiological adjustment). A shift in species composition as well as physiological adjustments in species can lead to changes in fatty acid composition that determine the food quality for zooplankton consumers. We used phytoplankton communities consisting of five species and exposed them to two different light intensities, two light conditions (constant and variable), and two levels of phosphorus supply. Changes in fatty acid and species composition were analyzed. We compared community pairs differing in one factor by calculating the Bray-Curtis similarity index for the composition of both variables. Comparing the Bray-Curtis similarity index of the species composition with the index of the fatty acid composition was used to estimate the effects of species sorting and physiological plasticity. Changes in nutrient supply influenced fatty acid responses based on species sorting and physiological plasticity the most. On one hand, the relevance of physiological plasticity was highest at cultivation in different nutrient supplies but the same light environment. Conversely with low nutrients species sorting appeared to dominate the response to changes in light, while at high nutrients physiological plasticity appeared to influence the response. Overall, under low phosphorus supply the communities showed a lower total fatty acid content per carbon and had increased proportions of saturated and monounsaturated fatty acids. Instead, communities in low light produced more of eicosapentaenoic acid. Our results suggest that the relevance of species sorting and physiological plasticity in shaping the community response highly depends on the environmental factors that influence the system. Nutrient supply had the largest effect, while light had more limited conditional effects. However, all of these factors are important in shaping the food quality of the phytoplankton community for higher trophic levels.},
  language  = {en}
}
@article{HempelAdolphsLandwehretal.2020,
  author    = {Hempel, Sabrina and Adolphs, Julian and Landwehr, Niels and Janke, David and Amon, Thomas},
  title     = {How the selection of training data and modeling approach affects the estimation of ammonia emissions from a naturally ventilated dairy barn—classical statistics versus machine learning},
  series = {Sustainability},
  volume    = {12},
  journal   = {Sustainability},
  number    = {3},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2071-1050},
  doi       = {10.3390/su12031030},
  pages     = {18},
  year      = {2020},
  abstract  = {Environmental protection efforts can only be effective in the long term with a reliable quantification of pollutant gas emissions as a first step to mitigation. Measurement and analysis strategies must permit the accurate extrapolation of emission values. We systematically analyzed the added value of applying modern machine learning methods in the process of monitoring emissions from naturally ventilated livestock buildings to the atmosphere. We considered almost 40 weeks of hourly emission values from a naturally ventilated dairy cattle barn in Northern Germany. We compared model predictions using 27 different scenarios of temporal sampling, multiple measures of model accuracy, and eight different regression approaches. The error of the predicted emission values with the tested measurement protocols was, on average, well below 20\%. The sensitivity of the prediction to the selected training dataset was worse for the ordinary multilinear regression. Gradient boosting and random forests provided the most accurate and robust emission value predictions, accompanied by the second-smallest model errors. Most of the highly ranked scenarios involved six measurement periods, while the scenario with the best overall performance was: One measurement period in summer and three in the transition periods, each lasting for 14 days.},
  language  = {en}
}
@article{FoersterAsratRamseyetal.2022,
  author    = {Foerster, Verena and Asrat, Asfawossen and Ramsey, Christopher Bronk and Brown, Erik T. and Chapot, Melissa S. and Deino, Alan and D{\"u}sing, Walter and Grove, Matthew and Hahn, Annette and Junginger, Annett and Kaboth-Bahr, Stefanie and Lane, Christine S. and Opitz, Stephan and Noren, Anders and Roberts, Helen M. and Stockhecke, Mona and Tiedemann, Ralph and Vidal, Celine M. and Vogelsang, Ralf and Cohen, Andrew S. and Lamb, Henry F. and Schaebitz, Frank and Trauth, Martin H.},
  title     = {Pleistocene climate variability in eastern Africa influenced hominin evolution},
  series = {Nature geoscience},
  volume    = {15},
  journal   = {Nature geoscience},
  number    = {10},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {1752-0894},
  doi       = {10.1038/s41561-022-01032-y},
  pages     = {805 -- 811},
  year      = {2022},
  abstract  = {Despite more than half a century of hominin fossil discoveries in eastern Africa, the regional environmental context of hominin evolution and dispersal is not well established due to the lack of continuous palaeoenvironmental records from one of the proven habitats of early human populations, particularly for the Pleistocene epoch. Here we present a 620,000-year environmental record from Chew Bahir, southern Ethiopia, which is proximal to key fossil sites. Our record documents the potential influence of different episodes of climatic variability on hominin biological and cultural transformation. The appearance of high anatomical diversity in hominin groups coincides with long-lasting and relatively stable humid conditions from similar to 620,000 to 275,000 years bp (episodes 1-6), interrupted by several abrupt and extreme hydroclimate perturbations. A pattern of pronounced climatic cyclicity transformed habitats during episodes 7-9 (similar to 275,000-60,000 years bp), a crucial phase encompassing the gradual transition from Acheulean to Middle Stone Age technologies, the emergence of Homo sapiens in eastern Africa and key human social and cultural innovations. Those accumulative innovations plus the alignment of humid pulses between northeastern Africa and the eastern Mediterranean during high-frequency climate oscillations of episodes 10-12 (similar to 60,000-10,000 years bp) could have facilitated the global dispersal of H. sapiens.},
  language  = {en}
}
@article{MalinovaKoesslerOrawetzetal.2019,
  author    = {Malinova, Irina and K{\"o}ssler, Stella and Orawetz, Tom and Matthes, Ulrike and Orzechowski, Slawomir and Koch, Anke and Fettke, J{\"o}rg},
  title     = {Identification of two Arabidopsis thaliana plasma membrane transporters able to transport glucose 1-phosphate},
  series = {Plant \& cell physiology},
  volume    = {61},
  journal   = {Plant \& cell physiology},
  number    = {2},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {0032-0781},
  doi       = {10.1093/pcp/pcz206},
  pages     = {381 -- 392},
  year      = {2019},
  abstract  = {Primary carbohydrate metabolism in plants includes several sugar and sugar-derivative transport processes. Over recent years, evidences have shown that in starch-related transport processes, in addition to glucose 6-phosphate, maltose, glucose and triose-phosphates, glucose 1-phosphate also plays a role and thereby increases the possible fluxes of sugar metabolites in planta. In this study, we report the characterization of two highly similar transporters, At1g34020 and At4g09810, in Arabidopsis thaliana, which allow the import of glucose 1-phosphate through the plasma membrane. Both transporters were expressed in yeast and were biochemically analyzed to reveal an antiport of glucose 1-phosphate/phosphate. Furthermore, we showed that the apoplast of Arabidopsis leaves contained glucose 1-phosphate and that the corresponding mutant of these transporters had higher glucose 1-phosphate amounts in the apoplast and alterations in starch and starch-related metabolism.},
  language  = {en}
}
@article{JiaAnslanChenetal.2022,
  author    = {Jia, Weihan and Anslan, Sten and Chen, Fahu and Cao, Xianyong and Dong, Hailiang and Dulias, Katharina and Gu, Zhengquan and Heinecke, Liv and Jiang, Hongchen and Kruse, Stefan and Kang, Wengang and Li, Kai and Liu, Sisi and Liu, Xingqi and Liu, Ying and Ni, Jian and Schwalb, Antje and Stoof-Leichsenring, Kathleen R. and Shen, Wei and Tian, Fang and Wang, Jing and Wang, Yongbo and Wang, Yucheng and Xu, Hai and Yang, Xiaoyan and Zhang, Dongju and Herzschuh, Ulrike},
  title     = {Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: overview and prospects},
  series = {Quaternary science reviews : the international multidisciplinary research and review journal},
  volume    = {293},
  journal   = {Quaternary science reviews : the international multidisciplinary research and review journal},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0277-3791},
  doi       = {10.1016/j.quascirev.2022.107703},
  pages     = {14},
  year      = {2022},
  abstract  = {Alpine ecosystems on the Tibetan Plateau are being threatened by ongoing climate warming and intensified human activities. Ecological time-series obtained from sedimentary ancient DNA (sedaDNA) are essential for understanding past ecosystem and biodiversity dynamics on the Tibetan Plateau and their responses to climate change at a high taxonomic resolution. Hitherto only few but promising studies have been published on this topic. The potential and limitations of using sedaDNA on the Tibetan Plateau are not fully understood. Here, we (i) provide updated knowledge of and a brief introduction to the suitable archives, region-specific taphonomy, state-of-the-art methodologies, and research questions of sedaDNA on the Tibetan Plateau; (ii) review published and ongoing sedaDNA studies from the Tibetan Plateau; and (iii) give some recommendations for future sedaDNA study designs. Based on the current knowledge of taphonomy, we infer that deep glacial lakes with freshwater and high clay sediment input, such as those from the southern and southeastern Tibetan Plateau, may have a high potential for sedaDNA studies. Metabarcoding (for microorganisms and plants), metagenomics (for ecosystems), and hybridization capture (for prehistoric humans) are three primary sedaDNA approaches which have been successfully applied on the Tibetan Plateau, but their power is still limited by several technical issues, such as PCR bias and incompleteness of taxonomic reference databases. Setting up high-quality and open-access regional taxonomic reference databases for the Tibetan Plateau should be given priority in the future. To conclude, the archival, taphonomic, and methodological conditions of the Tibetan Plateau are favorable for performing sedaDNA studies. More research should be encouraged to address questions about long-term ecological dynamics at ecosystem scale and to bring the paleoecology of the Tibetan Plateau into a new era.},
  language  = {en}
}
@article{PetrichDunsingBoboneetal.2021,
  author    = {Petrich, Annett and Dunsing, Valentin and Bobone, Sara and Chiantia, Salvatore},
  title     = {Influenza A M2 recruits M1 to the plasma membrane},
  series = {Biophysical journal : BJ / ed. by the Biophysical Society},
  volume    = {120},
  journal   = {Biophysical journal : BJ / ed. by the Biophysical Society},
  number    = {24},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2021.11.023},
  pages     = {5478 -- 5490},
  year      = {2021},
  abstract  = {Influenza A virus (IAV) is a respiratory pathogen that causes seasonal epidemics with significant mortality. One of the most abundant proteins in IAV particles is the matrix protein 1 (M1), which is essential for the virus structural stability. M1 organizes virion assembly and budding at the plasma membrane (PM), where it interacts with other viral components. The recruitment of M1 to the PM as well as its interaction with the other viral envelope proteins (hemagglutinin [HA], neuraminidase, matrix protein 2 [M2]) is controversially discussed in previous studies. Therefore, we used fluorescence fluctuation microscopy techniques (i.e., scanning fluorescence cross-correlation spectroscopy and number and brightness) to quantify the oligomeric state of M1 and its interactions with other viral proteins in co-transfected as well as infected cells. Our results indicate that M1 is recruited to the PM by M2, as a consequence of the strong interaction between the two proteins. In contrast, only a weak interaction between M1 and HA was observed. M1-HA interaction occurred only in the event that M1 was already bound to the PM. We therefore conclude that M2 initiates the assembly of IAV by recruiting M1 to the PM, possibly allowing its further interaction with other viral proteins.},
  language  = {en}
}
@article{ReinhardGeisslerBlaum2022,
  author    = {Reinhard, Johanna E. and Geißler, Katja and Blaum, Niels},
  title     = {Grass and ground dwelling beetle community responses to holistic and wildlife grazing management using a cross-fence comparison in Western Kalahari rangeland, Namibia},
  series = {Journal of insect conservation : an international journal devoted to the conservation of insects and related invertebrates},
  volume    = {26},
  journal   = {Journal of insect conservation : an international journal devoted to the conservation of insects and related invertebrates},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1366-638X},
  doi       = {10.1007/s10841-022-00410-6},
  pages     = {711 -- 720},
  year      = {2022},
  abstract  = {Savannahs are often branded by livestock grazing with resulting land degradation. Holistic management of livestock was proposed to contribute to biodiversity conservation by simulating native wildlife grazing behaviour. This study attempts the comparison of the impact of a holistic management regime to a wildlife grazing management regime on grass and ground-dwelling beetle species diversity on neighboring farms in Namibian rangeland. Results show that the response of biodiversity in species richness and composition to holistic management of livestock differs substantially from wildlife grazing with a positive impact. From a total of 39 identified species of ground-dwelling beetles (Coleoptera: Tenebrionidae, Carabidae) from 29 genera, eight species were found to be indicators for holistic management of livestock and three were found to be indicators for wildlife grazed rangeland. Observations suggest that holistic management of livestock may contribute to biodiversity conservation, but the differential effect of grazing management on species assemblages suggests that livestock grazing cannot replace native wildlife herbivory. Implications for insect conservation An adaptive management strategy such as holistic management used in this study shows the potential to support high beetle biodiversity. Holistic management of livestock thus aspects in favour for a sustainable form of grazing management for insect conservation even though it does not functionally replace grazing by native wildlife.},
  language  = {en}
}
@article{WangLiMaetal.2021,
  author    = {Wang, Meng and Li, Panpan and Ma, Yao and Nie, Xiang and Grebe, Markus and Men, Shuzhen},
  title     = {Membrane sterol composition in Arabidopsis thaliana affects root elongation via auxin biosynthesis},
  series = {International journal of molecular sciences},
  volume    = {22},
  journal   = {International journal of molecular sciences},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms22010437},
  pages     = {20},
  year      = {2021},
  abstract  = {Plant membrane sterol composition has been reported to affect growth and gravitropism via polar auxin transport and auxin signaling. However, as to whether sterols influence auxin biosynthesis has received little attention. Here, by using the sterol biosynthesis mutant cyclopropylsterol isomerase1-1 (cpi1-1) and sterol application, we reveal that cycloeucalenol, a CPI1 substrate, and sitosterol, an end-product of sterol biosynthesis, antagonistically affect auxin biosynthesis. The short root phenotype of cpi1-1 was associated with a markedly enhanced auxin response in the root tip. Both were neither suppressed by mutations in polar auxin transport (PAT) proteins nor by treatment with a PAT inhibitor and responded to an auxin signaling inhibitor. However, expression of several auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) was upregulated in cpi1-1. Functionally, TAA1 mutation reduced the auxin response in cpi1-1 and partially rescued its short root phenotype. In support of this genetic evidence, application of cycloeucalenol upregulated expression of the auxin responsive reporter DR5:GUS (beta-glucuronidase) and of several auxin biosynthesis genes, while sitosterol repressed their expression. Hence, our combined genetic, pharmacological, and sterol application studies reveal a hitherto unexplored sterol-dependent modulation of auxin biosynthesis during Arabidopsis root elongation.},
  language  = {en}
}
@article{deOliveiraSilvaPiratelliZurelletal.2021,
  author    = {de Oliveira-Silva, Anna Elizabeth and Piratelli, Augusto Jo{\~a}o and Zurell, Damaris and da Silva, Fernando Rodrigues},
  title     = {Vegetation cover restricts habitat suitability predictions of endemic Brazilian Atlantic Forest birds},
  series = {Perspectives in Ecology and Conservation},
  volume    = {20},
  journal   = {Perspectives in Ecology and Conservation},
  number    = {1},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {2530-0644},
  doi       = {10.1016/j.pecon.2021.09.002},
  pages     = {1 -- 8},
  year      = {2021},
  abstract  = {Ecological niche models (ENMs) are often used to investigate how climatic variables from known occurrence records can estimate potential species range distribution. Although climate-based ENMs provide critical baseline information, the inclusion of non-climatic predictors related to vegetation cover might generate more realistic scenarios. This assumption is particularly relevant for species with life-history traits related to forest habitats and sensitive to habitat loss and fragmentation. Here, we developed ENMs for 36 Atlantic Forest endemic birds considering two sets of predictor variables: (i) climatic variables only and (ii) climatic variables combined with the percentage of remaining native vegetation. We hypothesized that the inclusion of native vegetation data would decrease the potential range distribution of forest-dependent species by limiting their occurrence in regions harboring small areas of native vegetation habitats, despite otherwise favorable climatic conditions. We also expected that habitat restriction in the climate-vegetation models would be more pronounced for highly forest-dependent birds. The inclusion of vegetation data in the modeling procedures restricted the final distribution ranges of 22 out of 36 modeled species, while the 14 remaining presented an expansion of their ranges. We observed that species with high and medium forest dependency showed higher restriction in range size predictions between predictor sets than species with low forest dependency, which showed no alteration or range expansion. Overall, our results suggest that ENMs based on climatic and landscape variables may be a useful tool for conservationists to better understand the dynamic of bird species distributions in threatened and highly fragmented regions such as the Atlantic Forest hotspot.(c) 2021 Associacao Brasileira de Cie circumflex accent ncia Ecol ogica e Conservacao. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/ ).},
  language  = {en}
}
@article{PetazziKoikkarahAjiTischleretal.2021,
  author    = {Petazzi, Roberto Arturo and Koikkarah Aji, Amit and Tischler, Nicole D. and Chiantia, Salvatore},
  title     = {Detection of envelope glycoprotein assembly from old world hantaviruses in the Golgi apparatus of living cells},
  series = {Journal of virology},
  volume    = {95},
  journal   = {Journal of virology},
  number    = {4},
  publisher = {American Society for Microbiology},
  address   = {Baltimore, Md.},
  issn      = {1098-5514},
  doi       = {10.1128/JVI.01238-20},
  pages     = {18},
  year      = {2021},
