TY  - JOUR
A1  - Zheng, Chunming
A1  - Toenjes, Ralf
A1  - Pikovskij, Arkadij
T1  - Transition to synchrony in a three-dimensional swarming model with helical trajectories
JF  - Physical review : E, Statistical, nonlinear and soft matter physics
N2  - We investigate the transition from incoherence to global collective motion in a three-dimensional swarming model of agents with helical trajectories, subject to noise and global coupling. Without noise this model was recently proposed as a generalization of the Kuramoto model and it was found that alignment of the velocities occurs discontinuously for arbitrarily small attractive coupling. Adding noise to the system resolves this singular limit and leads to a continuous transition, either to a directed collective motion or to center-of-mass rotations.
Y1  - 2021
U6  - https://doi.org/10.1103/PhysRevE.104.014216
SN  - 2470-0045
SN  - 2470-0053
VL  - 104
IS  - 1
PB  - American Physical Society
CY  - College Park
ER  - 
TY  - JOUR
A1  - Yildiz, Tugba
A1  - Leimkühler, Silke
T1  - TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli
JF  - Journal of bacteriology
N2  - To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U-34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation. <br /> IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm(5)s(2)U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm(5)s(2)U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis.
KW  - iron-sulfur clusters
KW  - tRNA thio modifications
KW  - FtsZ ring formation
KW  - cell
KW  - division
KW  - TusA
KW  - RpoS
KW  - Fis
KW  - FtsZ
Y1  - 2021
U6  - https://doi.org/10.1128/JB.00659-20
SN  - 1098-5530
VL  - 203
IS  - 7
PB  - American Society for Microbiology
CY  - Washington
ER  - 
TY  - JOUR
A1  - Xu, Xun
A1  - Nie, Yan
A1  - Wang, Weiwei
A1  - Ullah, Imran
A1  - Tung, Wing Tai
A1  - Ma, Nan
A1  - Lendlein, Andreas
T1  - Generation of 2.5D lung bud organoids from human induced pluripotent stem cells
JF  - Clinical hemorheology and microcirculation : blood flow and vessels
N2  - Human induced pluripotent stem cells (hiPSCs) are a promising cell source to generate the patient-specific lung organoid given their superior differentiation potential. However, the current 3D cell culture approach is tedious and time-consuming with a low success rate and high batch-to-batch variability. 

Here, we explored the establishment of lung bud organoids by systematically adjusting the initial confluence levels and homogeneity of cell distribution. 
The efficiency of single cell seeding and clump seeding was compared. Instead of the traditional 3D culture, we established a 2.5D organoid culture to enable the direct monitoring of the internal structure via microscopy. 
It was found that the cell confluence and distribution prior to induction were two key parameters, which strongly affected hiPSC differentiation trajectories. Lung bud organoids with positive expression of NKX 2.1, in a single-cell seeding group with homogeneously distributed hiPSCs at 70% confluence (SC 70% hom) or a clump seeding group with heterogeneously distributed cells at 90% confluence (CL 90% het), can be observed as early as 9 days post induction. 

These results suggest that a successful lung bud organoid formation with single-cell seeding of hiPSCs requires a moderate confluence and homogeneous distribution of cells, while high confluence would be a prominent factor to promote the lung organoid formation when seeding hiPSCs as clumps. 2.5D organoids generated with defined culture conditions could become a simple, efficient, and valuable tool facilitating drug screening, disease modeling and personalized medicine.
KW  - lung organoid
KW  - human induced pluripotent stem cell
KW  - cell culture
Y1  - 2021
U6  - https://doi.org/10.3233/CH-219111
SN  - 1386-0291
SN  - 1875-8622
VL  - 79
IS  - 1
SP  - 217
EP  - 230
PB  - IOS Press
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Xu, Rudan
A1  - Razaghi-Moghadam, Zahra
A1  - Nikoloski, Zoran
T1  - Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli
JF  - Bioinformatics
N2  - Motivation: 
Constraint-based modeling approaches allow the estimation of maximal in vivo enzyme catalytic rates that can serve as proxies for enzyme turnover numbers. Yet, genome-scale flux profiling remains a challenge in deploying these approaches to catalogue proxies for enzyme catalytic rates across organisms.

