Recent Submissions

  • Journal Article

    First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and their Comparative Genome Analysis 

    Friedrich, Ines; Hollensteiner, Jacqueline; Schneider, Dominik; Poehlein, Anja; Hertel, Robert; Daniel, Rolf
    Genome Biology and Evolution p.1-21
    We present the first two complete genomes of the Janthinobacterium lividum species, namely strains EIF1 and EIF2, which both possess the ability to synthesize violacein. The violet pigment violacein is a secondary metabolite with antibacterial, antifungal, antiviral, and antitumoral properties. Both strains were isolated from environmental oligotrophic water ponds in Göttingen. The strains were phylogenetically classified by ANI analysis and showed a species assignment to Janthinobacterium lividum with 97.72% (EIF1) and 97.66% (EIF2) identity. These are the first complete genome sequences of strains belonging to the species Janthinobacterium lividum. The genome of strain EIF1 consists of one circular chromosome (6,373,589 bp) with a GC-content of 61.98%. The genome contains 5,551 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA. The genome of EIF2 comprises one circular chromosome (6,399,352 bp) with a GC-content of 61.63% and a circular plasmid p356839 (356,839 bp) with a GC-content of 57.21%. The chromosome encodes 5,691 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA and the plasmid harbors 245 coding sequences. In addition to the highly conserved chromosomally encoded violacein operon, the plasmid comprises a non-ribosomal peptide synthetase cluster (NRPS) with similarity to xenoamicin, which is a bioactive compound effective against protozoan parasites.
    View Document Abstract
  • Journal Article

    Globally Abundant “Candidatus Udaeobacter” Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging 

    Willms, Inka M.; Rudolph, Anina Y.; Göschel, Isabell; Bolz, Simon H.; Schneider, Dominik; Penone, Caterina; Poehlein, Anja; Schöning, Ingo; Nacke, Heiko
    mSphere 2020; 5(4) p.1-17: Art. e00186-20
    Verrucomicrobia affiliated with “Candidatus Udaeobacter” belong to the most abundant soil bacteria worldwide. Although the synthesis of antibiotics presumably evolved in soil, and environmental pollution with antimicrobials increases, the impact of these complex molecules on “Ca. Udaeobacter” remains to be elucidated. In this study, we demonstrate that “Ca. Udaeobacter” representatives residing in grassland as well as forest soil ecosystems show multidrug resistance and even take advantage of antibiotics release. Soils treated with up to six different antibiotics exhibited a higher “Ca. Udaeobacter” abundance than corresponding controls after 3, 8, and 20 days of incubation. In this context, we provide evidence that “Ca. Udaeobacter” representatives may utilize nutrients which are released due to antibiotic-driven lysis of other soil microbes and thereby reduce energetically expensive synthesis of required biomolecules. Moreover, genomic analysis revealed the presence of genes conferring resistance to multiple classes of antibiotics and indicated that “Ca. Udaeobacter” representatives most likely oxidize the trace gas H$_2$ to generate energy. This energy might be required for long-term persistence in terrestrial habitats, as already suggested for other dominant soil bacteria. Our study illustrates, for the first time, that globally abundant “Ca. Udaeobacter” benefits from release of antibiotics, which confers advantages over other soil bacteria and represents a so-far overlooked fundamental lifestyle feature of this poorly characterized verrucomicrobial genus. Furthermore, our study suggests that “Ca. Udaeobacter” representatives can utilize H$_2$ as an alternative electron donor. IMPORTANCE Soil bacteria have been investigated for more than a century, but one of the most dominant terrestrial groups on Earth, “Candidatus Udaeobacter,” remains elusive and largely unexplored. Its natural habitat is considered a major reservoir of antibiotics, which directly or indirectly impact phylogenetically diverse microorganisms. Here, we found that “Ca. Udaeobacter” representatives exhibit multidrug resistance and not only evade harmful effects of antimicrobials but even benefit from antibiotic pressure in soil. Therefore, “Ca. Udaeobacter” evidently affects the composition of soil resistomes worldwide and might represent a winner of rising environmental pollution with antimicrobials. In addition, our study indicates that “Ca. Udaeobacter” representatives utilize H$_2$ and thereby contribute to global hydrogen cycling. The here-reported findings provide insights into elementary lifestyle features of “Ca. Udaeobacter,” potentially contributing to its successful global dissemination.
    View Document Abstract
  • Journal Article

