Recent Submissions

  • Journal Article

    Chirality enriched carbon nanotubes with tunable wrapping via corona phase exchange purification (CPEP) 

    Nißler, Robert; Mann, Florian A.; Preiß, Helen; Selvaggio, Gabriele; Herrmann, Niklas; Kruss, Sebastian
    Nanoscale 2019; 11(23) p.11159-11166
    Single-walled carbon nanotubes (SWCNTs) have unique photophysical properties and serve as building blocks for biosensors, functional materials and devices. For many applications it is crucial to use chirality-pure SWCNTs, which requires sophisticated processes. Purification procedures such as wrapping by certain polymers, phase separation, density gradient centrifugation or gel chromatography have been developed and yield distinct SWCNT species wrapped by a specific polymer or surfactant. However, many applications require a different organic functionalization (corona) around the SWCNTs instead of the one used for the purification process. Here, we present a novel efficient and straightforward process to gain chirality pure SWCNTs with tunable functionalization. Our approach uses polyfluorene (PFO) polymers to enrich certain chiralities but the polymer is removed again and finally exchanged to any desired organic phase. We demonstrate this concept by dispersing SWCNTs in poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(6,6'-{2,2'-bipyridine})] (PFO-BPy), which is known to preferentially solubilize (6,5)-SWCNTs. Then PFO-BPy is removed and recycled, while letting the SWCNTs adsorb/agglomerate on sodium chloride (NaCl) crystals, which act as a toluene-stable but water-soluble filler material. In the last step these purified SWCNTs are redispersed in different polymers, surfactants and ssDNA. This corona phase exchange purification (CPEP) approach was also extended to other PFO variants to enrich and functionalize (7,5)-SWCNTs. CPEP purified and functionalized SWCNTs display monodisperse nIR spectra, which are important for fundamental studies and applications that rely on spectral changes. We show this advantage for SWCNT-based nIR fluorescent sensors for the neurotransmitter dopamine and red-shifted sp3 defect peaks . In summary, CPEP makes use of PFO polymers for chirality enrichment but provides access to chirality enriched SWCNTs functionalized in any desired polymer, surfactant or biopolymer.
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  • Journal Article

    Fluorinated nanobodies for targeted molecular imaging of biological samples using nanoscale secondary ion mass spectrometry 

    Kabatas, Selda; Agüi-Gonzalez, Paola; Hinrichs, Rena; Jähne, Sebastian; Opazo, Felipe; Diederichsen, Ulf; Rizzoli, Silvio O.; Phan, Nhu T. N.
    Journal of Analytical Atomic Spectrometry 2019; 34(6) p.1083-1087
    Molecular imaging of targeted large biomolecules has been restricted in SIMS due to the limited number of probes containing SIMS-detectable isotopes. We introduce here new 19F-containing molecules that can be conjugated in a site-specific manner to nanobodies able to recognize fluorescent proteins (FPs) or mouse immunoglobulins (Igs). In this work, we demonstrate that it is possible to use the 19F-nanobodies to reveal the location of several cellular proteins previously tagged with FPs or Igs. This enables specific bio-imaging in SIMS for a vast repertoire of biomolecules, offering new opportunities to study specific structural and functional molecular interactions in biological specimens.
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  • Journal Article

    Electrification in granular gases leads to constrained fractal growth 

    Singh, Chamkor; Mazza, Marco G.
    Scientific Reports 2019; 9(1): Art. 9049
    The empirical observation of aggregation of dielectric particles under the influence of electrostatic forces lies at the origin of the theory of electricity. The growth of clusters formed of small grains underpins a range of phenomena from the early stages of planetesimal formation to aerosols. However, the collective effects of Coulomb forces on the nonequilibrium dynamics and aggregation process in a granular gas – a model representative of the above physical processes – have so far evaded theoretical scrutiny. Here, we establish a hydrodynamic description of aggregating granular gases that exchange charges upon collisions and interact via the long-ranged Coulomb forces. We analytically derive the governing equations for the evolution of granular temperature, charge variance, and number density for homogeneous and quasi-monodisperse aggregation. We find that, once the aggregates are formed, the granular temperature of the cluster population, the charge variance of the cluster population and the number density of the cluster population evolve in such a way that their non-dimensional combination obeys a physical constraint of nearly constant dimensionless ratio of characteristic electrostatic to kinetic energy. This constraint on the collective evolution of charged clusters is confirmed both by our theory and our detailed molecular dynamics simulations. The inhomogeneous aggregation of monomers and clusters in their mutual electrostatic field proceeds in a fractal manner. Our theoretical framework is extendable to more precise charge exchange mechanisms, a current focus of extensive experimentation. Furthermore, it illustrates the collective role of long-ranged interactions in dissipative gases and can lead to novel designing principles in particulate systems
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  • Journal Article