  abstract  = {Hantaviruses are emerging pathogens that occasionally cause deadly outbreaks in the human population. While the structure of the viral envelope has been characterized with high precision, protein-protein interactions leading to the formation of new virions in infected cells are not fully understood. We used quantitative fluorescence microscopy (i.e., number and brightness analysis and fluorescence fluctuation spectroscopy) to monitor the interactions that lead to oligomeric spike complex formation in the physiological context of living cells. To this aim, we quantified protein-protein interactions for the glycoproteins Gn and Gc from Puumala and Hantaan orthohantaviruses in several cellular models. The oligomerization of each protein was analyzed in relation to subcellular localization, concentration, and the concentration of its interaction partner. Our results indicate that, when expressed separately, Gn and Gc form, respectively, homo-tetrameric and homo-dimeric complexes, in a concentration-dependent manner. Site-directed mutations or deletion mutants showed the specificity of their homotypic interactions. When both glycoproteins were coexpressed, we observed in the Golgi apparatus clear indication of GnGc interactions and the formation of Gn-Gc multimeric protein complexes of different sizes, while using various labeling schemes to minimize the influence of the fluorescent tags. Such large glycoprotein multimers may be identified as multiple Gn viral spikes interconnected via Gc-Gc contacts. This observation provides the possible first evidence for the initial assembly steps of the viral envelope within this organelle, and does so directly in living cells. <br /> IMPORTANCE In this work, we investigate protein-protein interactions that drive the assembly of the hantavirus envelope. These emerging pathogens have the potential to cause deadly outbreaks in the human population. Therefore, it is important to improve our quantitative understanding of the viral assembly process in infected cells, from a molecular point of view. By applying advanced fluorescence microscopy methods, we monitored the formation of viral spike complexes in different cell types. Our data support a model for hantavirus assembly according to which viral spikes are formed via the clustering of hetero-dimers of the two viral glycoproteins Gn and Gc. Furthermore, the observation of large Gn-Gc hetero-multimers provide the possible first evidence for the initial assembly steps of the viral envelope, directly in the Golgi apparatus of living cells.},
  language  = {en}
}
@article{BognarSupalaYarmanetal.2022,
  author    = {Bogn{\´a}r, Zs{\´o}fia and Supala, Eszter and Yarman, Aysu and Zhang, Xiaorong and Bier, Frank Fabian and Scheller, Frieder W. and Gyurcsanyi, R{\´o}bert E.},
  title     = {Peptide epitope-imprinted polymer microarrays for selective protein recognition},
  series = {Chemical science / RSC, Royal Society of Chemistry},
  volume    = {13},
  journal   = {Chemical science / RSC, Royal Society of Chemistry},
  number    = {5},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {2041-6539},
  doi       = {10.1039/d1sc04502d},
  pages     = {1263 -- 1269},
  year      = {2022},
  abstract  = {We introduce a practically generic approach for the generation of epitope-imprinted polymer-based microarrays for protein recognition on surface plasmon resonance imaging (SPRi) chips. The SPRi platform allows the subsequent rapid screening of target binding kinetics in a multiplexed and label-free manner. The versatility of such microarrays, both as synthetic and screening platform, is demonstrated through developing highly affine molecularly imprinted polymers (MIPs) for the recognition of the receptor binding domain (RBD) of SARS-CoV-2 spike protein. A characteristic nonapeptide GFNCYFPLQ from the RBD and other control peptides were microspotted onto gold SPRi chips followed by the electrosynthesis of a polyscopoletin nanofilm to generate in one step MIP arrays. A single chip screening of essential synthesis parameters, including the surface density of the template peptide and its sequence led to MIPs with dissociation constants (K-D) in the lower nanomolar range for RBD, which exceeds the affinity of RBD for its natural target, angiotensin-convertase 2 enzyme. Remarkably, the same MIPs bound SARS-CoV-2 virus like particles with even higher affinity along with excellent discrimination of influenza A (H3N2) virus. While MIPs prepared with a truncated heptapeptide template GFNCYFP showed only a slightly decreased affinity for RBD, a single mismatch in the amino acid sequence of the template, i.e. the substitution of the central cysteine with a serine, fully suppressed the RBD binding.},
  language  = {en}
}
@article{SchulteLiLisovskietal.2022,
  author    = {Schulte, Luise and Li, Chenzhi and Lisovski, Simeon and Herzschuh, Ulrike},
  title     = {Forest-permafrost feedbacks and glacial refugia help explain the unequal distribution of larch across continents},
  series = {Journal of biogeography},
  volume    = {49},
  journal   = {Journal of biogeography},
  number    = {10},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0305-0270},
  doi       = {10.1111/jbi.14456},
  pages     = {1825 -- 1838},
  year      = {2022},
  abstract  = {Aim: The continental-scale distribution of plant functional types, such as evergreen and summergreen needle-leaf forest, is assumed to be determined by contemporary climate. However, the distribution of summergreen needle-leaf forest of larch (Larix Mill.) differs markedly between the continents, despite relatively similar climatic conditions. The reasons for these differences are little understood. Our aim is to identify potential triggers and drivers of the current distribution patterns by comparing species' bioclimatic niches, glacial refugia and postglacial recolonization patterns. Location: Northern hemisphere. Taxon: Species of the genus Larix (Mill.). Methods: We compare species distribution and dominance using species ranges and sites of dominance, as well as their occurrence on modelled permafrost extent, and active layer thickness (ALT). We compare the bioclimatic niches and calculate the niche overlap between species, using the same data in addition to modern climate data. We synthesize pollen, macrofossil and ancient DNA palaeo-evidence of past Larix occurrences of the last 60,000 years and track differences in distribution patterns through time. Results: Bioclimatic niches show large overlaps between Asian larch species and American Larix laricina. The distribution across various degrees of permafrost extent is distinctly different for Asian L. gmelinii and L. cajanderi compared to the other species, whereas the distribution on different depths of ALT is more similar among Asian and American species. Northern glacial refugia for Larix are only present in eastern Asia and Alaska. Main Conclusion: The dominance of summergreen larches in Asia, where evergreen conifers dominate most of the rest of the boreal forests, is dependent on the interaction of several factors which allows Asian L. gmelinii and L. cajanderi to dominate where these factors coincide. These factors include the early postglacial spread out of northern glacial refugia in the absence of competitors as well as a positive feedback mechanism between frozen ground and forest.},
  language  = {en}
}
@article{GuentherSchmidtQuittetal.2021,
  author    = {G{\"u}nther, Kerstin and Schmidt, Marcus and Quitt, Heinz and Heinken, Thilo},
  title     = {Ver{\"a}nderungen der Waldvegetation im Elbe-Havelwinkel von 1960 bis 2015},
  series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft},
  journal   = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft},
  number    = {41},
  publisher = {Floristisch-Soziologische Arbeitsgemeinschaft},
  address   = {G{\"o}ttingen},
  issn      = {0722-494X},
  doi       = {10.14471/2021.41.005},
  pages     = {53 -- 85},
  year      = {2021},
  abstract  = {Forest ecosystems are subject to a variety of influences such as forest management, nitrogen deposition, changes in the groundwater level or the immigration of invasive species. The repetition of historical releves is an important means of documenting the resulting changes in plant communities and determining their main drivers. In 2015, we examined the vegetation change in 140 semi-permanent plots in managed forests in the Elbe valley in the NE German lowlands (Saxony-Anhalt, Brandenburg). The first survey took place from 1956 to 1963. The releves cover an almost uniquely broad spectrum of different site conditions, ranging from wet forests (alluvial, swamp and bog forests of Alnion incanae, Alnion glutinosae and Betulion pubescentis) to acidic mixed oak forests (Quercion roboris) up to acidic, mostly dry pine forests with different nutrient status (Dicrano-Pinion). We analyzed the changes in the vegetation with the help of forest stand data, winner and loser species, alpha- and beta-diversity as well as the Ellenberg indicator values for nitrogen, reaction, moisture and light. In contrast to previous resurvey studies, areas were also taken into account on which a complete change of forest stand had taken place before the second survey. Particularly in the wet forests and acidic forests with a moderately good nutrient supply, changes in the main tree species have been recorded, and many pine stands have been newly established in the meantime. The species richness has decreased overall and in almost all forest types, but the beta-diversity has remained unchanged or has increased. The Ellenberg values indicate a decrease in soil moisture in the wet forests, while the acidic pine forests in particular have become darker, richer in nutrients and more humid. The number of loser species is more than twice as high as that of the winner species, but with different developments in the individual forest types. In particular, the wet forests, the acidic mixed oak forests and the lichen-pine forests have lost most of their characteristic species. The resurvey after more than 50 years shows a different development of the individual forest types. Vegetation changes in the wet forests are mainly due to local groundwater level drawdown and the resulting increased availability of nutrients. The alluvial forests were also strongly influenced by forest interventions. The reasons for the trend towards more humid and more nutrient-rich conditions in formerly dry acidic pine and oak forests are nitrogen depositions and a succession after the abandonment of historical forms of forest use (litter raking, forest pasture). Although the individual forest types have developed differently, eutrophication, falling groundwater levels and silviculture are the most important causes for the changes in vegetation. Silvicultural interventions such as clear cutting and stand conversion with a change of tree species are at the same time the main reason why the vegetation has not been homogenized despite the leveling of the site gradient as measured by the beta-diversity.},
  language  = {de}
}
@article{BiermannBachKlaeringetal.2022,
  author    = {Biermann, Robin Tim and Bach, Linh T. and Kl{\"a}ring, Hans-Peter and Baldermann, Susanne and B{\"o}rnke, Frederik and Schwarz, Dietmar},
  title     = {Discovering tolerance-A computational approach to assess abiotic stress tolerance in tomato under greenhouse conditions},
  series = {Frontiers in sustainable food systems},
  volume    = {6},
  journal   = {Frontiers in sustainable food systems},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2571-581X},
  doi       = {10.3389/fsufs.2022.878013},
  pages     = {12},
  year      = {2022},
  abstract  = {Modern plant cultivars often possess superior growth characteristics, but within a limited range of environmental conditions. Due to climate change, crops will be exposed to distressing abiotic conditions more often in the future, out of which heat stress is used as example for this study. To support identification of tolerant germplasm and advance screening techniques by a novel multivariate evaluation method, a diversity panel of 14 tomato genotypes, comprising Mediterranean landraces of Solanum lycopersicum, the cultivar "Moneymaker" and Solanum pennellii LA0716, which served as internal references, was assessed toward their tolerance against long-term heat stress. After 5 weeks of growth, young tomato plants were exposed to either control (22/18 degrees C) or heat stress (35/25 degrees C) conditions for 2 weeks. Within this period, water consumption, leaf angles and leaf color were determined. Additionally, gas exchange and leaf temperature were investigated. Finally, biomass traits were recorded. The resulting multivariate dataset on phenotypic plasticity was evaluated to test the hypothesis, that more tolerant genotypes have less affected phenotypes upon stress adaptation. For this, a cluster-analysis-based approach was developed that involved a principal component analysis (PCA), dimension reduction and determination of Euclidean distances. These distances served as measure for the phenotypic plasticity upon heat stress. Statistical evaluation allowed the identification and classification of homogeneous groups consisting each of four putative more or less heat stress tolerant genotypes. The resulting classification of the internal references as "tolerant" highlights the applicability of our proposed tolerance assessment model. PCA factor analysis on principal components 1-3 which covered 76.7\% of variance within the phenotypic data, suggested that some laborious measure such as the gas exchange might be replaced with the determination of leaf temperature in larger heat stress screenings. Hence, the overall advantage of the presented method is rooted in its suitability of both, planning and executing screenings for abiotic stress tolerance using multivariate phenotypic data to overcome the challenge of identifying abiotic stress tolerant plants from existing germplasms and promote sustainable agriculture for the future.},
  language  = {en}
}
@article{SchneebergerSchulzeScheffleretal.2021,
  author    = {Schneeberger, Karin and Schulze, Michael and Scheffler, Ingo and Caspers, Barbara A.},
  title     = {Evidence of female preference for odor of distant over local males in a bat with female dispersal},
  series = {Behavioral ecology : the official journal of the International Society for Behavioral Ecology},
  volume    = {32},
  journal   = {Behavioral ecology : the official journal of the International Society for Behavioral Ecology},
  number    = {4},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {1045-2249},
  doi       = {10.1093/beheco/arab003},
  pages     = {657 -- 661},
  year      = {2021},
  abstract  = {Geographic variation of sexually selected male traits is common in animals. Female choice also varies geographically and several studies found female preference for local males, which is assumed to lead to local adaptation and, therefore, increases fitness. As females are the nondispersing sex in most mammalian taxa, this preference for local males might be explained by the learning of male characteristics. Studies on the preference of females in female-dispersing species are lacking so far. To find out whether such females would also show preferences for local males, we conducted a study on greater sac-winged bats (Saccopteryx bilineata), a species where females disperse and males stay in their natal colony. Male greater sac-winged bats possess a wing pouch that is filled with odoriferous secretion and fanned toward females during courtship display. In a combination of chemical analysis and behavioral preference tests, we analyzed whether the composition of wing sac secretion varies between two geographically distinct populations (300 km), and whether females show a preference for local or distant male scent. Using gas chromatography, we found significant differences in the composition of the wing sac odors between the two geographically distinct populations. In addition, the behavioral preference experiments revealed that females of both populations preferred the scent of geographically distant males over local males. The wing sac odor might thus be used to guarantee optimal outbreeding when dispersing to a new colony. This is-to our knowledge-the first study on odor preference of females of a species with female-biased dispersal.},
  language  = {en}
}
@article{KlauschiesIsantaNavarro2022,
  author    = {Klauschies, Toni and Isanta-Navarro, Jana},
  title     = {The joint effects of salt and 6PPD contamination on a freshwater herbivore},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {829},
  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.2022.154675},
  pages     = {6},
  year      = {2022},
  abstract  = {Using sodium chloride (NaCl) for de-icing roads is known to have severe consequences on freshwater organisms when washed into water bodies. N-(1,3-dimethylbutyl)-N '-phenyl-p-phenylenediamine, also known as 6PPD, is an antiozonant mainly found in automobile tire rubber to prevent ozone mediated cracking or wear-out. Especially the ozonated derivate, 6PPD-quinone, which is washed into streams after storm events, has been found to be toxic for coho salmon. Studies on other freshwater organisms could not confirm those findings, pointing towards distinct species-specific differences. Storm events result in greater run-offs from all water-soluble contaminants into freshwater bodies, potentially enhancing the concentrations of both chloride and 6PPD during winter. Here we show that these two contaminants have synergistic negative effects on the population growth of the rotifer Brachionus calyciflorus, a common freshwater herbivore. Hence, while only high concentrations of 6PPD and even higher concentrations of 6PPD-quinone, beyond environmentally relevant concentrations, had lethal effects on rotifers, the addition of NaCl enhanced the sensitivity of the rotifers towards the application of 6PPD so that their negative effects were more pronounced at lower concentrations. Similarly, 6PPD increased the lethal effect of NaCl. Our results support the species-specific toxicity of 6PPD and demonstrate a synergistic effect of the antiozonant on the toxicity of other environmentally relevant stressors, such as road salt contamination.},
  language  = {en}
}
@article{KruseHerzschuh2022,
  author    = {Kruse, Stefan and Herzschuh, Ulrike},
  title     = {Regional opportunities for tundra conservation in the next 1000 years},
  series = {eLife},
  volume    = {11},
  journal   = {eLife},
  publisher = {eLife Sciences Publications},
  address   = {Cambridge},
  issn      = {2050-084X},
  doi       = {10.7554/eLife.75163},
  pages     = {24},
  year      = {2022},
  abstract  = {The biodiversity of tundra areas in northern high latitudes is threatened by invasion of forests under global warming. However, poorly understood nonlinear responses of the treeline ecotone mean the timing and extent of tundra losses are unclear, but policymakers need such information to optimize conservation efforts. Our individual-based model LAVESI, developed for the Siberian tundra-taiga ecotone, can help improve our understanding. Consequently, we simulated treeline migration trajectories until the end of the millennium, causing a loss of tundra area when advancing north. Our simulations reveal that the treeline follows climate warming with a severe, century-long time lag, which is overcompensated by infilling of stands in the long run even when temperatures cool again. Our simulations reveal that only under ambitious mitigation strategies (relative concentration pathway 2.6) will ~30\% of original tundra areas remain in the north but separated into two disjunct refugia.},
  language  = {en}
}
@article{ApanasewiczGrothScheffleretal.2020,
  author    = {Apanasewicz, Anna and Groth, Detlef and Scheffler, Christiane and Hermanussen, Michael and Piosek, Magdalena and Wychowaniec, Patrycja and Babiszewska, Magdalena and Barbarska, Olga and Ziomkiewicz, Anna},
  title     = {Traumatized women's infants are bigger than children of mothers without traumas},
  series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger},
  volume    = {77},
  journal   = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger},
  number    = {5},
  publisher = {Schweizerbart science publishers},
  address   = {Stuttgart},
  issn      = {0003-5548},
  doi       = {10.1127/anthranz/2020/1285},
  pages     = {359 -- 374},
  year      = {2020},