    Testate Amoeba Species- and Trait-Based Transfer Functions for Reconstruction of Hydrological Regime in Tropical Peatland of Central Sumatra, Indonesia 

    Krashevska, Valentyna; Tsyganov, Andrey N.; Esaulov, Anton S.; Mazei, Yuri A.; Hapsari, Kartika Anggi; Saad, Asmadi; Sabiham, Supiandi; Behling, Hermann; Biagioni, Siria
    Frontiers in Ecology and Evolution 2020; 8 p.1-15: Art. 225
    Tropical peatlands play an important role in carbon storage and in water regulation on a landscape level. However, our understanding of their ecology and long-term hydrological dynamics remains limited. Transfer functions, constructed on the basis of biological indicators (proxies) with known ecological preferences, allow us to infer past environmental conditions and serve as a basis for prediction of future changes in peatlands. Here, we use testate amoebae to develop the first species- and functional trait-based transfer functions for the Southeast Asia. This provides a valuable tool for future reconstructions of past hydrological changes in tropical peatlands, their development, and climatic changes. Surface samples for testate amoeba analysis were taken in various biotopes along two transects across the Sungai Buluh peatland in Central Sumatra. The following environmental characteristics were measured: water table depth (WTD), light intensity, pH, total C and N concentrations. The analysis of the surface samples revealed 145 morphotypes of testate amoebae belonging to 25 genera. A significant fraction of the variance in testate amoeba morphotypes and functional trait composition was explained by WTD and pH. The wide WTD range (0–120 cm) seems more valuable for reconstruction than the extremely short pH gradient (2.5–3.8). Thus, transfer functions were developed only for WTD, based on weighted averaging model for morphotypes and multiple linear regression for functional traits. Both species- and trait-based model have a predictive ability for WTD reconstruction. For traits, the best performance of the model was reached by including five morphological traits: shell width, aperture shape, aperture invagination, shell shape and shell compression. We discuss the ecology of several taxa and highlight the traits, which reflect hydrological changes in this system. Though the hydrological preferences of some species are similar to those in high and middle latitude peatlands, we argue that latitudinal differences in morphospecies composition and variations in environmental relationships of species require the development of region-specific transfer functions. Moreover, our results indicate that ecological preferences of morphotypes within morphospecies also need to be considered and included in future studies.
    View Document Abstract
  • Journal Article

    Non-Human Primate iPSC Generation, Cultivation, and Cardiac Differentiation under Chemically Defined Conditions 

    Stauske, Michael; Rodriguez Polo, Ignacio; Haas, Wadim; Knorr, Debbra Yasemin; Borchert, Thomas; Streckfuss-Bömeke, Katrin; Dressel, Ralf; Bartels, Iris; Tiburcy, Malte; Zimmermann, Wolfram-Hubertus; et al.
    Behr, Rüdiger
    Cells 2020; 9(6) p.1-24: Art. 1349
    Non-human primates (NHP) are important surrogate models for late preclinical development of advanced therapy medicinal products (ATMPs), including induced pluripotent stem cell (iPSC)-based therapies, which are also under development for heart failure repair. For effective heart repair by remuscularization, large numbers of cardiomyocytes are required, which can be obtained by efficient differentiation of iPSCs. However, NHP-iPSC generation and long-term culture in an undifferentiated state under feeder cell-free conditions turned out to be problematic. Here we describe the reproducible development of rhesus macaque (Macaca mulatta) iPSC lines. Postnatal rhesus skin fibroblasts were reprogrammed under chemically defined conditions using non-integrating vectors. The robustness of the protocol was confirmed using another NHP species, the olive baboon (Papio anubis). Feeder-free maintenance of NHP-iPSCs was essentially dependent on concurrent Wnt-activation by GSK-inhibition (Gi) and Wnt-inhibition (Wi). Generated NHP-iPSCs were successfully differentiated into cardiomyocytes using a combined growth factor/GiWi protocol. The capacity of the iPSC-derived cardiomyocytes to self-organize into contractile engineered heart muscle (EHM) was demonstrated. Collectively, this study establishes a reproducible protocol for the robust generation and culture of NHP-iPSCs, which are useful for preclinical testing of strategies for cell replacement therapies in NHP.
    View Document Abstract
  • Journal Article

    Plant intraspecific functional trait variation is related to within‐habitat heterogeneity and genetic diversity in Trifolium montanum L. 