    Distributional semantics of objects in visual scenes in comparison to text 

    Lüddecke, Timo; Agostini, Alejandro; Fauth, Michael; Tamosiunaite, Minija; Wörgötter, Florentin
    Artificial Intelligence 2019; 274 p.44-65
    The distributional hypothesis states that the meaning of a concept is defined through the contexts it occurs in. In practice, often word co-occurrence and proximity are analyzed in text corpora for a given word to obtain a real-valued semantic word vector, which is taken to (at least partially) encode the meaning of this word. Here we transfer this idea from text to images, where pre-assigned labels of other objects or activations of convolutional neural networks serve as context. We propose a simple algorithm that extracts and processes object contexts from an image database and yields semantic vectors for objects. We show empirically that these representations exhibit on par performance with state-of-the-art distributional models over a set of conventional objects. For this we employ well-known word benchmarks in addition to a newly proposed object-centric benchmark.
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  • Journal Article

    Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests 

    Dukunde, Amélie; Schneider, Dominik; Schmidt, Marcus; Veldkamp, Edzo; Daniel, Rolf
    Frontiers in Microbiology 2019; 10: Art. 1519
    Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.
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  • Journal Article

    Is implicit Theory of Mind real but hard to detect? Testing adults with different stimulus materials 

    Kulke, Louisa; Wübker, Marieke; Rakoczy, Hannes
    Royal Society Open Science 2019; 6(7): Art. 190068
    Recently, Theory of Mind (ToM) research has been revolutionized by new methods. Eye-tracking studies measuring subjects' looking times or anticipatory looking have suggested that implicit and automatic forms of ToM develop much earlier in ontogeny than traditionally assumed and continue to operate outside of subjects’ awareness throughout the lifespan. However, the reliability of these implicit methods has recently been put into question by an increasing number of non-replications. What remains unclear from these accumulating non-replication findings, though, is whether they present true negatives (there is no robust phenomenon of automatic ToM) or false ones (automatic ToM is real but difficult to tap). In order to address these questions, the current study implemented conceptual replications of influential anticipatory looking ToM tasks with a new variation in the stimuli. In two separate preregistered studies, we used increasingly realistic stimuli and controlled for potential confounds. Even with these more realistic stimuli, previous results could not be replicated. Rather, the anticipatory looking pattern found here remained largely compatible with more parsimonious explanations. In conclusion, the reality and robustness of automatic ToM remains controversial.
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  • Journal Article

    Doubly-charged Higgs boson at a future electron-proton collider 

    Dev, P. S. Bhupal; Khan, Sarif; Mitra, Manimala; Rai, Santosh Kumar
    Physical Review D 2019; 99(11)
    We explore the discovery prospect of the doubly-charged component of an SU(2)L-triplet scalar at the future e−p collider FCC-eh, proposed to operate with an electron beam energy of 60 GeV and a proton beam energy of 50 TeV. We consider the associated production of the doubly-charged Higgs boson along with leptons and jet(s), and its subsequent prompt decay to same-sign lepton pair. This occurs for O(1) Yukawa coupling of the scalar triplet with charged leptons, which is expected for reasonably small vacuum expectation values of the neutral component of the triplet field that governs the neutrino mass generation in the type-II seesaw. We present our analysis for two different final states, 3l+≥1j and an inclusive ≥2l+≥1j channel. Considering its decay to electrons only, we find that the doubly-charged Higgs boson with a mass around a TeV could be observed at the 3σ confidence level with O(200)  fb−1 of integrated luminosity, while masses up to 2 TeV could be probed within a few years of data accumulation. The signal proposed here becomes essentially background free, if it is triggered in the μμ mode and a 5σ discovery is achievable in this channel for a TeV-scale doubly-charged Higgs boson with an integrated luminosity as low as O(50)  fb−1. We also highlight the sensitivity of FCC-eh to the Yukawa coupling responsible for the production of the doubly-charged Higgs boson as a function of its mass in both the ee and μμ channels.
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  • Journal Article