Results:
Here, we formulate a constraint-based approach, termed NIDLE-flux, to estimate fluxes at a genome-scale level by using the principle of efficient usage of expressed enzymes. Using proteomics data from Escherichia coli, we show that the fluxes estimated by NIDLE-flux and the existing approaches are in excellent qualitative agreement (Pearson correlation > 0.9). We also find that the maximal in vivo catalytic rates estimated by NIDLE-flux exhibits a Pearson correlation of 0.74 with in vitro enzyme turnover numbers. However, NIDLE-flux results in a 1.4-fold increase in the size of the estimated maximal in vivo catalytic rates in comparison to the contenders. Integration of the maximum in vivo catalytic rates with publically available proteomics and metabolomics data provide a better match to fluxes estimated by NIDLE-flux. Therefore, NIDLE-flux facilitates more effective usage of proteomics data to estimate proxies for kcatomes.
Y1  - 2021
U6  - https://doi.org/10.1093/bioinformatics/btab575
SN  - 1367-4803
SN  - 1460-2059
VL  - 37
IS  - 21
SP  - 3848
EP  - 3855
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Wolff, Martin
A1  - Gast, Klaus
A1  - Evers, Andreas
A1  - Kurz, Michael
A1  - Pfeiffer-Marek, Stefania
A1  - Schüler, Anja
A1  - Seckler, Robert
A1  - Thalhammer, Anja
T1  - A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4
JF  - Biomolecules
N2  - Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.
KW  - biophysics
KW  - diabetes
KW  - peptides
KW  - oligomerization
KW  - conformational change
KW  - molecular modeling
KW  - static and dynamic light scattering
KW  - spectroscopy
Y1  - 2021
U6  - https://doi.org/10.3390/biom11091305
SN  - 2218-273X
VL  - 11
IS  - 9
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Wojcik, Laurie Anne
A1  - Ceulemans, Ruben
A1  - Gaedke, Ursula
T1  - Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs
JF  - Ecology and Evolution
N2  - Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems’ ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.
KW  - functional diversity
KW  - nutrient spike
KW  - pulse perturbation
KW  - regime shift
KW  - robustness
KW  - tritrophic food web
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.8214
SN  - 2045-7758
N1  - Wojcik and Ceulemans shared first authorship.
VL  - 11
IS  - 22
SP  - 15639
EP  - 15663
PB  - John Wiley & Sons, Inc.
CY  - Hoboken (New Jersey)
ER  - 
TY  - JOUR
A1  - Witte, Leonie
A1  - Linnemannstoens, Karen
A1  - Honemann-Capito, Mona
A1  - Groß, Julia Christina
T1  - Visualization and quantitation of Wg trafficking in the Drosophila wing imaginal epithelium
JF  - Bio-protocol
N2  - Secretory Wnt trafficking can be studied in the polarized epithelial monolayer of Drosophila wing imaginal discs (WID). In this tissue, Wg (Drosophila Wnt-I) is presented on the apical surface of its source cells before being internalized into the endosomal pathway. Long-range Wg secretion and spread depend on secondary secretion from endosomal compartments, but the exact post-endocytic fate of Wg is poorly understood. Here, we summarize and present three protocols for the immunofluorescencebased visualization and quantitation of different pools of intracellular and extracellular Wg in WID: (1) steady-state extracellular Wg; (2) dynamic Wg trafficking inside endosomal compartments; and (3) dynamic Wg release to the cell surface. Using a genetic driver system for gene manipulation specifically at the posterior part of the WID (EnGal4) provides a robust internal control that allows for direct comparison of signal intensities of control and manipulated compartments of the same WID. Therefore, it also circumvents the high degree of staining variability usually associated with whole-tissue samples. In combination with the genetic manipulation of Wg pathway components that is easily feasible in Drosophila, these methods provide a tool-set for the dissection of secretory Wg trafficking and can help us to understand how Wnt proteins travel along endosomal compartments for short-and long-range signal secretion.
KW  - Wingless/Wnt secretion
KW  - Morphogen signaling
KW  - Drosophila wing imaginal disc
KW  - Recycling assay
KW  - Extracelluar wingless
KW  - Imaginal disc dissection
Y1  - 2021
U6  - https://doi.org/10.21769/BioProtoc.4040
SN  - 2331-8325
VL  - 11
IS  - 11
PB  - bio-protocol.org
CY  - Sunnyvale, CA
ER  - 
TY  - JOUR
A1  - Witt, Barbara
A1  - Stiboller, Michael
A1  - Raschke, Stefanie
A1  - Friese, Sharleen
A1  - Ebert, Franziska
A1  - Schwerdtle, Tanja
T1  - Characterizing effects of excess copper levels in a human astrocytic cell line with focus on oxidative stress markers
JF  - Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements, GMS
N2  - Background: Being an essential trace element, copper is involved in diverse physiological processes. However, excess levels might lead to adverse effects. Disrupted copper homeostasis, particularly in the brain, has been associated with human diseases including the neurodegenerative disorders Wilson and Alzheimer?s disease. In this context, astrocytes play an important role in the regulation of the copper homeostasis in the brain and likely in the prevention against neuronal toxicity, consequently pointing them out as a potential target for the neurotoxicity of copper. Major toxic mechanisms are discussed to be directed against mitochondria probably via oxidative stress. However, the toxic potential and mode of action of copper in astrocytes is poorly understood, so far. Methods: In this study, excess copper levels affecting human astrocytic cell model and their involvement in the neurotoxic mode of action of copper, as well as, effects on the homeostasis of other trace elements (Mn, Fe, Ca and Mg) were investigated. Results: Copper induced substantial cytotoxic effects in the human astrocytic cell line following 48 h incubation (EC30: 250 ?M) and affected mitochondrial function, as observed via reduction of mitochondrial membrane potential and increased ROS production, likely originating from mitochondria. Moreover, cellular GSH metabolism was altered as well. Interestingly, not only cellular copper levels were affected, but also the homeostasis of other elements (Ca, Fe and Mn) were disrupted. Conclusion: One potential toxic mode of action of copper seems to be effects on the mitochondria along with induction of oxidative stress in the human astrocytic cell model. Moreover, excess copper levels seem to interact with the homeostasis of other essential elements such as Ca, Fe and Mn. Disrupted element homeostasis might also contribute to the induction of oxidative stress, likely involved in the onset and progression of neurodegenerative disorders. These insights in the toxic mechanisms will help to develop ideas and approaches for therapeutic strategies against copper-mediated diseases.
KW  - Copper
KW  - Astrocytes
KW  - Toxicity
KW  - Mitochondria
KW  - ROS
KW  - Trace elements
Y1  - 2021
U6  - https://doi.org/10.1016/j.jtemb.2021.126711
SN  - 1878-3252
VL  - 65
PB  - Elsevier
CY  - München
ER  - 
TY  - JOUR
A1  - Wilhelmi, Ilka
A1  - Neumann, Alexander
A1  - Jähnert, Markus
A1  - Ouni, Meriem
A1  - Schürmann, Annette
T1  - Enriched alternative splicing in islets of diabetes-susceptible mice
JF  - International journal of molecular sciences
N2  - Dysfunctional islets of Langerhans are a hallmark of type 2 diabetes (T2D). We hypothesize that differences in islet gene expression alternative splicing which can contribute to altered protein function also participate in islet dysfunction. RNA sequencing (RNAseq) data from islets of obese diabetes-resistant and diabetes-susceptible mice were analyzed for alternative splicing and its putative genetic and epigenetic modulators. We focused on the expression levels of chromatin modifiers and SNPs in regulatory sequences. We identified alternative splicing events in islets of diabetes-susceptible mice amongst others in genes linked to insulin secretion, endocytosis or ubiquitin-mediated proteolysis pathways. The expression pattern of 54 histones and chromatin modifiers, which may modulate splicing, were markedly downregulated in islets of diabetic animals. Furthermore, diabetes-susceptible mice carry SNPs in RNA-binding protein motifs and in splice sites potentially responsible for alternative splicing events. They also exhibit a larger exon skipping rate, e.g., in the diabetes gene Abcc8, which might affect protein function. Expression of the neuronal splicing factor Srrm4 which mediates inclusion of microexons in mRNA transcripts was markedly lower in islets of diabetes-prone compared to diabetes-resistant mice, correlating with a preferential skipping of SRRM4 target exons. The repression of Srrm4 expression is presumably mediated via a higher expression of miR-326-3p and miR-3547-3p in islets of diabetic mice. Thus, our study suggests that an altered splicing pattern in islets of diabetes-susceptible mice may contribute to an elevated T2D risk.
KW  - alternative splicing
KW  - epigenetic
KW  - MicroRNA
KW  - RNAseq
KW  - diabetes
KW  - beta-cell
KW  - failure
Y1  - 2021
U6  - https://doi.org/10.3390/ijms22168597
SN  - 1422-0067
VL  - 22
IS  - 16
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - JOUR
A1  - Wigger, Dominik
A1  - Schumacher, Fabian
A1  - Schneider-Schaulies, Sibylle
A1  - Kleuser, Burkhard
T1  - Sphingosine 1-phosphate metabolism and insulin signaling
JF  - Cellular signalling
N2  - Insulin is the main anabolic hormone secreted by 13-cells of the pancreas stimulating the assimilation and storage of glucose in muscle and fat cells. It modulates the postprandial balance of carbohydrates, lipids and proteins via enhancing lipogenesis, glycogen and protein synthesis and suppressing glucose generation and its release from the liver. Resistance to insulin is a severe metabolic disorder related to a diminished response of peripheral tissues to the insulin action and signaling. This leads to a disturbed glucose homeostasis that precedes the onset of type 2 diabetes (T2D), a disease reaching epidemic proportions. A large number of studies reported an association between elevated circulating fatty acids and the development of insulin resistance. The increased fatty acid lipid flux results in the accumulation of lipid droplets in a variety of tissues. However, lipid intermediates such as diacylglycerols and ceramides are also formed in response to elevated fatty acid levels. These bioactive lipids have been associated with the pathogenesis of insulin resistance. More recently, sphingosine 1-phosphate (S1P), another bioactive sphingolipid derivative, has also been shown to increase in T2D and obesity. Although many studies propose a protective role of S1P metabolism on insulin signaling in peripheral tissues, other studies suggest a causal role of S1P on insulin resistance. In this review, we critically summarize the current state of knowledge of S1P metabolism and its modulating role on insulin resistance. A particular emphasis is placed on S1P and insulin signaling in hepatocytes, skeletal muscle cells, adipocytes and pancreatic 13-cells. In particular, modulation of receptors and enzymes that regulate S1P metabolism can be considered as a new therapeutic option for the treatment of insulin resistance and T2D.
KW  - Insulin resistance
KW  - Type 2 diabetes
KW  - Sphingolipids
KW  - Hepatocytes
KW  - Adipocytes
KW  - Skeletal muscle cells
Y1  - 2021
U6  - https://doi.org/10.1016/j.cellsig.2021.109959
SN  - 0898-6568
SN  - 1873-3913
VL  - 82
PB  - Elsevier Science
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Wetzel, Alexandra Nicole
A1  - Scholtka, Bettina
A1  - Schumacher, Fabian
A1  - Rawel, Harshadrai Manilal
A1  - Geisendörfer, Birte
A1  - Kleuser, Burkhard
T1  - Epigenetic DNA methylation of EBI3 modulates human interleukin-35 formation via NFkB signaling
BT  - a promising therapeutic option in ulcerative colitis
JF  - International journal of molecular sciences
N2  - Ulcerative colitis (UC), a severe chronic disease with unclear etiology that is associated with increased risk for colorectal cancer, is accompanied by dysregulation of cytokines. Epstein-Barr virus-induced gene 3 (EBI3) encodes a subunit in the unique heterodimeric IL-12 cytokine family of either pro- or anti-inflammatory function. After having recently demonstrated that upregulation of EBI3 by histone acetylation alleviates disease symptoms in a dextran sulfate sodium (DSS)-treated mouse model of chronic colitis, we now aimed to examine a possible further epigenetic regulation of EBI3 by DNA methylation under inflammatory conditions. Treatment with the DNA methyltransferase inhibitor (DNMTi) decitabine (DAC) and TNF alpha led to synergistic upregulation of EBI3 in human colon epithelial cells (HCEC). Use of different signaling pathway inhibitors indicated NF kappa B signaling was necessary and proportional to the synergistic EBI3 induction. MALDI-TOF/MS and HPLC-ESIMS/MS analysis of DAC/TNF alpha-treated HCEC identified IL-12p35 as the most probable binding partner to form a functional protein. EBI3/IL-12p35 heterodimers (IL-35) induce their own gene upregulation, something that was indeed observed in HCEC cultured with media from previously DAC/TNF alpha-treated HCEC. These results suggest that under inflammatory and demethylating conditions the upregulation of EBI3 results in the formation of anti-inflammatory IL-35, which might be considered as a therapeutic target in colitis.
KW  - decitabine
KW  - DNMT inhibitor
KW  - EBI3
KW  - inhibitory cytokines
KW  - interleukin-35
KW  - TNF alpha
KW  - Ulcerative colitis
Y1  - 2021
U6  - https://doi.org/10.3390/ijms22105329
SN  - 1422-0067
VL  - 22
IS  - 10
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Wendt, Martin
A1  - Senftleben, Nele
A1  - Gros, Patrick
A1  - Schmitt, Thomas
T1  - Coping with environmental extremes
BT  - population ecology and behavioural adaptation of Erebia pronoe, an Alpine butterfly species
JF  - Insects : open access journal
N2  - Simple Summary:& nbsp;High alpine meadows are home to numerous endemic butterfly species. A combination of climate change and changes in agricultural practices has led to a severe decline in many species. A seemingly unaffected representative of this habitat is Erebia pronoe. We studied the behaviour, resource use and population structure of this species to explain its resilience and estimate its future survival potential. This species shows pronounced protandry in combination with serial eclosion. Males were significantly more active and mobile and were also caught significantly more often than females, resulting in a pronounced shift in sex ratio in the predicted population structure. The adults use a wide range of nectar plants and establish homeranges in areas of high habitat quality. Thus, Erebia pronoe adults use a wide array of resources combined with a slight specialisation to avoid niche overlap with closely related species. The resulting ecological flexibility seems to be an adaptation to unpredictable environmental conditions, which should be the result of a long-lasting adaptation process. Moreover, the combination of opportunism and modest specialisation should also be a good basis for coping with future changes caused by climate and land-use change.</p> <br /> <br></p> <br /> A mark-recapture study of the nominotypical Erebia pronoe in the Alps was conducted to survey its ecological demands and characteristics. Population structure analysis revealed a combination of protandry (one-week earlier eclosion of males) and serial eclosion. Significant differences between both sexes were found in population density (males: 580/ha & PLUSMN; 37 SE; females: 241/ha & PLUSMN; 66 SE), sex-ratio (2.4) and behaviour (57.7 vs. 11.9% flying). Both sexes used a wide range of nectar plants (Asteraceae, 77.3%; Dipsacaceae, 12.3%; Gentianaceae, 9.7%). The use of nectar plants shows a non-specific spectrum, which, however, completely avoids overlap with the locally co-occurring species Erebia nivalis. Movement patterns show the establishment of homeranges, which significantly limits the migration potential. Due to its broad ecological niche, E. pronoe will probably be able to react plastically to the consequences of climate change. The formation of high population densities, the unconcerned endangerment status, the unspecific resource spectrum and the sedentary character of the species make E. pronoe a potential indicator of the quality and general resource occurrence of alpine rupicolous grasslands.
KW  - mark-release-recapture
KW  - movement patterns
KW  - opportunistic behaviour
KW  - partial protandry
KW  - population demography
Y1  - 2021
U6  - https://doi.org/10.3390/insects12100896
SN  - 2075-4450
VL  - 12
IS  - 10
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Wehrhan, Marc
A1  - Puppe, Daniel
A1  - Kaczorek, Danuta
A1  - Sommer, Michael
T1  - Spatial patterns of aboveground phytogenic Si stocks in a grass-dominated catchment
BT  - results from UAS-based high-resolution remote sensing
JF  - Biogeosciences : BG
N2  - Various studies have been performed to quantify silicon (Si) stocks in plant biomass and related Si fluxes in terrestrial biogeosystems. Most studies are deliberately designed on the plot scale to ensure low heterogeneity in soils and plant composition, hence similar environmental conditions. Due to the immanent spatial soil variability, the transferability of results to larger areas, such as catchments, is therefore limited. However, the emergence of new technical features and increasing knowledge on details in Si cycling lead to a more complex picture at landscape and catchment scales. Dynamic and static soil properties change along the soil continuum and might influence not only the species composition of natural vegetation but also its biomass distribution and related Si stocks. Maximum likelihood (ML) classification was applied to multispectral imagery captured by an unmanned aerial system (UAS) aiming at the identification of land cover classes (LCCs). Subsequently, the normalized difference vegetation index (NDVI) and ground-based measurements of biomass were used to quantify aboveground Si stocks in two Si-accumulating plants (Calamagrostis epige-jos and Phragmites australis) in a heterogeneous catchment and related corresponding spatial patterns of these stocks to soil properties. We found aboveground Si stocks of C. epige-jos and P. australis to be surprisingly high (maxima of Si stocks reach values up to 98 g Sim(-2)), i.e. comparable to or markedly exceeding reported values for the Si storage in aboveground vegetation of various terrestrial ecosystems. We further found spatial patterns of plant aboveground Si stocks to reflect spatial heterogeneities in soil properties. From our results, we concluded that (i) aboveground biomass of plants seems to be the main factor of corresponding phytogenic Si stock quantities, and (ii) a detection of biomass heterogeneities via UAS-based remote sensing represents a promising tool for the quantification of lifelike phytogenic Si pools at landscape scales.
Y1  - 2021
U6  - https://doi.org/10.5194/bg-18-5163-2021
SN  - 1726-4170
SN  - 1726-4189
VL  - 18
IS  - 18
SP  - 5163
EP  - 5183
PB  - Copernicus
CY  - Göttingen
ER  - 
TY  - JOUR
A1  - Wardelmann, Kristina
A1  - Rath, Michaela
A1  - Castro, José Pedro
A1  - Blümel, Sabine
A1  - Schell, Mareike
A1  - Hauffe, Robert
A1  - Schumacher, Fabian
A1  - Flore, Tanina
A1  - Ritter, Katrin
A1  - Wernitz, Andreas
A1  - Hosoi, Toru
A1  - Ozawa, Koichiro
A1  - Kleuser, Burkhard
A1  - Weiß, Jürgen
A1  - Schürmann, Annette
A1  - Kleinridders, André
T1  - Central acting Hsp10 regulates mitochondrial function, fatty acid metabolism and insulin sensitivity in the hypothalamus
JF  - Antioxidants
N2  - Mitochondria are critical for hypothalamic function and regulators of metabolism. Hypothalamic mitochondrial dysfunction with decreased mitochondrial chaperone expression is present in type 2 diabetes (T2D). Recently, we demonstrated that a dysregulated mitochondrial stress response (MSR) with reduced chaperone expression in the hypothalamus is an early event in obesity development due to insufficient insulin signaling. Although insulin activates this response and improves metabolism, the metabolic impact of one of its members, the mitochondrial chaperone heat shock protein 10 (Hsp10), is unknown. Thus, we hypothesized that a reduction of Hsp10 in hypothalamic neurons will impair mitochondrial function and impact brain insulin action. Therefore, we investigated the role of chaperone Hsp10 by introducing a lentiviral-mediated Hsp10 knockdown (KD) in the hypothalamic cell line CLU-183 and in the arcuate nucleus (ARC) of C57BL/6N male mice. We analyzed mitochondrial function and insulin signaling utilizing qPCR, Western blot, XF96 Analyzer, immunohistochemistry, and microscopy techniques. We show that Hsp10 expression is reduced in T2D mice brains and regulated by leptin in vitro. Hsp10 KD in hypothalamic cells induced mitochondrial dysfunction with altered fatty acid metabolism and increased mitochondria-specific oxidative stress resulting in neuronal insulin resistance. Consequently, the reduction of Hsp10 in the ARC of C57BL/6N mice caused hypothalamic insulin resistance with acute liver insulin resistance.
KW  - brain insulin signaling
KW  - mitochondria
KW  - oxidative stress
KW  - fatty acid metabolism
Y1  - 2021
U6  - https://doi.org/10.3390/antiox10050711
SN  - 2076-3921
VL  - 10
IS  - 5
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Wang, Wei
A1  - Cherstvy, Andrey G.
A1  - Kantz, Holger
A1  - Metzler, Ralf
A1  - Sokolov, Igor M.
T1  - Time averaging and emerging nonergodicity upon resetting of fractional Brownian motion and heterogeneous diffusion processes
JF  - Physical review : E, Statistical, nonlinear and soft matter physics
N2  - How different are the results of constant-rate resetting of anomalous-diffusion processes in terms of their ensemble-averaged versus time-averaged mean-squared displacements (MSDs versus TAMSDs) and how does stochastic resetting impact nonergodicity? We examine, both analytically and by simulations, the implications of resetting on the MSD- and TAMSD-based spreading dynamics of particles executing fractional Brownian motion (FBM) with a long-time memory, heterogeneous diffusion processes (HDPs) with a power-law space-dependent diffusivity D(x) = D0|x|gamma and their "combined" process of HDP-FBM. We find, inter alia, that the resetting dynamics of originally ergodic FBM for superdiffusive Hurst exponents develops disparities in scaling and magnitudes of the MSDs and mean TAMSDs indicating weak ergodicity breaking. For subdiffusive HDPs we also quantify the nonequivalence of the MSD and TAMSD and observe a new trimodal form of the probability density function. For reset FBM, HDPs and HDP-FBM we compute analytically and verify by simulations the short-time MSD and TAMSD asymptotes and long-time plateaus reminiscent of those for processes under confinement. We show that certain characteristics of these reset processes are functionally similar despite a different stochastic nature of their nonreset variants. Importantly, we discover nonmonotonicity of the ergodicitybreaking parameter EB as a function of the resetting rate r. For all reset processes studied we unveil a pronounced resetting-induced nonergodicity with a maximum of EB at intermediate r and EB similar to(1/r )-decay at large r. Alongside the emerging MSD-versus-TAMSD disparity, this r-dependence of EB can be an experimentally testable prediction. We conclude by discussing some implications to experimental systems featuring resetting dynamics.
Y1  - 2021
U6  - https://doi.org/10.1103/PhysRevE.104.024105
SN  - 2470-0045
SN  - 2470-0053
VL  - 104
IS  - 2
PB  - American Institute of Physics
CY  - Woodbury, NY
ER  - 
TY  - JOUR
A1  - Wang, Ningzhen
A1  - Daniels, Robert
A1  - Connelly, Liam
A1  - Sotzing, Michael
A1  - Wu, Chao
A1  - Gerhard, Reimund
A1  - Sotzing, Gregory A.
A1  - Cao, Yang
T1  - All-organic flexible ferroelectret nanogenerator with fabric-based electrodes for self-powered body area networks
JF  - Small : nano micro
N2  - Due to their electrically polarized air-filled internal pores, optimized ferroelectrets exhibit a remarkable piezoelectric response, making them suitable for energy harvesting. Expanded polytetrafluoroethylene (ePTFE) ferroelectret films are laminated with two fluorinated-ethylene-propylene (FEP) copolymer films and internally polarized by corona discharge. Poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS)-coated spandex fabric is employed for the electrodes to assemble an all-organic ferroelectret nanogenerator (FENG). The outer electret-plus-electrode double layers form active device layers with deformable electric dipoles that strongly contribute to the overall piezoelectric response in the proposed concept of wearable nanogenerators. Thus, the FENG with spandex electrodes generates a short-circuit current which is twice as high as that with aluminum electrodes. The stacking sequence spandex/FEP/ePTFE/FEP/ePTFE/FEP/spandex with an average pore size of 3 mu m in the ePTFE films yields the best overall performance, which is also demonstrated by the displacement-versus-electric-field loop results. The all-organic FENGs are stable up to 90 degrees C and still perform well 9 months after being polarized. An optimized FENG makes three light emitting diodes (LEDs) blink twice with the energy generated during a single footstep. The new all-organic FENG can thus continuously power wearable electronic devices and is easily integrated, for example, with clothing, other textiles, or shoe insoles.
KW  - all-organic ferroelectret nanogenerator (FENG)
KW  - all-organic
KW  - piezoelectric nanogenerator (PENG)
KW  - expanded polytetrafluoroethylene
KW  - ferroelectret
KW  - micro-energy harvesting
KW  - (PEDOT
KW  - PSS)-coated porous
KW  - fabric electrodes
KW  - wearable electronics
Y1  - 2021
U6  - https://doi.org/10.1002/smll.202103161
SN  - 1613-6810
SN  - 1613-6829
VL  - 17
IS  - 33
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Wang, Meng
A1  - Li, Panpan
A1  - Ma, Yao
A1  - Nie, Xiang
A1  - Grebe, Markus
A1  - Men, Shuzhen
T1  - Membrane sterol composition in Arabidopsis thaliana affects root elongation via auxin biosynthesis
JF  - International journal of molecular sciences
N2  - Plant membrane sterol composition has been reported to affect growth and gravitropism via polar auxin transport and auxin signaling. However, as to whether sterols influence auxin biosynthesis has received little attention. Here, by using the sterol biosynthesis mutant cyclopropylsterol isomerase1-1 (cpi1-1) and sterol application, we reveal that cycloeucalenol, a CPI1 substrate, and sitosterol, an end-product of sterol biosynthesis, antagonistically affect auxin biosynthesis. The short root phenotype of cpi1-1 was associated with a markedly enhanced auxin response in the root tip. Both were neither suppressed by mutations in polar auxin transport (PAT) proteins nor by treatment with a PAT inhibitor and responded to an auxin signaling inhibitor. However, expression of several auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) was upregulated in cpi1-1. Functionally, TAA1 mutation reduced the auxin response in cpi1-1 and partially rescued its short root phenotype. In support of this genetic evidence, application of cycloeucalenol upregulated expression of the auxin responsive reporter DR5:GUS (beta-glucuronidase) and of several auxin biosynthesis genes, while sitosterol repressed their expression. Hence, our combined genetic, pharmacological, and sterol application studies reveal a hitherto unexplored sterol-dependent modulation of auxin biosynthesis during Arabidopsis root elongation.
KW  - Arabidopsis thaliana
KW  - auxin
KW  - auxin biosynthesis
KW  - cycloeucalenol
KW  - CPI1
KW  - sitosterol
KW  - sterol
Y1  - 2021
U6  - https://doi.org/10.3390/ijms22010437
SN  - 1422-0067
VL  - 22
IS  - 1
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Wandt, Viktoria Klara Veronika
A1  - Winkelbeiner, Nicola Lisa
A1  - Bornhorst, Julia
A1  - Witt, Barbara
A1  - Raschke, Stefanie
A1  - Simon, Luise
A1  - Ebert, Franziska
A1  - Kipp, Anna Patricia
A1  - Schwerdtle, Tanja
T1  - A matter of concern
BT  - trace element dyshomeostasis and genomic stability in neurons
JF  - Redox Biology
N2  - Neurons are post-mitotic cells in the brain and their integrity is of central importance to avoid neurodegeneration. Yet, the inability of self-replenishment of post-mitotic cells results in the need to withstand challenges from numerous stressors during life. Neurons are exposed to oxidative stress due to high oxygen consumption during metabolic activity in the brain. Accordingly, DNA damage can occur and accumulate, resulting in genome instability. In this context, imbalances in brain trace element homeostasis are a matter of concern, especially regarding iron, copper, manganese, zinc, and selenium. Although trace elements are essential for brain physiology, excess and deficient conditions are considered to impair neuronal maintenance. Besides increasing oxidative stress, DNA damage response and repair of oxidative DNA damage are affected by trace elements. Hence, a balanced trace element homeostasis is of particular importance to safeguard neuronal genome integrity and prevent neuronal loss. This review summarises the current state of knowledge on the impact of deficient, as well as excessive iron, copper, manganese, zinc, and selenium levels on neuronal genome stability
Y1  - 2021
U6  - https://doi.org/10.1016/j.redox.2021.101877
VL  - 41
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - THES
A1  - Verbancic, Jana
T1  - Carbon supply and the regulation of primary cell wall synthesis in Arabidopsis thaliana
N2  - Cellulose is the most abundant biopolymer on Earth and cell wall (CW) synthesis is one of the major carbon consumers in the plant cell. Structure and several interaction partners of plasma membrane (PM)-bound cellulose synthase (CESA) complexes, CSCs, have been studied extensively, but much less is understood about the signals that activate and translocate CESAs to the PM and how exactly cellulose synthesis is being regulated during the diel cycle. The literature describes CSC regulation possibilities through interactions with accessory proteins upon stress conditions (e.g. CC1), post-translational modifications that regulate CSC speed and their possible anchoring in the PM (e.g. with phosphorylation and S-acylation, respectively). In this thesis, 13CO2 labeling and imaging techniques were employed in the same Arabidopsis seedling growth system to elucidate how and when new carbon is incorporated into cell wall (CW) sugars and UDP-glucose, and to follow CSC behavior during the diel cycle. Additionally, an ubiquitination analysis was performed to investigate a possible mechanism to affect CSC trafficking to and/or from the PM. Carbon is being incorporated into CW glucose at a 3-fold higher rate during the light period in comparison to the night in wild-type seedlings. Furthermore, CSC density at the PM, as an indication of active cellulose synthesizing machinery, is increasing in the light and falling during the night, showing that CW biosynthesis is more active in the light. Therefore, CW synthesis might be regulated by the carbon status of the cell. This regulation is broken in the starchless pgm mutant where light and dark carbon incorporation rates into CW glucose are similar, possibly due to the high soluble sugar content in pgm during the first part of the night. Strikingly, pgm CSC abundance at the PM is constantly low during the whole diel cycle, indicating little or no cellulose synthesis, but can be restored with exogenous sucrose or a longer photoperiod. Ubiquitination was explored as a possible regulating mechanism for translocation of primary CW CSCs from the PM and several potential ubiquitination sites have been identified.. The approach in this thesis enabled to study cellulose/CW synthesis from different angles but in the same growth system, allowing direct comparison of those methodologies, which could help understand the relationship between the amount of available carbon in a plant cell and the cells capacity to synthesize cellulose/CW. Understanding which factors contribute to cellulose synthesis regulation and addressing those fundamental questions can provide essential knowledge to manage the need for increased crop production.
KW  - cellulose
KW  - cell wall
KW  - 13CO2 labeling
KW  - UDP-glucose
KW  - ubiquitination
Y1  - 2021
ER  - 
TY  - THES
A1  - Uflewski, Michal
T1  - Characterizing the regulation of proton antiport across the thylakoid membrane
N2  - Die Energie, die zum Antrieb photochemischer Reaktionen benötigt wird, stammt aus der Ladungstrennung an der Thylakoidmembran. Aufrgrund des Unterschieds in der Protonenkonzentration zwischen dem Stroma der Chloroplasten und dem Thylakoidlumen wird eine Protonenmotorische Kraft (pmf) erzeugt. Die pmf setzt sich aus dem Protonengradienten (ΔpH) und dem Membranpotential (ΔΨ) zusammen, die gemeinsam die ATP-Synthese antreiben. In der Natur schwankt die Energiemenge, die die Photosynthese antreibt, aufgrund häufiger Änderungen der Lichtintensität. Der Thylakoid-Ionentransport kann den Energiefluss durch einen Photosyntheseapparat an die Lichtverfügbarkeit anpassen, indem er die pmf-Zusammensetzung verändert. Die Dissipation von ΔΨ verringert die Ladungsrekombination am Photosystem II, so dass ein Anstieg der ΔpH-Komponente eine Rückkopplung zur Herabregulierung der Photosynthese auslösen kann. Der durch den K+-Austausch-Antiporter 3 (KEA3) gesteuerte K+/H+-Antiport reduziert den ΔpH-Anteil von pmf und dämpft dadurch das nicht-photochemische Quenching (NPQ). Infolgedessen erhöht sich die Photosyntheseeffizienz beim Übergang zu geringerer Lichtintensität. Ziel dieser Arbeit war es, Antworten auf Fragen zur Regulierung der KEA3-Aktivität und ihrer Rolle in der Pflanzenentwicklung zu finden. Die vorgestellten Daten zeigen, dass KEA3 in Pflanzen, denen der Chloroplasten-ATP-Synthase-Assembly-Faktor CGL160 fehlt und die eine verminderte ATP-Synthase-Aktivität aufweisen, eine zentrale Rolle bei der Regulierung der Photosynthese und des Pflanzenwachstums unter stationären Bedingungen spielt. Das Fehlen von KEA3 in der cgl160-Mutante führt zu einer starken Beeinträchtigung des Wachstums, da die Photosynthese aufgrund des erhöhten pH-abhängigen NPQs und des verringerten Elektronenflusses durch den Cytochrom b6f-Komplex eingeschränkt ist. Die Überexpression von KEA3 in der cgl160-Mutante erhöht die Ladungsrekombination im Photosystem II und fördert die Photosynthese. In Zeiten geringer ATP-Synthase-Aktivität profitieren die Pflanzen also von der KEA3-Aktivität. KEA3 unterliegt einer Dimerisierung über seinen regulatorischen C-Terminus (RCT). Der RCT reagiert auf Veränderungen der Lichtintensität, da die Pflanzen, die KEA3 ohne diese Domäne exprimieren, einen reduzierten Lichtschutzmechanismus bei Lichtintensitätsschwankungen aufweisen. Allerdings fixieren diese Pflanzen während der Photosynthese-Induktionsphase mehr Kohlenstoff als Gegenleistung für einen langfristigen Photoprotektor, was die regulierende Rolle von KEA3 in der Pflanzenentwicklung zeigt. Der KEA3-RCT ist dem Thylakoidstroma zugewandt, so dass seine Regulierung von lichtinduzierten Veränderungen in der Stroma-Umgebung abhängt. Die Regulierung der KEA3-Aktivität überschneidet sich mit den pH-Änderungen im Stroma, die bei Lichtschwankungen auftreten. Es hat sich gezeigt, dass ATP und ADP eine Affinität zum heterolog exprimierten KEA3 RCT haben. Eine solche Wechselwirkung verursacht Konformationsänderungen in der RCT-Struktur. Die Faltung der RCT-Liganden-Interaktion hängt vom pH-Wert der Umgebung ab. Mit einer Kombination aus Bioinformatik und In-vitro-Ansatz wurde die ATP-Bindungsstelle am RCT lokalisiert. Das Einfügen einer Punktmutation in der KEA3-RCT Bindungsstelle in planta führte zu einer Deregulierung der Antiporteraktivität beim Übergang zu wenig Licht. Die in dieser Arbeit vorgestellten Daten ermöglichten es uns, die Rolle von KEA3 bei der Anpassung der Photosynthese umfassender zu bewerten und Modelle zur Regulierung der KEA3-Aktivität während des Übergangs zwischen verschiedenen Lichtintensitäten vorzuschlagen.
N2  - The energy required to drive photochemical reactions is derived from charge separation across the thylakoid membrane. As the consequence of difference in proton concentration between chloroplasts stroma and thylakoid lumen, a proton motive force (pmf) is generated. The pmf is composed out of the proton gradient (ΔpH) and membrane potential (ΔΨ), and together they drive the ATP synthesis. In nature, the amount of energy fueling photosynthesis varies due to frequent changes in the light intensity. Thylakoid ion transport can adapt the energy flow through a photosynthetic apparatus to the light availability by adjusting the pmf composition. Dissipation of ΔΨ reduces the charge recombination at the photosystem II, allowing for an increase in ΔpH component to trigger a feedback downregulation of photosynthesis. K+ Exchange Antiporter 3 (KEA3) driven K+/H+ antiport reduces the ΔpH fraction of pmf, thereby dampening a non-photochemical quenching (NPQ). As a result, it increases the photosynthesis efficiency during the transition to lower light intensity. This thesis aimed to find the answers for questions concerning KEA3 activity regulation and its role in plant development. Presented data shows that in plants lacking chloroplast ATP synthase assembly factor CGL160 with decreased ATP synthase activity, KEA3 has a pivotal role in photosynthesis regulation and plant growth during steady-state conditions. Lack of KEA3 in cgl160 mutant results in a strong growth impairment, as photosynthesis is limited due to increased pH-dependent NPQ and decreased electron flow through cytochrome b6f complex. Overexpression of KEA3 in cgl160 mutant increases charge recombination at photosystem II, promoting photosynthesis. Thus, during periods of low ATP synthase activity, plants benefit from KEA3 activity. The KEA3 undergoes dimerization via its regulatory C-terminus (RCT). The RCT responds to changes in light intensity as the plants expressing KEA3 without this domain show reduced photo-protective mechanism in light intensity transients. However, those plants fix more carbon during the photosynthesis induction phase as a trade-off for a long-term photoprotection, showing KEA3 regulatory role in plant development. The KEA3 RCT is facing thylakoid stroma, thus its regulation depends on light-induced changes in the stromal environment. KEA3 activity regulation overlaps with the stromal pH changes occurring during light fluctuations. The ATP and ADP has shown to have an affinity towards heterologously expressed KEA3 RCT. Such interaction causes conformational changes in RCT structure. The fold change of RCT-ligand interaction depends on the environmental pH value. With a combination of bioinformatics and in vitro approach, the ATP binding site at RCT was located. Introduction of binding site point mutation in planta KEA3 RCT resulted in antiporter activity deregulation during transition to low light. Together, the data presented in this thesis allowed us to assess more broadly a KEA3 role in photosynthesis adjustment and propose the models of KEA3 activity regulation throughout transition in light intensity.
KW  - plant
KW  - photosynthesis
KW  - thylakoid
KW  - ion transport
KW  - fluctuating light
KW  - Pflanze
KW  - Photosynthese
KW  - Thylakoid
KW  - Ionentransport
KW  - schwankendes Licht
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Tung, Wing Tai
A1  - Sun, Xianlei
A1  - Wang, Weiwei
A1  - Xu, Xun
A1  - Ma, Nan
A1  - Lendlein, Andreas
T1  - Structure, mechanical properties and degradation behavior of electrospun PEEU fiber meshes and films
JF  - MRS advances : a journal of the Materials Research Society (MRS)
N2  - The capability of a degradable implant to provide mechanical support depends on its degradation behavior. Hydrolytic degradation was studied for a polyesteretherurethane (PEEU70), which consists of poly(p-dioxanone) (PPDO) and poly(epsilon-caprolactone) (PCL) segments with a weight ratio of 70:30 linked by diurethane junction units. PEEU70 samples prepared in the form of meshes with average fiber diameters of 1.5 mu m (mesh1.5) and 1.2 mu m (mesh1.2), and films were sterilized and incubated in PBS at 37 degrees C with 5 vol% CO2 supply for 1 to 6 weeks. Degradation features, such as cracks or wrinkles, became apparent from week 4 for all samples. Mass loss was found to be 11 wt%, 6 wt%, and 4 wt% for mesh1.2, mesh1.5, and films at week 6. The elongation at break decreased to under 20% in two weeks for mesh1.2. In case of the other two samples, this level of degradation was achieved after 4 weeks. The weight average molecular weight of both PEEU70 mesh and film samples decreased to below 30 kg/mol when elongation at break dropped below 20%. The time period of sustained mechanical stability of PEEU70-based meshes depends on the fiber diameter and molecular weight.
Y1  - 2021
U6  - https://doi.org/10.1557/s43580-020-00001-0
SN  - 2059-8521
VL  - 6
IS  - 10
SP  - 276
EP  - 282
PB  - Springer Nature Switzerland AG
CY  - Cham
ER  - 
TY  - THES
A1  - Tung, Wing Tai
T1  - Polymeric fibrous scaffold on macro/microscale towards tissue regeneration
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Tong, Hao
A1  - Küken, Anika
A1  - Razaghi-Moghadam, Zahra
A1  - Nikoloski, Zoran
T1  - Characterization of effects of genetic variants via genome-scale metabolic modelling
JF  - Cellular and molecular life sciences : CMLS
N2  - Genome-scale metabolic networks for model plants and crops in combination with approaches from the constraint-based modelling framework have been used to predict metabolic traits and design metabolic engineering strategies for their manipulation. With the advances in technologies to generate large-scale genotyping data from natural diversity panels and other populations, genome-wide association and genomic selection have emerged as statistical approaches to determine genetic variants associated with and predictive of traits. Here, we review recent advances in constraint-based approaches that integrate genetic variants in genome-scale metabolic models to characterize their effects on reaction fluxes. Since some of these approaches have been applied in organisms other than plants, we provide a critical assessment of their applicability particularly in crops. In addition, we further dissect the inferred effects of genetic variants with respect to reaction rate constants, abundances of enzymes, and concentrations of metabolites, as main determinants of reaction fluxes and relate them with their combined effects on complex traits, like growth. Through this systematic review, we also provide a roadmap for future research to increase the predictive power of statistical approaches by coupling them with mechanistic models of metabolism.
KW  - Single-nucleotide polymorphisms
KW  - Metabolic models
KW  - Genome-wide
KW  - association studies
KW  - Genomic selection
Y1  - 2021
U6  - https://doi.org/10.1007/s00018-021-03844-4
SN  - 1420-682X
SN  - 1420-9071
VL  - 78
IS  - 12
SP  - 5123
EP  - 5138
PB  - Springer International Publishing AG
CY  - Cham
ER  - 
TY  - THES
A1  - Ting, Michael Kien Yin
T1  - Circadian-regulated dynamics of translation in Arabidopsis thaliana
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Tchewonpi Sagu, Sorel
A1  - Landgräber, Eva
A1  - Henkel, Ina M.
A1  - Huschek, Gerd
A1  - Homann, Thomas
A1  - Bußler, Sara
A1  - Schlüter, Oliver
A1  - Rawel, Harshadrai Manilal
T1  - Effect of cereal α-amylase/trypsin inhibitors on developmental characteristics and abundance of digestive enzymes of mealworm larvae (Tenebrio molitor L.)
JF  - Insects : open access journal
N2  - The objective of this work was to investigate the potential effect of cereal α-amylase/trypsin inhibitors (ATIs) on growth parameters and selective digestive enzymes of Tenebrio molitor L. larvae. The approach consisted of feeding the larvae with wheat, sorghum and rice meals containing different levels and composition of α-amylase/trypsin inhibitors. The developmental and biochemical characteristics of the larvae were assessed over feeding periods of 5 h, 5 days and 10 days, and the relative abundance of α-amylase and selected proteases in larvae were determined using liquid chromatography tandem mass spectrometry. Overall, weight gains ranged from 21% to 42% after five days of feeding. The larval death rate significantly increased in all groups after 10 days of feeding (p < 0.05), whereas the pupation rate was about 25% among larvae fed with rice (Oryza sativa L.) and Siyazan/Esperya wheat meals, and only 8% and 14% among those fed with Damougari and S35 sorghum meals. As determined using the Lowry method, the protein contents of the sodium phosphate extracts ranged from 7.80 ± 0.09 to 9.42 ± 0.19 mg/mL and those of the ammonium bicarbonate/urea reached 19.78 ± 0.16 to 37.47 ± 1.38 mg/mL. The total protein contents of the larvae according to the Kjeldahl method ranged from 44.0 and 49.9 g/100 g. The relative abundance of α-amylase, CLIP domain-containing serine protease, modular serine protease zymogen and C1 family cathepsin significantly decreased in the larvae, whereas dipeptidylpeptidase I and chymotrypsin increased within the first hours after feeding (p < 0.05). Trypsin content was found to be constant independently of time or feed material. Finally, based on the results we obtained, it was difficult to substantively draw conclusions on the likely effects of meal ATI composition on larval developmental characteristics, but their effects on the digestive enzyme expression remain relevant.
KW  - growth behavior
KW  - Tenebrio molitor larvae
KW  - feeding
KW  - cereal meals
KW  - α-amylase
KW  - digestive enzymes quantification
KW  - LC-MS/MS
KW  - trypsin inhibitors
Y1  - 2021
U6  - https://doi.org/10.3390/insects12050454
SN  - 2075-4450
VL  - 12
IS  - 5
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Tadjoung Waffo, Armel Franklin
A1  - Mitrova, Biljana
A1  - Tiedemann, Kim
A1  - Iobbi-Nivol, Chantal
A1  - Leimkühler, Silke
A1  - Wollenberger, Ulla
T1  - Electrochemical trimethylamine n-oxide biosensor with enzyme-based oxygen-scavenging membrane for long-term operation under ambient air
JF  - Biosensors : open access journal
N2  - An amperometric trimethylamine N-oxide (TMAO) biosensor is reported, where TMAO reductase (TorA) and glucose oxidase (GOD) and catalase (Cat) were immobilized on the electrode surface, enabling measurements of mediated enzymatic TMAO reduction at low potential under ambient air conditions. The oxygen anti-interference membrane composed of GOD, Cat and polyvinyl alcohol (PVA) hydrogel, together with glucose concentration, was optimized until the O-2 reduction current of a Clark-type electrode was completely suppressed for at least 3 h. For the preparation of the TMAO biosensor, Escherichia coli TorA was purified under anaerobic conditions and immobilized on the surface of a carbon electrode and covered by the optimized O-2 scavenging membrane. The TMAO sensor operates at a potential of -0.8 V vs. Ag/AgCl (1 M KCl), where the reduction of methylviologen (MV) is recorded. The sensor signal depends linearly on TMAO concentrations between 2 mu M and 15 mM, with a sensitivity of 2.75 +/- 1.7 mu A/mM. The developed biosensor is characterized by a response time of about 33 s and an operational stability over 3 weeks. Furthermore, measurements of TMAO concentration were performed in 10% human serum, where the lowest detectable concentration is of 10 mu M TMAO.
KW  - trimethylamine N-oxide
KW  - biosensor
KW  - TMAO-reductase
KW  - oxygen scavenger
KW  - immobilized enzyme
KW  - multienzyme electrode
KW  - viologen
Y1  - 2021
U6  - https://doi.org/10.3390/bios11040098
SN  - 2079-6374
VL  - 11
IS  - 4
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Stiegler, Jonas
A1  - Kiemel, Katrin
A1  - Eccard, Jana
A1  - Fischer, Christina
A1  - Hering, Robert
A1  - Ortmann, Sylvia
A1  - Strigl, Lea
A1  - Tiedemann, Ralph
A1  - Ullmann, Wiebke
A1  - Blaum, Niels
T1  - Seed traits matter
BT  - endozoochoric dispersal through a pervasive mobile linker
JF  - Ecology and evolution
N2  - Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes.
KW  - agricultural landscapes
KW  - endozoochory
KW  - Lepus europaeus
KW  - mobile links
KW  - seed dispersal
KW  - seed dispersal syndrome
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.8440
SN  - 2045-7758
VL  - 11
IS  - 24
SP  - 18477
EP  - 18491
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Stiegler, Jonas
A1  - Kiemel, Katrin
A1  - Eccard, Jana
A1  - Fischer, Christina
A1  - Hering, Robert
A1  - Ortmann, Sylvia
A1  - Strigl, Lea
A1  - Tiedemann, Ralph
T1  - Seed traits matter
BT  - Endozoochoric dispersal through a pervasive mobile linker
JF  - Ecology and Evolution
N2  - Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes.
KW  - agricultural landscapes
KW  - endozoochory
KW  - Lepus europaeus
KW  - mobile links
KW  - seed dispersal
KW  - seed dispersal syndrome
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.8440
SN  - 2045-7758
VL  - 11
IS  - 24
SP  - 18477
EP  - 18491
PB  - John Wiley & Sons, Inc.
ER  - 
TY  - JOUR
A1  - Steppert, Isabel
A1  - Schönfelder, Jessy
A1  - Schultz, Carolyn
A1  - Kuhlmeier, Dirk
T1  - Rapid in vitro differentiation of bacteria by ion mobility spectrometry
JF  - Applied Microbiology and Biotechnology
N2  - Rapid screening of infected people plays a crucial role in interrupting infection chains. However, the current methods for identification of bacteria are very tedious and labor intense. Fast on-site screening for pathogens based on volatile organic compounds (VOCs) by ion mobility spectrometry (IMS) could help to differentiate between healthy and potentially infected subjects. As a first step towards this, the feasibility of differentiating between seven different bacteria including resistant strains was assessed using IMS coupled to multicapillary columns (MCC-IMS). The headspace above bacterial cultures was directly drawn and analyzed by MCC-IMS after 90 min of incubation. A cluster analysis software and statistical methods were applied to select discriminative VOC clusters. As a result, 63 VOC clusters were identified, enabling the differentiation between all investigated bacterial strains using canonical discriminant analysis. These 63 clusters were reduced to 7 discriminative VOC clusters by constructing a hierarchical classification tree. Using this tree, all bacteria including resistant strains could be classified with an AUC of 1.0 by receiver-operating characteristic analysis. In conclusion, MCC-IMS is able to differentiate the tested bacterial species, even the non-resistant and their corresponding resistant strains, based on VOC patterns after 90 min of cultivation. Although this result is very promising, in vivo studies need to be performed to investigate if this technology is able to also classify clinical samples. With a short analysis time of 5 min, MCC-IMS is quite attractive for a rapid screening for possible infections in various locations from hospitals to airports. Key Points center dot Differentiation of bacteria by MCC-IMS is shown after 90-min cultivation. center dot Non-resistant and resistant strains can be distinguished. center dot Classification of bacteria is possible based on metabolic features.
KW  - Bacteria identification
KW  - Volatile organic compounds (VOC)
KW  - Ion mobility
KW  - spectrometry (IMS)
KW  - Antibiotic resistance
KW  - Infection
KW  - Diagnostic
Y1  - 2021
U6  - https://doi.org/10.1007/s00253-021-11315-w
SN  - 0175-7598
SN  - 1432-0614
VL  - 105
IS  - 10
SP  - 4297
EP  - 4307
PB  - Springer
CY  - New York
ER  - 
TY  - CHAP
A1  - Stephan, Mareike Sophia
A1  - Barbirz, Stefanie
A1  - Robinson, Tom
A1  - Yandrapalli, Naresh
A1  - Dimova, Rumiana
T1  - Bacterial mimetic systems for studying bacterial inactivation and infection
BT  - Meeting abstract: 65th Annual Meeting of the Biophysical Society (BPS), Feb. 22-26, 2021
T2  - Biophysical journal : BJ / ed. by the Biophysical Society
Y1  - 2021
U6  - https://doi.org/10.1016/j.bpj.2020.11.1087
SN  - 0006-3495
SN  - 1542-0086
VL  - 120
IS  - 3
SP  - 148A
EP  - 148A
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Stark, Markus
A1  - Bach, Moritz
A1  - Guill, Christian
T1  - Patch isolation and periodic environmental disturbances have idiosyncratic effects on local and regional population variabilities in meta-food chains
JF  - Theoretical ecology
N2  - While habitat loss is a known key driver of biodiversity decline, the impact of other landscape properties, such as patch isolation, is far less clear. When patch isolation is low, species may benefit from a broader range of foraging opportunities, but are at the same time adversely affected by higher predation pressure from mobile predators. Although previous approaches have successfully linked such effects to biodiversity, their impact on local and metapopulation dynamics has largely been ignored. Since population dynamics may also be affected by environmental disturbances that temporally change the degree of patch isolation, such as periodic changes in habitat availability, accurate assessment of its link with isolation is highly challenging. To analyze the effect of patch isolation on the population dynamics on different spatial scales, we simulate a three-species meta-food chain on complex networks of habitat patches and assess the average variability of local populations and metapopulations, as well as the level of synchronization among patches. To evaluate the impact of periodic environmental disturbances, we contrast simulations of static landscapes with simulations of dynamic landscapes in which 30 percent of the patches periodically become unavailable as habitat. We find that increasing mean patch isolation often leads to more asynchronous population dynamics, depending on the parameterization of the food chain. However, local population variability also increases due to indirect effects of increased dispersal mortality at high mean patch isolation, consequently destabilizing metapopulation dynamics and increasing extinction risk. In dynamic landscapes, periodic changes of patch availability on a timescale much slower than ecological interactions often fully synchronize the dynamics. Further, these changes not only increase the variability of local populations and metapopulations, but also mostly overrule the effects of mean patch isolation. This may explain the often small and inconclusive impact of mean patch isolation in natural ecosystems.
KW  - Metacommunity dynamics
KW  - Dispersal
KW  - Patch isolation
KW  - Stability
KW  - Synchronization
KW  - Disturbance
Y1  - 2021
U6  - https://doi.org/10.1007/s12080-021-00510-0
SN  - 1874-1738
SN  - 1874-1746
VL  - 14
IS  - 3
SP  - 489
EP  - 500
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Spikes, Montrai
A1  - Rodríguez-Silva, Rodet
A1  - Bennett, Kerri-Ann
A1  - Bräger, Stefan
A1  - Josaphat, James
A1  - Torres-Pineda, Patricia
A1  - Ernst, Anja
A1  - Havenstein, Katja
A1  - Schlupp, Ingo
A1  - Tiedemann, Ralph
T1  - A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario
JF  - BMC Research Notes
N2  - Objective
The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean.

