Refine
Year of publication
- 2022 (191) (remove)
Document Type
- Article (191) (remove)
Language
- English (191) (remove)
Is part of the Bibliography
- yes (191)
Keywords
- functional traits (4)
- land use (4)
- animal personality (3)
- giving-up density (3)
- light pollution (3)
- permafrost (3)
- pollen (3)
- AC electrokinetics (2)
- AFLP (2)
- ALAN (2)
Institute
- Institut für Biochemie und Biologie (191) (remove)
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.
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.
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.
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.
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.
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.
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.
Wildfires play an essential role in the ecology of boreal forests.
In eastern Siberia, fire activity has been increasing in recent years, challenging the livelihoods of local communities. Intensifying fire regimes also increase disturbance pressure on the boreal forests, which currently protect the permafrost beneath from accelerated degradation.
However, long-term relationships between changes in fire regime and forest structure remain largely unknown.
We assess past fire-vegetation feedbacks using sedimentary proxy records from Lake Satagay, Central Yakutia, Siberia, covering the past c. 10,800 years.
Results from macroscopic and microscopic charcoal analyses indicate high amounts of burnt biomass during the Early Holocene, and that the present-day, low-severity surface fire regime has been in place since c. 4,500 years before present.
A pollen-based quantitative reconstruction of vegetation cover and a terrestrial plant record based on sedimentary ancient DNA metabarcoding suggest a pronounced shift in forest structure toward the Late Holocene.
Whereas the Early Holocene was characterized by postglacial open larch-birch woodlands, forest structure changed toward the modern, mixed larch-dominated closed-canopy forest during the Mid-Holocene.
We propose a potential relationship between open woodlands and high amounts of burnt biomass, as well as a mediating effect of dense larch forest on the climate-driven intensification of fire regimes.
Considering the anticipated increase in forest disturbances (droughts, insect invasions, and wildfires), higher tree mortality may force the modern state of the forest to shift toward an open woodland state comparable to the Early Holocene.
Such a shift in forest structure may result in a positive feedback on currently intensifying wildfires.
These new long-term data improve our understanding of millennial-scale fire regime changes and their relationships to changes of vegetation in Central Yakutia, where the local population is already being confronted with intensifying wildfire seasons.
Hantaviruses are enveloped viruses that possess a tri-segmented, negative-sense RNA genome.
The viral S-segment encodes the multifunctional nucleocapsid protein (N), which is involved in genome packaging, intracellular protein transport, immunoregulation, and several other crucial processes during hantavirus infection.
In this study, we generated fluorescently tagged N protein constructs derived from Puumalavirus (PUUV), the dominant hantavirus species in Central, Northern, and Eastern Europe.
We comprehensively characterized this protein in the rodent cell line CHO-K1, monitoring the dynamics of N protein complex formation and investigating co-localization with host proteins as well as the viral glycoproteins Gc and Gn.
We observed formation of large, fibrillar PUUV N protein aggregates, rapidly coalescing from early punctate and spike-like assemblies.
Moreover, we found significant spatial correlation of N with vimentin, actin, and P-bodies but not with microtubules. N constructs also co-localized with Gn and Gc albeit not as strongly as the glycoproteins associated with each other.
Finally, we assessed oligomerization of N constructs, observing efficient and concentration-dependent multimerization, with complexes comprising more than 10 individual proteins.