    Karbstein, Kevin; Prinz, Kathleen; Hellwig, Frank; Römermann, Christine
    Ecology and Evolution 2020; 10(11) p.5015-5033
    Intraspecific trait variation (ITV), based on available genetic diversity, is one of the major means plant populations can respond to environmental variability. The study of functional trait variation and diversity has become popular in ecological research, for example, as a proxy for plant performance influencing fitness. Up to now, it is unclear which aspects of intraspecific functional trait variation (iFD$_{CV}$) can be attributed to the environment or genetics under natural conditions. Here, we examined 260 individuals from 13 locations of the rare (semi‐)dry calcareous grassland species Trifolium montanum L. in terms of iFD$_{CV}$, within‐habitat heterogeneity, and genetic diversity. The iFD$_{CV}$ was assessed by measuring functional traits (releasing height, biomass, leaf area, specific leaf area, leaf dry matter content, F$_v$/F$_m$, performance index, stomatal pore surface, and stomatal pore area index). Abiotic within‐habitat heterogeneity was derived from altitude, slope exposure, slope, leaf area index, soil depth, and further soil factors. Based on microsatellites, we calculated expected heterozygosity (He) because it best‐explained, among other indices, iFD$_{CV}$. We performed multiple linear regression models quantifying relationships among iFD$_{CV}$, abiotic within‐habitat heterogeneity and genetic diversity, and also between separate functional traits and abiotic within‐habitat heterogeneity or genetic diversity. We found that abiotic within‐habitat heterogeneity influenced iFD$_{CV}$ twice as strong compared to genetic diversity. Both aspects together explained 77% of variation in iFD$_{CV}$ ($R^2_{adj}$=.77, $F_{2,10}$ = 21.66, p < .001). The majority of functional traits (releasing height, biomass, specific leaf area, leaf dry matter content, F$_v$/F$_m$, and performance index) were related to abiotic habitat conditions indicating responses to environmental heterogeneity. In contrast, only morphology‐related functional traits (releasing height, biomass, and leaf area) were related to genetics. Our results suggest that both within‐habitat heterogeneity and genetic diversity affect iFD$_{CV}$ and are thus crucial to consider when aiming to understand or predict changes of plant species performance under changing environmental conditions.
    View Document Abstract
  • Journal Article

    First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna 

    Perez, María Florencia; Kurth, Daniel; Farías, María Eugenia; Soria, Mariana Noelia; Castillo Villamizar, Genis Andrés; Poehlein, Anja; Daniel, Rolf; Dib, Julián Rafael
    Frontiers in Microbiology 2020; 11 p.1-15: Art. 1343
    Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O$_2$ pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche.
    View Document Abstract
  • Journal Article

    Regeneration Dynamics Following the Formation of Understory Gaps in a Slovakian Beech Virgin Forest 

    Feldmann, Eike; Glatthorn, Jonas; Ammer, Christian; Leuschner, Christoph
    Forests 2020; 11(5) p.1-20: Art. 585
    The frequency and size of canopy gaps largely determine light transmission to lower canopy strata, controlling structuring processes in the understory. However, quantitative data from temperate virgin forests on the structure of regeneration in gaps and its dynamics over time are scarce. We studied the structure and height growth of tree regeneration by means of sapling density, shoot length growth and cumulative biomass in 17 understory gaps (29 to 931 m2 in size) in a Slovakian beech (Fagus sylvatica L.) virgin forest, and compared the gaps with the regeneration under closed-canopy conditions. Spatial differences in regeneration structure and growth rate within a gap and in the gap periphery were analyzed for their dependence on the relative intensities of direct and diffuse radiation (high vs. low). We tested the hypotheses that (i) the density and cumulative biomass of saplings are higher in gaps than in closed-canopy patches, (ii) the position in a gap influences the density and height growth of saplings, and (iii) height growth of saplings increases with gap size. Sapling density and biomass were significantly higher in understory gaps than under closed canopy. Density of saplings was positively affected by comparatively high direct, but low diffuse radiation, resulting in pronounced spatial differences. In contrast, sapling shoot length growth was positively affected by higher levels of diffuse radiation and also depended on sapling size, while direct radiation intensity was not influential. Conclusively, in this forest, regeneration likely becomes suppressed after a short period by lateral canopy expansion in small gaps (<100 m2), resulting in a heterogeneous understory structure. In larger gaps (≥100 m2) saplings may be capable even at low plant densities to fill the gap, often forming a cohort-like regeneration layer. Thus, gaps of different sizes imprint on the resulting canopy structure in different ways, enhancing spatial heterogeneity.
    View Document Abstract
  • Journal Article