Results
For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade.
KW  - Cytochrome b
KW  - Island biogeography
KW  - Fresh water fish
KW  - Phylogeny
Y1  - 2021
U6  - https://doi.org/10.1186/s13104-021-05843-x
SN  - 1756-0500
VL  - 14
SP  - 1
EP  - 8
PB  - BMC Research Notes / Biomed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Soeriyadi, Angela H.
A1  - Ongley, Sarah E.
A1  - Kehr, Jan-Christoph
A1  - Pickford, Russel
A1  - Dittmann, Elke
A1  - Neilan, Brett A.
T1  - Tailoring enzyme stringency masks the multispecificity of a lyngbyatoxin (indolactam alkaloid) nonribosomal peptide synthetase
JF  - ChemBioChem
N2  - Indolactam alkaloids are activators of protein kinase C (PKC) and are of pharmacological interest for the treatment of pathologies involving PKC dysregulation. The marine cyanobacterial nonribosomal peptide synthetase (NRPS) pathway for lyngbyatoxin biosynthesis, which we previously expressed in E. coli, was studied for its amenability towards the biosynthesis of indolactam variants. Modification of culture conditions for our E. coli heterologous expression host and analysis of pathway products suggested the native lyngbyatoxin pathway NRPS does possess a degree of relaxed specificity. Site-directed mutagenesis of two positions within the adenylation domain (A-domain) substrate-binding pocket was performed, resulting in an alteration of substrate preference between valine, isoleucine, and leucine. We observed relative congruence of in vitro substrate activation by the LtxA NRPS to in vivo product formation. While there was a preference for isoleucine over leucine, the substitution of alternative tailoring domains may unveil the true in vivo effects of the mutations introduced herein.
KW  - a domain
KW  - indolactams
KW  - MbtH
KW  - natural products
KW  - teleocidin
Y1  - 2021
U6  - https://doi.org/10.1002/cbic.202100574
SN  - 1439-4227
SN  - 1439-7633
VL  - 23
IS  - 3
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Smith, Taylor
A1  - Rheinwalt, Aljoscha
A1  - Bookhagen, Bodo
T1  - Topography and climate in the upper Indus Basin
BT  - Mapping elevation-snow cover relationships
JF  - The science of the total environment : an international journal for scientific research into the environment and its relationship with man
N2  - The Upper Indus Basin (UIB), which covers a wide range of climatic and topographic settings, provides an ideal venue to explore the relationship between climate and topography. While the distribution of snow and glaciers is spatially and temporally heterogeneous, there exist regions with similar elevation-snow relationships. In this work, we construct elevation-binned snow-cover statistics to analyze 3415 watersheds and 7357 glaciers in the UIB region. We group both glaciers and watersheds using a hierarchical clustering approach and find that (1) watershed clusters mirror large-scale moisture transport patterns and (2) are highly dependent on median watershed elevation. (3) Glacier clusters are spatially heterogeneous and are less strongly controlled by elevation, but rather by local topographic parameters that modify solar insolation. Our clustering approach allows us to clearly define self-similar snow-topographic regions. Eastern watersheds in the UIB show a steep snow cover-elevation relationship whereas watersheds in the central and western UIB have moderately sloped relationships, but cluster in distinct groups. We highlight this snow-cover-topographic transition zone and argue that these watersheds have different hydrologic responses than other regions. Our hierarchical clustering approach provides a potential new framework to use in defining climatic zones in the cyrosphere based on empirical data.
KW  - Snow-cover
KW  - Hierarchical clustering
KW  - Glaciers
KW  - Upper Indus Basin
Y1  - 2021
U6  - https://doi.org/10.1016/j.scitotenv.2021.147363
SN  - 0048-9697
SN  - 1879-1026
VL  - 786
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Smirnov, Lev A.
A1  - Bolotov, Maxim I.
A1  - Osipov, Grigorij V.
A1  - Pikovskij, Arkadij
T1  - Disorder fosters chimera in an array of motile particles
JF  - Physical review : E, Statistical, nonlinear and soft matter physics
N2  - We consider an array of nonlocally coupled oscillators on a ring, which for equally spaced units possesses a Kuramoto-Battogtokh chimera regime and a synchronous state. We demonstrate that disorder in oscillators positions leads to a transition from the synchronous to the chimera state. For a static (quenched) disorder we find that the probability of synchrony survival depends on the number of particles, from nearly zero at small populations to one in the thermodynamic limit. Furthermore, we demonstrate how the synchrony gets destroyed for randomly (ballistically or diffusively) moving oscillators. We show that, depending on the number of oscillators, there are different scalings of the transition time with this number and the velocity of the units.
Y1  - 2021
U6  - https://doi.org/10.1103/PhysRevE.104.034205
SN  - 2470-0045
SN  - 2470-0053
VL  - 104
IS  - 3
PB  - American Physical Society
CY  - Melville, NY
ER  - 
TY  - JOUR
A1  - Sen, Jaydip
A1  - Bogin, Barry
A1  - Mondal, Nitish
A1  - Dey, Sima
A1  - Roy, Shreysai
ED  - Scheffler, Christiane
ED  - Koziel, Slawomir
ED  - Hermanussen, Michael
ED  - Bogin, Barry
T1  - Groundwater arsenic contamination in the Bengal Delta Plain is an important public health issue
BT  - a review
T2  - Human Biology and Public Health
N2  - There is a close association between human biology, epidemiology and public health. Exposure to toxic elements is one area of such associations and global concerns. The Bengal Delta Plain (BDP) is a region where contamination of ground water by arsenic has assumed epidemic proportions. Apart from dermatological manifestations, chronic exposure to arsenic causes a heavy toll through several carcinogenic and non-carcinogenic disorders. This article provides a global overview of groundwater arsenic contamination in the BDP region, especially the sources, speciation, and mobility of arsenic, and critically reviews the effects of arsenic on human health. The present review also provides a summary of comprehensive knowledge on various measures required for mitigation and social consequences of the problem of arsenic contaminated groundwater in the BDP region.
KW  - public health
KW  - arsenic
KW  - groundwater
KW  - India
KW  - Bangladesh
KW  - Bengal Delta
Y1  - 2021
U6  - https://doi.org/10.52905/hbph.v1.7
SN  - 2748-9957
VL  - 2021
IS  - 1
SP  - 1
EP  - 31
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - JOUR
A1  - Schönemann, Eric
A1  - Koc, Julian
A1  - Karthäuser, Jana
A1  - Özcan, Onur
A1  - Schanzenbach, Dirk
A1  - Schardt, Lisa
A1  - Rosenhahn, Axel
A1  - Laschewsky, André
T1  - Sulfobetaine methacrylate polymers of unconventional polyzwitterion architecture and their antifouling properties
JF  - Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences
N2  - Combining high hydrophilicity with charge neutrality, polyzwitterions are intensely explored for their high biocompatibility and low-fouling properties. Recent reports indicated that in addition to charge neutrality, the zwitterion's segmental dipole orientation is an important factor for interacting with the environment. Accordingly, a series of polysulfobetaines with a novel architecture was designed, in which the cationic and anionic groups of the zwitterionic moiety are placed at equal distances from the backbone. They were investigated by in vitro biofouling assays, covering proteins of different charges and model marine organisms. All polyzwitterion coatings reduced the fouling effectively compared to model polymer surfaces of poly(butyl methacrylate), with a nearly equally good performance as the reference polybetaine poly(3-(N-(2-(methacryloyloxy)ethyl)-N,N-dimethylammonio)propanesulfonate). The specific fouling resistance depended on the detailed chemical structure of the polyzwitterions. Still, while clearly affecting the performance, the precise dipole orientation of the sulfobetaine group in the polyzwitterions seems overall to be only of secondary importance for their antifouling behavior.
Y1  - 2021
U6  - https://doi.org/10.1021/acs.biomac.0c01705
SN  - 1525-7797
SN  - 1526-4602
VL  - 22
IS  - 4
SP  - 1494
EP  - 1508
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Schneeberger, Karin
A1  - Schulze, Michael
A1  - Scheffler, Ingo
A1  - Caspers, Barbara A.
T1  - Evidence of female preference for odor of distant over local males in a bat with female dispersal
JF  - Behavioral ecology : the official journal of the International Society for Behavioral Ecology
N2  - Geographic variation of sexually selected male traits is common in animals. Female choice also varies geographically and several studies found female preference for local males, which is assumed to lead to local adaptation and, therefore, increases fitness. As females are the nondispersing sex in most mammalian taxa, this preference for local males might be explained by the learning of male characteristics. Studies on the preference of females in female-dispersing species are lacking so far. To find out whether such females would also show preferences for local males, we conducted a study on greater sac-winged bats (Saccopteryx bilineata), a species where females disperse and males stay in their natal colony. Male greater sac-winged bats possess a wing pouch that is filled with odoriferous secretion and fanned toward females during courtship display. In a combination of chemical analysis and behavioral preference tests, we analyzed whether the composition of wing sac secretion varies between two geographically distinct populations (300 km), and whether females show a preference for local or distant male scent. Using gas chromatography, we found significant differences in the composition of the wing sac odors between the two geographically distinct populations. In addition, the behavioral preference experiments revealed that females of both populations preferred the scent of geographically distant males over local males. The wing sac odor might thus be used to guarantee optimal outbreeding when dispersing to a new colony. This is-to our knowledge-the first study on odor preference of females of a species with female-biased dispersal.
KW  - bats
KW  - dispersal
KW  - female preference
KW  - male philopatry
KW  - odor
KW  - olfaction
Y1  - 2021
U6  - https://doi.org/10.1093/beheco/arab003
SN  - 1045-2249
SN  - 1465-7279
VL  - 32
IS  - 4
SP  - 657
EP  - 661
PB  - Oxford University Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Schirrmann, Michael
A1  - Landwehr, Niels
A1  - Giebel, Antje
A1  - Garz, Andreas
A1  - Dammer, Karl-Heinz
T1  - Early detection of stripe rust in winter wheat using deep residual neural networks
JF  - Frontiers in plant science : FPLS
N2  - Stripe rust (Pst) is a major disease of wheat crops leading untreated to severe yield losses. The use of fungicides is often essential to control Pst when sudden outbreaks are imminent. Sensors capable of detecting Pst in wheat crops could optimize the use of fungicides and improve disease monitoring in high-throughput field phenotyping. Now, deep learning provides new tools for image recognition and may pave the way for new camera based sensors that can identify symptoms in early stages of a disease outbreak within the field. The aim of this study was to teach an image classifier to detect Pst symptoms in winter wheat canopies based on a deep residual neural network (ResNet). For this purpose, a large annotation database was created from images taken by a standard RGB camera that was mounted on a platform at a height of 2 m. Images were acquired while the platform was moved over a randomized field experiment with Pst-inoculated and Pst-free plots of winter wheat. The image classifier was trained with 224 x 224 px patches tiled from the original, unprocessed camera images. The image classifier was tested on different stages of the disease outbreak. At patch level the image classifier reached a total accuracy of 90%. To test the image classifier on image level, the image classifier was evaluated with a sliding window using a large striding length of 224 px allowing for fast test performance. At image level, the image classifier reached a total accuracy of 77%. Even in a stage with very low disease spreading (0.5%) at the very beginning of the Pst outbreak, a detection accuracy of 57% was obtained. Still in the initial phase of the Pst outbreak with 2 to 4% of Pst disease spreading, detection accuracy with 76% could be attained. With further optimizations, the image classifier could be implemented in embedded systems and deployed on drones, vehicles or scanning systems for fast mapping of Pst outbreaks.
KW  - yellow rust
KW  - monitoring
KW  - deep learning
KW  - wheat crops
KW  - image recognition
KW  - camera sensor
KW  - ResNet
KW  - smart farming
Y1  - 2021
U6  - https://doi.org/10.3389/fpls.2021.469689
SN  - 1664-462X
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Schindler, Daniel
A1  - Moldenhawer, Ted
A1  - Stange, Maike
A1  - Lepro, Valentino
A1  - Beta, Carsten
A1  - Holschneider, Matthias
A1  - Huisinga, Wilhelm
T1  - Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows
JF  - PLoS Computational Biology : a new community journal
N2  - Amoeboid cell motility is essential for a wide range of biological processes including wound healing, embryonic morphogenesis, and cancer metastasis. It relies on complex dynamical patterns of cell shape changes that pose long-standing challenges to mathematical modeling and raise a need for automated and reproducible approaches to extract quantitative morphological features from image sequences. Here, we introduce a theoretical framework and a computational method for obtaining smooth representations of the spatiotemporal contour dynamics from stacks of segmented microscopy images. Based on a Gaussian process regression we propose a one-parameter family of regularized contour flows that allows us to continuously track reference points (virtual markers) between successive cell contours. We use this approach to define a coordinate system on the moving cell boundary and to represent different local geometric quantities in this frame of reference. In particular, we introduce the local marker dispersion as a measure to identify localized membrane expansions and provide a fully automated way to extract the properties of such expansions, including their area and growth time. The methods are available as an open-source software package called AmoePy, a Python-based toolbox for analyzing amoeboid cell motility (based on time-lapse microscopy data), including a graphical user interface and detailed documentation. Due to the mathematical rigor of our framework, we envision it to be of use for the development of novel cell motility models. We mainly use experimental data of the social amoeba Dictyostelium discoideum to illustrate and validate our approach. <br /> Author summary Amoeboid motion is a crawling-like cell migration that plays an important key role in multiple biological processes such as wound healing and cancer metastasis. This type of cell motility results from expanding and simultaneously contracting parts of the cell membrane. From fluorescence images, we obtain a sequence of points, representing the cell membrane, for each time step. By using regression analysis on these sequences, we derive smooth representations, so-called contours, of the membrane. Since the number of measurements is discrete and often limited, the question is raised of how to link consecutive contours with each other. In this work, we present a novel mathematical framework in which these links are described by regularized flows allowing a certain degree of concentration or stretching of neighboring reference points on the same contour. This stretching rate, the so-called local dispersion, is used to identify expansions and contractions of the cell membrane providing a fully automated way of extracting properties of these cell shape changes. We applied our methods to time-lapse microscopy data of the social amoeba Dictyostelium discoideum.
Y1  - 2021
U6  - https://doi.org/10.1371/journal.pcbi.1009268
SN  - 1553-734X
SN  - 1553-7358
VL  - 17
IS  - 8
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Scharnweber, Inga Kristin
A1  - Chaguaceda, Fernando
A1  - Eklöv, Peter
T1  - Fatty acid accumulation in feeding types of a natural freshwater fish population
JF  - Oecologia / in cooperation with the International Association for Ecology, Intecol
N2  - Fatty acids are widely used to study trophic interactions in food web assemblages. Generally, it is assumed that there is a very small modification of fatty acids from one trophic step to another, making them suitable as trophic biomarkers. However, recent literature provides evidence that many fishes possess genes encoding enzymes with a role in bioconversion, thus the capability for bioconversion might be more widespread than previously assumed. Nonetheless, empirical evidence for biosynthesis occurring in natural populations remains scarce. In this study, we investigated different feeding types of perch (Perca fluviatilis) that are specialized on specific resources with different levels of highly unsaturated fatty acids (HUFAs), and analyzed the change between HUFA proportions in perch muscle tissue compared to their resources. Perch showed matching levels to their resources for EPA, but ARA and especially DHA were accumulated. Compound-specific stable isotope analyses helped us to identify the origin of HUFA carbon. Our results suggest that perch obtain a substantial amount of DHA via bioconversion when feeding on DHA-poor benthic resources. Thus, our data indicate the capability of bioconversion of HUFAs in a natural freshwater fish population.
KW  - Fatty acid conversion
KW  - Compound-specific stable isotope analysis
KW  - Docosahexaenoic acid
KW  - Bioconversion
KW  - Trophic upgrading
Y1  - 2021
U6  - https://doi.org/10.1007/s00442-021-04913-y
SN  - 0029-8549
SN  - 1432-1939
VL  - 196
IS  - 1
SP  - 53
EP  - 63
PB  - Springer
CY  - Berlin ; Heidelberg [u.a.]
ER  - 
TY  - JOUR
A1  - Scharnweber, Inga Kristin
A1  - Andersson, Matilda L.
A1  - Chaguaceda, Fernando
A1  - Eklöv, Peter
T1  - Intraspecific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis)
JF  - Ecology and evolution
N2  - Stable isotopes represent a unique approach to provide insights into the ecology of organisms. δ13C and δ15N have specifically been used to obtain information on the trophic ecology and food-web interactions. Trophic discrimination factors (TDF, Δ13C and Δ15N) describe the isotopic fractionation occurring from diet to consumer tissue, and these factors are critical for obtaining precise estimates within any application of δ13C and δ15N values. It is widely acknowledged that metabolism influences TDF, being responsible for different TDF between tissues of variable metabolic activity (e.g., liver vs. muscle tissue) or species body size (small vs. large). However, the connection between the variation of metabolism occurring within a single species during its ontogeny and TDF has rarely been considered. Here, we conducted a 9-month feeding experiment to report Δ13C and Δ15N of muscle and liver tissues for several weight classes of Eurasian perch (Perca fluviatilis), a widespread teleost often studied using stable isotopes, but without established TDF for feeding on a natural diet. In addition, we assessed the relationship between the standard metabolic rate (SMR) and TDF by measuring the oxygen consumption of the individuals. Our results showed a significant negative relationship of SMR with Δ13C, and a significant positive relationship of SMR with Δ15N of muscle tissue, but not with TDF of liver tissue. SMR varies inversely with size, which translated into a significantly different TDF of muscle tissue between size classes. In summary, our results emphasize the role of metabolism in shaping-specific TDF (i.e., Δ13C and Δ15N of muscle tissue) and especially highlight the substantial differences between individuals of different ontogenetic stages within a species. Our findings thus have direct implications for the use of stable isotope data and the applications of stable isotopes in food-web studies.
KW  - fractionation factors
KW  - metabolism
KW  - ontogeny
KW  - standard metabolic rate
KW  - tissue types
KW  - δ13C
KW  - δ15N
Y1  - 2021
SN  - 2045-7758
VL  - 11
IS  - 14
SP  - 9804
EP  - 9814
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Sauer, Michael
A1  - Grebe, Markus
T1  - Plant cell biology
BT  - PIN polarity maintained
JF  - Current biology : CB
N2  - PIN-FORMED (PIN) polar protein localization directs transport of the growth and developmental regulator auxin in plants. Once established after cytokinesis, PIN polarity requires maintenance. Now, direct interactions between PIN, MAB4/MEL and PID proteins suggest self-reinforced maintenance of PIN polarity through limiting lateral diffusion.
Y1  - 2021
U6  - https://doi.org/10.1016/j.cub.2021.03.070
SN  - 0960-9822
SN  - 1879-0445
VL  - 31
IS  - 9
SP  - R449
EP  - R451
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Santamans, Carla Daniela
A1  - Cordoba, Francisco E.
A1  - Franco, María G.
A1  - Vignoni, Paula
A1  - Lupo, Liliana C.
T1  - Hydro-climatological variability in Lagunas de Vilama System, Argentinean Altiplano-Puna Plateau, Southern Tropical Andes (22 degrees S) and its response to large-scale climate forcings
JF  - The science of the total environment : an international journal for scientific research into the environment and its relationship with man
N2  - The Altiplano-Puna Plateau holds several shallow lakes, which are very sensitive to climate changes. This work is focused on a high-altitude lake system called Lagunas de Vilama (LVS), located in a complex climatic transition area with scarcity of continuous and homogeneous instrumental records. The objective of this study is to determine the regional spatial-temporal variability of precipitation and evaluate the seasonal and interannual lake responses. We use a lake-surfaces record derived from Landsat images to investigate links with regional precipitations and different climatic forcings. The results reveal that austral summer and autumn precipitations control the variability of the annual lake-surfaces. Also, we found intra-annual and interannual lags in the lake responses to precipitations, and identified several wet and dry stages. Our results show negative trends in precipitations and lake-surfaces, whose were strengthened by a shift to a warm phase of the Atlantic Multidecadal Oscillation in the 1990s. The El Nino Southern Oscillation, Pacific Decadal Oscillation, and Southern Annular Mode also exert a strong influence in the region. This study demonstrates that the variability of LVS lakes is strongly related to the South American Monsoon System dynamics and large-scale climate fordngs from the Pacific and Atlantic Oceans. This work provides novel indices which demonstrated to be good indicators of regional hydroclimatological variability for this region of South America.
KW  - Lake-surfaces variability
KW  - Precipitation variability
KW  - Hydro-meteorological indices
KW  - Regional forcings
KW  - South American Monsoon
KW  - System
KW  - Andean plateau
Y1  - 2021
U6  - https://doi.org/10.1016/j.scitotenv.2020.144926
SN  - 0048-9697
SN  - 1879-1026
VL  - 767
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Sandhage-Hofmann, Alexandra
A1  - Linstädter, Anja
A1  - Kindermann, Liana
A1  - Angombe, Simon
A1  - Amelung, Wulf
T1  - Conservation with elevated elephant densities sequesters carbon in soils despite losses of woody biomass
JF  - Global change biology
N2  - Nature conservation and restoration in terrestrial ecosystems is often focused on increasing the numbers of megafauna, expecting them to have positive impacts on ecological self-regulation processes and biodiversity. In sub-Saharan Africa, conservation efforts also aspire to protect and enhance biodiversity with particular focus on elephants. However, elephant browsing carries the risk of woody biomass losses. In this context, little is known about how increasing elephant numbers affects carbon stocks in soils, including the subsoils. We hypothesized that (1) increasing numbers of elephants reduce tree biomass, and thus the amount of C stored therein, resulting (2) in a loss of soil organic carbon (SOC). If true, a negative carbon footprint could limit the sustainability of elephant conservation from a global carbon perspective. To test these hypotheses, we selected plots of low, medium, and high elephant densities in two national parks and adjacent conservancies in the Namibian component of the Kavango Zambezi Transfrontier Area (KAZA), and quantified carbon storage in both woody vegetation and soils (1 m). Analyses were supplemented by the assessment of soil carbon isotopic composition. We found that increasing elephant densities resulted in a loss of tree carbon storage by 6.4 t ha(-1). However, and in contrast to our second hypothesis, SOC stocks increased by 4.7 t ha(-1) with increasing elephant densities. These higher SOC stocks were mainly found in the topsoil (0-30 cm) and were largely due to the formation of SOC from woody biomass. A second carbon input source into the soils was megaherbivore dung, which contributed with 0.02-0.323 t C ha(-1) year(-1) to ecosystem carbon storage in the low and high elephant density plots, respectively. Consequently, increasing elephant density does not necessarily lead to a negative C footprint, as soil carbon sequestration and transient C storage in dung almost compensate for losses in tree biomass.
KW  - carbon sequestration
KW  - conservation
KW  - elephants
KW  - soil organic carbon
KW  - woody biomass
Y1  - 2021
U6  - https://doi.org/10.1111/gcb.15779
SN  - 1354-1013
SN  - 1365-2486
VL  - 27
IS  - 19
SP  - 4601
EP  - 4614
PB  - Blackwell Science
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Rutschmann, Sereina
A1  - Chen, Ping
A1  - Zhou, Changfa
A1  - Monaghan, Michael T.
T1  - Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae)
JF  - Mitochondrial DNA Part B
N2  - Mayflies (Ephemeroptera) are a semi-aquatic insect order with comparatively few genomic data available despite their phylogenetic position at the root of the winged-insects and possession of ancestral traits. 