  abstract  = {Life history theory predicts that experiencing stress during the early period of life will result in accelerated growth and earlier maturation. Indeed, animal and some human studies documented a faster pace of growth in the offspring of stressed mothers. Recent advances in epigenetics suggest that the effects of early developmental stress might be passed across the generations. However, evidence for such intergenerational transmission is scarce, at least in humans. Here we report the results of the study investigating the association between childhood trauma in mothers and physical growth in their children during the first months of life. Anthropometric and psychological data were collected from 99 mothers and their exclusively breastfed children at the age of 5 months. The mothers completed the Early Life Stress Questionnaire to assess childhood trauma. The questionnaire includes questions about the most traumatic events that they had experienced before the age of 12 years. Infant growth was evaluated based on the anthropometric measurements of weight, length, and head circumference. Also, to control for the size of maternal investment, the composition of breast milk samples taken at the time of infant anthropometric measurements was investigated. The children of mothers with higher early life stress tended to have higher weight and bigger head circumference. The association between infant anthropometrics and early maternal stress was not affected by breast milk composition, suggesting that the effect of maternal stress on infant growth was independent of the size of maternal investment. Our results demonstrate that early maternal trauma may affect the pace of growth in the offspring and, in consequence, lead to a faster life history strategy. This effect might be explained via changes in offspring epigenetics.},
  language  = {en}
}
@article{XiaoLiuWangetal.2020,
  author    = {Xiao, Shangbin and Liu, Liu and Wang, Wei and Lorke, Andreas and Woodhouse, Jason Nicholas and Grossart, Hans-Peter},
  title     = {A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water},
  series = {Hydrology and earth system sciences : HESS},
  volume    = {24},
  journal   = {Hydrology and earth system sciences : HESS},
  number    = {7},
  publisher = {European Geosciences Union (EGU) ; Copernicus},
  address   = {Munich},
  issn      = {1027-5606},
  doi       = {10.5194/hess-24-3871-2020},
  pages     = {3871 -- 3880},
  year      = {2020},
  abstract  = {Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95\%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6\% and a measurement accuracy of 0.5\% for CH4. A similar performance was observed for dissolved CO2 (t(95\%) = 10 s, equilibration ratio 67.1 \%). An equilibration ratio as high as 91.8\% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.},
  language  = {en}
}
@article{HoffmannHoelkerEccard2022,
  author    = {Hoffmann, Julia and H{\"o}lker, Franz and Eccard, Jana},
  title     = {Welcome to the dark side},
  series = {Frontiers in ecology and evolution},
  volume    = {9},
  journal   = {Frontiers in ecology and evolution},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-701X},
  doi       = {10.3389/fevo.2021.779825},
  pages     = {11},
  year      = {2022},
  abstract  = {Differences in natural light conditions caused by changes in moonlight are known to affect perceived predation risk in many nocturnal prey species. As artificial light at night (ALAN) is steadily increasing in space and intensity, it has the potential to change movement and foraging behavior of many species as it might increase perceived predation risk and mask natural light cycles. We investigated if partial nighttime illumination leads to changes in foraging behavior during the night and the subsequent day in a small mammal and whether these changes are related to animal personalities. We subjected bank voles to partial nighttime illumination in a foraging landscape under laboratory conditions and in large grassland enclosures under near natural conditions. We measured giving-up density of food in illuminated and dark artificial seed patches and video recorded the movement of animals. While animals reduced number of visits to illuminated seed patches at night, they increased visits to these patches at the following day compared to dark seed patches. Overall, bold individuals had lower giving-up densities than shy individuals but this difference increased at day in formerly illuminated seed patches. Small mammals thus showed carry-over effects on daytime foraging behavior due to ALAN, i.e., nocturnal illumination has the potential to affect intra- and interspecific interactions during both night and day with possible changes in personality structure within populations and altered predator-prey dynamics.},
  language  = {en}
}
@article{TongKuekenRazaghiMoghadametal.2021,
  author    = {Tong, Hao and K{\"u}ken, Anika and Razaghi-Moghadam, Zahra and Nikoloski, Zoran},
  title     = {Characterization of effects of genetic variants via genome-scale metabolic modelling},
  series = {Cellular and molecular life sciences : CMLS},
  volume    = {78},
  journal   = {Cellular and molecular life sciences : CMLS},
  number    = {12},
  publisher = {Springer International Publishing AG},
  address   = {Cham},
  issn      = {1420-682X},
  doi       = {10.1007/s00018-021-03844-4},
  pages     = {5123 -- 5138},
  year      = {2021},
  abstract  = {Genome-scale metabolic networks for model plants and crops in combination with approaches from the constraint-based modelling framework have been used to predict metabolic traits and design metabolic engineering strategies for their manipulation. With the advances in technologies to generate large-scale genotyping data from natural diversity panels and other populations, genome-wide association and genomic selection have emerged as statistical approaches to determine genetic variants associated with and predictive of traits. Here, we review recent advances in constraint-based approaches that integrate genetic variants in genome-scale metabolic models to characterize their effects on reaction fluxes. Since some of these approaches have been applied in organisms other than plants, we provide a critical assessment of their applicability particularly in crops. In addition, we further dissect the inferred effects of genetic variants with respect to reaction rate constants, abundances of enzymes, and concentrations of metabolites, as main determinants of reaction fluxes and relate them with their combined effects on complex traits, like growth. Through this systematic review, we also provide a roadmap for future research to increase the predictive power of statistical approaches by coupling them with mechanistic models of metabolism.},
  language  = {en}
}
@article{IltisFrahmVoitetal.2022,
  author    = {Iltis, Peter W. and Frahm, Jens and Voit, Dirk and Wood, Danielle and Taylor, Scott},
  title     = {Oral cavity movements of the tongue during large interval slurs in high-level horn players br a descriptive study},
  series = {Medical problems of performing artists},
  volume    = {3},
  journal   = {Medical problems of performing artists},
  number    = {2},
  publisher = {Science \& Medicine, Inc.},
  address   = {Narberth},
  issn      = {0885-1158},
  doi       = {10.21091/mppa.2022.2014},
  pages     = {89 -- 97},
  year      = {2022},
  abstract  = {OBJECTIVE: Recent publications describing lingual movement strategies within the oral cavity of brass players have established the existence of efficient and predictable movement patterns in healthy performers for a variety of performance tasks. In this study we extend the research to include the playing of large interval slurs in horn players. METHODS: Real-time MRI films at 40-msec resolution were simultaneously obtained in the sagittal and coronal planes in 9 professional horn players as they performed 2 repetitions each of 3 slur sequences spanning 1 octave, 1 octave + 3rd, and 1 octave + 5th at a mezzo forte dynamic level. Nine profile lines were overlaid on the images allowing the measurement of dorsal tongue edge movement using a customized MATLAB toolkit. Movement along lines representing the anterior, middle, and posterior oral cavity in the sagittal plane, as well as the vertical height of an air channel observed in the coronal plane, are reported. RESULTS: Both sagittal and coronal views demonstrate patterned tongue movements that narrow and widen the air channel during ascending and descending slurs, respectively. The magnitude of these movements is greater during larger intervals, though not perfectly consistent within each slur sequence. Additionally, the tongue position during notes tends to drift in the direction of the subsequent note in each sequence. We suggest that the observed movements may help to modulate air speed through the lips, possible attenuating embouchure muscle tension changes by assisting changes in lip vibration frequency.},
  language  = {en}
}
@article{KiemelGurkeParaskevopoulouetal.2022,
  author    = {Kiemel, Katrin and Gurke, Marie and Paraskevopoulou, Sofia and Havenstein, Katja and Weithoff, Guntram and Tiedemann, Ralph},
  title     = {Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species},
  series = {Scientific reports},
  volume    = {12},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-022-27137-3},
  pages     = {14},
  year      = {2022},
  abstract  = {Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.},
  language  = {en}
}
@article{Pandey2023,
  author    = {Pandey, Yogesh},
  title     = {Enriched cell-free and cell-based native membrane derived vesicles (nMV) enabling rapid in-vitro electrophysiological analysis of the voltage-gated sodium channel 1.5.},
  series = {Biochimica et Biophysica Acta (BBA) - Biomembranes},
  volume    = {1865},
  journal   = {Biochimica et Biophysica Acta (BBA) - Biomembranes},
  number    = {5},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1879-2642},
  doi       = {10.1016/j.bbamem.2023.184144},
  year      = {2023},
  abstract  = {Here, we demonstrate the utility of native membrane derived vesicles (nMVs) as tools for expeditious electrophysiological analysis of membrane proteins. We used a cell-free (CF) and a cell-based (CB) approach for preparing protein-enriched nMVs. We utilized the Chinese Hamster Ovary (CHO) lysate-based cell-free protein synthesis (CFPS) system to enrich ER-derived microsomes in the lysate with the primary human cardiac voltage-gated sodium channel 1.5 (hNaV1.5; SCN5A) in 3 h. Subsequently, CB-nMVs were isolated from fractions of nitrogen-cavitated CHO cells overexpressing the hNaV1.5. In an integrative approach, nMVs were micro-transplanted into Xenopus laevis oocytes. CB-nMVs expressed native lidocaine-sensitive hNaV1.5 currents within 24 h; CF-nMVs did not elicit any response. Both the CB- and CF-nMV preparations evoked single-channel activity on the planar lipid bilayer while retaining sensitivity to lidocaine application. Our findings suggest a high usability of the quick-synthesis CF-nMVs and maintenance-free CB-nMVs as ready-to-use tools for in-vitro analysis of electrogenic membrane proteins and large, voltage-gated ion channels.},
  language  = {en}
}
@article{GlowinskiAutenrieth2023,
  author    = {Glowinski, Ingrid and Autenrieth, Marijke},
  title     = {Eigene Forschung im Labor, um naturwissenschaftliche Erkenntnisgewinnung kompetent unterrichten zu k{\"o}nnen?},
  series = {PSI-Potsdam: Ergebnisbericht zu den Aktivit{\"a}ten im Rahmen der Qualit{\"a}tsoffensive Lehrerbildung (2019-2023) (Potsdamer Beitr{\"a}ge zur Lehrerbildung und Bildungsforschung ; 3)},
  journal   = {PSI-Potsdam: Ergebnisbericht zu den Aktivit{\"a}ten im Rahmen der Qualit{\"a}tsoffensive Lehrerbildung (2019-2023) (Potsdamer Beitr{\"a}ge zur Lehrerbildung und Bildungsforschung ; 3)},
  number    = {3},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-568-2},
  issn      = {2626-3556},
  doi       = {10.25932/publishup-61792},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-617922},
  pages     = {273 -- 293},
  year      = {2023},
  abstract  = {Im Rahmen des PSI-Projekts wurde eine Lehrveranstaltung konzipiert, die Lehramtsstudierenden einen vertieften Einblick sowohl in den Ablauf von Forschung als auch eine Bearbeitung einer eigenen experimentellen Forschungsaufgabe erm{\"o}glichen soll. Anlass waren die Ber{\"u}cksichtigung eines „Wissens {\"u}ber Erkenntnisgewinnung in der Disziplin" im Modell des „Erweiterten Fachwissens f{\"u}r den schulischen Kontext" (PSI) sowie Erkenntnisse empirischer Studien, die die Relevanz eigener Forschungserfahrung f{\"u}r das Unterrichten naturwissenschaftlicher Erkenntnisgewinnungsprozesse zeigen. Hier stellen wir eine neue Lehrveranstaltung (4 SWS) vor, die den angehenden Lehrkr{\"a}ften Forschungserfahrung erm{\"o}glicht (Seminar und Praktikum). Die Lehrveranstaltung vermittelt Einblicke in Forschung und die „Natur der Naturwissenschaften", erm{\"o}glicht das Durchf{\"u}hren eigener wissenschaftlicher und schulrelevanter Experimente und bietet eine angemessene Reflexion {\"u}ber die verschiedenen Kurselemente. Die Evaluationsergebnisse sind {\"u}berwiegend positiv, zeigen aber auch, dass f{\"u}r die Studierenden die wahrgenommene Schulrelevanz und die fachdidaktischen Aspekte ein wichtiges Kriterium f{\"u}r die positive Bewertung sind.},
  language  = {de}
}
@article{ColeLiddleConsolandietal.2020,
  author    = {Cole, Matthew and Liddle, Corin and Consolandi, Giulia and Drago, Claudia and Hird, Cameron and Lindeque, Penelope Kate and Galloway, Tamara S.},
  title     = {Microplastics, microfibres and nanoplastics cause variable sub-lethal responses in mussels (Mytilus spp.)},
  series = {Marine pollution bulletin : the international journal for marine environmental scientists, engineers, administrators, politicians and lawyers},
  volume    = {160},
  journal   = {Marine pollution bulletin : the international journal for marine environmental scientists, engineers, administrators, politicians and lawyers},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0025-326X},
  doi       = {10.1016/j.marpolbul.2020.111552},
  pages     = {10},
  year      = {2020},
  abstract  = {We compare the toxicity of microplastics, microfibres and nanoplastics on mussels. Mussels (Mytilus spp.) were exposed to 500 ng mL(-1) of 20 mu m polystyrene microplastics, 10 x 30 mu m polyamide microfibres or 50 nm polystyrene nanoplastics for 24 h or 7 days. Biomarkers of immune response, oxidative stress response, lysosomal destabilisation and genotoxic damage were measured in haemolymph, digestive gland and gills. Microplastics and microfibres were observed in the digestive glands, with significantly higher plastic concentrations after 7-days exposure (ANOVA, P < 0.05). Nanoplastics had a significant effect on hyalinocytegranulocyte ratios (ANOVA, P < 0.05), indicative of a heightened immune response. SOD activity was significantly increased followed 24 h exposure to plastics (two-way ANOVA, P < 0.05), but returned to normal levels after 7-days exposure. No evidence of lysosomal destabilisation or genotoxic damage was observed from any form of plastic. The study highlights how particle size is a key factor in plastic particulate toxicity.},
  language  = {en}
}
@article{VillalbaKarnatakGrossartetal.2022,
  author    = {Villalba, Luis Alberto and Karnatak, Rajat and Grossart, Hans-Peter and Wollrab, Sabine},
  title     = {Flexible habitat choice of pelagic bacteria increases system stability and energy flow through the microbial loop},
  series = {Limnology and oceanography : L \& O},
  volume    = {67},
  journal   = {Limnology and oceanography : L \& O},
  number    = {6},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {0024-3590},
  doi       = {10.1002/lno.12091},
  pages     = {1402 -- 1415},
  year      = {2022},
  abstract  = {Pelagic bacteria can be classified into free-living and particle-attached life modes, which either dwell in the water column or attach to suspended particles. Bacteria with a generalist life style, however, can actively shift between these two habitats. Globally increasing densities of natural and artificial particles enhance habitat heterogeneity, with potential consequences for system stability and trophic transfer through aquatic food webs. To better decipher the dynamics of microbial communities, we investigated the influence of adaptive vs. fixed habitat choice on species coexistence for a simplified bacterial community by analyzing a corresponding food web model, consisting of two specialist bacterial prey species (free and attached), a generalist bacterial prey species with the ability to shift between both habitats, and two protist predators, specialized on either water or particle compartment. For simplicity we assume a shared resource pool, considering particles only for colonization but not as a source for nutrients or carbon, that is, inert particles like microplastics or inorganic sediments. The model predicts coexistence on a cyclic attractor between fixed and flexible bacteria, if the costs for adaptive habitat choice can be balanced by adaptation speed. The presence of adaptive prey dampens predator-prey cycle amplitudes, contributing to system stabilization resulting in higher mean predator biomass compared to specialist prey only. Thus, in pelagic microbial systems, flexible habitat choice at the prey level has important implications for system stability and magnitude of energy flow through the microbial loop.},
  language  = {en}
}
@article{IlicicGrossart2022,
  author    = {Ilicic, Doris and Grossart, Hans-Peter},
  title     = {Basal parasitic fungi in marine food webs-a mystery yet to unravel},
  series = {Journal of Fungi},
  volume    = {8},
  journal   = {Journal of Fungi},
  number    = {2},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2309-608X},
  doi       = {10.3390/jof8020114},
  pages     = {16},
  year      = {2022},
  abstract  = {Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.},
  language  = {en}
}
@article{EmaryMalchow2022,
  author    = {Emary, Clive and Malchow, Anne-Kathleen},
  title     = {Stability-instability transition in tripartite merged ecological networks},
  series = {Journal of mathematical biology},
  volume    = {85},
  journal   = {Journal of mathematical biology},
  number    = {3},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {0303-6812},
  doi       = {10.1007/s00285-022-01783-7},
  pages     = {18},
  year      = {2022},
  abstract  = {Although ecological networks are typically constructed based on a single type of interaction, e.g. trophic interactions in a food web, a more complete picture of ecosystem composition and functioning arises from merging networks of multiple interaction types. In this work, we consider tripartite networks constructed by merging two bipartite networks, one mutualistic and one antagonistic. Taking the interactions within each sub-network to be distributed randomly, we consider the stability of the dynamics of the network based on the spectrum of its community matrix. In the asymptotic limit of a large number of species, we show that the spectrum undergoes an eigenvalue phase transition, which leads to an abrupt destabilisation of the network as the ratio of mutualists to antagonists is increased. We also derive results that show how this transition is manifest in networks of finite size, as well as when disorder is introduced in the segregation of the two interaction types. Our random-matrix results will serve as a baseline for understanding the behaviour of merged networks with more realistic structures and/or more detailed dynamics.},
  language  = {en}
}
@article{ParrySchlaegelTiedemannetal.2022,
  author    = {Parry, Victor and Schl{\"a}gel, Ulrike E. and Tiedemann, Ralph and Weithoff, Guntram},
  title     = {Behavioural responses of defended and undefended prey to their predator},
  series = {Biology : open access journal},
  volume    = {11},
  journal   = {Biology : open access journal},
  number    = {8},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2079-7737},
  doi       = {10.3390/biology11081217},
  pages     = {14},
  year      = {2022},
  abstract  = {Many animals that have to cope with predation have evolved mechanisms to reduce their predation risk. One of these mechanisms is change in morphology, for example, the development of spines. These spines are induced, when mothers receive chemical signals of a predator (kairomones) and their daughters are then equipped with defensive spines. We studied the behaviour of a prey and its predator when the prey is either defended or undefended. We used common aquatic micro-invertebrates, the rotifers Brachionus calyciflorus (prey) and Asplanchna brightwellii (predator) as experimental animals. We found that undefended prey increased its swimming speed in the presence of the predator. The striking result was that the defended prey did not respond to the predator's presence. This suggests that defended prey has a different response behaviour to a predator than undefended conspecifics. Our study provides further insights into complex zooplankton predator-prey interactions. Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status.},
