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Simple Summary Gliomas are heterogenous types of cancer, therefore the therapy should be personalized and targeted toward specific pathways. We developed a methodology that corrected strong batch effects from The Cancer Genome Atlas datasets and estimated glioma grade-specific co-enrichment mechanisms using machine learning. Our findings created hypotheses for annotations, e.g., pathways, that should be considered as therapeutic targets. Gliomas develop and grow in the brain and central nervous system. Examining glioma grading processes is valuable for improving therapeutic challenges. One of the most extensive repositories storing transcriptomics data for gliomas is The Cancer Genome Atlas (TCGA). However, such big cohorts should be processed with caution and evaluated thoroughly as they can contain batch and other effects. Furthermore, biological mechanisms of cancer contain interactions among biomarkers. Thus, we applied an interpretable machine learning approach to discover such relationships. This type of transparent learning provides not only good predictability, but also reveals co-predictive mechanisms among features. In this study, we corrected the strong and confounded batch effect in the TCGA glioma data. We further used the corrected datasets to perform comprehensive machine learning analysis applied on single-sample gene set enrichment scores using collections from the Molecular Signature Database. Furthermore, using rule-based classifiers, we displayed networks of co-enrichment related to glioma grades. Moreover, we validated our results using the external glioma cohorts. We believe that utilizing corrected glioma cohorts from TCGA may improve the application and validation of any future studies. Finally, the co-enrichment and survival analysis provided detailed explanations for glioma progression and consequently, it should support the targeted treatment.
Spatially explicit knowledge on grassland extent and management is critical to understand and monitor the impact of grassland use intensity on ecosystem services and biodiversity. While regional studies allow detailed insights into land use and ecosystem service interactions, information on a national scale can aid biodiversity assessments. However, for most European countries this information is not yet widely available. We used an analysis-ready-data cube that contains dense time series of co-registered Sentinel-2 and Landsat 8 data, covering the extent of Germany. We propose an algorithm that detects mowing events in the time series based on residuals from an assumed undisturbed phenology, as an indicator of grassland use intensity. A self-adaptive ruleset enabled to account for regional variations in land surface phenology and non-stationary time series on a pixelbasis. We mapped mowing events for the years from 2017 to 2020 for permanent grassland areas in Germany. The results were validated on a pixel level in four of the main natural regions in Germany based on reported mowing events for a total of 92 (2018) and 78 (2019) grassland parcels. Results for 2020 were evaluated with combined time series of Landsat, Sentinel-2 and PlanetScope data. The mean absolute percentage error between detected and reported mowing events was on average 40% (2018), 36% (2019) and 35% (2020). Mowing events were on average detected 11 days (2018), 7 days (2019) and 6 days (2020) after the reported mowing. Performance measures varied between the different regions of Germany, and lower accuracies were found in areas that are revisited less frequently by Sentinel-2. Thus, we assessed the influence of data availability and found that the detection of mowing events was less influenced by data availability when at least 16 cloud-free observations were available in the grassland season. Still, the distribution of available observations throughout the season appeared to be critical. On a national scale our results revealed overall higher shares of less intensively mown grasslands and smaller shares of highly intensively managed grasslands. Hotspots of the latter were identified in the alpine foreland in Southern Germany as well as in the lowlands in the Northwest of Germany. While these patterns were stable throughout the years, the results revealed a tendency to lower management intensity in the extremely dry year 2018. Our results emphasize the ability of the approach to map the intensity of grassland management throughout large areas despite variations in data availability and environmental conditions.
Monitoring agricultural systems becomes increasingly important in the context of global challenges like climate change, biodiversity loss, population growth, and the rising demand for agricultural products. High-resolution, national-scale maps of agricultural land are needed to develop strategies for future sustainable agriculture.
However, the characterization of agricultural land cover over large areas and for multiple years remains challenging due to the locally diverse and temporally variable characteristics of cultivated land.
We here propose a workflow for generating national agricultural land cover maps on a yearly basis that accounts for varying environmental conditions. We tested the approach by mapping 24 agricultural land cover classes in Germany for the three years 2017, 2018, and 2019, in which the meteorological conditions strongly differed.
We used a random forest classifier and dense time series data from Sentinel-2 and Landsat 8 in combination with monthly Sentinel-1 composites and environmental data and evaluated the relative importance of optical, radar, and environmental data.
Our results show high overall accuracy and plausible class accuracies for the most dominant crop types across different years despite the strong inter-annual meteorological variability and the presence of drought and nondrought years. The maps show high spatial consistency and good delineation of field parcels.
Combining optical, SAR, and environmental data increased overall accuracies by 6% to 10% compared to single sensor approaches, in which optical data outperformed SAR. Overall accuracy ranged between 78% and 80%, and the mapped areas aligned well with agricultural statistics at the regional and national level.
Based on the multi-year dataset we mapped major crop sequences of cereals and leaf crops. Most crop sequences were dominated by winter cereals followed by summer cereals.
Monocultures of summer cereals were mainly revealed in the Northwest of Germany. We showcased that high spatial and thematic detail in combination with annual mapping will stimulate research on crop cycles and studies to assess the impact of environmental policies on management decisions.
Our results demonstrate the capabilities of integrated optical time series and SAR data in combination with variables describing local and seasonal environmental conditions for annual large-area crop type mapping.
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.
The Brachionus calyciflorus species complex was recently subdivided into four species, but genetic resources to resolve phylogenetic relationships within this complex are still lacking. We provide two complete mitochondrial (mt) genomes from B. calyciflorus sensu stricto (Germany, USA) and the mt coding sequences (cds) from a German B. fernandoi. Phylogenetic analysis placed our B. calyciflorus sensu stricto strains close to the published genomes of B. calyciflorus, forming the putative sister species to B. fernandoi. Global representatives of B. calyciflorus sensu stricto (i.e. Europe, USA, and China) are genetically closer related to each other than to B. fernandoi (average pairwise nucleotide diversity 0.079 intraspecific vs. 0.254 interspecific).
Air chemistry is affected by the emission of biogenic volatile organic compounds (BVOCs), which originate from almost all plants in varying qualities and quantities. They also vary widely among different crops, an aspect that has been largely neglected in emission inventories. In particular, bioenergy-related species can emit mixtures of highly reactive compounds that have received little attention so far. For such species, long-term field observations of BVOC exchange from relevant crops covering different phenological phases are scarcely available. Therefore, we measured and modeled the emission of three prominent European bioenergy crops (maize, ryegrass, and oil-seed rape) for full rotations in north-eastern Germany. Using a proton transfer reaction-mass spectrometer combined with automatically moving large canopy chambers, we were able to quantify the characteristic seasonal BVOC flux dynamics of each crop species. The measured BVOC fluxes were used to parameterize and evaluate the BVOC emission module (JJv) of the physiology-oriented LandscapeDNDC model, which was enhanced to cover de novo emissions as well as those from plant storage pools. Parameters are defined for each compound individually. The model is used for simulating total compound-specific reactivity over several years and also to evaluate the importance of these emissions for air chemistry. We can demonstrate substantial differences between the investigated crops with oil-seed rape having 37-fold higher total annual emissions than maize. However, due to a higher chemical reactivity of the emitted blend in maize, potential impacts on atmospheric OH-chemistry are only 6-fold higher.
The study of diamond frogs (genus Rhombophryne, endemic to Madagascar) has been historically hampered by the paucity of available specimens, because of their low detectability in the field. Over the last 10 years, 13 new taxa have been described, and 20 named species are currently recognized. Nevertheless, undescribed diversity within the genus is probably large, calling for a revision of the taxonomic identification of published records and an update of the known distribution of each lineage. Here we generate DNA sequences of the mitochondrial 16S rRNA gene of all specimens available to us, revise the genetic data from public databases, and report all deeply divergent mitochondrial lineages of Rhombophryne identifiable from these data. We also generate a multi-locus dataset (including five mitochondrial and eight nuclear markers; 9844 bp) to infer a species-level phylogenetic hypothesis for the diversification of this genus and revise the distribution of each lineage. We recognize a total of 10 candidate species, two of which are identified here for the first time. The genus Rhombophryne is here proposed to be divided into six main species groups, and phylogenetic relationships among some of them are not fully resolved. These frogs are primarily distributed in northern Madagascar, and most species are known from only few localities. A previous record of this genus from the Tsingy de Bemaraha (western Madagascar) is interpreted as probably due to a mislabelling and should not be considered further unless confirmed by new data. By generating this phylogenetic hypothesis and providing an updated distribution of each lineage, our findings will facilitate future species descriptions, pave the way for evolutionary studies, and provide valuable information for the urgent conservation of diamond frogs.
Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.
Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. 'Thermomemory' is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/ CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Ara bidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like atafl, anac055 mutants show improved thermomemory, revealing a potential co-control of both NACTFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.
Background: Network models are useful tools for researchers to simplify and understand investigated systems. Yet, the assessment of methods for network construction is often uncertain. Random resampling simulations can aid to assess methods, provided synthetic data exists for reliable network construction.
Objectives: We implemented a new Monte Carlo algorithm to create simulated data for network reconstruction, tested the influence of adjusted parameters and used simulations to select a method for network model estimation based on real-world data. We hypothesized, that reconstructs based on Monte Carlo data are scored at least as good compared to a benchmark.