Here, we provide three mitochondrial genomes (mtgenomes) from representatives of the two most species-rich families, Baetis rutilocylindratus and Cloeon dipterum (Baetidae), and Habrophlebiodes zijinensis (Leptophlebiidae). 
All mtgenomes had a complete set of 13 protein-coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. 
Phylogenetic reconstructions using 21 mayfly mtgenomes and representatives of seven additional orders recovered both Baetidae and Leptophlebiidae as well supported monophyletic clades, with Ephemeroptera as the sister-taxon to all other winged insects (i.e. Odonata and Neoptera).
KW  - Baetis
KW  - Cloeon
KW  - Habrophlebiodes
KW  - mayfly
KW  - mitochondrial phylogeny
Y1  - 2021
U6  - https://doi.org/10.1080/23802359.2021.1974966
SN  - 2380-2359
VL  - 6
IS  - 10
SP  - 2969
EP  - 2971
PB  - Routledge, Taylor & Francis Group
CY  - Abingdon
ER  - 
TY  - JOUR
A1  - Rottler, Erwin
A1  - Vormoor, Klaus Josef
A1  - Francke, Till
A1  - Bronstert, Axel
T1  - Hydro Explorer
BT  - an interactive web app to investigate changes in runoff timing and runoff seasonality all over the world
JF  - River research and applications
N2  - Climatic changes and anthropogenic modifications of the river basin or river network have the potential to fundamentally alter river runoff. In the framework of this study, we aim to analyze and present historic changes in runoff timing and runoff seasonality observed at river gauges all over the world. In this regard, we develop the Hydro Explorer, an interactive web app, which enables the investigation of >7,000 daily resolution discharge time series from the Global Runoff Data Centre (GRDC). The interactive nature of the developed web app allows for a quick comparison of gauges, regions, methods, and time frames. We illustrate the available analytical tools by investigating changes in runoff timing and runoff seasonality in the Rhine River Basin. Since we provide the source code of the application, existing analytical approaches can be modified, new methods added, and the tool framework can be re-used to visualize other data sets.
KW  - global runoff database
KW  - interactive web app
KW  - R Shiny
KW  - runoff
KW  - seasonality
KW  - runoff timing
Y1  - 2021
U6  - https://doi.org/10.1002/rra.3772
SN  - 1535-1459
SN  - 1535-1467
VL  - 37
IS  - 4
SP  - 544
EP  - 554
PB  - Wiley
CY  - New York
ER  - 
TY  - JOUR
A1  - Romero-Mujalli, Daniel
A1  - Rochow, Markus
A1  - Kahl, Sandra M.
A1  - Paraskevopoulou, Sofia
A1  - Folkertsma, Remco
A1  - Jeltsch, Florian
A1  - Tiedemann, Ralph
T1  - Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies
JF  - Ecology and Evolution
N2  - Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses  under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one  genotype–phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona
climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype–phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.
KW  - developmental canalization
KW  - environmental change
KW  - genetic accommodation
KW  - Individual-based models
KW  - limits
KW  - many-to-one genotype–phenotype map
KW  - noise color
KW  - phenotypic plasticity
KW  - reaction norms
KW  - stochastic fluctuations
Y1  - 2020
SN  - 2045-7758
VL  - 11
IS  - 11
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Rogol, Alan D.
ED  - Scheffler, Christiane
ED  - Koziel, Slawomir
ED  - Hermanussen, Michael
ED  - Bogin, Barry
T1  - Settings Perspective
BT  - Bridging the Gap between Human Biology and Public Health
T2  - Human Biology and Public Health
KW  - growth
KW  - maturation
KW  - populations
KW  - secular change
Y1  - 2021
U6  - https://doi.org/10.52905/hbph.v1.2
SN  - 2748-9957
VL  - 2021
IS  - 1
SP  - 1
EP  - 2
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - JOUR
A1  - Roe, Stephanie
A1  - Streck, Charlotte
A1  - Beach, Robert
A1  - Busch, Jonah
A1  - Chapman, Melissa
A1  - Daioglou, Vassilis
A1  - Deppermann, Andre
A1  - Doelman, Jonathan
A1  - Emmet-Booth, Jeremy
A1  - Engelmann, Jens
A1  - Fricko, Oliver
A1  - Frischmann, Chad
A1  - Funk, Jason
A1  - Grassi, Giacomo
A1  - Griscom, Bronson
A1  - Havlik, Petr
A1  - Hanssen, Steef
A1  - Humpenöder, Florian
A1  - Landholm, David
A1  - Lomax, Guy
A1  - Lehmann, Johannes
A1  - Mesnildrey, Leah
A1  - Nabuurs, Gert-Jan
A1  - Popp, Alexander
A1  - Rivard, Charlotte
A1  - Sanderman, Jonathan
A1  - Sohngen, Brent
A1  - Smith, Pete
A1  - Stehfest, Elke
A1  - Woolf, Dominic
A1  - Lawrence, Deborah
T1  - Land-based measures to mitigate climate change
BT  - potential and feasibility by country
JF  - Global change biology
N2  - Land-based climate mitigation measures have gained significant attention and importance in public and private sector climate policies. Building on previous studies, we refine and update the mitigation potentials for 20 land-based measures in >200 countries and five regions, comparing “bottom-up” sectoral estimates with integrated assessment models (IAMs). We also assess implementation feasibility at the country level. Cost-effective (available up to $100/tCO2eq) land-based mitigation is 8–13.8 GtCO2eq yr−1 between 2020 and 2050, with the bottom end of this range representing the IAM median and the upper end representing the sectoral estimate. The cost-effective sectoral estimate is about 40% of available technical potential and is in line with achieving a 1.5°C pathway in 2050. Compared to technical potentials, cost-effective estimates represent a more realistic and actionable target for policy. The cost-effective potential is approximately 50% from forests and other ecosystems, 35% from agriculture, and 15% from demand-side measures. The potential varies sixfold across the five regions assessed (0.75–4.8 GtCO2eq yr−1) and the top 15 countries account for about 60% of the global potential. Protection of forests and other ecosystems and demand-side measures present particularly high mitigation efficiency, high provision of co-benefits, and relatively lower costs. The feasibility assessment suggests that governance, economic investment, and socio-cultural conditions influence the likelihood that land-based mitigation potentials are realized. A substantial portion of potential (80%) is in developing countries and LDCs, where feasibility barriers are of greatest concern. Assisting countries to overcome barriers may result in significant quantities of near-term, low-cost mitigation while locally achieving important climate adaptation and development benefits. Opportunities among countries vary widely depending on types of land-based measures available, their potential co-benefits and risks, and their feasibility. Enhanced investments and country-specific plans that accommodate this complexity are urgently needed to realize the large global potential from improved land stewardship.
KW  - AFOLU
KW  - co-benefits
KW  - demand management
KW  - feasibility
KW  - land management
KW  - land sector
KW  - mitigation
KW  - natural climate solutions
KW  - nature-based solutions
Y1  - 2021
U6  - https://doi.org/10.1111/gcb.15873
SN  - 1365-2486
VL  - 27
IS  - 23
SP  - 6025
EP  - 6058
PB  - Wiley-Blackwell
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Robin, Koger
A1  - Katharina, Syböck
A1  - Emily, Weinelt
A1  - Beda, Hartmann
A1  - Kirchengast, Sylvia
ED  - Scheffler, Christiane
ED  - Koziel, Slawomir
ED  - Hermanussen, Michael
ED  - Bogin, Barry
T1  - Advanced maternal age and nicotine consumption during pregnancy
BT  - Additive effects on new-born parameters
T2  - Human Biology and Public Health
N2  - Background