  language  = {en}
}
@article{KiemelWeithoffTiedemann2022,
  author    = {Kiemel, Katrin and Weithoff, Guntram and Tiedemann, Ralph},
  title     = {DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity},
  series = {Molecular ecology},
  volume    = {32},
  journal   = {Molecular ecology},
  number    = {23},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0962-1083},
  doi       = {10.1111/mec.16627},
  pages     = {20},
  year      = {2022},
  abstract  = {Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.},
  language  = {en}
}
@article{MbebiTongNikoloski2021,
  author    = {Mbebi, Alain J. and Tong, Hao and Nikoloski, Zoran},
  title     = {L-2,L-1-norm regularized multivariate regression model with applications to genomic prediction},
  series = {Bioinformatics},
  volume    = {37},
  journal   = {Bioinformatics},
  number    = {18},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1367-4803},
  doi       = {10.1093/bioinformatics/btab212},
  pages     = {2896 -- 2904},
  year      = {2021},
  abstract  = {Motivation: Genomic selection (GS) is currently deemed the most effective approach to speed up breeding of agricultural varieties. It has been recognized that consideration of multiple traits in GS can improve accuracy of prediction for traits of low heritability. However, since GS forgoes statistical testing with the idea of improving predictions, it does not facilitate mechanistic understanding of the contribution of particular single nucleotide polymorphisms (SNP). Results: Here, we propose a L-2,L-1-norm regularized multivariate regression model and devise a fast and efficient iterative optimization algorithm, called L-2,L-1-joint, applicable in multi-trait GS. The usage of the L-2,L-1-norm facilitates variable selection in a penalized multivariate regression that considers the relation between individuals, when the number of SNPs is much larger than the number of individuals. The capacity for variable selection allows us to define master regulators that can be used in a multi-trait GS setting to dissect the genetic architecture of the analyzed traits. Our comparative analyses demonstrate that the proposed model is a favorable candidate compared to existing state-of-the-art approaches. Prediction and variable selection with datasets from Brassica napus, wheat and Arabidopsis thaliana diversity panels are conducted to further showcase the performance of the proposed model.},
  language  = {en}
}
@article{KimLeifheitMaassetal.2021,
  author    = {Kim, Shin Woong and Leifheit, Eva F. and Maaß, Stefanie and Rillig, Matthias C.},
  title     = {Time-dependent toxicity of tire particles on soil nematodes},
  series = {Frontiers in Environmental Science},
  volume    = {9},
  journal   = {Frontiers in Environmental Science},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-665X},
  doi       = {10.3389/fenvs.2021.744668},
  pages     = {9},
  year      = {2021},
  abstract  = {Tire-wear particles (TWPs) are being released into the environment by wearing down during car driving, and are considered an important microplastic pollution source. The chemical additive leaching from these polymer-based materials and its potential effects are likely temporally dynamic, since amounts of potentially toxic compounds can gradually increase with contact time of plastic particles with surrounding media. In the present study, we conducted soil toxicity tests using the soil nematode Caenorhabditis elegans with different soil pre-incubation (30 and 75 days) and exposure (short-term exposure, 2 days; lifetime exposure, 10 days) times. Soil pre-incubation increased toxicity of TWPs, and the effective concentrations after the pre-incubation were much lower than environmentally relevant concentrations. The lifetime of C. elegans was reduced faster in the TWP treatment groups, and the effective concentration for lifetime exposure tests were 100- to 1,000-fold lower than those of short-term exposure tests. Water-extractable metal concentrations (Cr, Cu, Ni, Pb, and Zn) in the TWP-soils showed no correlation with nominal TWP concentrations or pre-incubation times, and the incorporated metals in the TWPs may be not the main reason of toxicity in this study. Our results show that toxic effects of TWPs can be time-dependent, both in terms of the microplastic particles themselves and their interactions in the soil matrix, but also because of susceptibility of target organisms depending on developmental stage. It is vital that future works consider these aspects, since otherwise effects of microplastics and TWPs could be underestimated.},
  language  = {en}
}
@article{HerzschuhBoehmerLietal.2022,
  author    = {Herzschuh, Ulrike and B{\"o}hmer, Thomas and Li, Chenzhi and Cao, Xianyong and H{\´e}bert, Rapha{\"e}l and Dallmeyer, Anne and Telford, Richard J. and Kruse, Stefan},
  title     = {Reversals in temperature-precipitation correlations in the Northern Hemisphere extratropics during the Holocene},
  series = {Geophysical research letters},
  volume    = {49},
  journal   = {Geophysical research letters},
  number    = {22},
  publisher = {American Geophysical Union},
  address   = {Washington},
  issn      = {0094-8276},
  doi       = {10.1029/2022GL099730},
  pages     = {11},
  year      = {2022},
  abstract  = {Future precipitation levels remain uncertain because climate models have struggled to reproduce observed variations in temperature-precipitation correlations. Our analyses of Holocene proxy-based temperature-precipitation correlations and hydrological sensitivities from 2,237 Northern Hemisphere extratropical pollen records reveal a significant latitudinal dependence and temporal variations among the early, middle, and late Holocene. These proxy-based variations are largely consistent with patterns obtained from transient climate simulations (TraCE21k). While high latitudes and subtropical monsoon areas show mainly stable positive correlations throughout the Holocene, the mid-latitude pattern is temporally and spatially more variable. In particular, we identified a reversal from positive to negative temperature-precipitation correlations in the eastern North American and European mid-latitudes from the early to mid-Holocene that mainly related to slowed down westerlies and a switch to moisture-limited convection under a warm climate. Our palaeoevidence of past temperature-precipitation correlation shifts identifies those regions where simulating past and future precipitation levels might be particularly challenging.},
  language  = {en}
}
@article{OuedraogoZareKorbeogoetal.2021,
  author    = {Ou{\´e}draogo, Karim and Zar{\´e}, Alhassane and Korb{\´e}ogo, Gabin and Ou{\´e}draogo, Oumarou and Linst{\"a}dter, Anja},
  title     = {Resilience strategies of West African pastoralists in response to scarce forage resources},
  series = {Pastoralism : research, policy and practice},
  volume    = {11},
  journal   = {Pastoralism : research, policy and practice},
  number    = {1},
  publisher = {SpringerOpen},
  address   = {Heidelberg},
  issn      = {2041-7136},
  doi       = {10.1186/s13570-021-00210-8},
  pages     = {14},
  year      = {2021},
  abstract  = {Finding sufficient natural fodder resources to feed livestock has become a challenge for herders in the Sahel zone of Burkina Faso. Despite the existence of pastoral reserves, the issue of fodder shortage remains unsolved. This article highlights the changes in behaviour and the evolution of pastoral practices caused by the scarcity of forage resources. These changes are defined and classified as resilience strategies. Thus, this paper aims to analyse these strategies using new semantics that calls for other forms of perceptions or approach to the questions of pastoralists' resilience strategies. Interviews (semi-structured and casual conversations), ethnographic observations and ethnobotanical surveys were used to collect data. In rangelands, such high value fodder species as Andropogon gayanus, Pennisetum pedicellatum and Dactyloctenium aegyptium that were abundant herbaceous plants during the last decades are disappearing. Concomitantly, species with lower forage value, such as Senna obtusifolia, which are more resilient to ecological disturbance factors, are colonizing rangelands. Faced with these ecological changes, pastoralists are trying to redefine and reconfigure their practices, and this implies a redefinition of their identity. They use resilience strategies such as mowing grasses, building up fodder bundles, conserving crop residues, exploiting Senna obtusifolia (a previously neglected species), using woody fodder and adapting the type of livestock and the size of the herds to the ability of pastoralists to feed them. Strategies that are older than these are the integration of agriculture with livestock and decollectivized transhumance. It is these resilience strategies that this article exposes and analyses as defence mechanisms of Sahelian pastoralists in the face of the depletion of forage resources in their environments.},
  language  = {en}
}
@article{MeridaFettke2021,
  author    = {Merida, Angel and Fettke, J{\"o}rg},
  title     = {Starch granule initiation in Arabidopsis thaliana chloroplasts},
  series = {The plant journal},
  volume    = {107},
  journal   = {The plant journal},
  number    = {3},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.15359},
  pages     = {688 -- 697},
  year      = {2021},
  abstract  = {The initiation of starch granule formation and the mechanism controlling the number of granules per plastid have been some of the most elusive aspects of starch metabolism. This review covers the advances made in the study of these processes. The analyses presented herein depict a scenario in which starch synthase isoform 4 (SS4) provides the elongating activity necessary for the initiation of starch granule formation. However, this protein does not act alone; other polypeptides are required for the initiation of an appropriate number of starch granules per chloroplast. The functions of this group of polypeptides include providing suitable substrates (maltooligosaccharides) to SS4, the localization of the starch initiation machinery to the thylakoid membranes, and facilitating the correct folding of SS4. The number of starch granules per chloroplast is tightly regulated and depends on the developmental stage of the leaves and their metabolic status. Plastidial phosphorylase (PHS1) and other enzymes play an essential role in this process since they are necessary for the synthesis of the substrates used by the initiation machinery. The mechanism of starch granule formation initiation in Arabidopsis seems to be generalizable to other plants and also to the synthesis of long-term storage starch. The latter, however, shows specific features due to the presence of more isoforms, the absence of constantly recurring starch synthesis and degradation, and the metabolic characteristics of the storage sink organs.},
  language  = {en}
}
@article{JohnOlasMuellerRoeber2021,
  author    = {John, Sheeba and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {Regulation of alternative splicing in response to temperature variation in plants},
  series = {Journal of experimental botany},
  volume    = {72},
  journal   = {Journal of experimental botany},
  number    = {18},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0022-0957},
  doi       = {10.1093/jxb/erab232},
  pages     = {6150 -- 6163},
  year      = {2021},
  abstract  = {Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.},
  language  = {en}
}
@article{MummSchefflerHermanussen2022,
  author    = {Mumm, Rebekka and Scheffler, Christiane and Hermanussen, Michael},
  title     = {Locally structured correlation (LSC) plots describe inhomogeneity in normally distributed correlated bivariate variables},
  series = {Archives of public health = Archives belges de sant{\´e} publique = Belgisch archief voor volksgezondheid},
  volume    = {80},
  journal   = {Archives of public health = Archives belges de sant{\´e} publique = Belgisch archief voor volksgezondheid},
  number    = {1},
  publisher = {BMC},
  address   = {London},
  issn      = {0778-7367},
  doi       = {10.1186/s13690-021-00748-4},
  pages     = {6},
  year      = {2022},
  abstract  = {Background The association between bivariate variables may not necessarily be homogeneous throughout the whole range of the variables. We present a new technique to describe inhomogeneity in the association of bivariate variables. Methods We consider the correlation of two normally distributed random variables. The 45 degrees diagonal through the origin of coordinates represents the line on which all points would lie if the two variables completely agreed. If the two variables do not completely agree, the points will scatter on both sides of the diagonal and form a cloud. In case of a high association between the variables, the band width of this cloud will be narrow, in case of a low association, the band width will be wide. The band width directly relates to the magnitude of the correlation coefficient. We then determine the Euclidean distances between the diagonal and each point of the bivariate correlation, and rotate the coordinate system clockwise by 45 degrees. The standard deviation of all Euclidean distances, named "global standard deviation", reflects the band width of all points along the former diagonal. Calculating moving averages of the standard deviation along the former diagonal results in "locally structured standard deviations" and reflect patterns of "locally structured correlations (LSC)". LSC highlight inhomogeneity of bivariate correlations. We exemplify this technique by analyzing the association between body mass index (BMI) and hip circumference (HC) in 6313 healthy East German adults aged 18 to 70 years. Results The correlation between BMI and HC in healthy adults is not homogeneous. LSC is able to identify regions where the predictive power of the bivariate correlation between BMI and HC increases or decreases, and highlights in our example that slim people have a higher association between BMI and HC than obese people. Conclusion Locally structured correlations (LSC) identify regions of higher or lower than average correlation between two normally distributed variables.},
  language  = {en}
}
@article{MazzaGuenther2021,
  author    = {Mazza, Valeria and G{\"u}nther, Anja},
  title     = {City mice and country mice},
  series = {Animal behaviour},
  volume    = {172},
  journal   = {Animal behaviour},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0003-3472},
  doi       = {10.1016/j.anbehav.2020.12.007},
  pages     = {197 -- 210},
  year      = {2021},
  abstract  = {The ability to produce innovative behaviour is a key determinant in the successful coping with environmental challenges and changes. The expansion of human-altered environments presents wildlife with multiple novel situations in which innovativeness could be beneficial. A better understanding of the drivers of within-species variation in innovation propensity and its consequences will provide insights into the traits enabling animals to thrive in the face of human-induced rapid environmental change. We compared problem-solving performance of 31 striped field mice, Apodemus agrarius, originating from rural or urban environments in a battery of eight foraging extraction tasks. We tested whether differences in problem-solving performance were mediated by the extent and duration of the animal's exploration of the experimental set-ups, the time required to solve the tasks, and their persistence. In addition, we tested the influence of the diversity of motor responses, as well as of behavioural traits boldness and activity on problem-solving performance. Urban individuals were better problem solvers despite rural individuals approaching faster and interacting longer with the test set-ups. Participation rates and time required to solve a task did not differ between rural and urban individuals. However, in case of failure to solve a task, rural mice were more persistent. The best predictors of solving success, aside from the area of origin, were the time spent exploring the set-ups and boldness, while activity and diversity of motor responses did not explain it. Problem-solving ability could thus be a contributing factor to the successful coping with the rapid and recent expansion of human-altered environments.},
  language  = {en}
}
@article{DallmeyerKleinenClaussenetal.2022,
  author    = {Dallmeyer, Anne and Kleinen, Thomas and Claussen, Martin and Weitzel, Nils and Cao, Xianyong and Herzschuh, Ulrike},
  title     = {The deglacial forest conundrum},
  series = {Nature Communications},
  volume    = {13},
  journal   = {Nature Communications},
  number    = {1},
  publisher = {Nature Publishing Group UK},
  address   = {[London]},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-022-33646-6},
  pages     = {10},
  year      = {2022},
  abstract  = {How fast the Northern Hemisphere (NH) forest biome tracks strongly warming climates is largely unknown. Regional studies reveal lags between decades and millennia. Here we report a conundrum: Deglacial forest expansion in the NH extra-tropics occurs approximately 4000 years earlier in a transient MPI-ESM1.2 simulation than shown by pollen-based biome reconstructions. Shortcomings in the model and the reconstructions could both contribute to this mismatch, leaving the underlying causes unresolved. The simulated vegetation responds within decades to simulated climate changes, which agree with pollen-independent reconstructions. Thus, we can exclude climate biases as main driver for differences. Instead, the mismatch points at a multi-millennial disequilibrium of the NH forest biome to the climate signal. Therefore, the evaluation of time-slice simulations in strongly changing climates with pollen records should be critically reassessed. Our results imply that NH forests may be responding much slower to ongoing climate changes than Earth System Models predict. <br /> Deglacial forest expansion in the Northern Hemisphere poses a conundrum: Model results agree with the climate signal but are several millennia ahead of reconstructed forest dynamics. The underlying causes remain unsolved.},
  language  = {en}
}
@article{LauxWengerBieretal.2020,
  author    = {Laux, Eva-Maria and Wenger, Christian and Bier, Frank Fabian and Hoelzel, Ralph},
  title     = {AC electrokinetic immobilization of organic dye molecules},
  series = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry and Analusis},
  volume    = {412},
  journal   = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry and Analusis},
  number    = {16},
  publisher = {Springer},
  address   = {Berlin},
  issn      = {1618-2642},
  doi       = {10.1007/s00216-020-02480-4},
  pages     = {3859 -- 3870},
  year      = {2020},
  abstract  = {The application of inhomogeneous AC electric fields for molecular immobilization is a very fast and simple method that does not require any adaptions to the molecule's functional groups or charges. Here, the method is applied to a completely new category of molecules: small organic fluorescence dyes, whose dimensions amount to only 1 nm or even less. The presented setup and the electric field parameters used allow immobilization of dye molecules on the whole electrode surface as opposed to pure dielectrophoretic applications, where molecules are attracted only to regions of high electric field gradients, i.e., to the electrode tips and edges. In addition to dielectrophoresis and AC electrokinetic flow, molecular scale interactions and electrophoresis at short time scales are discussed as further mechanisms leading to migration and immobilization of the molecules.},
  language  = {en}
}
@article{LiWangHerzschuhetal.2022,
  author    = {Li, Zhen and Wang, Yongbo and Herzschuh, Ulrike and Cao, Xianyong and Ni, Jian and Zhao, Yan},
  title     = {Pollen-based biome reconstruction on the Qinghai-Tibetan Plateau during the past 15,000 years},
  series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences},
  volume    = {604},
  journal   = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0031-0182},
  doi       = {10.1016/j.palaeo.2022.111190},
  pages     = {12},
  year      = {2022},