Methods: Simulated data was generated in R using the Monte Carlo algorithm of the mcgraph package. Benchmark data was created by the huge package. Networks were reconstructed using six estimator functions and scored by four classification metrics. For compatibility tests of mean score differences, Welch’s t-test was used. Network model estimation based on real-world data was done by stepwise selection.
Samples: Simulated data was generated based on 640 input graphs of various types and sizes. The real-world dataset consisted of 67 medieval skeletons of females and males from the region of Refshale (Lolland) and Nordby (Jutland) in Denmark.
Results: Results after t-tests and determining confidence intervals (CI95%) show, that evaluation scores for network reconstructs based on the mcgraph package were at least as good compared to the benchmark huge. The results even indicate slightly better scores on average for the mcgraph package.
Conclusion: The results confirmed our objective and suggested that Monte Carlo data can keep up with the benchmark in the applied test framework. The algorithm offers the feature to use (weighted) un- and directed graphs and might be useful for assessing methods for network construction.
Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste
(2022)
Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill.
Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources.
The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol.
The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6%) and Nocardioides dubius KSL-104(T) (98.3%).
The genomic DNA G+C content of strain NGK65(T) was 68.2%.
Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides.
Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed.
The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)).
The discovery that certain diseases have specific miRNA signatures which correspond to disease progression opens a new biomarker category. The detection of these small non-coding RNAs is performed routinely using body fluids or tissues with real-time PCR, next-generation sequencing, or amplification-based miRNA assays. Antibody-based detection systems allow an easy onset handling compared to PCR or sequencing and can be considered as alternative methods to support miRNA diagnostic in the future. In this study, we describe the generation of a camelid heavy-chain-only antibody specifically recognizing miRNAs to establish an antibody-based detection method. The generation of nucleic acid-specific binders is a challenge. We selected camelid binders via phage display, expressed them as VHH as well as full-length antibodies, and characterized the binding to several miRNAs from a signature specific for dilated cardiomyopathy. The described workflow can be used to create miRNA-specific binders and establish antibody-based detection methods to provide an additional way to analyze disease-specific miRNA signatures.
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.
The terrestrial ecosystem in the Yellow River Source Area (YRSA) is sensitive to climate change and human impacts, although past vegetation change and the degree of human disturbance are still largely unknown. A 170-cm-long sediment core covering the last 7,400 years was collected from Lake Xingxinghai (XXH) in the YRSA. Pollen, together with a series of other environmental proxies (including grain size, total organic carbon (TOC) and carbonate content), were analysed to explore past vegetation and environmental changes for the YRSA. Dominant and common pollen components-Cyperaceae, Poaceae, Artemisia, Chenopodiaceae and Asteraceae-are stable throughout the last 7,400 years. Slight vegetation change is inferred from an increasing trend of Cyperaceae and decreasing trend of Poaceae, suggesting that alpine steppe was replaced by alpine meadow at ca. 3.5 ka cal bp. The vegetation transformation indicates a generally wetter climate during the middle and late Holocene, which is supported by increased amounts of TOC and Pediastrum (representing high water-level) and is consistent with previous past climate records from the north-eastern Tibetan Plateau. Our results find no evidence of human impact on the regional vegetation surrounding XXH, hence we conclude the vegetation change likely reflects the regional climate signal.
Dictyostelium cells undergo a semi-closed mitosis, during which the nuclear envelope (NE) persists; however, free diffusion between the cytoplasm and the nucleus takes place. To permit the formation of the mitotic spindle, the nuclear envelope must be permeabilized in order to allow diffusion of tubulin dimers and spindle assembly factors into the nucleus. In Aspergillus, free diffusion of proteins between the cytoplasm and the nucleus is achieved by a partial disassembly of the nuclear pore complexes (NPCs) prior to spindle assembly. In order to determine whether this is also the case in Dictyostelium, we analysed components of the NPC by immunofluorescence microscopy and live cell imaging and studied their behaviour during interphase and mitosis. We observed that the NPCs are absent from the contact area of the nucleoli and that some nucleoporins also localize to the centrosome and the spindle poles. In addition, we could show that, during mitosis, the central FG protein NUP62, two inner ring components and Gle1 depart from the NPCs, while all other tested NUPs remained at the NE. This leads to the conclusion that indeed a partial disassembly of the NPCs takes place, which contributes to permeabilisation of the NE during semi-closed mitosis.
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.
Background
Animal personality has emerged as a key concept in behavioral ecology. While many studies have demonstrated the influence of personality traits on behavioral patterns, its quantification, especially in wild animal populations, remains a challenge. Only a few studies have established a link between personality and recurring movements within home ranges, although these small-scale movements are of key importance for identifying ecological interactions and forming individual niches. In this regard, differences in space use among individuals might reflect different exploration styles between behavioral types along the shy-bold continuum.
Methods
We assessed among-individual differences in behavior in the European hare (Lepus europaeus), a characteristic mammalian herbivore in agricultural landscapes using a standardized box emergence test for captive and wild hares. We determined an individuals’ degree of boldness by measuring the latencies of behavioral responses in repeated emergence tests in captivity. During capture events of wild hares, we conducted a single emergence test and recorded behavioral responses proven to be stable over time in captive hares. Applying repeated novel environment tests in a near-natural enclosure, we further quantified aspects of exploration and activity in captive hares. Finally, we investigated whether and how this among-individual behavioral variation is related to general activity and space use in a wild hare population. Wild and captive hares were treated similarly and GPS-collared with internal accelerometers prior to release to the wild or the outdoor enclosure, respectively. General activity was quantified as overall dynamic body acceleration (ODBA) obtained from accelerometers. Finally, we tested whether boldness explained variation in (i) ODBA in both settings and (ii) variation in home ranges and core areas across different time scales of GPS-collared hares in a wild population.
Results
We found three behavioral responses to be consistent over time in captive hares. ODBA was positively related to boldness (i.e., short latencies to make first contact with the new environment) in both captive and wild hares. Space use in wild hares also varied with boldness, with shy individuals having smaller core areas and larger home ranges than bold conspecifics (yet in some of the parameter space, this association was just marginally significant).
Conclusions
Against our prediction, shy individuals occupied relatively large home ranges but with small core areas. We suggest that this space use pattern is due to them avoiding risky, and energy-demanding competition for valuable resources. Carefully validated, activity measurements (ODBA) from accelerometers provide a valuable tool to quantify aspects of animal personality along the shy-bold continuum remotely. Without directly observing—and possibly disturbing—focal individuals, this approach allows measuring variability in animal personality, especially in species that are difficult to assess with experiments. Considering that accelerometers are often already built into GPS units, we recommend activating them at least during the initial days of tracking to estimate individual variation in general activity and, if possible, match them with a simple novelty experiment. Furthermore, information on individual behavioral types will help to facilitate mechanistic understanding of processes that drive spatial and ecological dynamics in heterogeneous landscapes.
Review exploring the regulation of PHYTOCHROME-INTERACTING FACTORS by light, their role in abiotic stress tolerance and plant architecture, and their influence on crop productivity.
Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.
Biological dinitrogen (N-2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments.
Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water.
We argue that planktonic aggregates are important loci for energetically-expensive N-2 fixation by NCDs and propose a conceptual framework for aggregate-associated N-2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.
Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.
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.
Pollen-based biome reconstruction on the Qinghai-Tibetan Plateau during the past 15,000 years
(2022)
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.
Land-use intensification is the main factor for the catastrophic decline of insect pollinators. However, land-use intensification includes multiple processes that act across various scales and should affect pollinator guilds differently depending on their ecology. We aimed to reveal how two main pollinator guilds, wild bees and hoverflies, respond to different land-use intensification measures, that is, arable field cover (AFC), landscape heterogeneity (LH), and functional flower composition of local plant communities as a measure of habitat quality. We sampled wild bees and hoverflies on 22 dry grassland sites within a highly intensified landscape (NE Germany) within three campaigns using pan traps. We estimated AFC and LH on consecutive radii (60-3000 m) around the dry grassland sites and estimated the local functional flower composition. Wild bee species richness and abundance was positively affected by LH and negatively by AFC at small scales (140-400 m). In contrast, hoverflies were positively affected by AFC and negatively by LH at larger scales (500-3000 m), where both landscape parameters were negatively correlated to each other. At small spatial scales, though, LH had a positive effect on hoverfly abundance. Functional flower diversity had no positive effect on pollinators, but conspicuous flowers seem to attract abundance of hoverflies. In conclusion, landscape parameters contrarily affect two pollinator guilds at different scales. The correlation of landscape parameters may influence the observed relationships between landscape parameters and pollinators. Hence, effects of land-use intensification seem to be highly landscape-specific.
Land-use intensification is the main factor for the catastrophic decline of insect pollinators. However, land-use intensification includes multiple processes that act across various scales and should affect pollinator guilds differently depending on their ecology. We aimed to reveal how two main pollinator guilds, wild bees and hoverflies, respond to different land-use intensification measures, that is, arable field cover (AFC), landscape heterogeneity (LH), and functional flower composition of local plant communities as a measure of habitat quality. We sampled wild bees and hoverflies on 22 dry grassland sites within a highly intensified landscape (NE Germany) within three campaigns using pan traps. We estimated AFC and LH on consecutive radii (60–3000 m) around the dry grassland sites and estimated the local functional flower composition. Wild bee species richness and abundance was positively affected by LH and negatively by AFC at small scales (140–400 m). In contrast, hoverflies were positively affected by AFC and negatively by LH at larger scales (500–3000 m), where both landscape parameters were negatively correlated to each other. At small spatial scales, though, LH had a positive effect on hoverfly abundance. Functional flower diversity had no positive effect on pollinators, but conspicuous flowers seem to attract abundance of hoverflies. In conclusion, landscape parameters contrarily affect two pollinator guilds at different scales. The correlation of landscape parameters may influence the observed relationships between landscape parameters and pollinators. Hence, effects of land-use intensification seem to be highly landscape-specific.
Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems.
Background: Child growth is a dynamic process. When measured at short intervals, children’s growth shows characteristic patterns that can be of great importance for clinical purposes.
Objective: To study whether measuring height on a daily basis using an APP is practicable and user-friendly.
Methods: Recruitment took place via Snowball Sampling. Thirteen out of 14 contacted families signed up for a study period of 12 weeks with altogether 22 healthy children aged 3 to 13 years (response rate 93%). The study started with a visit to the family home for the setup of the measurement site, conventional height measuring and initial training of the new measurement process. Follow-up appointments were made at four, eight and 12 weeks. The children’s height was measured at daily intervals at their family homes over a period of three months.
Results: The parents altogether recorded 1704 height measurements and meticulously documented practicability and problems when using the device.
A 93% response rate in recruitment was achieved by maintaining a high motivation within the families. Contact with the principal investigator was permanently available, including open communication, personal training and attendance during the appointments at the family homes.
Conclusion: Measuring height by photographic display is interesting for children and parents and can be used for height measurements at home. A positive response rate of 13 out of 14 families with altogether 22 children highlights feasible recruitment and the high convenience and user-friendliness of daily APP-supported height measurements. Daily APP measurements appear to be a promising new tool for longitudinal growth studies.
PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments
(2022)
Recently, mass cytometry has enabled quantification of up to 50 parameters for millions of cells per sample. It remains a challenge to analyze such high-dimensional data to exploit the richness of the inherent information, even though many valuable new analysis tools have already been developed. We propose a novel algorithm "pattern recognition of immune cells (PRI)" to tackle these high-dimensional protein combinations in the data. PRI is a tool for the analysis and visualization of cytometry data based on a three or more-parametric binning approach, feature engineering of bin properties of multivariate cell data, and a pseudo-multiparametric visualization. Using a publicly available mass cytometry dataset, we proved that reproducible feature engineering and intuitive understanding of the generated bin plots are helpful hallmarks for re-analysis with PRI. In the CD4(+)T cell population analyzed, PRI revealed two bin-plot patterns (CD90/CD44/CD86 and CD90/CD44/CD27) and 20 bin plot features for threshold-independent classification of mice concerning ineffective and effective tumor treatment. In addition, PRI mapped cell subsets regarding co-expression of the proliferation marker Ki67 with two major transcription factors and further delineated a specific Th1 cell subset. All these results demonstrate the added insights that can be obtained using the non-cluster-based tool PRI for re-analyses of high-dimensional cytometric data.
Assessing the risk of yield loss in African drought-affected regions is key to identify feasible solutions for stable crop production. Recent studies have demonstrated that Copula-based probabilistic methods are well suited for such assessment owing to reasonably inferring important properties in terms of exceedance probability and joint dependence of different characterization. However, insufficient attention has been given to quantifying the probability of yield loss and determining the contribution of climatic factors. This study applies the Copula theory to describe the dependence between drought and crop yield anomalies for rainfed maize, millet, and sorghum crops in sub-Saharan Africa (SSA). The environmental policy integrated climate model, calibrated with Food and Agriculture Organization country-level yield data, was used to simulate yields across SSA (1980-2012). The results showed that the severity of yield loss due to drought had a higher magnitude than the severity of drought itself. Sensitivity analysis to identify factors contributing to drought and high-temperature stresses for all crops showed that the amount of precipitation during vegetation and grain filling was the main driver of crop yield loss, and the effect of temperature was stronger for sorghum than for maize and millet. The results demonstrate the added value of probabilistic methods for drought-impact assessment. For future studies, we recommend looking into factors influencing drought and high-temperature stresses as individual/concurrent climatic extremes.
Leaf area index (LAI) is a key variable in understanding and modeling crop-environment interactions.
With the advent of increasingly higher spatial resolution satellites and sensors mounted on remotely piloted aircrafts (RPAs), the use of remote sensing in precision agriculture is becoming more common.
Since also the availability of methods to retrieve LAI from image data have also drastically expanded, it is necessary to test simultaneously as many methods as possible to understand the advantages and disadvantages of each approach.
Ground-based LAI data from three years of barley experiments were related to remote sensing information using vegetation indices (VI), machine learning (ML) and radiative transfer models (RTM), to assess the relative accuracy and efficacy of these methods.
The optimized soil adjusted vegetation index and a modified version of the Weighted Difference Vegetation Index performed slightly better than any other retrieval method. However, all methods yielded coefficients of determination of around 0.7 to 0.9.
The best performing machine learning algorithms achieved higher accuracies when four Sentinel-2 bands instead of 12 were used.
Also, the good performance of VIs and the satisfactory performance of the 4-band RTM, strongly support the synergistic use of satellites and RPAs in precision agriculture. One of the methods used, Sen2-Agri, an open source ML-RTM-based operational system, was also able to accurately retrieve LAI, although it is restricted to Sentinel-2 and Landsat data.
This study shows the benefits of testing simultaneously a broad range of retrieval methods to monitor crops for precision agriculture.
Marine macroalgae are a key primary producer in coastal ecosystems, but are often overlooked in blue carbon inventories. Large quantities of macroalgal detritus deposit on beaches, but the fate of wrack carbon (C) is little understood. If most of the wrack carbon is respired back to CO2, there would be no net carbon sequestration. However, if most of the wrack carbon is converted to bicarbonate (alkalinity) or refractory DOC, wrack deposition would represent net carbon sequestration if at least part of the metabolic products (e.g., reduced Fe and S) are permanently removed (i.e., long-term burial) and the DOC is not remineralised. To investigate the release of macroalgal C via porewater and its potential to contribute to C sequestration (blue carbon), we monitored the degradation of Ecklonia radiata in flow-through mesocosms simulating tidal flushing on sandy beaches. Over 60 days, 81% of added E. radiata organic matter (OM) decomposed. Per 1 mol of detritus C, the degradation produced 0.48 +/- 0.34 mol C of dissolved organic carbon (DOC) (59%) and 0.25 +/- 0.07 mol C of dissolved inorganic carbon (DIC) (31%) in porewater, and a small amount of CO2 (0.3 +/- 0.0 mol C; ca. 3%) which was emitted to the atmosphere. A significant amount of carbonate alkalinity was found in porewater, equating to 33% (0.27 +/- 0.05 mol C) of the total degraded C. The degradation occurred in two phases. In the first phase (days 0-3), 27% of the OM degraded, releasing highly reactive DOC. In the second phase (days 4-60), the labile DOC was converted to DIC. The mechanisms underlying E. radiata degradation were sulphate reduction and ammonification. It is likely that the carbonate alkalinity was primarily produced through sulphate reduction. The formation of carbonate alkalinity and semi-labile or refractory DOC from beach wrack has the potential to play an overlooked role in coastal carbon cycling and contribute to marine carbon sequestration.
Die Professionsorientierung der Lehramtsstudiengänge ist ein zentrales Anliegen der universitären Potsdamer Lehrkräftebildung. Seit 1999 finden Evaluationen zur Professionsorientierung statt, die Diskrepanzen zwischen der gewünschten und der erfahrenen Professionsorientierung durch die Studierenden aufzeigen. Im Wintersemester 2013/14 wurden neue Studiengänge an der Universität Potsdam eingeführt. Inwieweit damit auch eine stärkere Professionsorientierung und ein stärkerer Berufsbezug erfolgt ist, ist bislang ungeklärt. In einer Onlinebefragung im Dezember 2018 wurden Studierende der Lehramtsstudiengänge der Universität Potsdam gebeten, die inhaltliche Gestaltung der Lehramtsstudiengänge sowie die Professionsorientierung der Praxisphasen, die Betreuung und Beratung im Rahmen der Praktika, den Nutzen der Praktika für Studium und Beruf und ihre Lehrer:innenkompetenz einzuschätzen. Der Beitrag stellt erste empirische Analysen dar und diskutiert Anregungen zur Weiterentwicklung der Studiengänge mit Bezug auf die Praxisstudien.
Several morphological and mitochondrial lineages of the alpine ringlet butterfly species Erebia pronoe have been described, indicating a complex phylogenetic structure. However, the existing data were insufficient and allow neither a reconstruction of the biogeographic history, nor an assessment of the genetic lineages. Therefore, we analysed mitochondrial (COI, NDI) and nuclear (EF1 alpha, RPS5) gene sequences and compared them with sequences from the sister species Erebia melas. Additionally, we combined this information with morphometric data of the male genitalia and the infection patterns with Wolbachia strains, based on a WSP analysis. We obtained a distinct phylogeographic structure within the E. pronoe-melas complex with eight well-distinguishable geographic groups, but also a remarkable mito-nuclear discordance. The mito-nuclear discordance in E. melas and E. pronoe glottis can be explained by different ages of Wolbachia infections with different Wolbachia strains, associated selective sweeps, and hybridisation inhibition. Additionally, we found indications for incipient speciation of E. pronoe glottis in the Pyrenees and a pronounced range dynamic within and among the other high mountain systems of Europe. Our results emphasize the importance of combined approaches in reconstructing biogeographic patterns and evaluating phylogeographic splits.