    FIMP dark matter candidate(s) in a B − L model with inverse seesaw mechanism 

    Abdallah, Waleed; Choubey, Sandhya; Khan, Sarif
    Journal of High Energy Physics 2019; 2019(6)
    Abstract: The non-thermal dark matter (DM) production via the so-called freeze-in mechanism provides a simple alternative to the standard thermal WIMP scenario. In this work, we consider a popular U(1)B�����L extension of the standard model (SM) in the context of inverse seesaw mechanism which has at least one (fermionic) FIMP DM candidate. Due to the added Z2 symmetry, a SM gauge singlet fermion, with mass of order keV, is stable and can be a warm DM candidate. Also, the same Z2 symmetry helps the lightest righthanded neutrino, with mass of order GeV, to be a stable or long-lived particle by making a corresponding Yukawa coupling very small. This provides a possibility of a two component DM scenario as well. Firstly, in the absence of a GeV DM component (i.e., without tuning its corresponding Yukawa coupling to be very small), we consider only a keV DM as a single component DM, which is produced by the freeze-in mechanism via the decay of the extra Z0 gauge boson associated to U(1)B�����L and can consistently explain the DM relic density measurements. In contrast with most of the existing literature, we have found a reasonable DM production from the annihilation processes. After numerically studying the DM production, we show the dependence of the DM relic density as a function of its relevant free parameters. We use these results to obtain the parameter space regions that are compatible with the DM relic density bound. Secondly, we study a two component DM scenario and emphasize that the current DM relic density bound can be satis ed for a wide range of parameter space.
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  • Journal Article

    The Ulakhan fault surface rupture and the seismicity of the Okhotsk–North America plate boundary 

    Hindle, David; Sedov, Boris; Lindauer, Susanne; Mackey, Kevin
    Solid Earth 2019; 10(2) p.561-580
    New field work, combined with analysis of high-resolution aerial photographs, digital elevation models, and satellite imagery, has identified an active fault that is traceable for ∼90 km across the Seymchan Basin and is part of the Ulakhan fault system, which is believed to form the Okhotsk–North America plate boundary. Age dating of alluvial fan sediments in a channel system that is disturbed by fault activity suggests the current scarp is a result of a series of large earthquakes (≥Mw 7.5) that have occurred since 11.6±2.7 ka. A possible channel feature offset by 62±4 m associated with these sediments yields a slip rate of 5.3±1.3 mm yr−1, in broad agreement with rates suggested from global plate tectonics. Our results clearly identify the Ulakhan fault as the Okhotsk–North America plate boundary and show that tectonic strain release is strongly concentrated on the boundaries of Okhotsk. In light of our results, the likelihood of recurrence of Mw 7.5 earthquakes is high, suggesting a previously underestimated seismic hazard across the region.
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  • Journal Article

    CuO-CeO2 nanocomposite catalysts produced by mechanochemical synthesis 

    Borchers, Ch.; Martin, M. L.; Vorobjeva, G. A.; Morozova, O. S.; Firsova, A. A.; Leonov, A. V.; Kurmaev, E. Z.; Kukharenko, A. I.; Zhidkov, I. S.; Cholakh, S. O.
    AIP Advances 2019; 9(6): Art. 065115
    Mechanochemical synthesis based on ball-milling of individual oxides was applied as a one-step preparation technique for CuO-CeO2 catalyst for preferential CO oxidation in H2 excess. The mechanical energy dose transferred to the original powder mixture determines both the catalyst composition and activity. It is found that after 90 min of milling (corresponding to a dose of 372 kJ mol–1), a mixture of 10 wt.% CuO-CeO2 powder exhibits a CO conversion of 97% at 423 K. Four active oxygen states, which are not observed in case of pure CeO2, were detected in the nanocomposite lattice and attributed to the presence of Cu in surface sites as well as in subsurface bulk sites of CeO2, in nearest neighbor and next nearest neighbor positions. Correspondingly, oxidation of CO to CO2 was found to occur in a two-stage process with Tmax = 395/460 K, and oxidation of H2 to H2O likewise in a four-stage process with Tmax = 426/448/468/516 K. The milled powder consists of CeO2 crystallites sized 8–10 nm agglomerated to somewhat larger aggregates, with CuO dispersed on the surface of the CeO2 crystallites, and to a lesser extent present as Cu2O.
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  • Journal Article