  abstract  = {Reconstruction of past vegetation change is critical for better understanding the potential impact of future global change on the fragile alpine ecosystems of the Qinghai-Tibetan Plateau (QTP). In this paper, pollen assemblages comprising 58 records from the QTP, spanning the past 15 kyrs, were collected to reconstruct biome compositions using a standard approach. Six forest biomes were identified mainly on the southeastern plateau, exhibiting a pattern of gradual expansion along the eastern margin during early to mid-Holocene times. The alpine meadow biome was separately identified based on an updated scheme, and showed notable westward expansions towards lower latitudes and higher altitudes during early Holocene times. Consistent patterns of migration could also be identified for the alpine steppe biome, which moved eastward during the late Holocene after 4 ka. As the dominant biome type, temperate steppe was distributed widely over the QTP with minor migration patterns, except for a progressive expansion to lower altitudes in the late Holocene times. The desert biome was inferred mainly as covering the northwestern plateau and the Qaidam Basin, in relatively restricted areas. The spatial distribution of the reconstructed biomes represent the large-scale vegetation gradient on the QTP. Monsoonal precipitation expressed predominant controls on the development of alpine ecosystems, while the variations in desert vegetation responded to regional moisture brought by the mid-latitude Westerlies. Temperature changes played relatively minor roles in the variations of alpine vegetation, but exerted more significant impacts on the forest biomes.},
  language  = {en}
}
@article{JaenickeGoddardSteinetal.2022,
  author    = {J{\"a}nicke, Clemens and Goddard, Adam and Stein, Susanne and Steinmann, Horst-Henning and Lakes, Tobia and Nendel, Claas and M{\"u}ller, Daniel},
  title     = {Field-level land-use data reveal heterogeneous crop sequences with distinct regional differences in Germany},
  series = {European journal of agronomy},
  volume    = {141},
  journal   = {European journal of agronomy},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1161-0301},
  doi       = {10.1016/j.eja.2022.126632},
  pages     = {12},
  year      = {2022},
  abstract  = {Crop cultivation intensifies globally, which can jeopardize biodiversity and the resilience of cropping systems. We investigate changes in crop rotations as one intensification metric for half of the croplands in Germany with annual field-level land-use data from 2005 to 2018. We proxy crop rotations with crop sequences and compare how these sequences changed among three seven-year periods. The results reveal an overall high diversity of crop sequences in Germany. Half of the cropland has crop sequences with four or more crops within a seven-year period, while continuous cultivation of the same crop is present on only 2\% of the cropland. Larger farms tend to have more diverse crop sequences and organic farms have lower shares of cereal crops. In three federal states, crop rotations became less structurally diverse over time, i.e. the number of crops and the number of changes between crops decreased. In one state, structural diversity increased and the proportion of monocropping decreased. The functional diversity of the crop sequences, which measures the share of winter and spring crops as well as the share of leaf and cereal crops per sequence, remained largely stable. Trends towards cereal-or leaf -crop dominated sequences varied between the states, and no clear overall dynamic could be observed. However, the share of winter crops per sequence decreased in all four federal states. Quantifying the dynamics of crop sequences at the field level is an important metric of land-use intensity and can reveal the patterns of land-use intensification.},
  language  = {en}
}
@article{GuerreroFickelBenhaiemetal.2020,
  author    = {Guerrero, Tania P. and Fickel, J{\"o}rns and Benhaiem, Sarah and Weyrich, Alexandra},
  title     = {Epigenomics and gene regulation in mammalian social systems},
  series = {Current zoology},
  volume    = {66},
  journal   = {Current zoology},
  number    = {3},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1674-5507},
  doi       = {10.1093/cz/zoaa005},
  pages     = {307 -- 319},
  year      = {2020},
  abstract  = {Social epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene-environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEls, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.},
  language  = {en}
}
@article{KruseKolmogorovPestryakovaetal.2020,
  author    = {Kruse, Stefan and Kolmogorov, Aleksey I. and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Long-lived larch clones may conserve adaptations that could restrict treeline migration in northern Siberia},
  series = {Ecology and evolution},
  volume    = {10},
  journal   = {Ecology and evolution},
  number    = {18},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.6660},
  pages     = {10017 -- 10030},
  year      = {2020},
  abstract  = {The occurrence of refugia beyond the arctic treeline and genetic adaptation therein play a crucial role of largely unknown effect size. While refugia have potential for rapidly colonizing the tundra under global warming, the taxa may be maladapted to the new environmental conditions. Understanding the genetic composition and age of refugia is thus crucial for predicting any migration response. Here, we genotype 194 larch individuals from an similar to 1.8 km(2)area in northcentral Siberia on the southern Taimyr Peninsula by applying an assay of 16 nuclear microsatellite markers. For estimating the age of clonal individuals, we counted tree rings at sections along branches to establish a lateral growth rate that was then combined with geographic distance. Findings reveal that the predominant reproduction type is clonal (58.76\%) by short distance spreading of ramets. One outlier of clones 1 km apart could have been dispersed by reindeer. In clonal groups and within individuals, we find that somatic mutations accumulate with geographic distance. Clonal groups of two or more individuals are observed. Clonal age estimates regularly suggest individuals as old as 2,200 years, which coincides with a major environmental change that forced a treeline retreat in the region. We conclude that individuals with clonal growth mode were naturally selected as it lowers the likely risk of extinction under a harsh environment. We discuss this legacy from the past that might now be a maladaptation and hinder expansion under currently strongly increasing temperatures.},
  language  = {en}
}
@article{StieglerKiemelEccardetal.2021,
  author    = {Stiegler, Jonas and Kiemel, Katrin and Eccard, Jana and Fischer, Christina and Hering, Robert and Ortmann, Sylvia and Strigl, Lea and Tiedemann, Ralph and Ullmann, Wiebke and Blaum, Niels},
  title     = {Seed traits matter},
  series = {Ecology and evolution},
  volume    = {11},
  journal   = {Ecology and evolution},
  number    = {24},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.8440},
  pages     = {18477 -- 18491},
  year      = {2021},
  abstract  = {Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51\%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes.},
  language  = {en}
}
@article{GuoSchwitallaBenndorfetal.2020,
  author    = {Guo, Huijuan and Schwitalla, Jan W. and Benndorf, Ren{\´e} and Baunach, Martin and Steinbeck, Christoph and G{\"o}rls, Helmar and de Beer, Z. Wilhelm and Regestein, Lars and Beemelmanns, Christine},
  title     = {Gene cluster activation in a bacterial symbiont leads to halogenated angucyclic maduralactomycins and spirocyclic actinospirols},
  series = {Organic letters},
  volume    = {22},
  journal   = {Organic letters},
  number    = {7},
  publisher = {American Chemical Society},
  address   = {Washington, DC},
  issn      = {1523-7060},
  doi       = {10.1021/acs.orglett.0c00601},
  pages     = {2634 -- 2638},
  year      = {2020},
  abstract  = {Growth from spores activated a biosynthetic gene cluster in Actinomadura sp. RB29, resulting in the identification of two novel groups of halogenated polyketide natural products, named maduralactomycins and actinospirols. The unique tetracyclic and spirocyclic structures were assigned based on a combination of NMR analysis, chemoinformatic calculations, X-ray crystallography, and C-13 labeling studies. On the basis of HRMS2 data, genome mining, and gene expression studies, we propose an underlying noncanonical angucycline biosynthesis and extensive post-polyketide synthase (PKS) oxidative modifications.},
  language  = {en}
}
@article{ZiegeHermannKriestenetal.2020,
  author    = {Ziege, Madlen and Hermann, Bernd Timo and Kriesten, Stefanie and Merker, Stefan and Ullmann, Wiebke and Streit, Bruno and Wenninger, Sandra and Plath, Martin},
  title     = {Ranging behavior of European rabbits (Oryctolagus cuniculus) in urban and suburban landscapes},
  series = {Mammal research / Mammal Research Institute, Polish Academy of Sciences},
  volume    = {65},
  journal   = {Mammal research / Mammal Research Institute, Polish Academy of Sciences},
  number    = {3},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {2199-2401},
  doi       = {10.1007/s13364-020-00490-2},
  pages     = {607 -- 614},
  year      = {2020},
  abstract  = {Various mammals, particularly carnivores, reportedly establish smaller home ranges in urban compared with rural areas. This may be because urban environments provide optimal resources within a small area, negating the requirement to range further, or because habitat fragmentation constrains ranging behavior. Comparable information on urban populations of herbivorous mammalian species (such as European rabbits) is scarce. To fill this knowledge gap, we radio-tracked 13 individuals (seven females and six males) equipped with radio collars in a suburban and an urban study site in the city of Frankfurt am Main in Germany during the reproductive season (March to September) of 2012. The study sites differed in levels of habitat fragmentation. We report the smallest home ranges ever described for this species, with mean 95\% minimum convex polygons (MCPs) covering 0.50 ha, while no consistent differences between sites were uncovered. We occasionally tracked individuals crossing streets underground (in burrows), suggesting that streets may restrict the ranging behavior of rabbits-and possibly other burrowing species-to a much lesser extent than previously thought. We conclude that heterogeneous landscape structures, made up of a diverse mosaic of buildings, parks, and gardens, provide sufficient food and shelter in close proximity to burrows at both study sites. Therefore, our data support the hypothesis that optimal resources constrain ranges in this case rather than habitat fragmentation.},
  language  = {en}
}
@article{BarlowHartmannGonzalezetal.2020,
  author    = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.},
  title     = {Consensify},
  series = {Genes / Molecular Diversity Preservation International},
  volume    = {11},
  journal   = {Genes / Molecular Diversity Preservation International},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes11010050},
  pages     = {22},
  year      = {2020},
  abstract  = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.},
  language  = {en}
}
@article{WicaksonoBraunBernhardtetal.2022,
  author    = {Wicaksono, Wisnu Adi and Braun, Maria and Bernhardt, J{\"o}rg and Riedel, Katharina and Cernava, Tomislav and Berg, Gabriele},
  title     = {Trade-off for survival},
  series = {Environment international : a journal of science, technology, health, monitoring and policy},
  volume    = {168},
  journal   = {Environment international : a journal of science, technology, health, monitoring and policy},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {1873-6750},
  doi       = {10.1016/j.envint.2022.107474},
  pages     = {13},
  year      = {2022},
  abstract  = {The environmental micmbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen as a bioindicator organism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native micmbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments.},
  language  = {en}
}
@article{LehmannZhengRyoetal.2020,
  author    = {Lehmann, Anika and Zheng, Weishuang and Ryo, Masahiro and Soutschek, Katharina and Roy, Julien and Rongstock, Rebecca and Maaß, Stefanie and Rillig, Matthias C.},
  title     = {Fungal traits important for soil aggregation},
  series = {Frontiers in microbiology},
  volume    = {10},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2019.02904},
  pages     = {13},
  year      = {2020},
  abstract  = {Soil structure, the complex arrangement of soil into aggregates and pore spaces, is a key feature of soils and soil biota. Among them, filamentous saprobic fungi have well-documented effects on soil aggregation. However, it is unclear what properties, or traits, determine the overall positive effect of fungi on soil aggregation. To achieve progress, it would be helpful to systematically investigate a broad suite of fungal species for their trait expression and the relation of these traits to soil aggregation. Here, we apply a trait-based approach to a set of 15 traits measured under standardized conditions on 31 fungal strains including Ascomycota, Basidiomycota, and Mucoromycota, all isolated from the same soil. We find large differences among these fungi in their ability to aggregate soil, including neutral to positive effects, and we document large differences in trait expression among strains. We identify biomass density, i.e., the density with which a mycelium grows (positive effects), leucine aminopeptidase activity (negative effects) and phylogeny as important factors explaining differences in soil aggregate formation (SAF) among fungal strains; importantly, growth rate was not among the important traits. Our results point to a typical suite of traits characterizing fungi that are good soil aggregators, and our findings illustrate the power of employing a trait-based approach to unravel biological mechanisms underpinning soil aggregation. Such an approach could now be extended also to other soil biota groups. In an applied context of restoration and agriculture, such trait information can inform management, for example to prioritize practices that favor the expression of more desirable fungal traits.},
  language  = {en}
}
@article{RadosavljevicLantuitKnoblauchetal.2022,
  author    = {Radosavljevic, Boris and Lantuit, Hugues and Knoblauch, Christian and Couture, Nicole and Herzschuh, Ulrike and Fritz, Michael},
  title     = {Arctic nearshore sediment dynamics - an example from Herschel Island - Qikiqtaruk, Canada},
  series = {Journal of marine science and engineering},
  volume    = {10},
  journal   = {Journal of marine science and engineering},
  number    = {11},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2077-1312},
  doi       = {10.3390/jmse10111589},
  pages     = {18},
  year      = {2022},
  abstract  = {Increasing arctic coastal erosion rates imply a greater release of sediments and organic matter into the coastal zone. With 213 sediment samples taken around Herschel Island-Qikiqtaruk, Canadian Beaufort Sea, we aimed to gain new insights on sediment dynamics and geochemical properties of a shallow arctic nearshore zone. Spatial characteristics of nearshore sediment texture (moderately to poorly sorted silt) are dictated by hydrodynamic processes, but ice-related processes also play a role. We determined organic matter (OM) distribution and inferred the origin and quality of organic carbon by C/N ratios and stable carbon isotopes delta C-13. The carbon content was higher offshore and in sheltered areas (mean: 1.0 wt.\%., S.D.: 0.9) and the C/N ratios also showed a similar spatial pattern (mean: 11.1, S.D.: 3.1), while the delta C-13 (mean: -26.4 parts per thousand VPDB, S.D.: 0.4) distribution was more complex. We compared the geochemical parameters of our study with terrestrial and marine samples from other studies using a bootstrap approach. Sediments of the current study contained 6.5 times and 1.8 times less total organic carbon than undisturbed and disturbed terrestrial sediments, respectively. Therefore, degradation of OM and separation of carbon pools take place on land and continue in the nearshore zone, where OM is leached, mineralized, or transported beyond the study area.},
  language  = {en}
}
@article{WarmtFenzelHenkeletal.2021,
  author    = {Warmt, Christian and Fenzel, Carolin Kornelia and Henkel, J{\"o}rg and Bier, Frank Fabian},
  title     = {Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {[London]},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-99774-z},
  pages     = {9},
  year      = {2021},
  abstract  = {In this report we describe Cy5-dUTP labelling of recombinase-polymerase-amplification (RPA) products directly during the amplification process for the first time. Nucleic acid amplification techniques, especially polymerase-chain-reaction as well as various isothermal amplification methods such as RPA, becomes a promising tool in the detection of pathogens and target specific genes. Actually, RPA even provides more advantages. This isothermal method got popular in point of care diagnostics because of its speed and sensitivity but requires pre-labelled primer or probes for a following detection of the amplicons. To overcome this disadvantages, we performed an labelling of RPA-amplicons with Cy5-dUTP without the need of pre-labelled primers. The amplification results of various multiple antibiotic resistance genes indicating great potential as a flexible and promising tool with high specific and sensitive detection capabilities of the target genes. After the determination of an appropriate rate of 1\% Cy5-dUTP and 99\% unlabelled dTTP we were able to detect the bla(CTX-M15) gene in less than 1.6E-03 ng genomic DNA corresponding to approximately 200 cfu of Escherichia coli cells in only 40 min amplification time.},
  language  = {en}
}
@article{TebbeOttensmannHavensteinetal.2022,
  author    = {Tebbe, Jonas and Ottensmann, Meinolf and Havenstein, Katja and Efstratiou, Artemis and Lenz, Tobias L. and Caspers, Barbara A. and Forcada, Jaume and Tiedemann, Ralph and Hoffman, Joseph},
  title     = {Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals},
  series = {Scientific reports},
  volume    = {12},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Nature Publishing Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-022-21658-7},
  pages     = {14},
  year      = {2022},
  abstract  = {The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.},
  language  = {en}
}
@article{LiYangSunetal.2021,
  author    = {Li, Xiaoxiao and Yang, Wei and Sun, Tao and Gaedke, Ursula},
  title     = {Quantitative food web structure and ecosystem functions in a warm-temperate seagrass bed},
  series = {Marine biology : international journal on life in oceans and coastal waters},
  volume    = {168},
  journal   = {Marine biology : international journal on life in oceans and coastal waters},
  number    = {5},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg},
  issn      = {0025-3162},
  doi       = {10.1007/s00227-021-03878-z},
  pages     = {17},
  year      = {2021},
  abstract  = {Seagrass beds are important habitats in coastal areas but increasingly decline in area and quality, thus conservation measures are urgently needed. Quantitative food webs, describing the biomass distribution and energy fluxes among trophic groups, reveal structural and functional aspects of ecosystems. Their knowledge can improve ecological conservation. For the recently discovered large warm-temperate seagrass (Zostera japonica) habitat in China's Yellow River Delta wetland, we used delta C-13 and delta N-15 measurements and a Bayesian isotope mixing model to construct its food web diagram with quantitative estimations of consumer diet compositions, comprising detritus and 14 living trophic groups from primary producers to fish. We then estimated the quantitative food web fluxes based on biomass measurements and calculated corresponding ecosystem functions. Pelagic producers were significantly C-13-depleted compared to benthic sources. Consumers (except zooplankton) were increasingly C-13-depleted with increasing trophic positions even though the consumed benthic production surpassed the pelagic one. Bivalves dominated consumer biomasses and fluxes and were the first to connect the pelagic and benthic pathways, whereas zooplankton and gastropods were specialized on the two pathways, respectively. We found flat biomass and production pyramids indicating low trophic transfer efficiencies. Generally, the energetic structure of the quantitative food web was consistent with the stable isotope analysis, and the estimated net primary production and most estimated production to biomass ratios of the trophic groups fell within literature ranges. This study provides a systematical understanding of the quantitative trophic ecology of a seagrass bed and facilitates synergistic knowledge on management, conservation, and restoration.},