    Modeling and Measuring Pre-Service Teachers’ Assessment Literacy Regarding Experimentation Competences in Biology 

    Joachim, Cora; Hammann, Marcus; Carstensen, Claus H.; Bögeholz, Susanne
    Education Sciences 2020; 10(5) p.1-27: Art. 140
    Assessment literacy is a crucial aspect of teachers’ professional knowledge and relevant to fostering students’ learning. Concerning experimentation, teachers have to be able to assess student achievement when students form hypotheses, design experiments, and analyze data. Therefore, teachers need to be familiar with criteria for experimentation as well as student conceptions of experimentation. The present study modeled and measured 495 German pre-service teachers’ knowledge of what to assess regarding experimentation competences in biology. We applied an open-answer format for the measurement instrument. For modeling we used item response theory (IRT). We argue that knowledge of what to assess regarding experimentation competences is a one-dimensional construct and we provide evidence for the validity of the measurement. Furthermore, we describe qualitative findings of pre-service teachers’ knowledge of what to assess, in particular difficulties concerning the assessment of student conceptions as well as the use of scientific terms in the assessments. We discuss the findings in terms of implications for science teacher education and further research perspectives.
    View Document Abstract
  • Journal Article

    Sexual modulation in a polyploid grass: a reproductive contest between environmentally inducible sexual and genetically dominant apomictic pathways 

    Karunarathne, Piyal; Reutemann, Anna V.; Schedler, Mara; Glücksberg, Adriana; Martínez, Eric J.; Honfi, Ana I.; Hojsgaard, Diego H.
    Scientific Reports 2020; 10(1) p.1-14: Art. 8319
    In systems alternating between sexual and asexual reproduction, sex increases under unfavorable environmental conditions. In plants producing sexual and asexual (apomictic) seeds, studies on the influence of environmental factors on sex are equivocal. We used Paspalum intermedium to study environmental effects on the expression of sexual and apomictic developments, and on resulting reproductive fitness variables. Flow cytometric and embryological analyses were performed to characterize ploidy and reproductive modes, and effects of local climatic conditions on sexual and apomictic ovule and seed frequencies were determined. Seed set and germination data were collected and used to estimate reproductive fitness. Frequencies of sexual and apomictic ovules and seeds were highly variable within and among populations. Apomictic development exhibited higher competitive ability but lower overall fitness. Frequencies of sexual reproduction in facultative apomictic plants increased at lower temperatures and wider mean diurnal temperature ranges. We identified a two-fold higher fitness advantage of sexuality and a Tug of War between factors intrinsic to apomixis and environmental stressors promoting sexuality which influence the distribution of sex in apomictic populations. This points toward a crucial role of local ecological conditions in promoting a reshuffling of genetic variability that may be shaping the adaptative landscape in apomictic P. intermedium plants.
    View Document Abstract
  • Journal Article

    Epigenetic Patterns and Geographical Parthenogenesis in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae) 

    Schinkel, Christoph C. F.; Syngelaki, Eleni; Kirchheimer, Bernhard; Dullinger, Stefan; Klatt, Simone; Hörandl, Elvira
    International Journal of Molecular Sciences 2020; 21(9) p.1-20: Art. 3318
    Polyploidization and the shift to apomictic reproduction are connected to changes in DNA cytosine-methylation. Cytosine-methylation is further sensitive to environmental conditions. We, therefore, hypothesize that DNA methylation patterns would differentiate within species with geographical parthenogenesis, i.e., when diploid sexual and polyploid apomictic populations exhibit different spatial distributions. On natural populations of the alpine plant Ranunculus kuepferi, we tested differences in methylation patterns across two cytotypes (diploid, tetraploid) and three reproduction modes (sexual, mixed, apomictic), and their correlation to environmental data and geographical distributions. We used methylation-sensitive amplified fragment-length polymorphism (methylation-sensitive AFLPs) and scored three types of epiloci. Methylation patterns differed independently between cytotypes versus modes of reproduction and separated three distinct combined groups (2x sexual + mixed, 4x mixed, and 4x apomictic), with differentiation of 4x apomicts in all epiloci. We found no global spatial autocorrelation, but instead correlations to elevation and temperature gradients in 22 and 36 epiloci, respectively. Results suggest that methylation patterns in R. kuepferi were altered by cold conditions during postglacial recolonization of the Alps, and by the concomitant shift to facultative apomixis, and by polyploidization. Obligate apomictic tetraploids at the highest elevations established a distinct methylation profile. Methylation patterns reflect an ecological gradient rather than the geographical differentiation.
    View Document Abstract
  • Journal Article