Nicotine consumption during pregnancy and advanced maternal age are well known independent risk factors for poor pregnancy outcome and therefore serious public health problems.

Objectives

Considering the ongoing trend of delaying childbirth in our society, this study investigates potential additive effects of nicotine consumption during pregnancy and advanced maternal age on foetal growth.

Sample and Methods

In a medical record-based study, we analysed the impact of maternal age and smoking behaviour before and during pregnancy on newborn size among 4142 singleton births that took place in Vienna, Austria between 1990 and 1995.

Results

Birth weight (H=82.176, p<0.001), birth length (H=91.525, p<0.001) and head circumference (H=42.097, p<0.001) differed significantly according to maternal smoking behaviour. For birth weight, the adjusted mean differences between smokers and non-smokers increased from 101.8g for the < 18-year-old mothers to 254.8g for >35 year olds, with the respective values for birth length being 0.6 cm to 0.7cm, for head circumference from 0.3 cm to 0.6 cm.

Conclusion

Increasing maternal age amplified the negative effects of smoking during pregnancy on newborn parameters. Our findings identify older smoking mothers as a high-risk group which should be of special interest for public health systems.
KW  - advanced maternal age at first birth
KW  - maternal nicotine consumption
KW  - foetal growth
KW  - newborn size
KW  - birthweight
KW  - smoking
Y1  - 2021
U6  - https://doi.org/10.52905/hbph.v1.6
SN  - 2748-9957
VL  - 2021
IS  - 1
SP  - 1
EP  - 19
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - JOUR
A1  - Rebekka Mumm, 
A1  - Reimann, Anna
A1  - Scheffler, Christiane
ED  - Scheffler, Christiane
ED  - Koziel, Slawomir
ED  - Hermanussen, Michael
ED  - Bogin, Barry
T1  - Estimation of percentage of body fat in field studies – a method based on relative elbow breadth (Frame Index) and BMI
T2  - Human Biology and Public Health
N2  - Background

Over the last 20 years, a decreasing trend in external skeletal robusticity and an increasing trend in overweight and obesity was observed worldwide in adults and children as modern lifestyles in nutritional and activity behavior have changed. However, body mass index (BMI) as a measure for overweight is not an ideal predictor of % body fat (%BF) either in children and adolescents or in adults. On the contrary, it disguises a phenomenon called “hidden obesity”.

Objectives

We aim to approximate %BF by combining skeletal robusticity and BMI and develop an estimation-based tool to identify normal weight obese children and adolescents.

Sample and Methods

We analyzed cross-sectional data on height, weight, elbow breadth, and skinfold thickness (triceps and subscapular) of German children aged 6 to 18 years (N=15,034). We used modified Hattori charts and multiple linear regression to develop a tool, the “%BF estimator”, to estimate %BF by using BMI and skeletal robusticity measured as Frame Index.

Results

Independent of sex and age an increase in BMI is associated with an increase in %BF, an increase in Frame Index is associated with a decrease in %BF. The developed tool “%BF estimator” allows the estimation of %BF per sex and age group after calculation of BMI and Frame Index.

Conclusion

The “%BF estimator” is an easily applicable tool for the estimation of %BF in respect of body composition for clinical practice, screening, and public health research. It is non-invasive and has high accuracy. Further, it allows the identification of normal weight obese children and adolescents.
KW  - body fat estimator
KW  - body composition
KW  - skeletal robusticity
KW  - hidden obesity
KW  - normal weigh obese
Y1  - 2021
U6  - https://doi.org/10.52905/hbph.v1.3
SN  - 2748-9957
VL  - 2021
IS  - 1
SP  - 1
EP  - 12
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - JOUR
A1  - Rausch, Ann-Kristin
A1  - Brockmeyer, Robert
A1  - Schwerdtle, Tanja
T1  - Development, validation, and application of a multi-method for the determination of mycotoxins, plant growth regulators, tropane alkaloids, and pesticides in cereals by two-dimensional liquid chromatography tandem mass spectrometry
JF  - Analytical & bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica
N2  - Mycotoxins and pesticides regularly co-occur in agricultural products worldwide. Thus, humans can be exposed to both toxic contaminants and pesticides simultaneously, and multi-methods assessing the occurrence of various food contaminants and residues in a single method are necessary. A two-dimensional high performance liquid chromatography tandem mass spectrometry method for the analysis of 40 (modified) mycotoxins, two plant growth regulators, two tropane alkaloids, and 334 pesticides in cereals was developed. After an acetonitrile/water/formic acid (79:20:1, v/v/v) multi-analyte extraction procedure, extracts were injected into the two-dimensional setup, and an online clean-up was performed. The method was validated according to Commission Decision (EC) no. 657/2002 and document N° SANTE/12682/2019. Good linearity (R2 > 0.96), recovery data between 70-120%, repeatability and reproducibility values < 20%, and expanded measurement uncertainties < 50% were obtained for a wide range of analytes, including very polar substances like deoxynivalenol-3-glucoside and methamidophos. However, results for fumonisins, zearalenone-14,16-disulfate, acid-labile pesticides, and carbamates were unsatisfying. Limits of quantification meeting maximum (residue) limits were achieved for most analytes. Matrix effects varied highly (−85 to +1574%) and were mainly observed for analytes eluting in the first dimension and early-eluting analytes in the second dimension. The application of the method demonstrated the co-occurrence of different types of cereals with 28 toxins and pesticides. Overall, 86% of the samples showed positive findings with at least one mycotoxin, plant growth regulator, or pesticide.
KW  - 2D-LC-MS/MS
KW  - Multi-method
KW  - Mycotoxins
KW  - Modified mycotoxins
KW  - Pesticides
KW  - Cereals
Y1  - 2021
U6  - https://doi.org/10.1007/s00216-021-03239-1
SN  - 1618-2650
SN  - 1618-2642
VL  - 413
IS  - 11
SP  - 3041
EP  - 3054
PB  - Springer
CY  - Berlin
ER  - 
TY  - JOUR
A1  - Ranisch, Robert
T1  - Consultation with Doctor Twitter
BT  - consent Fatigue, and the role of developers in digital medical ethics
JF  - The American journal of bioethics : ajob
Y1  - 2021
U6  - https://doi.org/10.1080/15265161.2021.1926595
SN  - 1526-5161
SN  - 1536-0075
VL  - 21
IS  - 7
SP  - 24
EP  - 25
PB  - Routledge, Taylor & Francis Group
CY  - Philadelphia, Pa.
ER  - 
TY  - CHAP
A1  - Ramadan, Shahenda
A1  - Guerrero, Paula
A1  - Nedielkov, Ruslan
A1  - Klishin, Nikolai
A1  - Dimova, Rumiana
A1  - Silva, Daniel V.
A1  - Möller, Heiko
T1  - Building a mimetic system for unraveling protein-protein interactions on membranes
T2  - European biophysics journal : with biophysics letters ; an international journal of biophysics
Y1  - 2021
U6  - https://doi.org/10.1007/s00249-021-01558-w
SN  - 0175-7571
SN  - 1432-1017
VL  - 50
IS  - SUPPL 1
SP  - S153
EP  - S153
PB  - Springer
CY  - Berlin ; Heidelberg ; New York
ER  - 
TY  - JOUR
A1  - Raju, Rajarshi Roy
A1  - Koetz, Joachim
T1  - Inner rotation of Pickering Janus emulsions
JF  - Nanomaterials : open access journal
N2  - Janus droplets were prepared by vortex mixing of three non-mixable liquids, i.e., olive oil, silicone oil and water, in the presence of gold nanoparticles (AuNPs) in the aqueous phase and magnetite nanoparticles (MNPs) in the olive oil. The resulting Pickering emulsions were stabilized by a red-colored AuNP layer at the olive oil/water interface and MNPs at the oil/oil interface. The core–shell droplets can be stimulated by an external magnetic field. Surprisingly, an inner rotation of the silicon droplet is observed when MNPs are fixed at the inner silicon droplet interface. This is the first example of a controlled movement of the inner parts of complex double emulsions by magnetic manipulation via interfacially confined magnetic nanoparticles.
KW  - Janus droplets
KW  - Pickering emulsions
KW  - magnetic manipulation
KW  - gold nanoparticles
KW  - magnetite nanoparticles
Y1  - 2021
U6  - https://doi.org/10.3390/nano11123312
SN  - 2079-4991
VL  - 11
IS  - 12
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Rainer, Edda M.
A1  - Seppey, Christophe Victor William
A1  - Hammer, Caroline
A1  - Svenning, Mette M.
A1  - Tveit, Alexander Tosdal
T1  - The influence of above-ground herbivory on the response of Arctic soil methanotrophs to increasing CH4 concentrations and temperatures
JF  - Microorganisms : open access journal
N2  - Rising temperatures in the Arctic affect soil microorganisms, herbivores, and peatland vegetation, thus directly and indirectly influencing microbial CH4 production. It is not currently known how methanotrophs in Arctic peat respond to combined changes in temperature, CH4 concentration, and vegetation. We studied methanotroph responses to temperature and CH4 concentration in peat exposed to herbivory and protected by exclosures. The methanotroph activity was assessed by CH4 oxidation rate measurements using peat soil microcosms and a pure culture of Methylobacter tundripaludum SV96, qPCR, and sequencing of pmoA transcripts. Elevated CH4 concentrations led to higher CH4 oxidation rates both in grazed and exclosed peat soils, but the strongest response was observed in grazed peat soils. Furthermore, the relative transcriptional activities of different methanotroph community members were affected by the CH4 concentrations. While transcriptional responses to low CH4 concentrations were more prevalent in grazed peat soils, responses to high CH4 concentrations were more prevalent in exclosed peat soils. We observed no significant methanotroph responses to increasing temperatures. We conclude that methanotroph communities in these peat soils respond to changes in the CH4 concentration depending on their previous exposure to grazing. This "conditioning " influences which strains will thrive and, therefore, determines the function of the methanotroph community.
KW  - methanotroph
KW  - methane oxidation
KW  - pmoA amplicon sequencing
KW  - Methylobacter
KW  - grazing pressure
KW  - peat soil microcosms
KW  - temperature
KW  - Arctic
Y1  - 2021
U6  - https://doi.org/10.3390/microorganisms9102080
SN  - 2076-2607
VL  - 9
IS  - 10
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Raatz, Larissa
A1  - Pirhofer-Walzl, Karin
A1  - Müller, Marina E.H.
A1  - Scherber, Christoph
A1  - Joshi, Jasmin Radha
T1  - Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats?
JF  - Ecology and Evolution
N2  - Semi-natural habitats (SNHs) are becoming increasingly scarce in modern agricultural landscapes. This may reduce natural ecosystem services such as pest control with its putatively positive effect on crop production. In agreement with other studies, we recently reported wheat yield reductions at field borders which were linked to the type of SNH and the distance to the border. In this experimental landscape-wide study, we asked whether these yield losses have a biotic origin while analyzing fungal seed and fungal leaf pathogens, herbivory of cereal leaf beetles, and weed cover as hypothesized mediators between SNHs and yield. We established experimental winter wheat plots of a single variety within conventionally managed wheat fields at fixed distances either to a hedgerow or to an in-field kettle hole. For each plot, we recorded the fungal infection rate on seeds, fungal infection and herbivory rates on leaves, and weed cover. Using several generalized linear mixed-effects models as well as a structural equation model, we tested the effects of SNHs at a field scale (SNH type and distance to SNH) and at a landscape scale (percentage and diversity of SNHs within a 1000-m radius). In the dry year of 2016, we detected one putative biotic culprit: Weed cover was negatively associated with yield values at a 1-m and 5-m distance from the field border with a SNH. None of the fungal and insect pests, however, significantly affected yield, neither solely nor depending on type of or distance to a SNH. However, the pest groups themselves responded differently to SNH at the field scale and at the landscape scale. Our findings highlight that crop losses at field borders may be caused by biotic culprits; however, their negative impact seems weak and is putatively reduced by conventional farming practices.
KW  - arable weeds
KW  - cereal leaf beetle
KW  - fungal pathogens
KW  - herbivory
KW  - structural equation model
KW  - wheat
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.8046
SN  - 1467-6435
VL  - 11
SP  - 13232
EP  - 13246
PB  - Wiley-Blackwell
CY  - Oxford
ET  - 19
ER  - 
TY  - JOUR
A1  - Quinzan, Francesco
A1  - Göbel, Andreas
A1  - Wagner, Markus
A1  - Friedrich, Tobias
T1  - Evolutionary algorithms and submodular functions
BT  - benefits of heavy-tailed mutations
JF  - Natural computing : an innovative journal bridging biosciences and computer sciences ; an international journal
N2  - A core operator of evolutionary algorithms (EAs) is the mutation. Recently, much attention has been devoted to the study of mutation operators with dynamic and non-uniform mutation rates. Following up on this area of work, we propose a new mutation operator and analyze its performance on the (1 + 1) Evolutionary Algorithm (EA). Our analyses show that this mutation operator competes with pre-existing ones, when used by the (1 + 1) EA on classes of problems for which results on the other mutation operators are available. We show that the (1 + 1) EA using our mutation operator finds a (1/3)-approximation ratio on any non-negative submodular function in polynomial time. We also consider the problem of maximizing a symmetric submodular function under a single matroid constraint and show that the (1 + 1) EA using our operator finds a (1/3)-approximation within polynomial time. This performance matches that of combinatorial local search algorithms specifically designed to solve these problems and outperforms them with constant probability. Finally, we evaluate the performance of the (1 + 1) EA using our operator experimentally by considering two applications: (a) the maximum directed cut problem on real-world graphs of different origins, with up to 6.6 million vertices and 56 million edges and (b) the symmetric mutual information problem using a four month period air pollution data set. In comparison with uniform mutation and a recently proposed dynamic scheme, our operator comes out on top on these instances.
KW  - Evolutionary algorithms
KW  - Mutation operators
KW  - Submodular functions
KW  - Matroids
Y1  - 2021
U6  - https://doi.org/10.1007/s11047-021-09841-7
SN  - 1572-9796
VL  - 20
IS  - 3
SP  - 561
EP  - 575
PB  - Springer Science + Business Media B.V.
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Pitzen, Valentin
A1  - Sander, Sophia
A1  - Baumann, Otto
A1  - Gräf, Ralph
A1  - Meyer, Irene
T1  - Cep192, a novel missing link between the centrosomal core and corona in Dictyostelium amoebae
JF  - Cells : open access journal
N2  - The Dictyostelium centrosome is a nucleus-associated body with a diameter of approx. 500 nm. It contains no centrioles but consists of a cylindrical layered core structure surrounded by a microtubule-nucleating corona. At the onset of mitosis, the corona disassembles and the core structure duplicates through growth, splitting, and reorganization of the outer core layers. During the last decades our research group has characterized the majority of the 42 known centrosomal proteins. In this work we focus on the conserved, previously uncharacterized Cep192 protein. We use superresolution expansion microscopy (ExM) to show that Cep192 is a component of the outer core layers. Furthermore, ExM with centrosomal marker proteins nicely mirrored all ultrastructurally known centrosomal substructures. Furthermore, we improved the proximity-dependent biotin identification assay (BioID) by adapting the biotinylase BioID2 for expression in Dictyostelium and applying a knock-in strategy for the expression of BioID2-tagged centrosomal fusion proteins. Thus, we were able to identify various centrosomal Cep192 interaction partners, including CDK5RAP2, which was previously allocated to the inner corona structure, and several core components. Studies employing overexpression of GFP-Cep192 as well as depletion of endogenous Cep192 revealed that Cep192 is a key protein for the recruitment of corona components during centrosome biogenesis and is required to maintain a stable corona structure.
KW  - Cep192
KW  - SPD-2
KW  - centrosome
KW  - Dictyostelium
KW  - microtubule-organization
KW  - MTOC
Y1  - 2021
U6  - https://doi.org/10.3390/cells10092384
SN  - 2073-4409
VL  - 10
IS  - 9
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Picconi, David
T1  - Nonadiabatic quantum dynamics of the coherent excited state intramolecular proton transfer of 10-hydroxybenzo[h]quinoline
JF  - Photochemical & photobiological sciences
N2  - The photoinduced nonadiabatic dynamics of the enol-keto isomerization of 10-hydroxybenzo[h]quinoline (HBQ) are studied computationally using high-dimensional quantum dynamics. The simulations are based on a diabatic vibronic coupling Hamiltonian, which includes the two lowest pi pi* excited states and a n pi* state, which has high energy in the Franck-Condon zone, but significantly stabilizes upon excited state intramolecular proton transfer. A procedure, applicable to large classes of excited state proton transfer reactions, is presented to parametrize this model using potential energies, forces and force constants, which, in this case, are obtained by time-dependent density functional theory. The wave packet calculations predict a time scale of 10-15 fs for the photoreaction, and reproduce the time constants and the coherent oscillations observed in time- resolved spectroscopic studies performed on HBQ. In contrast to the interpretation given to the most recent experiments, it is found that the reaction initiated by 1 pi pi* <- S-0 photoexcitation proceeds essentially on a single potential energy surface, and the observed coherences bear signatures of Duschinsky mode-mixing along the reaction path. The dynamics after the 2 pi pi* <- S-0 excitation are instead nonadiabatic, and the n pi* state plays a major role in the relaxation process. The simulations suggest a mainly active role of the proton in the isomerization, rather than a passive migration assisted by the vibrations of the benzoquinoline backbone. <br /> [GRAPHICS] <br /> .
KW  - Excited state proton transfer
KW  - Quantum dynamics
KW  - Nonadiabatic effects
KW  - Spectroscopy
KW  - Coherences
Y1  - 2021
U6  - https://doi.org/10.1007/s43630-021-00112-z
SN  - 1474-905X
SN  - 1474-9092
VL  - 20
IS  - 11
SP  - 1455
EP  - 1473
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Petrović, Saša
A1  - Wendler, Petra
T1  - A RADD approach to probing AAA plus protein function
JF  - Nature structural & molecular biology
N2  - AAA+ proteins (ATPases associated with various cellular activities) catalyze the energy-dependent movement or rearrangement of macromolecules. A new study addresses the important question of how to design a selective chemical inhibitor for specific proteins in this diverse superfamily. The powerful chemical genetics approach adds to a growing toolbox of applications that allow dissection of the functions of distinct AAA+ proteins in vivo, facilitating the first steps toward effective drug development.
Y1  - 2021
U6  - https://doi.org/10.1038/s41594-021-00579-5
SN  - 1545-9993
SN  - 1545-9985
VL  - 28
IS  - 4
SP  - 329
EP  - 330
PB  - Nature Publishing Group
CY  - Berlin
ER  - 
TY  - JOUR
A1  - Petrich, Annett
A1  - Dunsing, Valentin
A1  - Bobone, Sara
A1  - Chiantia, Salvatore
T1  - Influenza A M2 recruits M1 to the plasma membrane
BT  - a fluorescence fluctuation microscopy study
JF  - Biophysical journal : BJ / ed. by the Biophysical Society
N2  - Influenza A virus (IAV) is a respiratory pathogen that causes seasonal epidemics with significant mortality. One of the most abundant proteins in IAV particles is the matrix protein 1 (M1), which is essential for the virus structural stability. M1 organizes virion assembly and budding at the plasma membrane (PM), where it interacts with other viral components. The recruitment of M1 to the PM as well as its interaction with the other viral envelope proteins (hemagglutinin [HA], neuraminidase, matrix protein 2 [M2]) is controversially discussed in previous studies. Therefore, we used fluorescence fluctuation microscopy techniques (i.e., scanning fluorescence cross-correlation spectroscopy and number and brightness) to quantify the oligomeric state of M1 and its interactions with other viral proteins in co-transfected as well as infected cells. Our results indicate that M1 is recruited to the PM by M2, as a consequence of the strong interaction between the two proteins. In contrast, only a weak interaction between M1 and HA was observed. M1-HA interaction occurred only in the event that M1 was already bound to the PM. We therefore conclude that M2 initiates the assembly of IAV by recruiting M1 to the PM, possibly allowing its further interaction with other viral proteins.
Y1  - 2021
U6  - https://doi.org/10.1016/j.bpj.2021.11.023
SN  - 0006-3495
SN  - 1542-0086
VL  - 120
IS  - 24
SP  - 5478
EP  - 5490
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Petazzi, Roberto Arturo
A1  - Koikkarah Aji, Amit
A1  - Tischler, Nicole D.
A1  - Chiantia, Salvatore
T1  - Detection of envelope glycoprotein assembly from old world hantaviruses in the Golgi apparatus of living cells
JF  - Journal of virology
N2  - Hantaviruses are emerging pathogens that occasionally cause deadly outbreaks in the human population. While the structure of the viral envelope has been characterized with high precision, protein-protein interactions leading to the formation of new virions in infected cells are not fully understood. We used quantitative fluorescence microscopy (i.e., number and brightness analysis and fluorescence fluctuation spectroscopy) to monitor the interactions that lead to oligomeric spike complex formation in the physiological context of living cells. To this aim, we quantified protein-protein interactions for the glycoproteins Gn and Gc from Puumala and Hantaan orthohantaviruses in several cellular models. The oligomerization of each protein was analyzed in relation to subcellular localization, concentration, and the concentration of its interaction partner. Our results indicate that, when expressed separately, Gn and Gc form, respectively, homo-tetrameric and homo-dimeric complexes, in a concentration-dependent manner. Site-directed mutations or deletion mutants showed the specificity of their homotypic interactions. When both glycoproteins were coexpressed, we observed in the Golgi apparatus clear indication of GnGc interactions and the formation of Gn-Gc multimeric protein complexes of different sizes, while using various labeling schemes to minimize the influence of the fluorescent tags. Such large glycoprotein multimers may be identified as multiple Gn viral spikes interconnected via Gc-Gc contacts. This observation provides the possible first evidence for the initial assembly steps of the viral envelope within this organelle, and does so directly in living cells. <br /> IMPORTANCE In this work, we investigate protein-protein interactions that drive the assembly of the hantavirus envelope. These emerging pathogens have the potential to cause deadly outbreaks in the human population. Therefore, it is important to improve our quantitative understanding of the viral assembly process in infected cells, from a molecular point of view. By applying advanced fluorescence microscopy methods, we monitored the formation of viral spike complexes in different cell types. Our data support a model for hantavirus assembly according to which viral spikes are formed via the clustering of hetero-dimers of the two viral glycoproteins Gn and Gc. Furthermore, the observation of large Gn-Gc hetero-multimers provide the possible first evidence for the initial assembly steps of the viral envelope, directly in the Golgi apparatus of living cells.
KW  - fluorescence fluctuation microscopy
KW  - number and brightness
KW  - virus
KW  - assembly
KW  - fluorescence correlation spectroscopy
KW  - protein-protein
KW  - interaction
KW  - fluorescence microscopy
KW  - fluorescent image analysis
Y1  - 2021
U6  - https://doi.org/10.1128/JVI.01238-20
SN  - 1098-5514
VL  - 95
IS  - 4
PB  - American Society for Microbiology
CY  - Baltimore, Md.
ER  - 
TY  - JOUR
A1  - Perscheid, Cindy
T1  - Integrative biomarker detection on high-dimensional gene expression data sets
BT  - a survey on prior knowledge approaches
JF  - Briefings in bioinformatics
N2  - Gene expression data provide the expression levels of tens of thousands of genes from several hundred samples. These data are analyzed to detect biomarkers that can be of prognostic or diagnostic use. Traditionally, biomarker detection for gene expression data is the task of gene selection. The vast number of genes is reduced to a few relevant ones that achieve the best performance for the respective use case. Traditional approaches select genes based on their statistical significance in the data set. This results in issues of robustness, redundancy and true biological relevance of the selected genes. Integrative analyses typically address these shortcomings by integrating multiple data artifacts from the same objects, e.g. gene expression and methylation data. When only gene expression data are available, integrative analyses instead use curated information on biological processes from public knowledge bases. With knowledge bases providing an ever-increasing amount of curated biological knowledge, such prior knowledge approaches become more powerful. This paper provides a thorough overview on the status quo of biomarker detection on gene expression data with prior biological knowledge. We discuss current shortcomings of traditional approaches, review recent external knowledge bases, provide a classification and qualitative comparison of existing prior knowledge approaches and discuss open challenges for this kind of gene selection.
KW  - gene selection
KW  - external knowledge bases
KW  - biomarker detection
KW  - gene
KW  - expression
KW  - prior knowledge
Y1  - 2021
U6  - https://doi.org/10.1093/bib/bbaa151
SN  - 1467-5463
SN  - 1477-4054
VL  - 22
IS  - 3
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Perscheid, Cindy
T1  - Comprior
BT  - Facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets
JF  - BMC Bioinformatics
N2  - Background
Reproducible benchmarking is important for assessing the effectiveness of novel feature selection approaches applied on gene expression data, especially for prior knowledge approaches that incorporate biological information from online knowledge bases. However, no full-fledged benchmarking system exists that is extensible, provides built-in feature selection approaches, and a comprehensive result assessment encompassing classification performance, robustness, and biological relevance. Moreover, the particular needs of prior knowledge feature selection approaches, i.e. uniform access to knowledge bases, are not addressed. As a consequence, prior knowledge approaches are not evaluated amongst each other, leaving open questions regarding their effectiveness.