  language  = {en}
}
@article{HebertHerzschuhLaepple2022,
  author    = {H{\´e}bert, Rapha{\"e}l and Herzschuh, Ulrike and Laepple, Thomas},
  title     = {Millennial-scale climate variability over land overprinted by ocean temperature fluctuations},
  series = {Nature geoscience},
  volume    = {15},
  journal   = {Nature geoscience},
  number    = {11},
  publisher = {Nature portfolio},
  address   = {Berlin},
  issn      = {1752-0894},
  doi       = {10.1038/s41561-022-01056-4},
  pages     = {899},
  year      = {2022},
  abstract  = {Variations in regional temperature have widespread implications for society, but our understanding of the amplitude and origin of long-term natural variability is insufficient for accurate regional projections. This is especially the case for terrestrial temperature variability, which is currently thought to be weak over long timescales. By performing spectral analysis on climate reconstructions, produced using sedimentary pollen records from the Northern Hemisphere over the last 8,000 years, coupled with instrumental data, we provide a comprehensive estimate of regional temperature variability from annual to millennial timescales. We show that short-term random variations are overprinted by strong ocean-driven climate variability on multi-decadal and longer timescales. This may cause substantial and potentially unpredictable regional climatic shifts in the coming century, in contrast to the relatively muted and homogeneous warming projected by climate models. Due to the marine influence, regions characterized by stable oceanic climate at sub-decadal timescales experience stronger long-term variability, and continental regions with higher sub-decadal variability show weaker long-term variability. This fundamental relationship between the timescales provides a unique insight into the emergence of a marine-driven low-frequency regime governing terrestrial climate variability and sets the basis to project the amplitude of temperature fluctuations on multi-decadal timescales and longer. Temperature variability over land is enhanced by ocean temperature fluctuations on millennial timescales, with implications for regional-scale climate change, according to an analysis of Northern Hemisphere proxy records and observations.},
  language  = {en}
}
@article{RuthsatzScherzVences2021,
  author    = {Ruthsatz, Katharina and Scherz, Mark D. and Vences, Miguel},
  title     = {Dissecting the tree of life},
  series = {Zootaxa : an international journal of zootaxonomy ;},
  volume    = {5016},
  journal   = {Zootaxa : an international journal of zootaxonomy ;},
  number    = {3},
  publisher = {Magnolia Press},
  address   = {Auckland},
  issn      = {1175-5326},
  doi       = {10.11646/zootaxa.5016.3.10},
  pages     = {448 -- 450},
  year      = {2021},
  language  = {en}
}
@article{LanghammerGrimm2020,
  author    = {Langhammer, Maria and Grimm, Volker},
  title     = {Mitigating bioenergy-driven biodiversity decline},
  series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog},
  volume    = {416},
  journal   = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3800},
  doi       = {10.1016/j.ecolmodel.2019.108914},
  pages     = {13},
  year      = {2020},
  abstract  = {The cultivation of energy crops leads to direct and indirect land use changes that impair the biodiversity of the agricultural landscape. In our study, we analyse the effects of mitigation measures on the European brown hare (Lepus europaeus), which is directly affected by ongoing land use change and has experienced widespread decline throughout Europe since the 1960s. Therefore, we developed a spatially explicit and individual-based ecological model to study the effects of different landscape configurations and compositions on hare population development. As an input, we used two 4 x 4 km large model landscapes, which were generated by a landscape generator based on real field sizes and crop proportions and differed in average field size and crop composition. The crops grown annually are evaluated in terms of forage suitability, breeding suitability and crop richness for the hare. In six mitigation scenarios, we investigated the effects of a 10 \% increase in the following measures: (1) mixed silphie, (2) miscanthus, (3) grass-clover ley, (4) alfalfa, (5) set-aside, and (6) general crop richness. All mitigation measures had significant effects on hare population development. Compared to the base scenario, the relative change in hare abundance ranged from a factor of 0.56 in the grass-clover ley scenario to-0.16 in the miscanthus scenario. The mitigation measures of mixed silphie, grass-clover ley and increased crop richness led to distinct increases in hare abundance in both landscapes ( > 0.3). The results show that both landscape configuration and composition have a significant effect on hare population development, which responds particularly strongly to compositional changes. The increase in crop diversity, e.g., through the cultivation of alternative energy crops such as mixed silphie and grass-clover ley, proves to be beneficial for the brown hare.},
  language  = {en}
}
@article{BaunachChowdhuryStallforthetal.2021,
  author    = {Baunach, Martin and Chowdhury, Somak and Stallforth, Pierre and Dittmann-Th{\"u}nemann, Elke},
  title     = {The landscape of recombination events that create nonribosomal peptide diversity},
  series = {Molecular biology and evolution : MBE},
  volume    = {38},
  journal   = {Molecular biology and evolution : MBE},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msab015},
  pages     = {2116 -- 2130},
  year      = {2021},
  abstract  = {Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing andmatching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the A(core) domains, yet domain interfaces and the flexible A(sub) domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.},
  language  = {en}
}
@article{SchaelickeHeimMartinCreuzburgetal.2020,
  author    = {Sch{\"a}licke, Svenja and Heim, Silvia and Martin-Creuzburg, Dominik and Wacker, Alexander},
  title     = {Inter- and intraspecific differences in rotifer fatty acid composition during acclimation to low-quality food},
  series = {Philosophical transactions of the Royal Society of London : B, Biological sciences},
  volume    = {375},
  journal   = {Philosophical transactions of the Royal Society of London : B, Biological sciences},
  number    = {1804},
  publisher = {Royal Society},
  address   = {London},
  issn      = {0962-8436},
  doi       = {10.1098/rstb.2019.0644},
  pages     = {8},
  year      = {2020},
  abstract  = {Biochemical food quality constraints affect the performance of consumers and mediate trait variation among and within consumer species. To assess inter- and intraspecific differences in fatty acid retention and conversion in freshwater rotifers, we provided four strains of two closely related rotifer species,Brachionus calyciflorussensustricto andBrachionus fernandoi, with food algae differing in their fatty acid composition. The rotifers grazed for 5 days on eitherNannochloropsis limneticaorMonoraphidium minutum, two food algae with distinct polyunsaturated fatty acid (PUFA) profiles, before the diets were switched to PUFA-freeSynechococcus elongatus, which was provided for three more days. We found between- and within-species differences in rotifer fatty acid compositions on the respective food sources and, in particular, highly specific acclimation reactions to the PUFA-free diet. The different reactions indicate inter- but also intraspecific differences in physiological traits, such as PUFA retention, allocation and bioconversion capacities, within the genusBrachionusthat are most likely accompanied by differences in their nutritional demands. Our data suggest that biochemical food quality constraints act differently on traits of closely related species and of strains of a particular species and thus might be involved in shaping ecological interactions and evolutionary processes. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.},
  language  = {en}
}
@article{SchneebergerRoederTaborsky2020,
  author    = {Schneeberger, Karin and R{\"o}der, Gregory and Taborsky, Michael},
  title     = {The smell of hunger},
  series = {PLoS biology},
  volume    = {18},
  journal   = {PLoS biology},
  number    = {3},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1544-9173},
  doi       = {10.1371/journal.pbio.3000628},
  pages     = {13},
  year      = {2020},
  abstract  = {When individuals exchange helpful acts reciprocally, increasing the benefit of the receiver can enhance its propensity to return a favour, as pay-offs are typically correlated in iterated interactions. Therefore, reciprocally cooperating animals should consider the relative benefit for the receiver when deciding to help a conspecific. Norway rats (Rattus norvegicus) exchange food reciprocally and thereby take into account both the cost of helping and the potential benefit to the receiver. By using a variant of the sequential iterated prisoner's dilemma paradigm, we show that rats may determine the need of another individual by olfactory cues alone. In an experimental food-exchange task, test subjects were provided with odour cues from hungry or satiated conspecifics located in a different room. Our results show that wild-type Norway rats provide help to a stooge quicker when they receive odour cues from a hungry rather than from a satiated conspecific. Using chemical analysis by gas chromatography-mass spectrometry (GC-MS), we identify seven volatile organic compounds that differ in their abundance between hungry and satiated rats. Combined, this "smell of hunger" can apparently serve as a reliable cue of need in reciprocal cooperation, which supports the hypothesis of honest signalling.},
  language  = {en}
}
@article{MunjonjiAyisiMudongoetal.2020,
  author    = {Munjonji, Lawrence and Ayisi, Kingsley Kwabena and Mudongo, Edwin I. and Mafeo, Tieho Paulus and Behn, Kai and Mokoka, Malesela Vincent and Linst{\"a}dter, Anja},
  title     = {Disentangling drought and grazing effects on soil carbon stocks and CO2 fluxes in a semi-arid African Savanna},
  series = {Frontiers in Environmental Science},
  volume    = {8},
  journal   = {Frontiers in Environmental Science},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-665X},
  doi       = {10.3389/fenvs.2020.590665},
  pages     = {14},
  year      = {2020},
  abstract  = {Grasslands cover ca. 30\% of the global land surface and provide critical ecosystem services. Among them, carbon storage is one of the most important. However, grasslands are increasingly threatened by drought and overgrazing which might negatively affect soil carbon stocks. Despite this threat, there is a dearth of information on how drought and grazing jointly impact soil carbon stocks and CO2 fluxes in dryland grasslands. With the aid of a large field experiment, we studied the combined effects of a 5-year extreme drought and moderate grazing on soil carbon stocks, CO2 fluxes and soil chemical properties. Extreme drought was induced by reducing ambient rainfall by 66\% using large rainout shelters. We found CO2 fluxes to strongly respond to the 5-year experimental drought. Extreme drought reduced CO2 emission rates by 32\% compared to ambient conditions. CO2 fluxes averaged 5.7 mg m(-2)min(-1) under drought compared to 8.3 mg m(-2) min(-1) under ambient conditions. CO2 fluxes were, however, not influenced by grazing. At the end of the growth period, grazed plots under ambient rainfall had released 16.3 tons of CO2 ha(-1) which was 58\% higher than observed on grazed plots subjected to severe drought. Soil carbon stocks were higher under drought conditions due to slower decomposition rates. Drought resulted in increased concentrations of primary macronutrients (N, P, and K), micronutrients (Zn and Mn) and pH in the top 30 cm of the soil relative to ambient conditions. The results also showed that grazing reduced the concentration of N and P in the topsoil compared to the ungrazed plots. This study provided insights on the soil carbon storage, CO2 emission rates and nutrient dynamics in a semi-arid dryland grassland as influenced by both drought and grazing. Our study also revealed that long-term extreme drought may be favorable in terms of preserving the existing soil carbon stocks through reduced CO2 release. This finding is critical for understanding future soil carbon dynamics in dryland grasslands in the face of climate change.},
  language  = {en}
}
@article{HuangHerzschuhPestryakovaetal.2020,
  author    = {Huang, Sichao and Herzschuh, Ulrike and Pestryakova, Luidmila Agafyevna and Zimmermann, Heike Hildegard and Davydova, Paraskovya and Biskaborn, Boris and Shevtsova, Iuliia and Stoof-Leichsenring, Kathleen Rosemarie},
  title     = {Genetic and morphologic determination of diatom community composition in surface sediments from glacial and thermokarst lakes in the Siberian Arctic},
  series = {Journal of paleolimnolog},
  volume    = {64},
  journal   = {Journal of paleolimnolog},
  number    = {3},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0921-2728},
  doi       = {10.1007/s10933-020-00133-1},
  pages     = {225 -- 242},
  year      = {2020},
  abstract  = {Lakes cover large parts of the climatically sensitive Arctic landscape and respond rapidly to environmental change. Arctic lakes have different origins and include the predominant thermokarst lakes, which are small, young and highly dynamic, as well as large, old and stable glacial lakes. Freshwater diatoms dominate the primary producer community in these lakes and can be used to detect biotic responses to climate and environmental change. We used specific diatom metabarcoding on sedimentary DNA, combined with next-generation sequencing and diatom morphology, to assess diatom diversity in five glacial and 15 thermokarst lakes within the easternmost expanse of the Siberian treeline ecotone in Chukotka, Russia. We obtained 163 verified diatom sequence types and identified 176 diatom species morphologically. Although there were large differences in taxonomic assignment using the two approaches, they showed similar high abundances and diversity of Fragilariceae and Aulacoseiraceae. In particular, the genetic approach detected hidden within-lake variations of fragilarioids in glacial lakes and dominance of centric Aulacoseira species, whereas Lindavia ocellata was predominant using morphology. In thermokarst lakes, sequence types and valve counts also detected high diversity of Fragilariaceae, which followed the vegetation gradient along the treeline. Ordination analyses of the genetic data from glacial and thermokarst lakes suggest that concentrations of sulfate (SO42-), an indicator of the activity of sulfate-reducing microbes under anoxic conditions, and bicarbonate (HCO3-), which relates to surrounding vegetation, have a significant influence on diatom community composition. For thermokarst lakes, we also identified lake depth as an important variable, but SO42- best explains diatom diversity derived from genetic data, whereas HCO3- best explains the data from valve counts. Higher diatom diversity was detected in glacial lakes, most likely related to greater lake age and different edaphic settings, which gave rise to diversification and endemism. In contrast, small, dynamic thermokarst lakes are inhabited by stress-tolerant fragilarioids and are related to different vegetation types along the treeline ecotone. Our study demonstrated that genetic investigations of lake sediments can be used to interpret climate and environmental responses of diatoms. It also showed how lake type affects diatom diversity, and that such genetic analyses can be used to track diatom community changes under ongoing warming in the Arctic.},
  language  = {en}
}
@article{LyallNikoloskiGechev2020,
  author    = {Lyall, Rafe and Nikoloski, Zoran and Gechev, Tsanko},
  title     = {Comparative analysis of ROS network genes in extremophile Eukaryotes},
  series = {International journal of molecular sciences},
  volume    = {21},
  journal   = {International journal of molecular sciences},
  number    = {23},
  publisher = {Molecular Diversity Preservation International (MDPI)},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms21239131},
  pages     = {27},
  year      = {2020},
  abstract  = {The reactive oxygen species (ROS) gene network, consisting of both ROS-generating and detoxifying enzymes, adjusts ROS levels in response to various stimuli. We performed a cross-kingdom comparison of ROS gene networks to investigate how they have evolved across all Eukaryotes, including protists, fungi, plants and animals. We included the genomes of 16 extremotolerant Eukaryotes to gain insight into ROS gene evolution in organisms that experience extreme stress conditions. Our analysis focused on ROS genes found in all Eukaryotes (such as catalases, superoxide dismutases, glutathione reductases, peroxidases and glutathione peroxidase/peroxiredoxins) as well as those specific to certain groups, such as ascorbate peroxidases, dehydroascorbate/monodehydroascorbate reductases in plants and other photosynthetic organisms. ROS-producing NADPH oxidases (NOX) were found in most multicellular organisms, although several NOX-like genes were identified in unicellular or filamentous species. However, despite the extreme conditions experienced by extremophile species, we found no evidence for expansion of ROS-related gene families in these species compared to other Eukaryotes. Tardigrades and rotifers do show ROS gene expansions that could be related to their extreme lifestyles, although a high rate of lineage-specific horizontal gene transfer events, coupled with recent tetraploidy in rotifers, could explain this observation. This suggests that the basal Eukaryotic ROS scavenging systems are sufficient to maintain ROS homeostasis even under the most extreme conditions.},
  language  = {en}
}
@article{SteppertSteppertBollingeretal.2020,
  author    = {Steppert, Claus and Steppert, Isabel and Bollinger, Thomas and Sterlacci, William},
  title     = {Rapid non-invasive detection of Influenza-A-infection by multicapillary column coupled ion mobility spectrometry},
  series = {Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR)},
  volume    = {15},
  journal   = {Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR)},
  number    = {1},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1752-7163},
  doi       = {10.1088/1752-7163/abb762},
  pages     = {5},
  year      = {2020},
  abstract  = {Infectious pathogens are a global issue. Global air travel offers an easy and fast opportunity not only for people but also for infectious diseases to spread around the world within a few days. Also, large public events facilitate increasing infection numbers. Therefore, rapid on-site screening for infected people is urgently needed. Due to the small size and easy handling, ion mobility spectrometry coupled with a multicapillary column (MCC-IMS) is a very promising, sensitive method for the on-site identification of infectious pathogens based on scents, representing volatile organic compounds (VOCs). The purpose of this study was to prospectively assess whether identification of Influenza-A-infection based on VOCs by MCC-IMS is possible in breath. Nasal breath was investigated in 24 consecutive persons with and without Influenza-A-infection by MCC-IMS. In 14 Influenza-A-infected patients, infection was proven by PCR of nasopharyngeal swabs. Four healthy staff members and six patients with negative PCR result served as controls. For picking up relevant VOCs in MCC-IMS spectra, software based on cluster analysis followed by multivariate statistical analysis was applied. With only four VOCs canonical discriminant analysis was able to distinguish Influenza-A-infected patients from those not infected with 100\% sensitivity and 100\% specificity. This present proof-of-concept-study yields encouraging results showing a rapid diagnosis of viral infections in nasal breath within 5 min by MCC-IMS. The next step is to validate the results with a greater number of patients with Influenza-A-infection as well as other viral diseases, especially COVID-19. Registration number at ClinicalTrials.gov NCT04282135.},
  language  = {en}
}
@article{NguyenMamonekeneVateretal.2020,