    Encoding Information From Rotations Too Rapid To Be Consciously Perceived as Rotating: A Replication of the Motion Bridging Effect on a Liquid Crystal Display 

    Stein, Maximilian; Fendrich, Robert; Mattler, Uwe
    i-Perception 2020; 11(3) p.1-11: Art. 204166952092511
    A ring of points that is rotated so rapidly is perceived as a stationary outline circle that can induce an illusory rotation with the same spin direction in a subsequently presented ring of stationary points. This motion bridging effect (MBE) demonstrates that motion information can be conveyed by temporal frequencies generally thought to exceed the processing capabilities of the human visual system. It was first described in displays shown with an analog oscilloscope, but the rapid rotation rates needed to produce the MBE have heretofore prevented it from being investigated with conventional raster scan monitors. Here, we demonstrate the MBE can be reliably generated using the new generation of 240 Hz LCD gaming monitors, and exhibits basic characteristics similar to those reported previously. These monitors therefore provide a readily available resource for research on the MBE and the studies of the visual processing rapid motions in general.
    View Document Abstract
  • Journal Article

    Apomixis Technology: Separating the Wheat from the Chaff 

    Hojsgaard, Diego
    Genes 2020; 11(4) p.1-24: Art. 411
    Projections indicate that current plant breeding approaches will be unable to incorporate the global crop yields needed to deliver global food security. Apomixis is a disruptive innovation by which a plant produces clonal seeds capturing heterosis and gene combinations of elite phenotypes. Introducing apomixis into hybrid cultivars is a game-changing development in the current plant breeding paradigm that will accelerate the generation of high-yield cultivars. However, apomixis is a developmentally complex and genetically multifaceted trait. The central problem behind current constraints to apomixis breeding is that the genomic configuration and molecular mechanism that initiate apomixis and guide the formation of a clonal seed are still unknown. Today, not a single explanation about the origin of apomixis o er full empirical coverage, and synthesizing apomixis by manipulating individual genes has failed or produced little success. Overall evidence suggests apomixis arise from a still unknown single event molecular mechanism with multigenic e ects. Disentangling the genomic basis and complex genetics behind the emergence of apomixis in plants will require the use of novel experimental approaches benefiting from Next Generation Sequencing technologies and targeting not only reproductive genes, but also the epigenetic and genomic configurations associated with reproductive phenotypes in homoploid sexual and apomictic carriers. A comprehensive picture of most regulatory changes guiding apomixis emergence will be central for successfully installing apomixis into the target species by exploiting genetic modification techniques.
    View Document Abstract
  • Journal Article

    Effects of Temperature Treatments on Cytosine-Methylation Profiles of Diploid and Autotetraploid Plants of the Alpine Species Ranunculus kuepferi (Ranunculaceae) 