    Impact of Nitriles on Bacterial Communities 

    Egelkamp, Richard; Zimmermann, Till; Schneider, Dominik; Hertel, Robert; Daniel, Rolf
    Frontiers in Environmental Science 2019; 7: Art. 103
    Nitriles are organic molecules with –C≡N as functional group and often toxic for living organisms. Detoxification can occur via nitrilases that degrade nitriles directly to carboxylic acids and ammonia, or with nitrile hydratases and amidases that convert nitriles to amides and subsequently to carboxylic acids and ammonia. Despite the knowledge of enzymatic degradation pathways, the influence of these compounds on the composition of bacterial communities is unknown. The tolerances of four phylogenetically different bacterial strains without known nitrile detoxification systems (Agrobacterium tumefaciens, Bacillus subtilis, Corynebacterium glutamicum, and Escherichia coli) to the toxic effects of nine nitriles and the corresponding carboxylic acids were determined. Based on these results, the effect of nitriles on diversity and composition of compost-derived bacterial communities was monitored over time by 16S rRNA gene amplicon-based andmetagenome analyses. Acetone cyanohydrin, 2-phenylpropionitrile, and pyruvonitrile exhibited a lethal, phenylacetonitrile, 4-hydroxybenzonitrile, and cyclohexanecarbonitrile a growth-suppressing and succinonitrile, acetonitrile, and crotononitrile a growth-promoting effect on the studied communities. Furthermore, each nitrile had a specific community-shaping effect, e.g., communities showing growth-suppression exhibited high relative abundance of Paenibacillus. In general, analysis of all data indicated a higher resistance of Gram-positive than Gram-negative bacterial community members and test organisms to growth-suppressing nitriles. More than 70 putative nitrilase-encoding and over 20 potential nitrile hydratase-encoding genes were identified during analysis of metagenomes derived from nitrile-enrichments, underlining the high yet often unexplored abundance of nitrile-degrading enzymes.
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  • Journal Article

    COP9 Signalosome Interaction with UspA/Usp15 Deubiquitinase Controls VeA-Mediated Fungal Multicellular Development 

    Meister, Cindy; Thieme; Karl G.; Thieme, Sabine; Köhler, Anna M.; Schmitt, Kerstin; Valerius, Oliver; Braus, Gerhard H.
    Biomolecules 2019; 9(6): Art. 238
    COP9 signalosome (CSN) and Den1/A deneddylases physically interact and promote multicellular development in fungi. CSN recognizes Skp1/cullin-1/Fbx E3 cullin-RING ligases (CRLs) without substrate and removes their posttranslational Nedd8 modification from the cullin scaffold. This results in CRL complex disassembly and allows Skp1 adaptor/Fbx receptor exchange for altered substrate specificity. We characterized the novel ubiquitin-specific protease UspA of the mold Aspergillus nidulans, which corresponds to CSN-associated human Usp15 and interacts with six CSN subunits. UspA reduces amounts of ubiquitinated proteins during fungal development, and the uspA gene expression is repressed by an intact CSN. UspA is localized in proximity to nuclei and recruits proteins related to nuclear transport and transcriptional processing, suggesting functions in nuclear entry control. UspA accelerates the formation of asexual conidiospores, sexual development, and supports the repression of secondary metabolite clusters as the derivative of benzaldehyde (dba) genes. UspA reduces protein levels of the fungal NF-kappa B-like velvet domain protein VeA, which coordinates differentiation and secondary metabolism. VeA stability depends on the Fbx23 receptor, which is required for light controlled development. Our data suggest that the interplay between CSN deneddylase, UspA deubiquitinase, and SCF-Fbx23 ensures accurate levels of VeA to support fungal development and an appropriate secondary metabolism.
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  • Journal Article

    Cold-water corals and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz) – living on the edge 