  author    = {Nguyen, Manh Duy Linh and Mamonekene, Victor and Vater, Marianne and Bartsch, Peter and Tiedemann, Ralph and Kirschbaum, Frank},
  title     = {Ontogeny of electric organ and electric organ discharge in Campylomormyrus rhynchophorus (Teleostei: Mormyridae)},
  series = {Journal of comparative physiology; A, Neuroethology, sensory, neural, and behavioral physiology},
  volume    = {206},
  journal   = {Journal of comparative physiology; A, Neuroethology, sensory, neural, and behavioral physiology},
  number    = {3},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg},
  issn      = {0340-7594},
  doi       = {10.1007/s00359-020-01411-z},
  pages     = {453 -- 466},
  year      = {2020},
  abstract  = {The aim of this study was a longitudinal description of the ontogeny of the adult electric organ of Campylomormyrus rhynchophorus which produces as adult an electric organ discharge of very long duration (ca. 25 ms). We could indeed show (for the first time in a mormyrid fish) that the electric organ discharge which is first produced early during ontogeny in 33-mm-long juveniles is much shorter in duration and has a different shape than the electric organ discharge in 15-cm-long adults. The change from this juvenile electric organ discharges into the adult electric organ discharge takes at least a year. The increase in electric organ discharge duration could be causally linked to the development of surface evaginations, papillae, at the rostral face of the electrocyte which are recognizable for the first time in 65-mm-long juveniles and are most prominent at the periphery of the electrocyte.},
  language  = {en}
}
@article{ZimmermannStoofLeichsenringKruseetal.2020,
  author    = {Zimmermann, Heike Hildegard and Stoof-Leichsenring, Kathleen Rosemarie and Kruse, Stefan and M{\"u}ller, Juliane and Stein, Ruediger and Tiedemann, Ralf and Herzschuh, Ulrike},
  title     = {Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30 000 years},
  series = {Ocean science},
  volume    = {16},
  journal   = {Ocean science},
  number    = {5},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1812-0784},
  doi       = {10.5194/os-16-1017-2020},
  pages     = {1017 -- 1032},
  year      = {2020},
  abstract  = {The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are scarce, rarely exceed the Holocene, and contain sparse information about past richness and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA (sedaDNA) metabarcoding. Amplifying a short, partial rbcL marker from samples of sediment core MSM05/5-712-2 resulted in 95.7\% of our sequences being assigned to diatoms across 18 different families, with 38.6\% of them being resolved to species and 25.8\% to genus level. Independent replicates show a high similarity of PCR products, especially in the oldest samples. Diatom sedaDNA richness is highest in the Late Weichselian and lowest in Mid- and Late Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice-associated diatoms and suggests several reorganisations - after the Last Glacial Maximum, after the Younger Dryas, and after the Early and after the Mid-Holocene. Different sequences assigned to, amongst others, Chaetoceros socialis indicate the detectability of intra-specific diversity using sedaDNA. We detect no clear pattern between our diatom sedaDNA record and the previously published IP25 record of this core, although proportions of pennate diatoms increase with higher IP25 concentrations and proportions of Nitzschia cf. frigida exceeding 2\% of the assemblage point towards past sea-ice presence.},
  language  = {en}
}
@article{KoekerAkcaalanDittmannetal.2021,
  author    = {K{\"o}ker, Latife and Ak{\c{c}}aalan, Reyhan and Dittmann, Elke and Albay, Meri{\c{c}}},
  title     = {Depth profiles of protein-bound microcystin in K{\"u}{\c{c}}{\"u}k{\c{c}}ekmece Lagoon},
  series = {Toxicon : an international journal devoted to the exchange of knowledge on the poisons derived from the tissues of plants and animals ; official journal of the International Society on Toxinology},
  volume    = {198},
  journal   = {Toxicon : an international journal devoted to the exchange of knowledge on the poisons derived from the tissues of plants and animals ; official journal of the International Society on Toxinology},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0041-0101},
  doi       = {10.1016/j.toxicon.2021.05.005},
  pages     = {156 -- 163},
  year      = {2021},
  abstract  = {Microcystis is the most commonly found toxic cyanobacterial genus around the world and has a negative impact on the ecosystem. As a predominant producer of the potent hepatotoxin microcystin (MC), the genus causes outbreaks in freshwaters worldwide. Standard analytical methods that are used for the detection of microcystin variants can only measure the free form of microcystin in cells. Since microcystin was found as free and proteinbound forms in the cells, a significant proportion of microcystin is underestimated with analytical methods. The aim of the study was to measure protein-bound microcystins and determine the environmental factors that affect the binding of microcystin to proteins. Samples were taken at depths of surface, 1 m, 5 m, 10 m, 15 m, and 18 m in Kucukcekmece Lagoon to analyze depth profiles of two different microcystin forms from June to September 2012 at regular monthly intervals. Our findings suggest that the most important parameter affecting proteinbound microcystin at surface water is high light. Due to favorable environmental conditions such as temperature, light, and physicochemical parameters, the higher microcystin contents, both free and protein-bound MCs, were found in summer periods.},
  language  = {en}
}
@article{PriesRazaghiMoghadamKopkaetal.2021,
  author    = {Pries, Christopher and Razaghi-Moghadam, Zahra and Kopka, Joachim and Nikoloski, Zoran},
  title     = {Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-84114-y},
  pages     = {12},
  year      = {2021},
  abstract  = {Ribosome biogenesis is tightly associated to plant metabolism due to the usage of ribosomes in the synthesis of proteins necessary to drive metabolic pathways. Given the central role of ribosome biogenesis in cell physiology, it is important to characterize the impact of different components involved in this process on plant metabolism. Double mutants of the Arabidopsis thaliana cytosolic 60S maturation factors REIL1 and REIL2 do not resume growth after shift to moderate 10 degrees C chilling conditions. To gain mechanistic insights into the metabolic effects of this ribosome biogenesis defect on metabolism, we developed TC-iReMet2, a constraint-based modelling approach that integrates relative metabolomics and transcriptomics time-course data to predict differential fluxes on a genome-scale level. We employed TC-iReMet2 with metabolomics and transcriptomics data from the Arabidopsis Columbia 0 wild type and the reil1-1 reil2-1 double mutant before and after cold shift. We identified reactions and pathways that are highly altered in a mutant relative to the wild type. These pathways include the Calvin-Benson cycle, photorespiration, gluconeogenesis, and glycolysis. Our findings also indicated differential NAD(P)/NAD(P)H ratios after cold shift. TC-iReMet2 allows for mechanistic hypothesis generation and interpretation of system biology experiments related to metabolic fluxes on a genome-scale level.},
  language  = {en}
}
@article{RoedelAbdelilahSeyfried2021,
  author    = {R{\"o}del, Claudia Jasmin and Abdelilah-Seyfried, Salim},
  title     = {A zebrafish toolbox for biomechanical signaling in cardiovascular development and disease},
  series = {Current opinion in hematology},
  volume    = {28},
  journal   = {Current opinion in hematology},
  number    = {3},
  publisher = {Lippincott Williams \& Wilkins},
  address   = {Philadelphia},
  issn      = {1065-6251},
  doi       = {10.1097/MOH.0000000000000648},
  pages     = {198 -- 207},
  year      = {2021},
  abstract  = {Purpose of review The zebrafish embryo has emerged as a powerful model organism to investigate the mechanisms by which biophysical forces regulate vascular and cardiac cell biology during development and disease. A versatile arsenal of methods and tools is available to manipulate and analyze biomechanical signaling. This review aims to provide an overview of the experimental strategies and tools that have been utilized to study biomechanical signaling in cardiovascular developmental processes and different vascular disease models in the zebrafish embryo. Within the scope of this review, we focus on work published during the last two years. Recent findings Genetic and pharmacological tools for the manipulation of cardiac function allow alterations of hemodynamic flow patterns in the zebrafish embryo and various types of transgenic lines are available to report endothelial cell responses to biophysical forces. These tools have not only revealed the impact of biophysical forces on cardiovascular development but also helped to establish more accurate models for cardiovascular diseases including cerebral cavernous malformations, hereditary hemorrhagic telangiectasias, arteriovenous malformations, and lymphangiopathies. Summary The zebrafish embryo is a valuable vertebrate model in which in-vivo manipulations of biophysical forces due to cardiac contractility and blood flow can be performed. These analyses give important insights into biomechanical signaling pathways that control endothelial and endocardial cell behaviors. The technical advances using this vertebrate model will advance our understanding of the impact of biophysical forces in cardiovascular pathologies.},
  language  = {en}
}
@article{FloederYongKlauschiesetal.2021,
  author    = {Fl{\"o}der, Sabine and Yong, Joanne and Klauschies, Toni and Gaedke, Ursula and Poprick, Tobias and Brinkhoff, Thorsten and Moorthi, Stefanie},
  title     = {Intraspecific trait variation alters the outcome of competition in freshwater ciliates},
  series = {Ecology and evolution},
  volume    = {11},
  journal   = {Ecology and evolution},
  number    = {15},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.7828},
  pages     = {10225 -- 10243},
  year      = {2021},
  abstract  = {Trait variation among heterospecific and conspecific organisms may substantially affect community and food web dynamics. While the relevance of competition and feeding traits have been widely studied for different consumer species, studies on intraspecific differences are more scarce, partly owing to difficulties in distinguishing different clones of the same species. Here, we investigate how intraspecific trait variation affects the competition between the freshwater ciliates Euplotes octocarinatus and Coleps hirtus in a nitrogen-limited chemostat system. The ciliates competed for the microalgae Cryptomonas sp. (Cry) and Navicula pelliculosa (Nav), and the bacteria present in the cultures over a period of 33 days. We used monoclonal Euplotes and three different Coleps clones (Col 1, Col 2, and Col 3) in the experiment that could be distinguished by a newly developed rDNA-based molecular assay based on the internal transcribed spacer (ITS) regions. While Euplotes feeds on Cry and on bacteria, the Coleps clones cannot survive on bacteria alone but feed on both Cry and Nav with clone-specific rates. Experimental treatments comprised two-species mixtures of Euplotes and one or all of the three different Coleps clones, respectively. We found intraspecific variation in the traits "selectivity" and "maximum ingestion rate" for the different algae to significantly affect the competitive outcome between the two ciliate species. As Nav quickly escaped top-down control and likely reached a state of low food quality, ciliate competition was strongly determined by the preference of different Coleps clones for Cry as opposed to feeding on Nav. In addition, the ability of Euplotes to use bacteria as an alternative food source strengthened its persistence once Cry was depleted. Hence, trait variation at both trophic levels codetermined the population dynamics and the outcome of species competition.},
  language  = {en}
}
@article{SchneebergerEccard2021,
  author    = {Schneeberger, Karin and Eccard, Jana},
  title     = {Experience of social density during early life is associated with attraction to conspecific odour in the common vole (Microtus arvalis)},
  series = {Ethology : international journal of behavioural biology},
  volume    = {127},
  journal   = {Ethology : international journal of behavioural biology},
  number    = {10},
  publisher = {Wiley-Blackwell},
  address   = {Berlin},
  issn      = {0179-1613},
  doi       = {10.1111/eth.13211},
  pages     = {908 -- 913},
  year      = {2021},
  abstract  = {Social organisation in species with fluctuating population sizes can change with density. Therefore, information on (future) density obtained during early life stages may be associated with social behaviour. Olfactory cues may carry important social information. We investigated whether early life experience of different experimental densities was subsequently associated with differences in attraction to adult conspecific odours. We used common voles (Microtus arvalis), a rodent species undergoing extreme density fluctuations. We found that individuals originating from high experimental density populations kept in large outdoor enclosures invested more time in inspecting conspecific olfactory cues than individuals from low-density populations. Generally, voles from both treatments spent more time with the olfactory cues than expected by chance and did not differ in their latency to approach the odour samples. Our findings indicate either that early experience affects odour sensitivity or that animals evaluate the social information contained in conspecific odours differently, depending on their early life experience of conspecific density.},
  language  = {en}
}
@article{OrzechowskiSitnickaGrabowskaetal.2021,
  author    = {Orzechowski, Slawomir and Sitnicka, Dorota and Grabowska, Agnieszka and Compart, Julia and Fettke, J{\"o}rg and Zdunek-Zastocka, Edyta},
  title     = {Effect of short-term cold treatment on carbohydrate metabolism in potato leaves},
  series = {International journal of molecular sciences},
  volume    = {22},
  journal   = {International journal of molecular sciences},
  number    = {13},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms22137203},
  pages     = {17},
  year      = {2021},
  abstract  = {Plants are often challenged by an array of unfavorable environmental conditions. During cold exposure, many changes occur that include, for example, the stabilization of cell membranes, alterations in gene expression and enzyme activities, as well as the accumulation of metabolites. In the presented study, the carbohydrate metabolism was analyzed in the very early response of plants to a low temperature (2 degrees C) in the leaves of 5-week-old potato plants of the Russet Burbank cultivar during the first 12 h of cold treatment (2 h dark and 10 h light). First, some plant stress indicators were examined and it was shown that short-term cold exposure did not significantly affect the relative water content and chlorophyll content (only after 12 h), but caused an increase in malondialdehyde concentration and a decrease in the expression of NDA1, a homolog of the NADH dehydrogenase gene. In addition, it was shown that the content of transitory starch increased transiently in the very early phase of the plant response (3-6 h) to cold treatment, and then its decrease was observed after 12 h. In contrast, soluble sugars such as glucose and fructose were significantly increased only at the end of the light period, where a decrease in sucrose content was observed. The availability of the monosaccharides at constitutively high levels, regardless of the temperature, may delay the response to cold, involving amylolytic starch degradation in chloroplasts. The decrease in starch content, observed in leaves after 12 h of cold exposure, was preceded by a dramatic increase in the transcript levels of the key enzymes of starch degradation initiation, the alpha-glucan, water dikinase (GWD-EC 2.7.9.4) and the phosphoglucan, water dikinase (PWD-EC 2.7.9.5). The gene expression of both dikinases peaked at 9 h of cold exposure, as analyzed by real-time PCR. Moreover, enhanced activities of the acid invertase as well as of both glucan phosphorylases during exposure to a chilling temperature were observed. However, it was also noticed that during the light phase, there was a general increase in glucan phosphorylase activities for both control and cold-stressed plants irrespective of the temperature. In conclusion, a short-term cold treatment alters the carbohydrate metabolism in the leaves of potato, which leads to an increase in the content of soluble sugars.},
  language  = {en}
}
@article{KuekenWenderingLangaryetal.2021,
  author    = {K{\"u}ken, Anika and Wendering, Philipp and Langary, Damoun and Nikoloski, Zoran},
  title     = {A structural property for reduction of biochemical networks},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-96835-1},
  pages     = {11},
  year      = {2021},
  abstract  = {Large-scale biochemical models are of increasing sizes due to the consideration of interacting organisms and tissues. Model reduction approaches that preserve the flux phenotypes can simplify the analysis and predictions of steady-state metabolic phenotypes. However, existing approaches either restrict functionality of reduced models or do not lead to significant decreases in the number of modelled metabolites. Here, we introduce an approach for model reduction based on the structural property of balancing of complexes that preserves the steady-state fluxes supported by the network and can be efficiently determined at genome scale. Using two large-scale mass-action kinetic models of Escherichia coli, we show that our approach results in a substantial reduction of 99\% of metabolites. Applications to genome-scale metabolic models across kingdoms of life result in up to 55\% and 85\% reduction in the number of metabolites when arbitrary and mass-action kinetics is assumed, respectively. We also show that predictions of the specific growth rate from the reduced models match those based on the original models. Since steady-state flux phenotypes from the original model are preserved in the reduced, the approach paves the way for analysing other metabolic phenotypes in large-scale biochemical networks.},
  language  = {en}
}
@article{WuestenhagenLukasMuelleretal.2020,
  author    = {W{\"u}stenhagen, Doreen Anja and Lukas, Phil and M{\"u}ller, Christian and Aubele, Simone A. and Hildebrandt, Jan-Peter and Kubick, Stefan},
  title     = {Cell-free synthesis of the hirudin variant 1 of the blood-sucking leech Hirudo medicinalis},
  series = {Scientific reports},
  volume    = {10},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-020-76715-w},
  pages     = {13},
  year      = {2020},
  abstract  = {Synthesis and purification of peptide drugs for medical applications is a challenging task. The leech-derived factor hirudin is in clinical use as an alternative to heparin in anticoagulatory therapies. So far, recombinant hirudin is mainly produced in bacterial or yeast expression systems. We describe the successful development and application of an alternative protocol for the synthesis of active hirudin based on a cell-free protein synthesis approach. Three different cell lysates were compared, and the effects of two different signal peptide sequences on the synthesis of mature hirudin were determined. The combination of K562 cell lysates and the endogenous wild-type signal peptide sequence was most effective. Cell-free synthesized hirudin showed a considerably higher anti-thrombin activity compared to recombinant hirudin produced in bacterial cells.},
  language  = {en}
}
@article{SeepRazaghiMoghadamNikoloski2021,
  author    = {Seep, Lea and Razaghi-Moghadam, Zahra and Nikoloski, Zoran},
  title     = {Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-87643-8},
  pages     = {11},
  year      = {2021},