    Syngelaki, Eleni; Schinkel, Christoph C. F.; Klatt, Simone; Hörandl, Elvira
    Frontiers in Plant Science 2020; 11 p.1-13: Art. 435
    The exposure to environmental stress can trigger epigenetic variation, which may have several evolutionary consequences. Polyploidy seems to affect the DNA methylation profiles. Nevertheless, it abides unclear whether temperature stress can induce methylations changes in different cytotypes and to what extent a treatment shift is translated to an epigenetic response. A suitable model system for studying these questions is Ranunculus kuepferi, an alpine perennial herb. Diploid and autotetraploid individuals of R. kuepferi were exposed to cold (+7°C day/+2°C night; frost treatment −1° C cold shocks for 3 nights per week) and warm (+15° day/+10°C night) conditions in climate growth chambers for two consecutive flowering periods and shifted from one condition to the other after the first flowering period. Methylation-sensitive amplified fragment-length polymorphism markers were applied for both years, to track down possible alterations induced by the stress treatments. Patterns of methylation suggested that cytotypes differed significantly in their profiles, independent from year of treatment. Likewise, the treatment shift had an impact on both cytotypes, resulting in significantly less epiloci, regardless the shift's direction. The AMOVAs revealed higher variation within than among treatments in diploids. In tetraploids, internally-methylated loci had a higher variation among than within treatments, as a response to temperature's change in both directions, and support the hypothesis of temperature stress affecting the epigenetic variation. Results suggest that the temperature-sensitivity of DNA methylation patterns shows a highly dynamic phenotypic plasticity in R. kuepferi, as both cytotypes responded to temperature shifts. Furthermore, ploidy level, even without effects of hybridization, has an important effect on epigenetic background variation, which may be correlated with the DNA methylation dynamics during cold acclimation.
    View Document Abstract
  • Journal Article

    A Comparison of the Affectiva iMotions Facial Expression Analysis Software With EMG for Identifying Facial Expressions of Emotion 

    Kulke, Louisa; Feyerabend, Dennis; Schacht, Annekathrin
    Frontiers in Psychology 2020; 11 p.1-9: Art. 329
    Human faces express emotions, informing others about their affective states. In order to measure expressions of emotion, facial Electromyography (EMG) has widely been used, requiring electrodes and technical equipment. More recently, emotion recognition software has been developed that detects emotions from video recordings of human faces. However, its validity and comparability to EMG measures is unclear. The aim of the current study was to compare the Affectiva Affdex emotion recognition software by iMotions with EMG measurements of the zygomaticus mayor and corrugator supercilii muscle, concerning its ability to identify happy, angry and neutral faces. Twenty participants imitated these facial expressions while videos and EMG were recorded. Happy and angry expressions were detected by both the software and by EMG above chance, while neutral expressions were more often falsely identified as negative by EMG compared to the software. Overall, EMG and software values correlated highly. In conclusion, Affectiva Affdex software can identify facial expressions and its results are comparable to EMG findings.
    View Document Abstract
  • Journal Article

    Ploidy-Dependent Effects of Light Stress on the Mode of Reproduction in the Ranunculus auricomus Complex (Ranunculaceae) 

    Ulum, Fuad Bahrul; Costa Castro, Camila; Hörandl, Elvira
    Frontiers in Plant Science 2020; 11 p.1-11: Art. 104
    Polyploidy in angiosperms is an influential factor to trigger apomixis, the reproduction of asexual seeds. Apomixis is usually facultative, which means that both sexual and apomictic seeds can be formed by the same plant. Environmental abiotic stress, e.g. light stress, can change the frequency of apomixis. Previous work suggested effects of stress treatments on meiosis and megasporogenesis. We hypothesized that polyploidy would alter the stress response and hence reproductive phenotypes of different cytotypes. The main aims of this research were to explore with prolonged photoperiods, whether polyploidy alters proportions of sexual ovule and sexual seed formation under light stress conditions. We used three facultative apomictic, pseudogamous cytotypes of the Ranunculus auricomus complex (diploid, tetraploid, and hexaploid). Stress treatments were applied by extended light periods (16.5 h) and control (10 h) in climate growth chambers. Proportions of apomeiotic vs. meiotic development in the ovule were evaluated with clearing methods, and mode of seed formation was examined by single seed flow cytometric seed screening (ssFCSS). We further studied pollen stainability to understand effects of pollen quality on seed formation. Results revealed that under extended photoperiod, all cytotypes produced significantly more sexual ovules than in the control, with strongest effects on diploids. The stress treatment affected neither the frequency of seed set nor the proportion of sexual seeds nor pollen quality. Successful seed formation appears to be dependent on balanced maternal: paternal genome contributions. Diploid cytotypes had mostly sexual seed formation, while polyploid cytotypes formed predominantly apomictic seeds. Pollen quality was in hexaploids better than in diploids and tetraploids. These findings confirm our hypothesis that megasporogenesis is triggered by light stress treatments. Comparisons of cytotypes support the hypothesis that ovule development in polyploid plants is less sensitive to prolonged photoperiods and responds to a lesser extent with sexual ovule formation. Polyploids may better buffer environmental stress, which releases the potential for aposporous ovule development from somatic cells, and may facilitate the establishment of apomictic seed formation.
    View Document Abstract
  • Journal Article