Quantifying the capacity for contemporary trait changes to drive intermittent predator-prey cycles
(2022)
A large and growing body of theory has demonstrated how the presence of trait variation in prey or predator populations may affect the amplitude and phase of predator-prey cycles. Less attention has been given to so-called intermittent cycles, in which predator-prey oscillations recurrently disappear and re-appear, despite such dynamics being observed in empirical systems and modeling studies. A comprehensive understanding of the conditions under which trait changes may drive intermittent predator-prey dynamics, as well as their potential ecological implications, is therefore missing. Here we provide a first systematic analysis of the eco-evolutionary conditions that may give rise to intermittent predator-prey cycles, investigating 16 models that incorporate different types of trait variation within prey, predators, or both. Our results show that intermittent dynamics often arise through predator-prey coevolution, but only very rarely when only one trophic level can adapt. Additionally, the frequency of intermittent cycles depends on the source of trait variation (genetic variation or phenotypic plasticity) and the genetic architecture (Mendelian or quantitative traits), with intermittency occurring most commonly through Mendelian evolution, and very rarely through phenotypic plasticity. Further analysis identified three necessary conditions for when trait variation can drive intermittent cycles. First, the intrinsic stability of the predator-prey system must depend on the traits of prey, predators, or both. Second, there must be a mechanism causing the recurrent alternation between stable and unstable states, leading to a "trait" cycle superimposed on the population dynamics. Finally, these trait dynamics must be significantly slower than the predator-prey cycles. We show how these conditions explain all the abovementioned patterns. We further show an important unexpected consequence of these necessary conditions: they are most easily met when intraspecific trait variation is at high risk of being lost. As trait diversity is positively associated with ecosystem functioning, this can have potentially severe negative consequences. This novel result highlights the importance of identifying and understanding intermittent cycles in theoretical studies and natural systems. The new approach for detecting and quantifying intermittency we develop here will be instrumental in enabling future study.
Plants show remarkable phenotypic plasticity and are able to adjust their morphology and development to diverse environmental stimuli. Morphological acclimation responses to elevated ambient temperatures are collectively termed thermomorphogenesis. In Arabidopsis thaliana, morphological changes are coordinated to a large extent by the transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), which in turn is regulated by several thermosensing mechanisms and modulators. Here, we review recent advances in the identification of factors that regulate thermomorphogenesis of Arabidopsis seedlings by affecting PIF4 expression and PIF4 activity. We summarize newly identified thermosensing mechanisms and highlight work on the emerging topic of organ- and tissue-specificity in the regulation of thermomorphogenesis.
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.
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.
Crop model intercomparison studies have mostly focused on the assessment of predictive capabilities for crop development using weather and basic soil data from the same location. Still challenging is the model performance when considering complex interrelations between soil and crop dynamics under a changing climate. The objective of this study was to test the agronomic crop and environmental flux-related performance of a set of crop models. The aim was to predict weighing lysimeter-based crop (i.e., agronomic) and water-related flux or state data (i.e., environmental) obtained for the same soil monoliths that were taken from their original environment and translocated to regions with different climatic conditions, after model calibration at the original site. Eleven models were deployed in the study. The lysimeter data (2014-2018) were from the Dedelow (Dd), Bad Lauchstadt (BL), and Selhausen (Se) sites of the TERENO (TERrestrial ENvironmental Observatories) SOILCan network. Soil monoliths from Dd were transferred to the drier and warmer BL site and the wetter and warmer Se site, which allowed a comparison of similar soil and crop under varying climatic conditions. The model parameters were calibrated using an identical set of crop- and soil-related data from Dd. Environmental fluxes and crop growth of Dd soil were predicted for conditions at BL and Se sites using the calibrated models. The comparison of predicted and measured data of Dd lysimeters at BL and Se revealed differences among models. At site BL, the crop models predicted agronomic and environmental components similarly well. Model performance values indicate that the environmental components at site Se were better predicted than agronomic ones. The multi-model mean was for most observations the better predictor compared with those of individual models. For Se site conditions, crop models failed to predict site-specific crop development indicating that climatic conditions (i.e., heat stress) were outside the range of variation in the data sets considered for model calibration. For improving predictive ability of crop models (i.e., productivity and fluxes), more attention should be paid to soil-related data (i.e., water fluxes and system states) when simulating soil-crop-climate interrelations in changing climatic conditions.
Introduction: The ongoing COVID-19 pandemic situation caused by SARS-CoV-2 and variants of concern such as B.1.617.2 (Delta) and recently, B.1.1.529 (Omicron) is posing multiple challenges to humanity. The rapid evolution of the virus requires adaptation of diagnostic and therapeutic applications.
Objectives: In this study, we describe camelid heavy-chain-only antibodies (hcAb) as useful tools for novel in vitro diagnostic assays and for therapeutic applications due to their neutralizing capacity.
Methods: Five antibody candidates were selected out of a naïve camelid library by phage display and expressed as full length IgG2 antibodies. The antibodies were characterized by Western blot, enzyme-linked immunosorbent assays, surface plasmon resonance with regard to their specificity to the recombinant SARS-CoV-2 Spike protein and to SARS-CoV-2 virus-like particles. Neutralization assays were performed with authentic SARS-CoV-2 and pseudotyped viruses (wildtype and Omicron).
Results: All antibodies efficiently detect recombinant SARS-CoV-2 Spike protein and SARS-CoV-2 virus-like particles in different ELISA setups. The best combination was shown with hcAb B10 as catcher antibody and HRP-conjugated hcAb A7.2 as the detection antibody. Further, four out of five antibodies potently neutralized authentic wildtype SARS-CoV-2 and particles pseudotyped with the SARS-CoV-2 Spike proteins of the wildtype and Omicron variant, sublineage BA.1 at concentrations between 0.1 and 0.35 ng/mL (ND50).
Conclusion: Collectively, we report novel camelid hcAbs suitable for diagnostics and potential therapy.
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.
Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.
Gases like H-2, N-2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N-2, CO2, and CO and the production of H-2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N-2 fixation by nitrogenase and H-2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
All plant cells are encased in primary cell walls that determine plant morphology, but also protect the cells against the environment. Certain cells also produce a secondary wall that supports mechanically demanding processes, such as maintaining plant body stature and water transport inside plants. Both these walls are primarily composed of polysaccharides that are arranged in certain patterns to support cell functions. A key requisite for patterned cell walls is the arrangement of cortical microtubules that may direct the delivery of wall polymers and/or cell wall producing enzymes to certain plasma membrane locations. Microtubules also steer the synthesis of cellulose-the load-bearing structure in cell walls-at the plasma membrane. The organization and behaviour of the microtubule array are thus of fundamental importance to cell wall patterns. These aspects are controlled by the coordinated effort of small GTPases that probably coordinate a Turing's reaction-diffusion mechanism to drive microtubule patterns. Here, we give an overview on how wall patterns form in the water-transporting xylem vessels of plants. We discuss systems that have been used to dissect mechanisms that underpin the xylem wall patterns, emphasizing the VND6 and VND7 inducible systems, and outline challenges that lay ahead in this field.
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.
Arctic and alpine aquatic ecosystems are changing rapidly under recent global warming, threatening water resources by diminishing trophic status and changing biotic composition. Macrophytes play a key role in the ecology of freshwaters and we need to improve our understanding of long-term macrophytes diversity and environmental change so far limited by the sporadic presence of macrofossils in sediments.
In our study, we applied metabarcoding using the trnL P6 loop marker to retrieve macrophyte richness and composition from 179 surface-sediment samples from arctic Siberian and alpine Chinese lakes and three representative lake cores.
The surface-sediment dataset suggests that macrophyte richness and composition are mostly affected by temperature and conductivity, with highest richness when mean July temperatures are higher than 12 degrees C and conductivity ranges between 40 and 400 mu S cm(-1). Compositional turnover during the Late Pleistocene/Holocene is minor in Siberian cores and characterized by a less rich, but stable emergent macrophyte community. Richness decreases during the Last Glacial Maximum and rises during wetter and warmer climate in the Late-glacial and Mid-Holocene.
In contrast, we detect a pronounced change from emergent to submerged taxa at 14 ka in the Tibetan alpine core, which can be explained by increasing temperature and conductivity due to glacial runoff and evaporation.
Our study provides evidence for the suitability of the trnL marker to recover modern and past macrophyte diversity and its applicability for the response of macrophyte diversity to lake-hydrochemical and climate variability predicting contrasting macrophyte changes in arctic and alpine lakes under intensified warming and human impact.
Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set
(2022)
A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.
Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.
Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling in conservation and restoration. Of 650 reviewed publications, 217 publications had a clear management application and were included in our quantitative analyses. Overall, modelling studies were biased towards static models (79%), towards the species and population level (80%) and towards conservation (rather than restoration) applications (71%). Correlative niche models were the most widely used model type. Dynamic models as well as the gene-to-individual level and the community-to-ecosystem level were underrepresented, and explicit cost optimisation approaches were only used in 10% of the studies. We present a new model typology for selecting models for animal conservation and restoration, characterising model types according to organisational levels, biological processes of interest and desired management applications. This typology will help to more closely link models to management goals. Additionally, future efforts need to overcome important challenges related to data integration, model integration and decision-making. We conclude with five key recommendations, suggesting that wider usage of spatially explicit models for decision support can be achieved by 1) developing a toolbox with multiple, easier-to-use methods, 2) improving calibration and validation of dynamic modelling approaches and 3) developing best-practise guidelines for applying these models. Further, more robust decision-making can be achieved by 4) combining multiple modelling approaches to assess uncertainty, and 5) placing models at the core of adaptive management. These efforts must be accompanied by long-term funding for modelling and monitoring, and improved communication between research and practise to ensure optimal conservation and restoration outcomes.
Species community structures of Afrotropical butterflies differ depending on the monitoring method
(2022)
Standardised biodiversity assessment is crucial to understand community structures and population dynamics of animals.
There exist various methods to monitor biodiversity. Approaches differ depending on the target species group and the aim of study, and show advantages and disadvantages.
The obtained data and results are influenced by local environmental conditions and seasonal variability.
In a comparative approach, we studied butterfly diversity and community structure in the dryland savannah biome of south-eastern Kenya with two different methods, transect counts and bait trapping.
We repeatedly collected data throughout the dry and rainy seasons, in both near natural and anthropogenically influenced landscapes. Significantly more species and individuals were recorded by transect counts than by bait trapping, though the larger and more mobile Nymphalid species (and in particular representatives of the genus Charaxes) were comparatively overrepresented in traps.
The transect data revealed much more pronounced effects of land-use and seasonality than the trap data. These results show that the choice of data collection methods must depend on the general research question, habitat conditions and season. To study the relative variation of species diversity and abundance, the collection of a fraction of the total species diversity might be sufficient.
However, if the focus is on a largely complete recording of species diversity, the use of various collection methods is essential. More specifically, our data clearly demonstrate that transect counts represent a reasonable method for assessing butterfly diversity for the African dryland savannah region, but fails to fully capture occurrences of all species. Bait trapping can be used only as a supplementary method for assessing some few highly mobile low-density species.
The Lena Delta in Siberia is the largest delta in the Arctic and as a snow-dominated ecosystem particularly vulnerable to climate change.
Using the two decades of MODerate resolution Imaging Spectroradiometer satellite acquisitions, this study investigates interannual and spatial variability of snow-cover duration and summer vegetation vitality in the Lena Delta.
We approximated snow by the application of the normalized difference snow index and vegetation greenness by the normalized difference vegetation index (NDVI). We consolidated the analyses by integrating reanalysis products on air temperature from 2001 to 2021, and air temperature, ground temperature, and the date of snow-melt from time-lapse camera (TLC) observations from the Samoylov observatory located in the central delta.
We extracted spring snow-cover duration determined by a latitudinal gradient. The 'regular year' snow-melt is transgressing from mid-May to late May within a time window of 10 days across the delta.
We calculated yearly deviations per grid cell for two defined regions, one for the delta, and one focusing on the central delta. We identified an ensemble of early snow-melt years from 2012 to 2014, with snow-melt already starting in early May, and two late snow-melt years in 2004 and 2017, with snow-melt starting in June. In the times of TLC recording, the years of early and late snow-melt were confirmed.
In the three summers after early snow-melt, summer vegetation greenness showed neither positive nor negative deviations. Whereas, vegetation greenness was reduced in 2004 after late snow-melt together with the lowest June monthly air temperature of the time series record. Since 2005, vegetation greenness is rising, with maxima in 2018 and 2021.
The NDVI rise since 2018 is preceded by up to 4 degrees C warmer than average June air temperature. The ongoing operation of satellite missions allows to monitor a wide range of land surface properties and processes that will provide urgently needed data in times when logistical challenges lead to data gaps in land-based observations in the rapidly changing Arctic.
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.
Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates mu'. Subsets of cells that did not show net growth mu'SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.
Large quantities of the antibiotic florfenicol are used in animal farming and aquaculture, contaminating the ecosystem with antibiotic residues and promoting antimicrobial resistance, ultimately leading to untreatable multidrug-resistant pathogens. Florfenicol-resistant bacteria often activate export mechanisms that result in resistance to various structurally unrelated antibiotics. We devised novel strategies for the enzymatic inactivation of florfenicol in different media, such as saltwater or milk. Using a combinatorial approach and selection, we optimized a hydrolase (EstDL136) for florfenicol cleavage. Reaction kinetics were followed by time-resolved NMR spectroscopy. Importantly, the hydrolase remained active in different media, such as saltwater or cow milk. Various environmentally-friendly application strategies for florfenicol inactivation were developed using the optimized hydrolase. As a potential filter device for cost-effective treatment of waste milk or aquacultural wastewater, the hydrolase was immobilized on Ni-NTA agarose or silica as carrier materials. In two further application examples, the hydrolase was used as cell extract or encapsulated with a semi-permeable membrane. This facilitated, for example, florfenicol inactivation in whole milk, which can help to treat waste milk from medicated cows, to be fed to calves without the risk of inducing antibiotic resistance. Enzymatic inactivation of antibiotics, in general, enables therapeutic intervention without promoting antibiotic resistance.
Solid organ transplant (SOT) recipients receive therapeutic immunosuppression that compromises their immune response to infections and vaccines. For this reason, SOT patients have a high risk of developing severe coronavirus disease 2019 (COVID-19) and an increased risk of death from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Moreover, the efficiency of immunotherapies and vaccines is reduced due to the constant immunosuppression in this patient group. Here, we propose adoptive transfer of SARS-CoV-2-specific T cells made resistant to a common immunosuppressant, tacrolimus, for optimized performance in the immunosuppressed patient. Using a ribonucleoprotein approach of CRISPR-Cas9 technology, we have generated tacrolimus-resistant SARS-CoV-2-specific T cell products from convalescent donors and demonstrate their specificity and function through characterizations at the single-cell level, including flow cytometry, single-cell RNA (scRNA) Cellular Indexing of Transcriptomes and Epitopes (CITE), and T cell receptor (TCR) sequencing analyses. Based on the promising results, we aim for clinical validation of this approach in transplant recipients. Additionally, we propose a combinatory approach with tacrolimus, to prevent an overshooting immune response manifested as bystander T cell activation in the setting of severe COVID-19 immunopathology, and tacrolimus-resistant SARS-CoV-2-specific T cell products, allowing for efficient clearance of viral infection. Our strategy has the potential to prevent severe COVID-19 courses in SOT or autoimmunity settings and to prevent immunopathology while providing viral clearance in severe non-transplant COVID-19 cases.
Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species.
Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites.
For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence.
In contrast, DNA sequence information has rarely been used.
Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions.
The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far.
However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data.
Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals.
Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species.
Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research.
Advanced catalysis triggered by photothermal conversion effects has aroused increasing interest due to its huge potential in environmental purification.
In this work, we developed a novel approach to the fast degradation of 4-nitrophenol (4-Nip) using porous MoS2 nanoparticles as catalysts, which integrate the intrinsic catalytic property of MoS2 with its photothermal conversion capability.
Using assembled polystyrene-b-poly(2-vinylpyridine) block copolymers as soft templates, various MoS 2 particles were prepared, which exhibited tailored morphologies (e.g., pomegranate-like, hollow, and open porous structures).
The photothermal conversion performance of these featured particles was compared under near-infrared (NIR) light irradiation.
Intriguingly, when these porous MoS2 particles were further employed as catalysts for the reduction of 4-Nip, the reaction rate constant was increased by a factor of 1.5 under NIR illumination.
We attribute this catalytic enhancement to the open porous architecture and light-to-heat conversion performance of the MoS2 particles. This contribution offers new opportunities for efficient photothermal-assisted catalysis.
The benefits of counting butterflies: recommendations for a successful citizen science project
(2022)
Citizen science (CS) projects, being popular across many fields of science, have recently also become a popular tool to collect biodiversity data. Although the benefits of such projects for science and policy making are well understood, relatively little is known about the benefits participants get from these projects as well as their personal backgrounds and motivations. Furthermore, very little is known about their expectations. We here examine these aspects, with the citizen science project "German Butterfly Monitoring" as an example. A questionnaire was sent to all participants of the project and the responses to the questionnaire indicated the following: center dot Most transect walkers do not have a professional background in this field, though they do have a high educational level, and are close to retirement, with a high number of females; center dot An important motivation to join the project is to preserve the natural environment and to contribute to scientific knowledge; center dot Participants benefit by enhancing their knowledge about butterflies and especially their ability to identify different species (taxonomic knowledge); center dot Participants do not have specific expectations regarding the project beyond proper management and coordination, but have an intrinsic sense of working for a greater good. The willingness to join a project is higher if the project contributes to the solution of a problem discussed in the media (here, insect decline). Based on our findings from the analysis of the questionnaire we can derive a set of recommendations for establishing a successful CS project. These include the importance of good communication, e.g., by explaining what the (scientific) purpose of the project is and what problems are to be solved with the help of the data collected in the project. The motivation to join a CS project is mostly intrinsic and CS is a good tool to engage people during difficult times such as the COVID-19 pandemic, giving participants the feeling of doing something useful.
The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines
(2022)
Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood.
Here, we analysed the impact of plant-related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe.