  abstract  = {Thermodynamic metabolic flux analysis (TMFA) can narrow down the space of steady-state flux distributions, but requires knowledge of the standard Gibbs free energy for the modelled reactions. The latter are often not available due to unknown Gibbs free energy change of formation ,Delta fG0, of metabolites. To optimize the usage of data on thermodynamics in constraining a model, reaction lumping has been proposed to eliminate metabolites with unknown Delta fG0. However, the lumping procedure has not been formalized nor implemented for systematic identification of lumped reactions. Here, we propose, implement, and test a combined procedure for reaction lumping, applicable to genome-scale metabolic models. It is based on identification of groups of metabolites with unknown Delta fG0 whose elimination can be conducted independently of the others via: (1) group implementation, aiming to eliminate an entire such group, and, if this is infeasible, (2) a sequential implementation to ensure that a maximal number of metabolites with unknown Delta fG0 are eliminated. Our comparative analysis with genome-scale metabolic models of Escherichia coli, Bacillus subtilis, and Homo sapiens shows that the combined procedure provides an efficient means for systematic identification of lumped reactions. We also demonstrate that TMFA applied to models with reactions lumped according to the proposed procedure lead to more precise predictions in comparison to the original models. The provided implementation thus ensures the reproducibility of the findings and their application with standard TMFA.},
  language  = {en}
}
@article{EnzingmuellerPrechtl2021,
  author    = {Enzingm{\"u}ller, Carolin and Prechtl, Helmut},
  title     = {Constructing graphs in biology class},
  series = {International journal of science and mathematics education},
  volume    = {19},
  journal   = {International journal of science and mathematics education},
  number    = {1},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1571-0068},
  doi       = {10.1007/s10763-019-09975-2},
  pages     = {1 -- 19},
  year      = {2021},
  abstract  = {There has been a growing awareness that graphing is an essential part of the science curriculum. While much research has focused on student conceptions and abilities regarding graphical representations, only few studies have investigated what teachers think about them and how they use graphs in science class. The purpose of this study is to explore educational beliefs, motivation, and teaching practices of German secondary biology teachers regarding graph construction. Via questionnaire surveys, 71 teachers from different regions in Germany rated their beliefs and motivation as well as the frequency of different graph construction activities in biology class. The teachers surveyed in this study were quite motivated in their teaching of graph construction. Furthermore, they tended to believe that graph construction should be practiced explicitly in biology class and that students should learn clear strategies for constructing graphs. We found that teaching subjects and own research experience make a difference in teachers' beliefs and motivation regarding graph construction in biology class. The self-report on classroom practices revealed that participants may provide limited opportunities for students to experience graphing as a social and iterative practice. Implications are drawn for teacher education and professional development as well as for further research in teacher education contexts.},
  language  = {en}
}
@article{TaguchiGotoMatsuokaetal.2023,
  author    = {Taguchi, Mioko and Goto, Mutsuo and Matsuoka, Koji and Tiedemann, Ralph and Pastene, Luis A.},
  title     = {Population genetic structure of Bryde's whales (Balaenoptera brydei) on the central and western North Pacific feeding grounds},
  series = {Canadian Journal of Fisheries and Aquatic Sciences},
  volume    = {80},
  journal   = {Canadian Journal of Fisheries and Aquatic Sciences},
  number    = {1},
  publisher = {Canadian science publishing},
  address   = {Ottawa},
  issn      = {0706-652X},
  doi       = {10.1139/cjfas-2022-0005},
  pages     = {142 -- 155},
  year      = {2023},
  abstract  = {The genetic structure of Bryde's whale (Balaenoptera brydei) on the central and western North Pacific feeding grounds was investigated using a total of 1195 mitochondrial control region sequences and 1182 microsatellite genotypes at 17 loci in specimens collected from three longitudinal areas, 1W (135 degrees E-165 degrees E), 1E (165 degrees E-180 degrees), and 2 (180 degrees-155 degrees W). Genetic diversities were similar among areas and a haplotype network did not show any geographic structure, while an analysis of molecular variance found evidence of genetic structure in this species. Pairwise FST and G'ST estimates and heterogeneity tests attributed this structure to weak but significant differentiation between areas 1W/1E and 2. A Mantel test and a high-resolution analysis of genetic diversity statistics showed a weak spatial cline of genetic differentiation. These findings could be reconciled by two possible stock structure scenarios: (1) a single population with kin-association affecting feeding ground preference and (2) two populations with feeding ground preference for either area 1W or area 2. An estimated dispersal rate between areas 1W and 2 indicates that both scenarios should be considered as a precautionary principle in stock assessments.},
  language  = {en}
}
@article{SteppertSteppertSterlaccietal.2021,
  author    = {Steppert, Claus and Steppert, Isabel and Sterlacci, William and Bollinger, Thomas},
  title     = {Rapid detection of SARS-CoV-2 infection by multicapillary column coupled ion mobility spectrometry (MCC-IMS) of breath},
  series = {Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR)},
  volume    = {15},
  journal   = {Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR)},
  number    = {2},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1752-7163},
  doi       = {10.1088/1752-7163/abe5ca},
  pages     = {8},
  year      = {2021},
  abstract  = {There is an urgent need for screening of patients with a communicable viral disease to cut infection chains. Recently, we demonstrated that ion mobility spectrometry coupled with a multicapillary column (MCC-IMS) is able to identify influenza-A infections in patients' breath. With a decreasing influenza epidemic and upcoming SARS-CoV-2 infections we proceeded further and analyzed patients with suspected SARS-CoV-2 infections. In this study, the nasal breath of 75 patients (34 male, 41 female, aged 64.4 +/- 15.4 years) was investigated by MCC-IMS for viral infections. Fourteen were positively diagnosed with influenza-A infection and sixteen with SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) of nasopharyngeal swabs. In one patient RT-PCR was highly suspicious of SARS-CoV-2 but initially inconclusive. The remaining 44 patients served as controls. Breath fingerprints for specific infections were assessed by a combination of cluster analysis and multivariate statistics. There were no significant differences in gender or age according to the groups. In the cross validation of the discriminant analysis 72 of the 74 clearly defined patients could be correctly classified to the respective group. Even the inconclusive patient could be mapped to the SARS-CoV-2 group by applying the discrimination functions. Conclusion: SARS-CoV-2 infection and influenza-A infection can be detected with the help of MCC-IMS in breath in this pilot study. As this method provides a fast non-invasive diagnosis it should be further developed in a larger cohort for screening of communicable viral diseases. A validation study is ongoing during the second wave of COVID-19. Trial registration: ClinicalTrial.gov, NCT04282135 Registered 20 February 2020-Retrospectively registered,},
  language  = {en}
}
@article{EilersKleineEckertetal.2021,
  author    = {Eilers, Elisabeth Johanna and Kleine, Sandra and Eckert, Silvia and Waldherr, Simon and M{\"u}ller, Caroline},
  title     = {Flower production, headspace volatiles, pollen nutrients, and florivory in tanacetum vulgare chemotypes},
  series = {Frontiers in plant science : FPLS},
  volume    = {11},
  journal   = {Frontiers in plant science : FPLS},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2020.611877},
  pages     = {17},
  year      = {2021},
  abstract  = {Floral volatiles and reward traits are major drivers for the behavior of mutualistic as well as antagonistic flower visitors, i.e., pollinators and florivores. These floral traits differ tremendously between species, but intraspecific differences and their consequences on organism interactions remain largely unknown. Floral volatile compounds, such as terpenoids, function as cues to advertise rewards to pollinators, but should at the same time also repel florivores. The reward composition, e.g., protein and lipid contents in pollen, differs between individuals of distinct plant families. Whether the nutritional value of rewards within the same plant species is linked to their chemotypes, which differ in their pattern of specialized metabolites, has yet not been investigated. In the present study, we compared Tanacetum vulgare plants of five terpenoid chemotypes with regard to flower production, floral headspace volatiles, pollen macronutrient and terpenoid content, and floral attractiveness to florivorous beetles. Our analyses revealed remarkable differences between the chemotypes in the amount and diameter of flower heads, duration of bloom period, and pollen nutritional quality. The floral headspace composition of pollen-producing mature flowers, but not of premature flowers, was correlated to that of pollen and leaves in the same plant individual. For two chemotypes, florivorous beetles discriminated between the scent of mature and premature flower heads and preferred the latter. In semi-field experiments, the abundance of florivorous beetles and flower tissue miners differed between T. vulgare chemotypes. Moreover, the scent environment affected the choice and beetles were more abundant in homogenous plots composed of one single chemotype than in plots with different neighboring chemotypes. In conclusion, flower production, floral metabolic composition and pollen quality varied to a remarkable extend within the species T. vulgare, and the attractiveness of floral scent differed also intra-individually with floral ontogeny. We found evidence for a trade-off between pollen lipid content and pollen amount on a per-plant-level. Our study highlights that chemotypes which are more susceptible to florivory are less attacked when they grow in the neighborhood of other chemotypes and thus gain a benefit from high overall chemodiversity.},
  language  = {en}
}
@article{RoeslerSchefflerHermanussen2023,
  author    = {R{\"o}sler, Antonia and Scheffler, Christiane and Hermanussen, Michael},
  title     = {No evidence of growth impairment after forced migration in Polish school children after World War II},
  series = {Human biology and public health},
  volume    = {1},
  journal   = {Human biology and public health},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph2023.1.68},
  pages     = {8},
  year      = {2023},
  abstract  = {Background: Migration is omnipresent. It can come hand in hand with emotional stress which is known to influence the growth of children. Objective: The aim of this study was to analyse whether type of migration (forced or voluntary) and the geographic direction had influenced the growth of Polish children after World War II. Sample and Methods: A sub dataset of 2,208 individuals between the ages of 2-20, created from data of the 2nd Polish Anthropological Survey carried out in 1966-1969, including anthropometrical data and social and demographic information based on questionnaire, was used to analyse migration effects. Results: No association could be found between the direction of migration and the height of the children. The confidence intervals of the means of all classified migration categories overlap significantly and the effect size of the influence of migration category on height is ds=.140, which is too low to see any effects, even if there were one. Conclusion: Neither forced nor voluntary migration in Poland after World War II led to a change in height in children of migrating families.},
  language  = {en}
}
@article{HakeBodenbergerGroth2023,
  author    = {Hake, Tim and Bodenberger, Bernhard and Groth, Detlef},
  title     = {In Python available: St. Nicolas House Algorithm (SNHA) with bootstrap support for improved performance in dense networks},
  series = {Human biology and public health},
  volume    = {1},
  journal   = {Human biology and public health},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph2023.1.63},
  pages     = {16},
  year      = {2023},
  abstract  = {The St. Nicolas House Algorithm (SNHA) finds association chains of direct dependent variables in a data set. The dependency is based on the correlation coefficient, which is visualized as an undirected graph. The network prediction is improved by a bootstrap routine. It enables the computation of the empirical p-value, which is used to evaluate the significance of the predicted edges. Synthetic data generated with the Monte Carlo method were used to firstly compare the Python package with the original R package, and secondly to evaluate the predicted network using the sensitivity, specificity, balanced classification rate and the Matthew's correlation coefficient (MCC). The Python implementation yields the same results as the R package. Hence, the algorithm was correctly ported into Python. The SNHA scores high specificity values for all tested graphs. For graphs with high edge densities, the other evaluation metrics decrease due to lower sensitivity, which could be partially improved by using bootstrap,while for graphs with low edge densities the algorithm achieves high evaluation scores. The empirical p-values indicated that the predicted edges indeed are significant.},
  language  = {en}
}
@article{GasparatosSchefflerHermanussen2023,
  author    = {Gasparatos, Nikolaos and Scheffler, Christiane and Hermanussen, Michael},
  title     = {Assessing the applicability of changepoint analysis to analyse short-term growth},
  series = {Human biology and public health},
  volume    = {1},
  journal   = {Human biology and public health},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph2023.1.62},
  pages     = {15},
  year      = {2023},
  abstract  = {Background: Assessing short-term growth in humans is still fraught with difficulties. Especially when looking for small variations and increments, such as mini growth spurts, high precision instruments or frequent measurements are necessary. Daily measurements however require a lot of effort, both for anthropologists and for the subjects. Therefore, new sophisticated approaches are needed that reduce fluctuations and reveal underlying patterns. Objectives: Changepoints are abrupt variations in the properties of time series data. In the context of growth, such variations could be variation in mean height. By adjusting the variance and using different growth models, we assessed the ability of changepoint analysis to analyse short-term growth and detect mini growth spurts. Sample and Methods: We performed Bayesian changepoint analysis on simulated growth data using the bcp package in R. Simulated growth patterns included stasis, linear growth, catch-up growth, and mini growth spurts. Specificity and a normalised variant of the Matthews correlation coefficient (MCC) were used to assess the algorithm's performance. Welch's t-test was used to compare differences of the mean. Results: First results show that changepoint analysis can detect mini growth spurts. However, the ability to detect mini growth spurts is highly dependent on measurement error. Data preparation, such as ranking and rotating time series data, showed negligible improvements. Missing data was an issue and may affect the prediction quality of the classification metrics. Conclusion: Changepoint analysis is a promising tool to analyse short-term growth. However, further optimisation and analysis of real growth data is needed to make broader generalisations.},
  language  = {en}
}
@article{GrothSchefflerHermanussen2023,
  author    = {Groth, Detlef and Scheffler, Christiane and Hermanussen, Michael},
  title     = {Human growth data analysis and statistics - the 5th G{\"u}lpe International Student Summer School},
  series = {Human biology and public health},
  volume    = {1},
  journal   = {Human biology and public health},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph2023.1.70},
  pages     = {5},
  year      = {2023},
  abstract  = {The Summer School in G{\"u}lpe (Ecological Station of the University of Potsdam) offers an exceptional learning opportunity for students to apply their knowledge and skills to real-world problems. With the guidance of experienced human biologists, statisticians, and programmers, students have the unique chance to analyze their own data and gain valuable insights. This interdisciplinary setting not only bridges different research areas but also leads to highly valuable outputs. The progress of students within just a few days is truly remarkable, especially when they are motivated and receive immediate feedback on their questions, problems, and results. The Summer School covers a wide range of topics, with this year's focus mainly on two areas: understanding the impact of socioeconomic and physiological factors on human development and mastering statistical techniques for analyzing data such as changepoint analysis and the St. Nicolas House Analysis (SNHA) to visualize interacting variables. The latter technique, born out of the Summer School's emphasis on gaining comprehensive data insights and understanding major relationships, has proven to be a valuable tool for researchers in the field. The articles in this special issue demonstrate that the Summer School in G{\"u}lpe stands as a testament to the power of practical learning and collaboration. Students who attend not only gain hands-on experience but also benefit from the expertise of professionals and the opportunity to engage with peers from diverse disciplines.},
  language  = {en}
}
@article{HermanussenSchefflerPulunganetal.2023,
  author    = {Hermanussen, Michael and Scheffler, Christiane and Pulungan, Aman B. and Bandyopadhyay, Arup Ratan and Ghosh, Jyoti Ratan and {\"O}zdemir, Ay{\c{s}}eg{\"u}l and Koca {\"O}zer, Ba{\c{s}}ak and Musalek, Martin and Lebedeva, Lidia and Godina, Elena and Bogin, Barry and Tutkuviene, Janina and Budrytė, Milda and Gervickaite, Simona and Limony, Yehuda and Kirchengast, Sylvia and Buston, Peter and Groth, Detlef and R{\"o}sler, Antonia and Gasparatos, Nikolaos and Erofeev, Sergei and Novine, Masiar and Navazo, B{\´a}rbara and Dahinten, Silvia and Gomuła, Aleksandra and Nowak-Szczepańska, Natalia and Kozieł, Sławomir},
  title     = {Environment, social behavior, and growth},
  series = {Human biology and public health},
  volume    = {1},
  journal   = {Human biology and public health},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph2023.1.59},
  pages     = {14},
  year      = {2023},
  abstract  = {Twenty-four scientists met for the annual Auxological conference held at Krobielowice castle, Poland, to discuss the diverse influences of the environment and of social behavior on growth following last year's focus on growth and public health concerns (Hermanussen et al., 2022b). Growth and final body size exhibit marked plastic responses to ecological conditions. Among the shortest are the pygmoid people of Rampasasa, Flores, Indonesia, who still live under most secluded insular conditions. Genetics and nutrition are usually considered responsible for the poor growth in many parts of this world, but evidence is accumulating on the prominent impact of social embedding on child growth. Secular trends not only in the growth of height, but also in body proportions, accompany the secular changes in the social, economic and political conditions, with major influences on the emotional and educational circumstances under which the children grow up (Bogin, 2021). Aspects of developmental tempo and aspects of sports were discussed, and the impact of migration by the example of women from Bangladesh who grew up in the UK. Child growth was considered in particular from the point of view of strategic adjustments of individual size within the network of its social group. Theoretical considerations on network characteristics were presented and related to the evolutionary conservation of growth regulating hypothalamic neuropeptides that have been shown to link behavior and physical growth in the vertebrate species. New statistical approaches were presented for the evaluation of short term growth measurements that permit monitoring child growth at intervals of a few days and weeks.},
  language  = {en}
}