    Characterization of an Immunoglobulin Binding Protein (IbpM) From $\text{Mycoplasma pneumoniae}$ 

    Blötz, Cedric; Singh, Neil; Dumke, Roger; Stülke, Jörg
    Frontiers in Microbiology 2020; 11 p.1-12: Art. 685
    Bacteria evolved many ways to invade, colonize and survive in the host tissue. Such complex infection strategies of other bacteria are not present in the cell-wall less $\textit{Mycoplasmas}$. Due to their strongly reduced genomes, these bacteria have only a minimal metabolism. $\textit{Mycoplasma pneumoniae}$ is a pathogenic bacterium using its virulence repertoire very efficiently, infecting the human lung. $\textit{M. pneumoniae}$ can cause a variety of conditions including fever, inflammation, atypical pneumoniae, and even death. Due to its strongly reduced metabolism, $\textit{M. pneumoniae}$ is dependent on nutrients from the host and aims to persist as long as possible, resulting in chronic diseases. $\textit{Mycoplasmas}$ evolved strategies to subvert the host immune system which involve proteins fending off immunoglobulins (Igs). In this study, we investigated the role of MPN400 as the putative factor responsible for Ig-binding and host immune evasion. MPN400 is a cell-surface localized protein which binds strongly to human IgG, IgA, and IgM. We therefore named the protein MPN400 immunoglobulin binding protein of $\textit{Mycoplasma}$ (IbpM). A strain devoid of IbpM is slightly compromised in cytotoxicity. Taken together, our study indicates that $\textit{M. pneumoniae}$ uses a refined mechanism for immune evasion.
    View Document Abstract
  • Journal Article

    The Economy of Canopy Space Occupation and Shade Production in Early- to Late-Successional Temperate Tree Species and Their Relation to Productivity 

    Leuschner, Christoph; Hagemeier, Marc
    Forests 2020; 11(3) p.1-18: Art. 317
    Light capture is linked to occupation of canopy space by tree crowns, which requires investment of carbon and nutrients. We hypothesize that (i) late-successional trees invest more in casting shade than in occupying space than early-successional trees, and (ii) shade production and crown volume expansion are generally greater in more productive species. For six Central European early-successional (Betula pendula, Pinus sylvestris), mid/late-successional (Quercus petraea, Carpinus betulus), and late-successional tree species (Tilia cordata, Fagus sylvatica), we measured through full-tree harvests (1) crown volume, (2) the costs of canopy space exploration (carbon (C) and nutrients invested to fill crown volume), of space occupation (annual foliage production per volume), and of shade production (foliage needed to reduce light transmittance), and (3) related the costs to aboveground productivity (ANPP). The C and nutrient costs of canopy volume exploration and occupation were independent of the species’ seral stage, but increased with ANPP. In contrast, the cost of shade production decreased from early-to late-successional species, suggesting that the economy of shade production is more decisive for the competitive superiority of late-successional species than the economy of canopy space exploration and occupation.
    View Document Abstract
  • Journal Article

    Biomass, Morphology, and Dynamics of the Fine Root System Across a 3,000-M Elevation Gradient on Mt. Kilimanjaro 

    Sierra Cornejo, Natalia; Hertel, Dietrich; Becker, Joscha N.; Hemp, Andreas; Leuschner, Christoph
    Frontiers in Plant Science 2020; 11 p.1-16: Art. 13
    Fine roots (≤2 mm) consume a large proportion of photosynthates and thus play a key role in the global carbon cycle, but our knowledge about fine root biomass, production, and turnover across environmental gradients is insufficient, especially in tropical ecosystems. Root system studies along elevation transects can produce valuable insights into root trait-environment relationships and may help to explore the evidence for a root economics spectrum (RES) that should represent a trait syndrome with a trade-off between resource acquisitive and conservative root traits. We studied fine root biomass, necromass, production, and mean fine root lifespan (the inverse of fine root turnover) of woody plants in six natural tropical ecosystems (savanna, four tropical mountain forest types, tropical alpine heathland) on the southern slope of Mt. Kilimanjaro (Tanzania) between 900 and 4,500 m a.s.l. Fine root biomass and necromass showed a unimodal pattern along the slope with a peak in the moist upper montane forest (~2,800 m), while fine root production varied little between savanna and upper montane forest to decrease toward the alpine zone. Root:shoot ratio (fine root biomass and production related to aboveground biomass) in the tropical montane forest increased exponentially with elevation, while it decreased with precipitation and soil nitrogen availability (decreasing soil C:N ratio). Mean fine root lifespan was lowest in the ecosystems with pronounced resource limitation (savanna at low elevation, alpine heathland at high elevation) and higher in the moist and cool forest belt (~1,800–3,700 m). The variation in root traits across the elevation gradient fits better with the concept of a multi-dimensional RES, as root tissue density and specific root length showed variable relations to each other, which does not agree with a simple trade-off between acquisitive and conservative root traits. In conclusion, despite large variation in fine root biomass, production, and morphology among the different plant species and ecosystems, a general belowground shift in carbohydrate partitioning is evident from 900 to 4,500 m a.s.l., suggesting that plant growth is increasingly limited by nutrient (probably N) shortage toward higher elevations.
    View Document Abstract
  • Journal Article