Results
We present the Comprior benchmark tool, which facilitates the rapid development and effortless benchmarking of feature selection approaches, with a special focus on prior knowledge approaches. Comprior is extensible by custom approaches, offers built-in standard feature selection approaches, enables uniform access to multiple knowledge bases, and provides a customizable evaluation infrastructure to compare multiple feature selection approaches regarding their classification performance, robustness, runtime, and biological relevance.

Conclusion
Comprior allows reproducible benchmarking especially of prior knowledge approaches, which facilitates their applicability and for the first time enables a comprehensive assessment of their effectiveness
KW  - Feature selection
KW  - Prior knowledge
KW  - Gene expression
KW  - Reproducible benchmarking
Y1  - 2021
U6  - https://doi.org/10.1186/s12859-021-04308-z
SN  - 1471-2105
VL  - 22
SP  - 1
EP  - 15
PB  - Springer Nature
CY  - London
ER  - 
TY  - JOUR
A1  - Perkins, Anita
A1  - Rose, Andrew
A1  - Grossart, Hans-Peter
A1  - Rojas-Jimenez, Keilor Osvaldo
A1  - Barroso Prescott, Selva Kiri
A1  - Oakes, Joanne M.
T1  - Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata
JF  - Frontiers in Microbiology
N2  - Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.
KW  - kelp
KW  - fungi
KW  - endophytes
KW  - carbon cycling
KW  - extracellular enzymes
KW  - cellulose polymeric organic matter
Y1  - 2021
U6  - https://doi.org/10.3389/fmicb.2021.726138
SN  - 1664-302X
VL  - 12
SP  - 1
EP  - 13
PB  - Frontiers in microbiology
CY  - Lausanne, Schweiz
ER  - 
TY  - JOUR
A1  - Paolini, Alessio
A1  - Fontana, Federica
A1  - Van-Cuong Pham, 
A1  - Rödel, Claudia Jasmin
A1  - Seyfried, Salim
T1  - Mechanosensitive Notch-Dll4 and Klf2-Wnt9 signaling pathways intersect in guiding valvulogenesis in zebrafish
JF  - Cell reports
N2  - In the zebrafish embryo, the onset of blood flow generates fluid shear stress on endocardial cells, which are specialized endothelial cells that line the interior of the heart. High levels of fluid shear stress activate both Notch and Klf2 signaling, which play crucial roles in atrioventricular valvulogenesis. However, it remains unclear why only individual endocardial cells ingress into the cardiac jelly and initiate valvulogenesis. Here, we show that lateral inhibition between endocardial cells, mediated by Notch, singles out Delta-like-4-positive endocardial cells. These cells ingress into the cardiac jelly, where they form an abluminal cell population. Delta-like-4-positive cells ingress in response to Wnt9a, which is produced in parallel through an Erk5Klf2-Wnt9a signaling cascade also activated by blood flow. Hence, mechanical stimulation activates parallel mechanosensitive signaling pathways that produce binary effects by driving endocardial cells toward either luminal or abluminal fates. Ultimately, these cell fate decisions sculpt cardiac valve leaflets.
Y1  - 2021
U6  - https://doi.org/10.1016/j.celrep.2021.109782
SN  - 2211-1247
VL  - 37
IS  - 1
PB  - Cell Press
CY  - Maryland Heights, MO
ER  - 
TY  - JOUR
A1  - Orzechowski, Slawomir
A1  - Sitnicka, Dorota
A1  - Grabowska, Agnieszka
A1  - Compart, Julia
A1  - Fettke, Jörg
A1  - Zdunek-Zastocka, Edyta
T1  - Effect of short-term cold treatment on carbohydrate metabolism in potato leaves
JF  - International journal of molecular sciences
N2  - Plants are often challenged by an array of unfavorable environmental conditions. During cold exposure, many changes occur that include, for example, the stabilization of cell membranes, alterations in gene expression and enzyme activities, as well as the accumulation of metabolites. In the presented study, the carbohydrate metabolism was analyzed in the very early response of plants to a low temperature (2 degrees C) in the leaves of 5-week-old potato plants of the Russet Burbank cultivar during the first 12 h of cold treatment (2 h dark and 10 h light). First, some plant stress indicators were examined and it was shown that short-term cold exposure did not significantly affect the relative water content and chlorophyll content (only after 12 h), but caused an increase in malondialdehyde concentration and a decrease in the expression of NDA1, a homolog of the NADH dehydrogenase gene. In addition, it was shown that the content of transitory starch increased transiently in the very early phase of the plant response (3-6 h) to cold treatment, and then its decrease was observed after 12 h. In contrast, soluble sugars such as glucose and fructose were significantly increased only at the end of the light period, where a decrease in sucrose content was observed. The availability of the monosaccharides at constitutively high levels, regardless of the temperature, may delay the response to cold, involving amylolytic starch degradation in chloroplasts. The decrease in starch content, observed in leaves after 12 h of cold exposure, was preceded by a dramatic increase in the transcript levels of the key enzymes of starch degradation initiation, the alpha-glucan, water dikinase (GWD-EC 2.7.9.4) and the phosphoglucan, water dikinase (PWD-EC 2.7.9.5). The gene expression of both dikinases peaked at 9 h of cold exposure, as analyzed by real-time PCR. Moreover, enhanced activities of the acid invertase as well as of both glucan phosphorylases during exposure to a chilling temperature were observed. However, it was also noticed that during the light phase, there was a general increase in glucan phosphorylase activities for both control and cold-stressed plants irrespective of the temperature. In conclusion, a short-term cold treatment alters the carbohydrate metabolism in the leaves of potato, which leads to an increase in the content of soluble sugars.
KW  - cold stress
KW  - alpha-glucan
KW  - water dikinase
KW  - phosphoglucan water dikinase
KW  - chloroplast isolation
KW  - glucan phosphorylase
KW  - acid invertase
Y1  - 2021
U6  - https://doi.org/10.3390/ijms22137203
SN  - 1422-0067
VL  - 22
IS  - 13
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Omranian, Sara
A1  - Angeleska, Angela
A1  - Nikoloski, Zoran
T1  - Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient
JF  - Computational and structural biotechnology journal
N2  - Identification of protein complexes from protein-protein interaction (PPI) networks is a key problem in PPI mining, solved by parameter-dependent approaches that suffer from small recall rates. Here we introduce GCC-v, a family of efficient, parameter-free algorithms to accurately predict protein complexes using the (weighted) clustering coefficient of proteins in PPI networks. Through comparative analyses with gold standards and PPI networks from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we demonstrate that GCC-v outperforms twelve state-of-the-art approaches for identification of protein complexes with respect to twelve performance measures in at least 85.71% of scenarios. We also show that GCC-v results in the exact recovery of similar to 35% of protein complexes in a pan-plant PPI network and discover 144 new protein complexes in Arabidopsis thaliana, with high support from GO semantic similarity. Our results indicate that findings from GCC-v are robust to network perturbations, which has direct implications to assess the impact of the PPI network quality on the predicted protein complexes. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
KW  - Protein complexes
KW  - Protein-protein interaction
KW  - Network clustering
KW  - Species comparison
Y1  - 2021
U6  - https://doi.org/10.1016/j.csbj.2021.09.014
SN  - 2001-0370
VL  - 19
SP  - 5255
EP  - 5263
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Omranian, Sara
A1  - Angeleska, Angela
A1  - Nikoloski, Zoran
T1  - PC2P
BT  - parameter-free network-based prediction of protein complexes
JF  - Bioinformatics
N2  - Motivation: 
Prediction of protein complexes from protein-protein interaction (PPI) networks is an important problem in systems biology, as they control different cellular functions. The existing solutions employ algorithms for network community detection that identify dense subgraphs in PPI networks. However, gold standards in yeast and human indicate that protein complexes can also induce sparse subgraphs, introducing further challenges in protein complex prediction. 