All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas.
The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae.
A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance.
Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring.
This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes.
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.
Background: Clinicians often refer anthropometric measures of a child to so-called “growth standards” and “growth references. Over 140 countries have meanwhile adopted WHO growth standards.
Objectives: The present study was conducted to thoroughly examine the idea of growth standards as a common yardstick for all populations. Weight depends on height. We became interested in whether also weight-for-height depends on height. First, we studied the age-group effect on weight-for-height. Thereafter, we tested the applicability of weight-for-height references in short and in historic populations.
Sample and Methods: We analyzed body height and body weight and weight-for-height of 3795 healthy boys and 3726 healthy girls aged 2 to 5 years measured in East-Germany between 1986 and 1990.
We chose contemporary height and weight charts from Germany, the UK, and the WHO growth chart and compared these with three geographically commensurable growth charts from the end of the 19th century.
Results: We analyzed body height and body weight and weight-for-height of 3795 healthy boys and 3726 healthy girls aged 2 to 5 years measured in East-Germany between 1986 and 1990.
We chose contemporary height and weight charts from Germany, the UK, and the WHO growth chart and compared these with three geographically commensurable growth charts of the end of the 19th century.
Conclusion: Weight-for-height depends on age and sex and apart from the nutritional state, reflects body proportion and body built particularly during infancy and early childhood. Populations with a relatively short average height are prone to high values of weight-for-height for arithmetic reasons independent of the nutritional state.
Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.
Phenotypic plasticity can increase individual fitness when environmental conditions change over time. Inducible defences are a striking example, allowing species to react to fluctuating predation pressure by only expressing their costly defended phenotype under high predation risk. Previous theoretical investigations have focused on how this affects predator–prey dynamics, but the impact on competitive outcomes and broader community dynamics has received less attention. Here we use a small food web model, consisting of two competing plastic autotrophic species exploited by a shared consumer, to study how the speed of inducible defences across three trade-off constellations affects autotroph coexistence, biomasses across trophic levels, and temporal variability. Contrary to the intuitive idea that faster adaptation increases autotroph fitness, we found that higher switching rates reduced individual fitness as it consistently provoked more maladaptive switching towards undefended phenotypes under high predation pressure. This had an unexpected positive impact on the consumer, increasing consumer biomass and lowering total autotroph biomass. Additionally, maladaptive switching strongly reduced autotroph coexistence through an emerging source-sink dynamic between defended and undefended phenotypes. The striking impact of maladaptive switching on species and food web dynamics indicates that this mechanism may be of more critical importance than previously recognized.
Phenotypic plasticity can increase individual fitness when environmental conditions change over time. Inducible defences are a striking example, allowing species to react to fluctuating predation pressure by only expressing their costly defended phenotype under high predation risk. Previous theoretical investigations have focused on how this affects predator–prey dynamics, but the impact on competitive outcomes and broader community dynamics has received less attention. Here we use a small food web model, consisting of two competing plastic autotrophic species exploited by a shared consumer, to study how the speed of inducible defences across three trade-off constellations affects autotroph coexistence, biomasses across trophic levels, and temporal variability. Contrary to the intuitive idea that faster adaptation increases autotroph fitness, we found that higher switching rates reduced individual fitness as it consistently provoked more maladaptive switching towards undefended phenotypes under high predation pressure. This had an unexpected positive impact on the consumer, increasing consumer biomass and lowering total autotroph biomass. Additionally, maladaptive switching strongly reduced autotroph coexistence through an emerging source-sink dynamic between defended and undefended phenotypes. The striking impact of maladaptive switching on species and food web dynamics indicates that this mechanism may be of more critical importance than previously recognized.
Plants use photoperiodism to activate flowering in response to a particular daylength. In rice, flowering is accelerated in short-day conditions, and even a brief exposure to light during the dark period (night-break) is sufficient to delay flowering. Although many of the genes involved in controlling flowering in rice have been uncovered, how the long- and short-day flowering pathways are integrated, and the mechanism of photoperiod perception is not understood. While many of the signaling components controlling photoperiod-activated flowering are conserved between Arabidopsis and rice, flowering in these two systems is activated by opposite photoperiods. Here we establish that photoperiodism in rice is controlled by the evening complex (EC). We show that mutants in the EC genes LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) paralogs abolish rice flowering. We also show that the EC directly binds and suppresses the expression of flowering repressors, including PRR37 and Ghd7. We further demonstrate that light acts via phyB to cause a rapid and sustained posttranslational modification of ELF3-1. Our results suggest a mechanism by which the EC is able to control both long- and short-day flowering pathways.
Consumers are increasingly demanding higher quality and safety standards for the products they consume, and one of this is wheat flour, the basis of a wide variety of processed products. This major component in the diet of many communities can be contaminated by microorganisms before the grain harvest, or during the grain storage right before processing. These microorganisms include several fungal species, many of which produce mycotoxins, secondary metabolites that can cause severe acute and chronic disorders. Yet, we still know little about the overall composition of fungal communities associated with wheat flour. In this study, we contribute to fill this gap by characterizing the fungal microbiome of different types of wheat flour using culture-dependent and -independent techniques. Qualitatively, these approaches suggested similar results, highlighting the presence of several fungal taxa able to produce mycotoxins. In-vitro isolation of fungal species suggest a higher frequency of Penicillium, while metabarcoding suggest a higher abundance of Alternaria. This discrepancy might reside on the targeted portion of the community (alive vs. overall) or in the specific features of each technique. Thus, this study shows that commercial wheat flour hosts a wide fungal diversity with several taxa potentially representing concerns for consumers, aspects that need more attention throughout the food production chain.
Understanding the complexity of metabolic networks has implications for manipulation of their functions. The complexity of metabolic networks can be characterized by identifying multireaction dependencies that are challenging to determine due to the sheer number of combinations to consider. Here, we propose the concept of concordant complexes that captures multireaction dependencies and can be efficiently determined from the algebraic structure and operational constraints of metabolic networks. The concordant complexes imply the existence of concordance modules based on which the apparent complexity of 12 metabolic networks of organisms from all kingdoms of life can be reduced by at least 78%. A comparative analysis against an ensemble of randomized metabolic networks shows that the metabolic network of Escherichia coli contains fewer concordance modules and is, therefore, more tightly coordinated than expected by chance. Together, our findings demonstrate that metabolic networks are considerably simpler than what can be perceived from their structure alone.
Resource polymorphism is common across taxa and can result in alternate ecotypes with specific morphologies, feeding modes, and behaviors that increase performance in a specific habitat. This can result in high intraspecific variation in the expression of specific traits and the extent to which these traits are correlated within a single population. Although metabolic rate influences resource acquisition and the overall pace of life of individuals it is not clear how metabolic rate interacts with the larger suite of traits to ultimately determine individual fitness. We examined the relationship between metabolic rates and the major differences (habitat use, morphology, and resource use) between littoral and pelagic ecotypes of European perch (Perca fluviatilis) from a single lake in Central Sweden. Standard metabolic rate (SMR) was significantly higher in pelagic perch but did not correlate with resource use or morphology. Maximum metabolic rate (MMR) was not correlated with any of our explanatory variables or with SMR. Aerobic scope (AS) showed the same pattern as SMR, differing across habitats, but contrary to expectations, was lower in pelagic perch. This study helps to establish a framework for future experiments further exploring the drivers of intraspecific differences in metabolism. In addition, since metabolic rates scale with temperature and determine predator energy requirements, our observed differences in SMR across habitats will help determine ecotype-specific vulnerabilities to climate change and differences in top-down predation pressure across habitats.
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.
Perceived predation risk varies in space and time creating a landscape of fear. This key feature of an animal's environment is classically studied as a species-specific property. However, individuals differ in how they solve the tradeoff between safety and reward and may, hence, differ consistently and predictively in perceived predation risk across landscapes. To test this hypothesis, we quantified among-individual differences in boldness and activity and exposed behaviourally phenotyped male bank voles Myodes glareolus individually to two different experimental landscapes of risks in large outdoor enclosures and provided resources as discrete food patches. We manipulated perceived predation risk via vegetation height between 2 and > 30 cm and quantified patch use indirectly via RFID-logging and giving-up densities. We statistically disentangled among-individual differences in microhabitat use from spatially varying perceived risk, i.e. landscape of fear. We found that individuals varied in mean vegetation height of their foraging microhabitats and that this microhabitat selection matched the intrinsic individual differences in perceived risk. As predicted by the patch use model, all individual's perceived higher risks when foraging in lower vegetation. However, individuals differed in their reaction norm slopes of perceived risk to vegetation height, and these differences in slopes were consistent across two different landscapes of risks and resources. We interpret these results as evidence for individual landscapes of fear, which could be predicted by among-individual differences in activity and boldness. Since perceived predation risk affects when and where to forage, among-individual differences in fear responses could act as a mode of intraspecific niche complementarity (i.e. individual niche specialization), help explain behavioural type by environment correlations, and will likely have cascading indirect effects on lower trophic levels.