    Notes on the leaf insects of the genus Phyllium of Sumatra and Java, Indonesia, including the description of two new species with purple coxae (Phasmatodea, Phylliidae) 

    Cumming, Royce T.; Bank, Sarah; Le Tirant, Stephane; Bradler, Sven; Cumming, Royce T.; Bank, Sarah; Le Tirant, Stephane; Bradler, Sven; Cumming, Royce T.; Bank, Sarah; et al.
    Le Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, SvenCumming, Royce T.Bank, SarahLe Tirant, StephaneBradler, Sven
    ZooKeys 2020; 913 p.89-126
    Within the last two years, the leaf insects of the genus Phyllium of both the islands of Java and Sumatra have been reviewed extensively based on morphological observations. However, cryptic species which cannot be differentiated morphologically may be present among the various populations. Since it has frequently been demonstrated that analyses based on molecular data can bring clarity in such cases, we conducted a phylogenetic analysis based on three genes (nuclear gene 28S and mitochondrial genes COI and 16S) from the Phyllium species of these islands. The results show distinct molecular divergence for several populations and suggest the presence of two new cryptic species, morphologically inseparable from Phyllium hausleithneri Brock, 1999. From Sumatra, the population originally thought to be a range expansion for Phyllium hausleithneri, is now here described as Phyllium nisus sp. nov., with the only consistent morphological difference being the color of the eggs between the two populations (dark brown in P. hausleithneri and tan in P. nisus sp. nov.). Further, an additional population with purple coxae from Java was morphologically examined and found to have no consistent features to separate it morphologically from the other purple coxae species. This cryptic species from Java was however shown to be molecularly distinct from the other purple coxae populations from Sumatra and Peninsular Malaysia and is here described as Phyllium gardabagusi sp. nov. In addition, Phyllium giganteum is here officially reported from Java for the first time based on both historic and modern records of male specimens.
    View Document Abstract
  • Journal Article

    Dbp5/DDX19 between Translational Readthrough and Nonsense Mediated Decay 

    Beißel, Christian; Grosse, Sebastian; Krebber, Heike
    International Journal of Molecular Sciences 2020; 21(3) p.1-13: Art. 1085
    The DEAD-box protein Dbp5 (human DDX19) remodels RNA-protein complexes. Dbp5 functions in ribonucleoprotein export and translation termination. Termination occurs, when the ribosome has reached a stop codon through the Dbp5 mediated delivery of the eukaryotic termination factor eRF1. eRF1 contacts eRF3 upon dissociation of Dbp5, resulting in polypeptide chain release and subsequent ribosomal subunit splitting. Mutations in DBP5 lead to stop codon readthrough, because the eRF1 and eRF3 interaction is not controlled and occurs prematurely. This identifies Dbp5/DDX19 as a possible potent drug target for nonsense suppression therapy. Neurodegenerative diseases and cancer are caused in many cases by the loss of a gene product, because its mRNA contained a premature termination codon (PTC) and is thus eliminated through the nonsense mediated decay (NMD) pathway, which is described in the second half of this review. We discuss translation termination andNMDin the light of Dbp5/DDX19 and subsequently speculate on reducing Dbp5/DDX19 activity to allow readthrough of the PTC and production of a full-length protein to detract the RNA from NMD as a possible treatment for diseases.
    View Document Abstract

View more