    Rincón-Tomás, Blanca; Duda, Jan-Peter; Somoza, Luis; González, Francisco Javier; Schneider, Dominik; Medialdea, Teresa; Santofimia, Esther; López-Pamo, Enrique; Madureira, Pedro; Hoppert, Michael; et al.
    Reitner, Joachim
    Biogeosciences 2019; 16(7) p.1607-1627
    Azooxanthellate cold-water corals (CWCs) have a global distribution and have commonly been found in areas of active fluid seepage. The relationship between the CWCs and these fluids, however, is not well understood. This study aims to unravel the relationship between CWC development and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz, Atlantic Ocean). This region is comprised of mud volcanoes (MVs), coral ridges and fields of coral mounds, which are all affected by the tectonically driven seepage of hydrocarbon-rich fluids. These types of seepage, for example, focused, scattered, diffused or eruptive, is tightly controlled by a complex system of faults and diapirs. Early diagenetic carbonates from the currently active Al Gacel MV exhibit δ13C signatures down to −28.77 ‰ Vienna Pee Dee Belemnite (VPDB), which indicate biologically derived methane as the main carbon source. The same samples contain 13C-depleted lipid biomarkers diagnostic for archaea such as crocetane (δ13C down to −101.2 ‰ VPDB) and pentamethylicosane (PMI) (δ13C down to −102.9 ‰ VPDB), which is evidence of microbially mediated anaerobic oxidation of methane (AOM). This is further supported by next generation DNA sequencing data, demonstrating the presence of AOM-related microorganisms (ANMEs, archaea, sulfate-reducing bacteria) in the carbonate. Embedded corals in some of the carbonates and CWC fragments exhibit less negative δ13C values (−8.08 ‰ to −1.39 ‰ VPDB), pointing against the use of methane as the carbon source. Likewise, the absence of DNA from methane- and sulfide-oxidizing microbes in sampled coral does not support the idea of these organisms having a chemosynthetic lifestyle. In light of these findings, it appears that the CWCs benefit rather indirectly from hydrocarbon-rich seepage by using methane-derived authigenic carbonates as a substratum for colonization. At the same time, chemosynthetic organisms at active sites prevent coral dissolution and necrosis by feeding on the seeping fluids (i.e., methane, sulfate, hydrogen sulfide), allowing cold-water corals to colonize carbonates currently affected by hydrocarbon-rich seepage.
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  • Journal Article

    Analysis of Economic Feasibility of Ash and Maple Lamella Production for Glued Laminated Timber 

    Schlotzhauer, Philipp; Kovryga, Andriy; Emmerich, Lukas; Bollmus, Susanne; Van de Kuilen, Jan-Willem; Militz, Holger
    Forests 2019; 10(7): Art. 529
    Background and Objectives: In the near future, in Europe a raised availability of hardwoods is expected. One possible sales market is the building sector, where medium dense European hardwoods could be used as load bearing elements. For the hardwood species beech, oak, and sweet chestnut technical building approvals already allow the production of hardwood glulam. For the species maple and ash this is not possible yet. This paper aims to evaluate the economic feasibility of glulam production from low dimension ash and maple timber from thinnings. Therefore, round wood qualities and the resulting lumber qualities are assessed and final as well as intermediate yields are calculated. Materials and Methods: 81 maple logs and 79 ash logs cut from trees from thinning operations in mixed (beech) forest stands were visually graded, cant sawn, and turned into strength-graded glulam lamellas. The volume yield of each production step was calculated. Results: The highest volume yield losses occur during milling of round wood (around 50%) and “presorting and planning” the dried lumber (56–60%). Strength grading is another key process in the production process. When grading according to DIN 4074-5 (2008), another 40–50% volume loss is reported, while combined visual and machine grading only produces 7–15% rejects. Conclusions: Yield raise potentials were identified especially in the production steps milling, presorting and planning and strength grading.
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  • Journal Article

    Advanced Aboveground Spatial Analysis as Proxy for the Competitive Environment Affecting Sapling Development 