Instrumental data show that the groundwater and lake levels in Northeast Germany have decreased over the past decades, and this process has accelerated over the past few years. In addition to global warming, the direct influence of humans on the local water balance is suspected to be the cause. Since the instrumental data usually go back only a few decades, little is known about the multidecadal to centennial-scale trend, which also takes long-term climate variation and the long-term influence by humans on the water balance into account. This study aims to quantitatively reconstruct the surface water areas in the Lower Havel Inner Delta and of adjacent Lake Gulpe in Brandenburg. The analysis includes the calculation of surface water areas from historical and modern maps from 1797 to 2020. The major finding is that surface water areas have decreased by approximately 30% since the pre-industrial period, with the decline being continuous. Our data show that the comprehensive measures in Lower Havel hydro-engineering correspond with groundwater lowering that started before recent global warming. Further, large-scale melioration measures with increasing water demands in the upstream wetlands beginning from the 1960s to the 1980s may have amplified the decline in downstream surface water areas.
Background:
One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.
Results:
Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies.
Conclusions:
Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health.
Environmental monitoring involves the quantification of microscopic cells and particles such as algae, plant cells, pollen, or fungal spores. Traditional methods using conventional microscopy require expert knowledge, are time-intensive and not well-suited for automated high throughput. Multispectral imaging flow cytometry (MIFC) allows measurement of up to 5000 particles per second from a fluid suspension and can simultaneously capture up to 12 images of every single particle for brightfield and different spectral ranges, with up to 60x magnification. The high throughput of MIFC has high potential for increasing the amount and accuracy of environmental monitoring, such as for plant-pollinator interactions, fossil samples, air, water or food quality that currently rely on manual microscopic methods. Automated recognition of particles and cells is also possible, when MIFC is combined with deep-learning computational techniques. Furthermore, various fluorescence dyes can be used to stain specific parts of the cell to highlight physiological and chemical features including: vitality of pollen or algae, allergen content of individual pollen, surface chemical composition (carbohydrate coating) of cells, DNA- or enzyme-activity staining. Here, we outline the great potential for MIFC in environmental research for a variety of research fields and focal organisms. In addition, we provide best practice recommendations.
This study examined how early childhood (EC) teachers' instructional quality predicted children's development in mathematics across two measurement occasions. Therefore, EC teachers' (n = 25) instructional quality was assessed using one standardized observation instrument covering both domain-specific and general aspects of instructional quality. Additionally, data on children's (n = 208) outcome in early number skills was collected applying a standardized test. Multilevel structural equation modeling was used accounting for nested data. Children's age and the average size of preschool groups were controlled for. Results revealed that EC teachers' instructional quality predicted children's development but was not associated with their initial achievement. The findings suggest that instruments covering domain-specific and general aspects might be helpful in order to measure EC teachers' instructional quality in mathematics and predict children's learning growth. Understanding the mechanisms between instructional quality and children's development may help EC teachers to enhance their math teaching in practice.
The role of the GMP nucleotides of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor of the DMSO reductase family has long been a subject of discussion. The recent characterization of the bis-molybdopterin (bis-Mo-MPT) cofactor present in the E. coli YdhV protein, which differs from bis-MGD solely by the absence of the nucleotides, now enables studying the role of the nucleotides of bis-MGD and bis-MPT cofactors in Moco insertion and the activity of molybdoenzymes in direct comparison. Using the well-known E. coli TMAO reductase TorA as a model enzyme for cofactor insertion, we were able to show that the GMP nucleotides of bis-MGD are crucial for the insertion of the bis-MGD cofactor into apo-TorA.
Background: In the animal kingdom body size is often linked to dominance and subsequently the standing in social hierarchy. Similarly, human growth has been associated and linked to socioeconomic factors, including one’s social status. This has already been proposed in the early 1900s where data on young German school girls from different social strata have been compared.
Objectives: This paper aims to summarize and analyze these results and make them accessible for non-German speakers. The full English translation of the historic work of Dikanski (Dikanski, 1914) is available as a supplement. Further, this work aims to compare the historical data with modern references, to test three hypotheses: (1) higher social class is positively associated with body height and weight, (2) affluent people from the used historical data match modern references in weight and height and (3) weight distributions are skewed in both modern and historical populations.
Methods: Comparison of historical data from 1914 with WHO and 1980s German data. The data sets, for both body weight and height for 6.0- and 7.0-year-old girls, were fitted onto centile curves and quantile correlation coefficients were calculated.
Results: In historical data social status is positively associated with body height and weight while both are also normally distributed, which marks a significant difference to modern references.
Conclusion: Social status is positively associated with height, signaling social dominance, making children of affluent classes taller. Children from the historical data do not reach the average height of modern children, even under the best environmental conditions. The children of the upper social class were not skewed in weight distribution, although they had the means to become as obese as modern children.
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.
The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ss-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ss-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ss-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ss-lactamase 1 expressing Enterobacteriaceae.
As a critical part of plant immunity, cells that are attacked by pathogens undergo rapid transcriptional reprogramming to minimize virulence. Many bacterial phytopathogens use type III effector (T3E) proteins to interfere with plant defense responses, including this transcriptional reprogramming. Here, we show that Xanthomonas outer protein S (XopS), a T3E of Xanthomonas campestris pv. vesicatoria (Xcv), interacts with and inhibits proteasomal degradation of WRKY40, a transcriptional regulator of defense gene expression. Virus-induced gene silencing of WRKY40 in pepper (Capsicum annuum) enhanced plant tolerance to Xcv infection, indicating that WRKY40 represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets, which include salicylic acid-responsive genes and the jasmonic acid signaling repressor JAZ8. Xcv bacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery by Xcv, as well as ectopic expression of XopS in Arabidopsis thaliana or Nicotiana benthamiana, prevented stomatal closure in response to bacteria and biotic elicitors. Silencing WRKY40 in pepper or N. benthamiana abolished XopS's ability to prevent stomatal closure. This suggests that XopS interferes with both preinvasion and apoplastic defense by manipulating WRKY40 stability and downstream gene expression, eventually altering phytohormone crosstalk to promote pathogen proliferation.
Boreal forests cover over half of the global permafrost area and protect underlying permafrost. Boreal forest development, therefore, has an impact on permafrost evolution, especially under a warming climate.
Forest disturbances and changing climate conditions cause vegetation shifts and potentially destabilize the carbon stored within the vegetation and permafrost. Disturbed permafrost-forest ecosystems can develop into a dry or swampy bush- or grasslands, shift toward broadleaf- or evergreen needleleaf-dominated forests, or recover to the pre-disturbance state.
An increase in the number and intensity of fires, as well as intensified logging activities, could lead to a partial or complete ecosystem and permafrost degradation. We study the impact of forest disturbances (logging, surface, and canopy fires) on the thermal and hydrological permafrost conditions and ecosystem resilience.
We use a dynamic multilayer canopy-permafrost model to simulate different scenarios at a study site in eastern Siberia. We implement expected mortality, defoliation, and ground surface changes and analyze the interplay between forest recovery and permafrost. We find that forest loss induces soil drying of up to 44%, leading to lower active layer thicknesses and abrupt or steady decline of a larch forest, depending on disturbance intensity.
Only after surface fires, the most common disturbances, inducing low mortality rates, forests can recover and overpass pre-disturbance leaf area index values. We find that the trajectory of larch forests after surface fires is dependent on the precipitation conditions in the years after the disturbance. Dryer years can drastically change the direction of the larch forest development within the studied period.
The generation of monoclonal antibodies using an in vitro immunization approach is a promising alternative to conventional hybridoma technology. As recently published, the in vitro approach enables an antigen-specific activation of B lymphocytes within 10-12 d followed by immortalization and subsequent selection of hybridomas. This in vitro process can be further improved by using a three-dimensional surrounding to stabilize the complex microenvironment required for a successful immune reaction. In this study, the suitability of Geltrex as a material for the generation of monoclonal antigen-specific antibodies by in vitro immunization was analyzed. We could show that dendritic cells, B cells, and T cells were able to travel through and interact inside of the matrix, leading to the antigen-specific activation of T and B cells. For cell recovery and subsequent hybridoma technique the suitability of dispase and Corning cell recovery solution (CRS) was compared. In our experiments, the use of dispase resulted in a severe alteration of cell surface receptor expression patterns and significantly higher cell death, while we could not detect an adverse effect of Corning CRS. Finally, an easy approach for high-density cell culture was established by printing an alginate ring inside a cell culture vessel. The ring was filled with Geltrex, cells, and medium to ensure a sufficient supply during cultivation. Using this approach, we were able to generate monoclonal hybridomas that produce antigen-specific antibodies against ovalbumin and the SARS-CoV-2 nucleocapsid protein.
Foraging by consumers acts as a biotic filtering mechanism for biodiversity at the trophic level of resources. Variation in foraging behaviour has cascading effects on abundance, diversity, and functional trait composition of the community of resource species. Here we propose diversity at giving-up density (DivGUD), i.e. when foragers quit exploiting a patch, as a novel concept and simple measure quantifying cascading effects at multiple spatial scales. In experimental landscapes with an assemblage of plant seeds, patch residency of wild rodents decreased local alpha-DivGUD (via elevated mortality of species with large seeds) and regional gamma-DivGUD, while dissimilarity among patches in a landscape (beta-DivGUD) increased. By linking theories of adaptive foraging behaviour with community ecology, DivGUD allows to investigate cascading indirect predation effects, e.g. the ecology-of-fear framework, feedbacks between functional trait composition of resource species and consumer communities, and effects of inter-individual differences among foragers on the biodiversity of resource communities.
Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.
Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.
Trade-off for survival
(2022)
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.
Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress
(2022)
Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.
Biodiversity conservation and agricultural production have been largely framed as separate goals for landscapes in the discourse on land use. Although there is an increasing tendency to move away from this dichotomy in theory, the tendency is perpetuated by the spatially explicit approaches used in research and management practice. Transition zones (TZ) have previously been defined as areas where two adjacent fields or patches interact, and so they occur abundantly throughout agricultural landscapes. Biodiversity patterns in TZ have been extensively studied, but their relationship to yield patterns and social-ecological dimensions has been largely neglected. Focusing on European, temperate agricultural landscapes, we outline three areas of research and management that together demonstrate how TZ might be used to facilitate an integrated landscape approach: (i) plant and animal species' use and response to boundaries and the resulting effects on yield, for a deeper understanding of how landscape structure shapes quantity and quality of TZ; (ii) local knowledge on field or patch-level management and its interactions with biodiversity and yield in TZ, and (iii) conflict prevention and collaborative management across land-use boundaries.
Trophic transfer efficiency (TTE) is usually calculated as the ratio of production rates between two consecutive trophic levels. Although seemingly simple, TTE estimates from lakes are rare. In our review, we explore the processes and structures that must be understood for a proper lake TTE estimate.
We briefly discuss measurements of production rates and trophic positions and mention how ecological efficiencies, nutrients (N, P) and other compounds (fatty acids) affect energy transfer between trophic levels and hence TTE.
Furthermore, we elucidate how TTE estimates are linked with size-based approaches according to the Metabolic Theory of Ecology, and how food-web models can be applied to study TTE in lakes.
Subsequently, we explore temporal and spatial heterogeneity of production and TTE in lakes, with a particular focus on the links between benthic and pelagic habitats and between the lake and the terrestrial environment.
We provide an overview of TTE estimates from lakes found in the published literature. Finally, we present two alternative approaches to estimating TTE. First, TTE can be seen as a mechanistic quantity informing about the energy and matter flow between producer and consumer groups.
This approach is informative with respect to food-web structure, but requires enormous amounts of data. The greatest uncertainty comes from the proper consideration of basal production to estimate TTE of omnivorous organisms.
An alternative approach is estimating food-chain and food-web efficiencies, by comparing the heterotrophic production of single consumer levels or the total sum of all heterotrophic production including that of heterotrophic bacteria to the total sum of primary production.
We close the review by pointing to a few research questions that would benefit from more frequent and standardized estimates of TTE in lakes.
Malagasy shrew tenrecs (Microgale) have increasingly been used to study speciation genetics over the last years. A previous study recently uncovered gene flow between the Shrew-toothed shrew tenrec (M. soricoides) and sympatric southern population of the Pale shrew tenrec (M. fotsifotsy). This gene flow has been suggested to be accompanied by complete mitochondrial replacement in M. fotsifotsy. To explore the temporal framework of this replacement, we assembled mitogenomes from publicly available sequencing data of ultra-conserved elements. We were able to assemble complete and partial mitogenomes for 19 specimens from five species of shrew tenrecs, which represents a multifold increase in mitogenomic resources available for all tenrecs. Phylogenetic inferences and sequence simulations support the close relationship between the mitochondrial lineages of M. soricoides and the southern population of M. fotsifotsy. Based on the nuclear divergence of northern and southern populations of M. fotsifotsy and the mitochondrial divergence between the latter and M. soricoides, there was a mean time window for replacement of similar to 350,000 years. This timeframe implies that the effective size of the ancestral M. fotsifotsy southern population was less 70,000.
Collagen-based biomaterials with oriented fibrils have shown great application potential in medicine. However, it is still challenging to control the type I collagen fibrillogenesis in ultrathin films. Here, we report an approach to produce cohesive and well-organized type I collagen ultrathin films of about 10 nm thickness using the Langmuir-Blodgett technique. Ellipsometry, rheology, and Brewster angle microscopy are applied to investigate in situ how the molecules behave at the air-water interface, both at room temperature and 37 degrees C. The interfacial storage modulus observed at room temperature vanishes upon heating, indicating the existence and disappearance of the network structure in the protein nanosheet. The films were spanning over holes as large as 1 mm diameter when transferred at room temperature, proving the strong cohesive interactions. A highly aligned and fibrillar structure was observed by atomic force microscopy (AFM) and optical microscopy.
Uncertainty in climate change impact studies for irrigated maize cropping systems in southern Spain
(2022)
This study investigates the main drivers of uncertainties in simulated irrigated maize yield under historical conditions as well as scenarios of increased temperatures and altered irrigation water availability.
Using APSIM, MONICA, and SIMPLACE crop models, we quantified the relative contributions of three irrigation water allocation strategies, three sowing dates, and three maize cultivars to the uncertainty in simulated yields.
The water allocation strategies were derived from historical records of farmer's allocation patterns in drip-irrigation scheme of the Genil-Cabra region, Spain (2014-2017).
By considering combinations of allocation strategies, the adjusted R-2 values (showing the degree of agreement between simulated and observed yields) increased by 29% compared to unrealistic assumptions of considering only near optimal or deficit irrigation scheduling. The factor decomposition analysis based on historic climate showed that irrigation strategies was the main driver of uncertainty in simulated yields (66%).
However, under temperature increase scenarios, the contribution of crop model and cultivar choice to uncertainty in simulated yields were as important as irrigation strategy. This was partially due to different model structure in processes related to the temperature responses.
Our study calls for including information on irrigation strategies conducted by farmers to reduce the uncertainty in simulated yields at field scale.
Poaching is driving many species toward extinction, and as a result, lowering poaching pressure is a conservation priority. This requires understanding where poaching pressure is high and which factors determine these spatial patterns. However, the cryptic and illegal nature of poaching makes this difficult.
Ranger patrol data, typically recorded in protected area logbooks, contain information on patrolling efforts and poaching detection and should thus provide opportunities for a better understanding of poaching pressure. However, these data are seldom analyzed and rarely used to inform adaptive management strategies.
We developed a novel approach to making use of analog logbook records to map poaching pressure and to test environmental criminology and predator-prey relationship hypotheses explaining poaching patterns. We showcase this approach for Golestan National Park in Iran, where poaching has substantially depleted ungulate populations. We digitized data from >4800 ranger patrols from 2014 to 2016 and used an occupancy modeling framework to relate poaching to (1) accessibility, (2) law enforcement, and (3) prey availability factors. Based on predicted poaching pressure and patrolling intensity, we provide suggestions for future patrol allocation strategies. Our results revealed a low probability (12%) of poacher detection during patrols. Poaching distribution was best explained by prey availability, indicating that poachers target areas with high concentrations of ungulates. Poaching pressure was estimated to be high (>0.49) in 39% of our study area. To alleviate poaching pressure, we recommend ramping up patrolling intensity in 12% of the national park, which could be achievable by reducing excess patrols in about 20% of the park.
However, our results suggest that for 27% of the park, it is necessary to improve patrolling quality to increase detection probability of poaching, for example, by closing temporal patrolling gaps or expanding informant networks. Our approach illustrates that analog ranger logbooks are an untapped resource for evidence-based and adaptive planning of protected area management. Using this wealth of data can open up new avenues to better understand poaching and its determinants, to expand effectiveness assessments to the past, and, more generally, to allow for strategic conservation planning in protected areas.
Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens
(2022)
Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urban-ization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sedi-ments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urban-ization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts.
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.
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.
The nature of the interaction between prehistoric humans and their environment, especially the vegetation, has long been of interest. The Qinghai Lake Basin in North China is well-suited to exploring the interactions between prehistoric humans and vegetation in the Tibetan Plateau, because of the comparatively dense distribution of archaeological sites and the ecologically fragile environment. Previous pollen studies of Qinghai Lake have enabled a detailed reconstruction of the regional vegetation, but they have provided relatively little information on vegetation change within the Qinghai Lake watershed. To address the issue we conducted a pollen-based vegetation reconstruction for an archaeological site (YWY), located on the southern shore of Qinghai Lake. We used high temporal-resolution pollen records from the YWY site and from Qinghai Lake, spanning the interval since the last deglaciation (15.3 kyr BP to the present) to quantitatively reconstruct changes in the local and regional vegetation using Landscape Reconstruction Algorithm models. The results show that, since the late glacial, spruce forest grew at high altitudes in the surrounding mountains, while the lakeshore environment was occupied mainly by shrub-steppe. From the lateglacial to the middle Holocene, coniferous woodland began to expand downslope and reached the YWY site at 7.1 kyr BP. The living environment of the local small groups of Paleolithic-Epipaleolithic humans (during 15.3-13.1 kyr BP and 9-6.4 kyr BP) changed from shrub-steppe to coniferous forest-steppe. The pollen record shows no evidence of pronounced changes in the vegetation community corresponding to human activity. However, based on a comparison of the local and regional vegetation reconstructions, low values of biodiversity and a significant increase in two indicators of vegetation degradation, Chenopodiaceae and Rosaceae, suggest that prehistoric hunters-gatherers likely disturbed the local vegetation during 9.0-6.4 kyr BP. Our findings are a preliminary attempt to study human-environment interactions at Paleolithic-Epipaleolithic sites in the region, and they contribute to ongoing environmental archaeology research in the Tibetan Plateau.
Welcome to the dark side
(2022)
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.
Welcome to the Dark Side
(2022)
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.