Results: 
To address this issue, we formalize protein complexes as biclique spanned subgraphs, which include both sparse and dense subgraphs. We then cast the problem of protein complex prediction as a network partitioning into biclique spanned subgraphs with removal of minimum number of edges, called coherent partition. Since finding a coherent partition is a computationally intractable problem, we devise a parameter-free greedy approximation algorithm, termed Protein Complexes from Coherent Partition (PC2P), based on key properties of biclique spanned subgraphs. Through comparison with nine contenders, we demonstrate that PC2P: (i) successfully identifies modular structure in networks, as a prerequisite for protein complex prediction, (ii) outperforms the existing solutions with respect to a composite score of five performance measures on 75% and 100% of the analyzed PPI networks and gold standards in yeast and human, respectively, and (iii,iv) does not compromise GO semantic similarity and enrichment score of the predicted protein complexes. Therefore, our study demonstrates that clustering of networks in terms of biclique spanned subgraphs is a promising framework for detection of complexes in PPI networks.
Y1  - 2021
U6  - https://doi.org/10.1093/bioinformatics/btaa1089
SN  - 1367-4811
VL  - 37
IS  - 1
SP  - 73
EP  - 81
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Omel'chenko, Oleh
A1  - Ocampo-Espindola, Jorge Luis
A1  - Kiss, István Z.
T1  - Asymmetry-induced isolated fully synchronized state in coupled oscillator populations
JF  - Physical review : E, Statistical, nonlinear and soft matter physics
N2  - A symmetry-breaking mechanism is investigated that creates bistability between fully and partially synchronized states in oscillator networks. Two populations of oscillators with unimodal frequency distribution and different amplitudes, in the presence of weak global coupling, are shown to simplify to a modular network with asymmetrical coupling. With increasing the coupling strength, a synchronization transition is observed with an isolated fully synchronized state. The results are interpreted theoretically in the thermodynamic limit and confirmed in experiments with chemical oscillators.
Y1  - 2021
U6  - https://doi.org/10.1103/PhysRevE.104.L022202
SN  - 2470-0045
SN  - 2470-0053
VL  - 104
IS  - 2
PB  - American Physical Society
CY  - Melville, NY
ER  - 
TY  - JOUR
A1  - Olas, Justyna Jadwiga
A1  - Apelt, Federico
A1  - Watanabe, Mutsumi
A1  - Höfgen, Rainer
A1  - Wahl, Vanessa
T1  - Developmental stage-specific metabolite signatures in Arabidopsis thaliana under optimal and mild nitrogen limitation
JF  - Plant science : an international journal of experimental plant biology
N2  - Metabolites influence flowering time, and thus are among the major determinants of yield. Despite the reported role of trehalose 6-phosphate and nitrate signaling on the transition from the vegetative to the reproductive phase, little is known about other metabolites contributing and responding to developmental phase changes. To increase our understanding which metabolic traits change throughout development in Arabidopsis thaliana and to identify metabolic markers for the vegetative and reproductive phases, especially among individual amino acids (AA), we profiled metabolites of plants grown in optimal (ON) and limited nitrogen (N) (LN) conditions, the latter providing a mild but consistent limitation of N. We found that although LN plants adapt their growth to a decreased level of N, their metabolite profiles are strongly distinct from ON plant profiles, with N as the driving factor for the observed differences. We demonstrate that the vegetative and the reproductive phase are not only marked by growth parameters such as biomass and rosette area, but also by specific metabolite signatures including specific single AA. In summary, we identified N-dependent and -independent indicators manifesting developmental stages, indicating that the plant's metabolic status also reports on the developmental phases.
KW  - Amino acids
KW  - Floral induction
KW  - Flowering time
KW  - Nitrogen
KW  - Metabolites
KW  - Vegetative phase
KW  - Reproductive phase
Y1  - 2021
U6  - https://doi.org/10.1016/j.plantsci.2020.110746
SN  - 0168-9452
SN  - 1873-2259
VL  - 303
PB  - Elsevier Science
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Nwosu, Ebuka Canisius
A1  - Roeser, Patricia Angelika
A1  - Yang, Sizhong
A1  - Ganzert, Lars
A1  - Dellwig, Olaf
A1  - Pinkerneil, Sylvia
A1  - Brauer, Achim
A1  - Dittmann, Elke
A1  - Wagner, Dirk
A1  - Liebner, Susanne
T1  - From water into sediment-tracing freshwater cyanobacteria via DNA analyses
JF  - Microorganisms : open access journal
N2  - Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May-October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.
KW  - Aphanizomenon
KW  - Planktothrix
KW  - Snowella
KW  - cyanobacteria sedimentation
KW  - lake monitoring
KW  - sedimentary ancient DNA
KW  - sediment traps
KW  - environmental reconstruction
Y1  - 2021
U6  - https://doi.org/10.3390/microorganisms9081778
SN  - 2076-2607
VL  - 9
IS  - 8
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Nwosu, Ebuka Canisius
A1  - Brauer, Achim
A1  - Kaiser, Jérôme
A1  - Horn, Fabian
A1  - Wagner, Dirk
A1  - Liebner, Susanne
T1  - Evaluating sedimentary DNA for tracing changes in cyanobacteria dynamics from sediments spanning the last 350 years of Lake Tiefer See, NE Germany
JF  - Journal of paleolimnology
N2  - Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, delta C-13 data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.
KW  - Late Holocene
KW  - Methylheptadecanes
KW  - Varves
KW  - Anthropocene
KW  - Sericytochromatia
KW  - Melainabacteria
Y1  - 2021
U6  - https://doi.org/10.1007/s10933-021-00206-9
SN  - 0921-2728
SN  - 1573-0417
VL  - 66
IS  - 3
SP  - 279
EP  - 296
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - THES
A1  - Nieschalke, Kai
T1  - Proteinaddukte und Urinmetaboliten des Nagetierkanzerogens Methyleugenol als Biomarker der Exposition
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Neffe, Axel T.
A1  - Löwenberg, Candy
A1  - Julich-Gruner, Konstanze K.
A1  - Behl, Marc
A1  - Lendlein, Andreas
T1  - Thermally-induced shape-memory behavior of degradable gelatin-based networks
JF  - International journal of molecular sciences
N2  - Shape-memory hydrogels (SMH) are multifunctional, actively-moving polymers of interest in biomedicine. In loosely crosslinked polymer networks, gelatin chains may form triple helices, which can act as temporary net points in SMH, depending on the presence of salts. Here, we show programming and initiation of the shape-memory effect of such networks based on a thermomechanical process compatible with the physiological environment. The SMH were synthesized by reaction of glycidylmethacrylated gelatin with oligo(ethylene glycol) (OEG) alpha,omega-dithiols of varying crosslinker length and amount. Triple helicalization of gelatin chains is shown directly by wide-angle X-ray scattering and indirectly via the mechanical behavior at different temperatures. The ability to form triple helices increased with the molar mass of the crosslinker. Hydrogels had storage moduli of 0.27-23 kPa and Young's moduli of 215-360 kPa at 4 degrees C. The hydrogels were hydrolytically degradable, with full degradation to water-soluble products within one week at 37 degrees C and pH = 7.4. A thermally-induced shape-memory effect is demonstrated in bending as well as in compression tests, in which shape recovery with excellent shape-recovery rates R-r close to 100% were observed. In the future, the material presented here could be applied, e.g., as self-anchoring devices mechanically resembling the extracellular matrix.
KW  - shape-memory hydrogel
KW  - active polymer
KW  - biopolymer
KW  - mechanical
KW  - properties
KW  - degradation
Y1  - 2021
U6  - https://doi.org/10.3390/ijms22115892
SN  - 1422-0067
SN  - 1661-6596
VL  - 22
IS  - 11
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - JOUR
A1  - Neffe, Axel T.
A1  - Izraylit, Victor
A1  - Hommes-Schattmann, Paul J.
A1  - Lendlein, Andreas
T1  - Soft, formstable (Co)polyester blend elastomers
JF  - Nanomaterials : open access journal
N2  - High crystallization rate and thermomechanical stability make polylactide stereocomplexes effective nanosized physical netpoints. Here, we address the need for soft, form-stable degradable elastomers for medical applications by designing such blends from (co)polyesters, whose mechanical properties are ruled by their nanodimensional architecture and which are applied as single components in implants. By careful controlling of the copolymer composition and sequence structure of poly[(L-lactide)-co-(epsilon-caprolactone)], it is possible to prepare hyperelastic polymer blends formed through stereocomplexation by adding poly(D-lactide) (PDLA). Low glass transition temperature T-g <= 0 degrees C of the mixed amorphous phase contributes to the low Young's modulus E. The formation of stereocomplexes is shown in DSC by melting transitions T-m > 190 degrees C and in WAXS by distinct scattering maxima at 2 theta = 12 degrees and 21 degrees. Tensile testing demonstrated that the blends are soft (E = 12-80 MPa) and show an excellent hyperelastic recovery R-rec = 66-85% while having high elongation at break epsilon(b) up to >1000%. These properties of the blends are attained only when the copolymer has 56-62 wt% lactide content, a weight average molar mass >140 kg center dot mol(-1), and number average lactide sequence length >= 4.8, while the blend is formed with a content of 5-10 wt% of PDLA. The devised strategy to identify a suitable copolymer for stereocomplexation and blend formation is transferable to further polymer systems and will support the development of thermoplastic elastomers suitable for medical applications.
KW  - thermoplastic elastomer
KW  - biomaterial
KW  - stereocomplexes
KW  - mechanical
KW  - properties
KW  - form stability
KW  - crystallinity
Y1  - 2021
U6  - https://doi.org/10.3390/nano11061472
SN  - 2079-4991
VL  - 11
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Naser, Eyad
A1  - Kadow, Stephanie
A1  - Schumacher, Fabian
A1  - Mohamed, Zainelabdeen H.
A1  - Kappe, Christian
A1  - Hessler, Gabriele
A1  - Pollmeier, Barbara
A1  - Kleuser, Burkhard
A1  - Arenz, Christoph
A1  - Becker, Katrin Anne
A1  - Gulbins, Erich
A1  - Carpinteiro, Alexander
T1  - Characterization of the small molecule ARC39
BT  - a direct and specific inhibitor of acid sphingomyelinase in vitro[S]
JF  - Journal of Lipid Research
N2  - Inhibition of acid sphingomyelinase (ASM), a lysosomal enzyme that catalyzes the hydrolysis of sphingomyelin into ceramide and phosphorylcholine, may serve as an investigational tool or a therapeutic intervention to control many diseases. Specific ASM inhibitors are currently not sufficiently characterized. Here, we found that 1-aminodecylidene bis-phosphonic acid (ARC39) specifically and efficiently (>90%) inhibits both lysosomal and secretory ASM in vitro. Results from investigating sphingomyelin phosphodiesterase 1 (SMPD1/Smpd1) mRNA and ASM protein levels suggested that ARC39 directly inhibits ASM's catalytic activity in cultured cells, a mechanism that differs from that of functional inhibitors of ASM. We further provide evidence that ARC39 dose- and time-dependently inhibits lysosomal ASM in intact cells, and we show that ARC39 also reduces platelet- and ASM-promoted adhesion of tumor cells. The observed toxicity of ARC39 is low at concentrations relevant for ASM inhibition in vitro, and it does not strongly alter the lysosomal compartment or induce phospholipidosis in vitro. When applied intraperitoneally in vivo, even subtoxic high doses administered short-term induced sphingomyelin accumulation only locally in the peritoneal lavage without significant accumulation in plasma, liver, spleen, or brain. These findings require further investigation with other possible chemical modifications. In conclusion, our results indicate that ARC39 potently and selectively inhibits ASM in vitro and highlight the need for developing compounds that can reach tissue concentrations sufficient for ASM inhibition in vivo.
KW  - sphingolipids
KW  - sphingomyelin
KW  - cerami-des
KW  - lipid metabolism
KW  - enzymology
KW  - lysosome
KW  - lysosomal hydrolases
KW  - acid ceramidase
KW  - bisphosphonates
KW  - functional inhibitors of acid sphin-gomyelinase
KW  - 1-aminodecylidene bis-phosphonic acid
Y1  - 2021
U6  - https://doi.org/10.1194/jlr.RA120000682
SN  - 1539-7262
SN  - 0022-2275
VL  - 61
IS  - 6
SP  - 896
EP  - 910
PB  - American Society for Biochemistry and Molecular Biology
CY  - Bethesda
ER  - 
TY  - THES
A1  - Nacak, Selma
T1  - Synthesis and Characterization of Upconversion Nanaparticles for Applications in Life Sciences
Y1  - 2021
ER  - 
TY  - JOUR
A1  - Münch, Juliane
A1  - Abdelilah-Seyfried, Salim
T1  - Sensing and responding of cardiomyocytes to changes of tissue stiffness in the diseased heart
JF  - Frontiers in cell developmental biology
N2  - Cardiomyocytes are permanently exposed to mechanical stimulation due to cardiac contractility. Passive myocardial stiffness is a crucial factor, which defines the physiological ventricular compliance and volume of diastolic filling with blood. Heart diseases often present with increased myocardial stiffness, for instance when fibrotic changes modify the composition of the cardiac extracellular matrix (ECM). Consequently, the ventricle loses its compliance, and the diastolic blood volume is reduced. Recent advances in the field of cardiac mechanobiology revealed that disease-related environmental stiffness changes cause severe alterations in cardiomyocyte cellular behavior and function. Here, we review the molecular mechanotransduction pathways that enable cardiomyocytes to sense stiffness changes and translate those into an altered gene expression. We will also summarize current knowledge about when myocardial stiffness increases in the diseased heart. Sophisticated in vitro studies revealed functional changes, when cardiomyocytes faced a stiffer matrix. Finally, we will highlight recent studies that described modulations of cardiac stiffness and thus myocardial performance in vivo. Mechanobiology research is just at the cusp of systematic investigations related to mechanical changes in the diseased heart but what is known already makes way for new therapeutic approaches in regenerative biology.
KW  - mechanobiology
KW  - tissue stiffness
KW  - cardiomyocyte
KW  - heart regeneration
KW  - titin
KW  - collagen
KW  - agrin
KW  - extracellular matrix
Y1  - 2020
U6  - https://doi.org/10.3389/fcell.2021.642840
SN  - 2296-634X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Merida, Angel
A1  - Fettke, Jörg
T1  - Starch granule initiation in Arabidopsis thaliana chloroplasts
JF  - The plant journal
N2  - The initiation of starch granule formation and the mechanism controlling the number of granules per plastid have been some of the most elusive aspects of starch metabolism. This review covers the advances made in the study of these processes. The analyses presented herein depict a scenario in which starch synthase isoform 4 (SS4) provides the elongating activity necessary for the initiation of starch granule formation. However, this protein does not act alone; other polypeptides are required for the initiation of an appropriate number of starch granules per chloroplast. The functions of this group of polypeptides include providing suitable substrates (maltooligosaccharides) to SS4, the localization of the starch initiation machinery to the thylakoid membranes, and facilitating the correct folding of SS4. The number of starch granules per chloroplast is tightly regulated and depends on the developmental stage of the leaves and their metabolic status. Plastidial phosphorylase (PHS1) and other enzymes play an essential role in this process since they are necessary for the synthesis of the substrates used by the initiation machinery. The mechanism of starch granule formation initiation in Arabidopsis seems to be generalizable to other plants and also to the synthesis of long-term storage starch. The latter, however, shows specific features due to the presence of more isoforms, the absence of constantly recurring starch synthesis and degradation, and the metabolic characteristics of the storage sink organs.
KW  - starch granules
KW  - starch metabolism
KW  - starch granule initiation
KW  - starch
KW  - granule number per chloroplast
KW  - starch morphology
KW  - Arabidopsis thaliana
Y1  - 2021
U6  - https://doi.org/10.1111/tpj.15359
SN  - 0960-7412
SN  - 1365-313X
VL  - 107
IS  - 3
SP  - 688
EP  - 697
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Mbebi, Alain J.
A1  - Tong, Hao
A1  - Nikoloski, Zoran
T1  - L-2,L-1-norm regularized multivariate regression model with applications to genomic prediction
JF  - Bioinformatics
N2  - Motivation: 
Genomic selection (GS) is currently deemed the most effective approach to speed up breeding of agricultural varieties. It has been recognized that consideration of multiple traits in GS can improve accuracy of prediction for traits of low heritability. However, since GS forgoes statistical testing with the idea of improving predictions, it does not facilitate mechanistic understanding of the contribution of particular single nucleotide polymorphisms (SNP). 