    Annighöfer, Peter; Seidel, Dominik; Mölder, Andreas; Ammer, Christian
    Frontiers in Plant Science 2019; 10: Art. 690
    Tree saplings are exposed to a competitive growth environment in which resources are limited and the ability to adapt determines general vitality and specific growth performance. In this study we analyzed the aboveground spatial neighborhood of oak [Quercus petraea (Matt.) Liebl.] and beech (Fagus sylvatica L.) saplings growing in Germany, by using hemispherical photography and terrestrial laser scanning as proxy for the competitive pressure saplings were exposed to. The hemispherical images were used to analyze the light availability and the three-dimensional (3D) point clouds from the laser scanning were used to assess the space and forest structure around the saplings. The aim was to increase the precision with which the biomass allocation, growth, and morphology of the saplings could be predicted by including more detailed information of their environment. The predictive strength of the models was especially increased through direct neighborhood variables (e.g., relative space filling), next to the light availability being the most important predictor variable. The biomass allocation patterns within the more light demanding oak were strongly driven by the space availability around the saplings. Diameter and height growth variables of both species reacted significantly to changes in light availability, and partly also to the neighborhood variables. The leaf morphology [as leaf-area ratio (LAR)] was also driven by light availability and decreased with increasing light availability. However, the branch morphology (as mean branch weight) could not be explained for oak and the model outcome for beech was hard to interpret. The results could show that individuals of the same species perform differently under constant light conditions but differing neighborhoods. Assessing the neighborhood of trees with highly precise measurement devices, like terrestrial laser scanners, proved to be useful. However, the primary response to a dense neighborhood seemed to be coping with a reduction of the lateral light availability aboveground, rather than responding to an increase of competition belowground. The results suggest continuing efforts to increase the precision with which plant environments can be described through innovative and efficient methods, like terrestrial laser scanning.
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  • Journal Article

    Indications of Genetic Admixture in the Transition Zone between Fagus sylvatica L. and Fagus sylvatica ssp. orientalis Greut. & Burd 

    Müller, Markus; Lopez, Precious Annie; Papageorgiou, Aristotelis C.; Tsiripidis, Ioannis; Gailing, Oliver
    Diversity 2019; 11(6): Art. 90
    Two subspecies of European beech (Fagus sylvatica L.) can be found in southeast Europe: Fagus sylvatica ssp. sylvatica L. and Fagus sylvatica ssp. orientalis (Lipsky) Greut. &Burd. (Fagus orientalis Lipsky). In a previous study, based on genetic diversity patterns and morphological characters, indications of hybridization between both subspecies were found in northeastern Greece, a known contact zone of F. sylvatica and F. orientalis. Nevertheless, potential genetic admixture has not been investigated systematically before. Here, we investigated genetic diversity and genetic structure of 14 beech populations originating from Greece and Turkey as well as of two reference F. sylvatica populations from Germany based on nine expressed sequence tag-simple sequence repeat (EST-SSR) markers. Very low genetic di erentiation was detected among F. sylvatica populations (mean GST: 0.005) as well as among F. orientalis populations (mean GST: 0.008), but substantial di erentiation was detected between populations of the two subspecies (mean GST: 0.122). Indications for hybridization between both subspecies were revealed for one population in Greece. One of the genetic markers showed specific allele frequencies for F. sylvatica and F. orientalis and may be used as a diagnostic marker in future studies to discriminate both subspecies.
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  • Journal Article

    Functional Metagenomics Reveals a New Catalytic Domain, the Metallo-β-Lactamase Superfamily Domain, Associated with Phytase Activity 

    Castillo Villamizar, Genis Andrés; Funkner, Katrina; Nacke, Heiko; Foerster, Karolin; Daniel, Rolf
    mSphere 2019; 4(3)
    Inositol-6-phosphate, also known as phytic acid, is a phosphorus source that plays several important roles in the phosphorus cycle and in cell metabolism. The known characterized enzymes responsible for its degradation, the phytases, are mostly derived from cultured individual microorganisms. The catalytic signatures of phytases are restricted to the molecular domains of four protein superfamilies: histidine phosphatases, protein tyrosine phosphatases, the purple acid phosphatases and the β-propeller phosphatases. During function-based screening of previously generated forest soil metagenomic libraries for Escherichia coli clones conferring phytase activity, two positive clones harboring the plasmids pLP05 and pLP12 were detected. Analysis of the insert sequences revealed the absence of classic phosphatase/phytase signatures of the proteins deduced from the putative genes, but the genes mblp01 (pLP05) and mblp02 (pLP12) encoded putative metallo-β-lactamases (MBLs). Several MBL representatives are promiscuous proteins with phosphoesterase activity, but phytase activity was previously not reported. Both mblp01 and mblp02 were subcloned, expressed, and analyzed. Mblp01 and Mblp02 are members of the lactamase B2 family. Protein modeling showed that the closest structural homologue of both proteins was ZipD of E. coli Mblp01 and Mblp02 showed activity toward the majority of the tested phosphorylated substrates, including phytate. The maximal enzyme activities were recorded for Mblp01 at 50°C under acidic conditions and for Mblp02 at 35°C and a neutral pH. In the presence of Cu2+ or SDS, the activities of Mblp01 and Mblp02 were strongly inhibited. Analyses of the minimal inhibitory concentrations of several β-lactam antibiotics revealed that recombinant E. coli cells carrying mblp01 or mblp02 showed reduced sensitivity toward β-lactam antibiotics.IMPORTANCE Phytic acid is a phosphorus storage molecule in many plant tissues, a source of phosphorus alternative to phosphate rocks, but it can also be a problematic antinutrient. In comparison to other phosphorus sources, phytic acid exhibits reduced bioavailability. Additionally, it influences functions of secondary messengers and acts as antioxidant in tumor growth prevention. The enzymatic capability to process phytate has been reported for a limited number of protein families. This might be due to the almost exclusive use of proteins derived from individual microorganisms to analyze phytase activity. With such a restriction, the study of the complexity and diversity of the phytases remains incomplete. By using metagenome-derived samples, this study demonstrates the existence of phytase activity in one of the most promiscuous superfamilies, the metallo-β-lactamases. Our results increase the general knowledge on phytase diversity in environmental samples and could provide new avenues for the study and engineering of new biocatalysts.
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  • Journal Article

    Sacred groves hold distinct bird assemblages within an Afrotropical savanna 

    Kühnert, Katharina; Grass, Ingo; Waltert, Matthias
    Global Ecology and Conservation 2019; 18: Art. e00656
    Riparian forests, an integral part of savanna ecosystems, are threatened across West Africa by agricultural expansion. However, some patches of original riparian vegetation are protected by traditional beliefs as ‘Sacred Groves’. We assessed the role of Sacred Groves in maintaining landscape-scale bird assemblages by conducting 144 1-h point counts, distributed over 24 plots in eastern Guinea-Bissau. The plots were situated in three riparian habitat types with different levels of human modification (Sacred Grove, Young Secondary Forest, Annual Cultures) and the adjacent Wooded Savanna. We accumulated 4572 records of 174 species and compared total species richness, composition, and functional traits among the four habitat types. At the plot level, species richness was higher in Wooded Savannas and Annual Cultures compared to Secondary Forests and Sacred Groves. Bird communities in Wooded Savannas were similar to those in Annual Cultures and differed the most from those of Sacred Groves. Bird community composition in Young Secondary Forests was similar to that in Annual Cultures but showed a shift towards the community composition found in Sacred Groves. Certain traits were strongly specific to habitat type. For example, Sacred Groves were characterized by a high number of forest specialists and insectivorous birds. Our results suggest that the rapid successional dynamics in riparian habitats enable disturbance tolerant forest species to recolonize fallow areas after a relatively short period of time. However, Sacred Groves hold a distinct avifauna and their conservation may therefore be crucial for forest specialist species and the re-establishment of bird assemblages in fallow riparian areas. Our findings also stress the importance of respecting and strengthening traditional forms of nature protection.
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  • Journal Article

    Review of the mite genus Ololaelaps (Acari, Laelapidae) and redescription of O. formidabilis Berlese 

    Beaulieu, Frédéric; Quintero-Gutiérrez, Edwin Javier; Sandmann, Dorotee; Klarner, Bernhard; Widyastuti, Rahayu; Cómbita-Heredia, Orlando; Scheu, Stefan
    ZooKeys 2019; 853 p.1-36
    A species of laelapid mite, Ololaelapsformidabilis, is redescribed based on male and female adults from soil in Sumatra, Indonesia. This species is distinguished from other Ololaelaps species by its metapodal platelet narrowly fused with the parapodal plate and by its hologastric shield having two inverted-V-like ridges. The genus is redescribed based on a review of the literature and examination of specimens of some species. Valid species of Ololaelaps are listed and accompanied by notes on morphological characters to assist future revision of the genus.
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  • Journal Article

    Genetics of adaptation in modern chicken 

    Qanbari, Saber; Rubin, Carl-Johan; Maqbool, Khurram; Weigend, Steffen; Weigend, Annett; Geibel, Johannes; Kerje, Susanne; Wurmser, Christine; Peterson, Andrew Townsend; Brisbin, I. Lehr; et al.
    Preisinger, RuediFries, RuediSimianer, HennerAndersson, Leif
    PLOS Genetics 2019; 15(4): Art. e1007989
    We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5×10-6). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding.
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