Results: 
Here, we propose a L-2,L-1-norm regularized multivariate regression model and devise a fast and efficient iterative optimization algorithm, called L-2,L-1-joint, applicable in multi-trait GS. The usage of the L-2,L-1-norm facilitates variable selection in a penalized multivariate regression that considers the relation between individuals, when the number of SNPs is much larger than the number of individuals. The capacity for variable selection allows us to define master regulators that can be used in a multi-trait GS setting to dissect the genetic architecture of the analyzed traits. Our comparative analyses demonstrate that the proposed model is a favorable candidate compared to existing state-of-the-art approaches. Prediction and variable selection with datasets from Brassica napus, wheat and Arabidopsis thaliana diversity panels are conducted to further showcase the performance of the proposed model.
Y1  - 2021
U6  - https://doi.org/10.1093/bioinformatics/btab212
SN  - 1367-4803
SN  - 1460-2059
VL  - 37
IS  - 18
SP  - 2896
EP  - 2904
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Mazza, Valeria
A1  - Czyperreck, Inken
A1  - Eccard, Jana
A1  - Dammhahn, Melanie
T1  - Cross-Context Responses to Novelty in Rural and Urban Small Mammals
JF  - Frontiers in Ecology and Evolution
N2  - The Anthropocene is the era of urbanization. The accelerating expansion of cities occurs at the expense of natural reservoirs of biodiversity and presents animals with challenges for which their evolutionary past might not have prepared them. Cognitive and behavioral adjustments to novelty could promote animals’ persistence under these altered conditions. We investigated the structure of, and covariance between, different aspects of responses to novelty in rural and urban small mammals of two non-commensal rodent species. We ran replicated experiments testing responses to three novelty types (object, food, or space) of 47 individual common voles (Microtus arvalis) and 41 individual striped field mice (Apodemus agrarius). We found partial support for the hypothesis that responses to novelty are structured, clustering (i) speed of responses, (ii) intensity of responses, and (iii) responses to food into separate dimensions. Rural and urban small mammals did not differ in most responses to novelty, suggesting that urban habitats do not reduce neophobia in these species. Further studies investigating whether comparable response patters are found throughout different stages of colonization, and along synurbanization processes of different duration, will help illuminate the dynamics of animals’ cognitive adjustments to urban life.
KW  - animal cognition
KW  - anthropogenic environment
KW  - HIREC
KW  - novelty
KW  - neophobia
KW  - neophilia
KW  - rodents
KW  - urbanization
Y1  - 2021
U6  - https://doi.org/10.3389/fevo.2021.661971
SN  - 2296-701X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Marzetz, Vanessa
A1  - Wacker, Alexander
T1  - Evaluating the relevance of species sorting and physiological plasticity of phytoplankton communities grown in a multifactor environment
JF  - Freshwater biology / Freshwater Biological Association
N2  - The two important mechanisms influencing the response of phytoplankton communities to alterations of abiotic factors in their environment are difficult to distinguish: species sorting resulting from a change in interspecific competitive pressure, and phenotypic plasticity (here explicitly physiological plasticity i.e. species-specific physiological adjustment). A shift in species composition as well as physiological adjustments in species can lead to changes in fatty acid composition that determine the food quality for zooplankton consumers. We used phytoplankton communities consisting of five species and exposed them to two different light intensities, two light conditions (constant and variable), and two levels of phosphorus supply. Changes in fatty acid and species composition were analyzed. We compared community pairs differing in one factor by calculating the Bray-Curtis similarity index for the composition of both variables. Comparing the Bray-Curtis similarity index of the species composition with the index of the fatty acid composition was used to estimate the effects of species sorting and physiological plasticity. Changes in nutrient supply influenced fatty acid responses based on species sorting and physiological plasticity the most. On one hand, the relevance of physiological plasticity was highest at cultivation in different nutrient supplies but the same light environment. Conversely with low nutrients species sorting appeared to dominate the response to changes in light, while at high nutrients physiological plasticity appeared to influence the response. Overall, under low phosphorus supply the communities showed a lower total fatty acid content per carbon and had increased proportions of saturated and monounsaturated fatty acids. Instead, communities in low light produced more of eicosapentaenoic acid. Our results suggest that the relevance of species sorting and physiological plasticity in shaping the community response highly depends on the environmental factors that influence the system. Nutrient supply had the largest effect, while light had more limited conditional effects. However, all of these factors are important in shaping the food quality of the phytoplankton community for higher trophic levels.
KW  - fatty acid composition
KW  - light intensity
KW  - light variability
KW  - nutrient
KW  - supply
KW  - resource competition
Y1  - 2021
U6  - https://doi.org/10.1111/fwb.13810
SN  - 0046-5070
SN  - 1365-2427
VL  - 66
IS  - 10
SP  - 1992
EP  - 2003
PB  - Wiley-Blackwell
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Marot, Medhi
A1  - Chevalère, Johann
A1  - Spatola, Nicolas
T1  - Depressed mood, a better predictor of social-distancing compliance and candidate for intervention compared to working memory capacity
JF  - Proceedings of the National Academy of Sciences of the United States of America
Y1  - 2021
U6  - https://doi.org/10.1073/pnas.2024017118
SN  - 0027-8424
SN  - 1091-6490
VL  - 118
IS  - 8
PB  - National Academy of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Malchow, Anne-Kathleen
A1  - Bocedi, Greta
A1  - Palmer, Stephen C. F.
A1  - Travis, Justin M. J.
A1  - Zurell, Damaris
T1  - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes
JF  - Ecography
N2  - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.
KW  - connectivity
KW  - conservation
KW  - dispersal
KW  - evolution
KW  - population dynamics
KW  - range dynamics
Y1  - 2021
SN  - 1600-0587
VL  - 44
IS  - 10
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Malchow, Anne-Kathleen
A1  - Bocedi, Greta
A1  - Palmer, Stephen C. F.
A1  - Travis, Justin M. J.
A1  - Zurell, Damaris
T1  - RangeShiftR
BT  - an R package for individual-based simulation of spatial changes
JF  - Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos
N2  - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.
KW  - connectivity
KW  - conservation
KW  - dispersal
KW  - evolution
KW  - population dynamics
KW  - range dynamics
Y1  - 2021
U6  - https://doi.org/10.1111/ecog.05689
SN  - 1600-0587
VL  - 44
IS  - 10
SP  - 1443
EP  - 1452
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - López-Sánchez, Aida
A1  - Bareth, Georg
A1  - Bolten, Andreas
A1  - Rose, Laura E.
A1  - Mansfeldt, Tim
A1  - Sapp, Melanie
A1  - Linstädter, Anja
T1  - Effects of declining oak vitality on ecosystem multifunctionality
BT  - lessons from a Spanish oak woodland
JF  - Forest ecology and management
N2  - Mediterranean oak woodlands are currently facing unprecedented degradation threats from oak decline. The Iberian oak decline "Seca", related to Phytophthora infection, causes crown defoliation that may adversely affect ecosystem services (ESs). We aim to improve our understanding of how Seca-induced declines in crown foliation affect the provision of multiple ecosystem services from understory vegetation. We selected holm (Quercus ilex) and cork oak (Q. suber) trees in a Spanish oak woodland and evaluated three proxies of canopy effects. One proxy (crown defoliation) solely captured Seca-dependent effects, one proxy solely captured Seca-independent effects (tree dimensions such as diameter and height), while the third proxy (tree vigor) captured overall canopy effects. We then used the best-performing proxies to assess canopy effects on key ecosystem services (ESs) such as aboveground net primary production (ANPP), grass and legume biomass, species diversity, litter decomposition rates, and a combined index of ecosystem multifunctionality. <br /> We found that both types of canopy effects (i.e. Seca-dependent and Seca-independent effects) were related, indicating that ANPP was disproportionally more affected by Seca when defoliated trees were large. Responses of other ESs were mostly not significant, although lower species diversity was found under trees with intermediate vigor. Our results underline that a Seca-related decline in canopy density triggered a homogenization of ecosystem service delivery on the ecosystem scale. The ecosystem functions (EFs) under trees of low vigor are similar to that in adjacent open microsites indicating that the presence of vigorous (i.e. old and vital) trees is critical for maintaining EFs at a landscape level. Our results also highlight the importance of quantifying not only defoliation but also tree dimensions as both factors jointly and interactively modify canopy effects on ecosystem multifunctionality.
KW  - ANPP
KW  - Decomposition
KW  - Microsite degradation
KW  - Herb diversity
KW  - Seca
Y1  - 2021
U6  - https://doi.org/10.1016/j.foreco.2021.118927
SN  - 0378-1127
SN  - 1872-7042
VL  - 484
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - CHAP
A1  - Loßow, Kristina
A1  - Schwarz, Maria
A1  - Kopp, Johannes
A1  - Schwerdtle, Tanja
A1  - Kipp, Anna Patricia
T1  - Age- and sex-dependent changes of trace elements and redox parameters in mice
T2  - Free radical biology and medicine : the official journal of the Oxygen Society, a constituent member of the International Society for Free Radical Research
Y1  - 2021
U6  - https://doi.org/10.1016/j.freeradbiomed.2020.12.346
SN  - 0891-5849
SN  - 1873-4596
VL  - 165
IS  - Suppl. 1
SP  - 34
PB  - Elsevier
CY  - New York
ER  - 
TY  - JOUR
A1  - Lozano, Yudi M.
A1  - Aguilar-Trigueros, Carlos A.
A1  - Onandia, Gabriela
A1  - Maaß, Stefanie
A1  - Zhao, Tingting
A1  - Rillig, Matthias C.
T1  - Effects of microplastics and drought on soil ecosystem functions and multifunctionality
JF  - Journal of applied ecology : an official journal of the British Ecological Society
N2  - 1. Microplastics in soils have become an important threat for terrestrial systems as they may potentially alter the geochemical/biophysical soil environment and can interact with drought. As microplastics may affect soil water content, this could exacerbate the well-known negative effects of drought on ecosystem functionality. Thus, functions including litter decomposition, soil aggregation or those related with nutrient cycling can be altered. Despite this potential interaction, we know relatively little about how microplastics, under different soil water conditions, affect ecosystem functions and multifunctionality. 
2. To address this gap, we performed an experiment using grassland plant communities growing in microcosms. Microplastic fibres (absent, present) and soil water conditions (well-watered, drought) were applied in a fully factorial design. At harvest, we measured soil ecosystem functions related to nutrient cycling (beta-glucosaminidase, beta-D-cellobiosidase, phosphatase, beta-glucosidase enzymes), respiration, nutrient retention, pH, litter decomposition and soil aggregation (water stable aggregates). As terrestrial systems provide these functions simultaneously, we also assessed ecosystem multifunctionality, an index that encompasses the array of ecosystem functions measured here. 
3. We found that the interaction between microplastic fibres and drought affected ecosystem functions and multifunctionality. Drought had negatively affected nutrient cycling by decreasing enzymatic activities by up to similar to 39%, while microplastics increased soil aggregation by similar to 18%, soil pH by similar to 4% and nutrient retention by up to similar to 70% by diminishing nutrient leaching. Microplastic fibres also impacted soil enzymes, respiration and ecosystem multifunctionality, but importantly, the direction of these effects depended on soil water status. That is, under well-watered conditions, these functions decreased with microplastic fibres by up to similar to 34% while under drought they had similar values irrespective of the microplastic presence, or tended to increase with microplastics. Litter decomposition had a contrary pattern increasing with microplastics by similar to 6% under well-watered conditions while decreasing to a similar percentage under drought. 
4. Synthesis and applications. Single ecosystem functions can be positively or negatively affected by microplastics fibres depending on soil water status. However, our results suggest that microplastic fibres may cause negative effects on ecosystem soil multifunctionality of a similar magnitude as drought. Thus, strategies to counteract this new global change factor are necessary.
KW  - enzymatic activities
KW  - grasslands ecosystem
KW  - litter decomposition
KW  - nutrient cycling
KW  - nutrient leaching
KW  - soil aggregation
KW  - soil pH
KW  - soil respiration
Y1  - 2021
U6  - https://doi.org/10.1111/1365-2664.13839
SN  - 1365-2664
VL  - 58
IS  - 5
SP  - 988
EP  - 996
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Lozada-Gobilard, Sissi Donna
A1  - Jeltsch, Florian
A1  - Zhu, Jinlei
T1  - High matrix vegetation decreases mean seed dispersal distance but increases long wind dispersal probability connecting local plant populations in agricultural landscapes
JF  - Agriculture, ecosystems & environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere
N2  - Seed dispersal plays an important role in population dynamics in agricultural ecosystems, but the effects of surrounding vegetation height on seed dispersal and population connectivity on the landscape scale have rarely been studied. Understanding the effects of surrounding vegetation height on seed dispersal will provide important information for land-use management in agricultural landscapes to prevent the spread of undesired weeds or enhance functional connectivity. We used two model species, Phragmites australis and Typha latifolia, growing in small natural ponds known as kettle holes, in an agricultural landscape to evaluate the effects of surrounding vegetation height on wind dispersal and population connectivity between kettle holes. Seed dispersal distance and the probability of long-distance dispersal (LDD) were simulated with the mechanistic WALD model under three scenarios of "low", "dynamic" and "high" surrounding vegetation height. Connectivity between the origin and target kettle holes was quantified with a connectivity index adapted from Hanski and Thomas (1994). Our results show that mean seed dispersal distance decreases with the height of surrounding matrix vegetation, but the probability of long-distance dispersal (LDD) increases with vegetation height. This indicates an important vegetation-based trade-off between mean dispersal distance and LDD, which has an impact on connectivity. Matrix vegetation height has a negative effect on mean seed dispersal distance but a positive effect on the probability of LDD. This positive effect and its impact on connectivity provide novel insights into landscape level (meta-)population and community dynamics - a change in matrix vegetation height by land-use or climatic changes could strongly affect the spread and connectivity of wind-dispersed plants. The opposite effect of vegetation height on mean seed dispersal distance and the probability of LDD should therefore be considered in management and analyses of future land-use and climate change effects.
KW  - Seed dispersal by wind
KW  - Long-distance seed dispersal
KW  - Matrix vegetation
KW  - Kettle holes
KW  - Agricultural landscapes
KW  - Metapopulation dynamics
Y1  - 2021
U6  - https://doi.org/10.1016/j.agee.2021.107678
SN  - 0167-8809
SN  - 1873-2305
VL  - 322
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Liu, Qingting
A1  - Li, Xiaoping
A1  - Fettke, Jörg
T1  - Starch granules in Arabidopsis thaliana mesophyll and guard cells show similar morphology but differences in size and number
JF  - International journal of molecular sciences
N2  - Transitory starch granules result from complex carbon turnover and display specific situations during starch synthesis and degradation. The fundamental mechanisms that specify starch granule characteristics, such as granule size, morphology, and the number per chloroplast, are largely unknown. However, transitory starch is found in the various cells of the leaves of Arabidopsis thaliana, but comparative analyses are lacking. Here, we adopted a fast method of laser confocal scanning microscopy to analyze the starch granules in a series of Arabidopsis mutants with altered starch metabolism. This allowed us to separately analyze the starch particles in the mesophyll and in guard cells. In all mutants, the guard cells were always found to contain more but smaller plastidial starch granules than mesophyll cells. The morphological properties of the starch granules, however, were indiscernible or identical in both types of leaf cells.
KW  - starch granules
KW  - starch granule number per chloroplast
KW  - starch morphology
KW  - mesophyll cell
KW  - guard cell
KW  - LCSM
KW  - Arabidopsis thaliana
KW  - starch granule initiation
KW  - starch metabolism
Y1  - 2021
U6  - https://doi.org/10.3390/ijms22115666
SN  - 1422-0067
SN  - 1661-6596
VL  - 22
IS  - 11
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - JOUR
A1  - Li, Xiaoxiao
A1  - Yang, Wei
A1  - Sun, Tao
A1  - Gaedke, Ursula
T1  - Quantitative food web structure and ecosystem functions in a warm-temperate seagrass bed
JF  - Marine biology : international journal on life in oceans and coastal waters
N2  - Seagrass beds are important habitats in coastal areas but increasingly decline in area and quality, thus conservation measures are urgently needed. Quantitative food webs, describing the biomass distribution and energy fluxes among trophic groups, reveal structural and functional aspects of ecosystems. Their knowledge can improve ecological conservation. For the recently discovered large warm-temperate seagrass (Zostera japonica) habitat in China's Yellow River Delta wetland, we used delta C-13 and delta N-15 measurements and a Bayesian isotope mixing model to construct its food web diagram with quantitative estimations of consumer diet compositions, comprising detritus and 14 living trophic groups from primary producers to fish. We then estimated the quantitative food web fluxes based on biomass measurements and calculated corresponding ecosystem functions. Pelagic producers were significantly C-13-depleted compared to benthic sources. Consumers (except zooplankton) were increasingly C-13-depleted with increasing trophic positions even though the consumed benthic production surpassed the pelagic one. Bivalves dominated consumer biomasses and fluxes and were the first to connect the pelagic and benthic pathways, whereas zooplankton and gastropods were specialized on the two pathways, respectively. We found flat biomass and production pyramids indicating low trophic transfer efficiencies. Generally, the energetic structure of the quantitative food web was consistent with the stable isotope analysis, and the estimated net primary production and most estimated production to biomass ratios of the trophic groups fell within literature ranges. This study provides a systematical understanding of the quantitative trophic ecology of a seagrass bed and facilitates synergistic knowledge on management, conservation, and restoration.
Y1  - 2021
U6  - https://doi.org/10.1007/s00227-021-03878-z
SN  - 0025-3162
SN  - 1432-1793
VL  - 168
IS  - 5
PB  - Springer
CY  - Berlin ; Heidelberg
ER  - 
TY  - JOUR
A1  - Lau, Skadi
A1  - Maier, Anna
A1  - Braune, Steffen
A1  - Gossen, Manfred
A1  - Lendlein, Andreas
T1  - Effect of endothelial culture medium composition on platelet responses to polymeric biomaterials
JF  - International journal of molecular sciences
N2  - Near-physiological in vitro thrombogenicity test systems for the evaluation of blood-contacting endothelialized biomaterials requires co-cultivation with platelets (PLT). However, the addition of PLT has led to unphysiological endothelial cell (EC) detachment in such in vitro systems. A possible cause for this phenomenon may be PLT activation triggered by the applied endothelial cell medium, which typically consists of basal medium (BM) and nine different supplements. To verify this hypothesis, the influence of BM and its supplements was systematically analyzed regarding PLT responses. For this, human platelet rich plasma (PRP) was mixed with BM, BM containing one of nine supplements, or with BM containing all supplements together. PLT adherence analysis was carried out in six-channel slides with plasma-treated cyclic olefin copolymer (COC) and poly(tetrafluoro ethylene) (PTFE, as a positive control) substrates as part of the six-channel slides in the absence of EC and under static conditions. PLT activation and aggregation were analyzed using light transmission aggregometry and flow cytometry (CD62P). Medium supplements had no effect on PLT activation and aggregation. In contrast, supplements differentially affected PLT adherence, however, in a polymer- and donor-dependent manner. Thus, the use of standard endothelial growth medium (BM + all supplements) maintains functionality of PLT under EC compatible conditions without masking the differences of PLT adherence on different polymeric substrates. These findings are important prerequisites for the establishment of a near-physiological in vitro thrombogenicity test system assessing polymer-based cardiovascular implant materials in contact with EC and PLT.
KW  - cyclic olefin copolymer
KW  - poly(tetrafluoroethylene)
KW  - endothelial cells
KW  - platelets
KW  - in vitro thrombogenicity testing
Y1  - 2021
U6  - https://doi.org/10.3390/ijms22137006
SN  - 1422-0067
SN  - 1661-6596
VL  - 22
IS  - 13
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - JOUR
A1  - Kürschner, Tobias
A1  - Scherer, Cédric
A1  - Radchuk, Viktoriia
A1  - Blaum, Niels
A1  - Kramer-Schadt, Stephanie
T1  - Movement can mediate temporal mismatches between resource availability and biological events in host-pathogen interactions
JF  - Ecology and evolution
N2  - Global change is shifting the timing of biological events, leading to temporal mismatches between biological events and resource availability. These temporal mismatches can threaten species' populations. Importantly, temporal mismatches not only exert strong pressures on the population dynamics of the focal species, but can also lead to substantial changes in pairwise species interactions such as host-pathogen systems. We adapted an established individual-based model of host-pathogen dynamics. The model describes a viral agent in a social host, while accounting for the host's explicit movement decisions. We aimed to investigate how temporal mismatches between seasonal resource availability and host life-history events affect host-pathogen coexistence, that is, disease persistence. Seasonal resource fluctuations only increased coexistence probability when in synchrony with the hosts' biological events. However, a temporal mismatch reduced host-pathogen coexistence, but only marginally. In tandem with an increasing temporal mismatch, our model showed a shift in the spatial distribution of infected hosts. It shifted from an even distribution under synchronous conditions toward the formation of disease hotspots, when host life history and resource availability mismatched completely. The spatial restriction of infected hosts to small hotspots in the landscape initially suggested a lower coexistence probability due to the critical loss of susceptible host individuals within those hotspots. However, the surrounding landscape facilitated demographic rescue through habitat-dependent movement. Our work demonstrates that the negative effects of temporal mismatches between host resource availability and host life history on host-pathogen coexistence can be reduced through the formation of temporary disease hotspots and host movement decisions, with implications for disease management under disturbances and global change.
KW  - classical swine fever
KW  - dynamic landscapes
KW  - global change
KW  - host– pathogen dynamics
KW  - individual‐ based model
KW  - movement ecology
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.7478
SN  - 2045-7758
VL  - 11
IS  - 10
SP  - 5728
EP  - 5741
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Köker, Latife
A1  - Akçaalan, Reyhan
A1  - Dittmann, Elke
A1  - Albay, Meriç
T1  - Depth profiles of protein-bound microcystin in Küçükçekmece Lagoon
JF  - Toxicon : an international journal devoted to the exchange of knowledge on the poisons derived from the tissues of plants and animals ; official journal of the International Society on Toxinology
N2  - Microcystis is the most commonly found toxic cyanobacterial genus around the world and has a negative impact on the ecosystem. As a predominant producer of the potent hepatotoxin microcystin (MC), the genus causes outbreaks in freshwaters worldwide. Standard analytical methods that are used for the detection of microcystin variants can only measure the free form of microcystin in cells. Since microcystin was found as free and proteinbound forms in the cells, a significant proportion of microcystin is underestimated with analytical methods. The aim of the study was to measure protein-bound microcystins and determine the environmental factors that affect the binding of microcystin to proteins. Samples were taken at depths of surface, 1 m, 5 m, 10 m, 15 m, and 18 m in Kucukcekmece Lagoon to analyze depth profiles of two different microcystin forms from June to September 2012 at regular monthly intervals. Our findings suggest that the most important parameter affecting proteinbound microcystin at surface water is high light. Due to favorable environmental conditions such as temperature, light, and physicochemical parameters, the higher microcystin contents, both free and protein-bound MCs, were found in summer periods.
KW  - Microcystis
KW  - Microcystin
KW  - Protein-bound microcystin
KW  - Mcy gene
KW  - Kucukcekmece Lagoon
Y1  - 2021
U6  - https://doi.org/10.1016/j.toxicon.2021.05.005
SN  - 0041-0101
SN  - 1879-3150
VL  - 198
SP  - 156
EP  - 163
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Kraus, Sara Milena
A1  - Mathew-Stephen, Mariet
A1  - Schapranow, Matthieu-Patrick
T1  - Eatomics
BT  - Shiny exploration of quantitative proteomics data
JF  - Journal of proteome research
N2  - Quantitative proteomics data are becoming increasingly more available, and as a consequence are being analyzed and interpreted by a larger group of users. However, many of these users have less programming experience. Furthermore, experimental designs and setups are getting more complicated, especially when tissue biopsies are analyzed. Luckily, the proteomics community has already established some best practices on how to conduct quality control, differential abundance analysis and enrichment analysis. However, an easy-to-use application that wraps together all steps for the exploration and flexible analysis of quantitative proteomics data is not yet available. For Eatomics, we utilize the R Shiny framework to implement carefully chosen parts of established analysis workflows to (i) make them accessible in a user-friendly way, (ii) add a multitude of interactive exploration possibilities, and (iii) develop a unique experimental design setup module, which interactively translates a given research hypothesis into a differential abundance and enrichment analysis formula. In this, we aim to fulfill the needs of a growing group of inexperienced quantitative proteomics data analysts. Eatomics may be tested with demo data directly online via https://we.analyzegenomes.com/now/eatomics/or with the user's own data by installation from the Github repository at https://github.com/Millchmaedchen/Eatomics.
KW  - R Shiny
KW  - application
KW  - label-free
KW  - proteomics
KW  - analysis
KW  - differential
KW  - abundance
KW  - experimental design
Y1  - 2021
U6  - https://doi.org/10.1021/acs.jproteome.0c00398
SN  - 1535-3893
SN  - 1535-3907
VL  - 20
IS  - 1
SP  - 1070
EP  - 1078
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Krahé, Barbara
A1  - Schuster, Isabell
A1  - Tomaszewska, Paulina
T1  - Prevalence of sexual aggression victimization and perpetration in a German university student sample
JF  - Archives of sexual behavior : the official publication of the International Academy of Sex Research
N2  - This study examined the prevalence of sexual aggression perpetration and victimization in a sample of 1,172 students (755 female, 417 male) from four universities in Germany. All participants were asked about both victimization by, and perpetration of, sexual aggression since the age of 14 years, using the Sexual Aggression and Victimization Scale (SAV-S). Prevalence rates were established for different coercive strategies, sexual acts, and victim-perpetrator relationships. Both same-sex and opposite-sex victim-perpetrator constellations were examined. The overall victimization rate was 62.1% for women and 37.5% for men. The overall perpetration rate was 17.7% for men and 9.4% for women. Prevalence rates of both victimization and perpetration were higher for participants who had sexual contacts with both opposite-sex and same-sex partners than for participants with exclusively opposite-sex partners. Significant overlap was found between victim and perpetrator status for men and women as well as for participants with only opposite-sex and both opposite-sex and same-sex partners. A disparity between (higher) victimization and (lower) perpetration reports was found for both men and women, suggesting a general underreporting of perpetration rather than a gendered explanation in terms of social desirability or the perception of consent cues. The findings are placed in the international research literature on the prevalence of sexual aggression before and after the #metoo campaign, and their implications for prevention efforts are discussed.
KW  - Sexual aggression
KW  - Sexual victimization
KW  - Male victims
KW  - Female perpetrators
KW  - Same-sex relationships
Y1  - 2021
U6  - https://doi.org/10.1007/s10508-021-01963-4
SN  - 0004-0002
SN  - 1573-2800
VL  - 50
IS  - 5
SP  - 2109
EP  - 2121
PB  - Springer
CY  - New York
ER  - 
TY  - THES
A1  - Knox-Brown, Patrick Frank
T1  - Towards understanding the sequence-structure-function relationship of intrinsically disordered LEA_4 proteins from Arabidopsis thaliana
N2  - Water-deficits can cause lethal damage to organisms, which is rooted in cellular dehydration. Many plant species, but also other organisms have developed mechanisms to tolerate such stresses, such as the expression of LEA proteins. Many studies report on physiological protective functions of LEA proteins but lack information about their precise mechanisms on a molecular level. Most LEA proteins are intrinsically disordered in dilute solution but may adopt a distinct secondary structure upon changes in solvent conditions. Understanding the molecular mechanism of how LEA proteins contribute to the counteraction of cellular damage during water-deficits may in the long-term pave the way for breeding crops that are resistant to the effects of global warming. The objective of the work at hand is to improve the biophysical understanding of the sequencestructure-function relationship of LEA proteins as membrane stabilizers, based on the LEA_4 family of the model plant A. thaliana. This is pursued by using a combination of spectroscopic and scattering techniques, supported by bioinformatics and computational analyses. Eight out of the 18 LEA_4 proteins are experimentally assessed revealing that a coil-helix transition in response to water-deficit is a common feature, as predicted for the entire family. In addition, they all stabilize simple membrane models during a freeze/ thaw cycle. Three-dimensional structure prediction of representative members suggests that their completely folded states are represented by a sequential arrangement of alpha-helical segments connected by unstructured linkers, which is experimentally verified for the LEA_4 protein COR15A. The unstructured linker region of COR15A represents a conserved motif among its closest homologs and is, therefore, of particular interest. Facilitating a set of seven designed and investigated COR15A mutants uncovers a complex interplay of transient interactions between the amphipathic alpha-helical segments, mediated by the linker, which fine-tunes folding transitions and structural ensembles upon reduced water-availability. Finally, alpha-helicity is also induced in COR15A upon temperature decrease, which is enhanced in the presence of osmolytes. In addition, high solution osmolarity induced secondary structure is followed by oligomerization of COR15A. Interestingly, the functionality of COR15A, in terms of liposome stabilization, strongly correlates with its alpha-helix ratio in the folded state. The present work significantly improves the understanding of the sequence-structure-function relationship for LEA_4 proteins and offers novel findings on folding mechanisms and oligomerization of COR15A.
N2  - Wasserdefizite können zu letalem Schaden von Organismen führen, der letztendlich aus zellulärer Dehydrierung resultiert. Viele Pflanzen, aber auch andere Organismen haben Mechanismen entwickelt, um solche Stressfaktoren zu tolerieren, z.B. die Expression von LEAProteinen. Diverse Studien beschreiben deren physiologische Schutzfunktionen, es fehlen jedoch Informationen ihrer präzisen Mechanismen auf molekularer Ebene. Die meisten LEA-Proteine sind in wässriger Lösung intrinsisch unstrukturiert, können jedoch in Reaktion auf veränderte Lösungsmittelbedingungen geordnete Strukturen ausbilden. Ein solides Verständnis ihrer molekularen Mechanismen führt daher über die Entschlüsselung ihrer Sequenz-StrukturFunktions-Beziehungen, welche langfristig den Weg zur Entwicklung von Pflanzen ebnen, die Resistenzen gegen die Auswirkungen der globalen Erwärmung aufweisen.. Ziel der vorliegenden Arbeit ist, das Verständnis der Sequenz-Struktur-Funktions-Beziehung der LEA_4-Familie aus der Modellpflanze A. thaliana zu verbessern. Dazu wird eine Kombination von Spektroskopie- und Streutechniken (unterstützt durch prädiktive Computeranalysen) verwendet. Alle acht experimentell untersuchten der insgesamt 18 LEA_4-Proteine zeigen einen Coil-Helix-Übergang in Reaktion auf Wasserdefizit als gemeinsames Merkmal und stabilisieren einfache Membranmodelle während eines Gefrier-/ Tau-Vorgang. Die dreidimensionale Strukturvorhersage repräsentativer LEA_4-Proteine deutet an, dass der gefaltete Zustand einer Abfolge alpha-helikaler Segmente unterbrochen durch unstrukturierte Domänen entspricht, was für das LEA_4-Protein COR15A experimentell belegt wird. Der unstrukturierte Linker, der die beiden alpha-helikalen Segmente von COR15A verbindet, stellt ein Motiv dar, das innerhalb der nächsten Homologen konserviert ist und ist daher von besonderem Interesse. Mithilfe von sieben entworfenen und untersuchten COR15A-Mutanten kann der komplexe Zusammenhang transienter Wechselwirkungen zwischen den amphipathischen, alpha-helikalen Segmenten, vermittelt durch den Linker, gezeigt werden. Dieser spielt eine zentrale Rolle in der Feinabstimmung von Faltungsübergängen und strukturellen Ensembles bei verringerter Wasserverfügbarkeit. Ferner wird gezeigt, dass alpha-helikale Struktur auch durch Temperaturerniedrigung induziert werden kann, was in Gegenwart von Osmolyten stärker ausgeprägt ist. Hohe Osmolaritäten induzieren außerdem eine Oligomerisierung von COR15A. Interessanterweise korreliert die Funktionalität von COR15A (die Stabilisierung von Liposomen) stark mit dem relativen alpha-Helix-Anteil im gefalteten Zustand. Die vorliegende Arbeit verbessert erheblich das Verständnis für eine Sequenz-StrukturFunktions-Beziehung für LEA_4-Proteine und bietet neue Erkenntnisse zu Faltungsmechanismen und Oligomerisierung von COR15A.
KW  - IDPs
KW  - alpha-helix
KW  - coil-helix
KW  - linker
KW  - structure-function
KW  - protein-folding
KW  - LEA
Y1  - 2021
ER  -