TY  - JOUR
A1  - Thirumalaikumar, Venkatesh P.
A1  - Gorka, Michal
A1  - Schulz, Karina
A1  - Masclaux-Daubresse, Celine
A1  - Sampathkumar, Arun
A1  - Skirycz, Aleksandra
A1  - Vierstra, Richard D.
A1  - Balazadeh, Salma
T1  - Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1
JF  - Autophagy
N2  - In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS.
KW  - Arabidopsis thaliana
KW  - heat stress
KW  - HSFA2
KW  - HSP90.1
KW  - NBR1
KW  - ROF1
KW  - selective autophagy
KW  - stress memory
KW  - stress recovery
Y1  - 2020
U6  - https://doi.org/10.1080/15548627.2020.1820778
SN  - 1554-8635
VL  - 17
IS  - 9
SP  - 2184
EP  - 2199
PB  - Taylor & Francis
CY  - Abingdon
ER  - 
TY  - JOUR
A1  - Friedrich, Thomas
A1  - Oberkofler, Vicky
A1  - Trindade, Inês
A1  - Altmann, Simone
A1  - Brzezinka, Krzysztof
A1  - Lämke, Jörn S.
A1  - Gorka, Michal
A1  - Kappel, Christian
A1  - Sokolowska, Ewelina
A1  - Skirycz, Aleksandra
A1  - Graf, Alexander
A1  - Bäurle, Isabel
T1  - Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis
JF  - Nature Communications
N2  - Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory. Moderate heat stress primes plants to acquire tolerance to subsequent, more severe heat stress. Here the authors show that the HSFA3 transcription factor forms a heteromeric complex with HSFA2 to sustain activated transcription of genes required for acquired thermotolerance by promoting H3K4 hyper-methylation.
Y1  - 2021
U6  - https://doi.org/10.1038/s41467-021-23786-6
SN  - 2041-1723
VL  - 12
IS  - 1
PB  - Nature Publishing Group UK
CY  - [London]
ER  - 
TY  - JOUR
A1  - Carpio Arias, Tannia Valeria
A1  - Arias Mogrovejo, Diana Carolina
A1  - Nicolalde Cifuentes, Tomás Marcelo
A1  - Tapia Veloz, Estephany Carolina
A1  - Zeeuw, Chris I. de
A1  - Vinueza Veloz, Maria Fernanda
T1  - Sleep quality does not mediate the negative effects of chronodisruption on body composition and metabolic syndrome in healthcare workers in Ecuador
JF  - Diabetes & metabolic syndrome : clinical research & reviews ; the official journal of DiabetesIndia
N2  - Background and aims: 
The objective of the present work was to determine to what extent sleep quality may mediate the association between chronodisruption (CD) and metabolic syndrome (MS), and between CD and body composition (BC). 

Methodology:
Cross-sectional study which included 300 adult health workers, 150 of whom were night shift workers and thereby exposed to CD. Diagnosis of MS was made based on Adult Treatment Panel III criteria. Sleep quality was measured using the Pittsburgh Sleep Quality Index. Body mass index (BMI), fat mass percentage, and visceral fat percentage were measured as indicators of body composition (BC). Data were analyzed using logistic, linear regression and structural equation models. 

Results: 
The odds of health workers exposed to CD to suffer MS was 22.13 (IC95 8.68-66.07) when the model was adjusted for age, gender, physical activity and energy consumption. CD was also significantly associated with an increase in fat mass and visceral fat percentages, but not to BMI. Surprisingly, there was not enough evidence supporting the hypothesis that sleep quality contributes to the association between CD and MS or between CD and BC. 

Conclusions:
Sleep quality does not mediate the negative effects of CD on MS nor on BC.
KW  - Shift work
KW  - Metabolic syndrome
KW  - Sleep quality
KW  - Chronodisruption
KW  - Body composition
Y1  - 2021
U6  - https://doi.org/10.1016/j.dsx.2021.01.017
SN  - 1871-4021
SN  - 1878-0334
VL  - 15
IS  - 1
SP  - 397
EP  - 402
PB  - Elsevier
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Huß, Sebastian
A1  - Judd, Rika Siedah
A1  - Koper, Kaan
A1  - Maeda, Hiroshi A.
A1  - Nikoloski, Zoran
T1  - An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana
JF  - The plant journal
N2  - Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating N-15 isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future N-15-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.
KW  - atom mapping
KW  - genome-scale metabolic model
KW  - isotopic labeling
KW  - metabolic
KW  - flux analysis
KW  - technical advance
Y1  - 2022
U6  - https://doi.org/10.1111/tpj.15903
SN  - 0960-7412
SN  - 1365-313X
VL  - 111
IS  - 5
SP  - 1486
EP  - 1500
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Ostermann-Miyashita, Emu-Felicitas
A1  - König, Hannes J.
A1  - Pernat, Nadja
A1  - Bellingrath-Kimura, Sonoko Dorothea
A1  - Hibler, Sophia
A1  - Kiffner, Christian
T1  - Knowledge of returning wildlife species and willingness to participate in citizen science projects among wildlife park visitors in Germany
JF  - People and nature
N2  - Successful conservation efforts have led to recent increases of large mammals such as European bison Bison bonasus, moose Alces alces and grey wolf Canis lupus and their return to former habitats in central Europe. 
While embraced by some, the recovery of these species is a controversial topic and holds potential for human-wildlife conflicts. 
Involving the public has been suggested to be an effective method for monitoring wildlife and mitigating associated conflicts. 
To assess two interrelated prerequisites for engaging people in Citizen Science (CS)-knowledge of returning species and respondents' readiness to participate in CS activities for monitoring and managing these species-we conducted a survey (questionnaire) in two wildlife parks located in different states of Germany. 
Based on 472 complete questionnaires, we developed generalized linear models to understand how sociodemographic variables and exposure to the species affected visitors' knowledge of each species, and to investigate if sociodemographic variables and knowledge influenced the likelihood of visitors to participate in CS activities. 
Almost all visitors were aware of the returning wolf population, while knowledge and awareness about bison and moose were significantly lower. 
Knowledge of the two herbivores differed geographically (higher knowledge of moose in the north-eastern state), possibly indicating a positive association between exposure to the species and knowledge. 
However, models generally performed poorly in predicting knowledge about wildlife, suggesting that such specific knowledge is insufficiently explained by sociodemographic variables. Our model, which explained stated willingness in CS indicated that younger participants and those with higher knowledge scores in the survey were more willing to engage in CS activities. 
Overall, our analyses highlight how exposure to large mammals, knowledge about wildlife and human demographics are interrelated-insights that are helpful for effectively recruiting citizen scientists for wildlife conservation. 
Read the free Plain Language Summary for this article on the Journal blog.
KW  - environmental awareness
KW  - human-animal relationships
KW  - human-wildlife conflicts
KW  - social-ecological system
KW  - wildlife conservation
KW  - wildlife knowledge
Y1  - 2022
U6  - https://doi.org/10.1002/pan3.10379
SN  - 2575-8314
VL  - 4
IS  - 5
SP  - 1201
EP  - 1215
PB  - British Ecological Society; Wiley
CY  - London; Hoboken, NJ
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  - Leins, Johannes A.
A1  - Banitz, Thomas
A1  - Grimm, Volker
A1  - Drechsler, Martin
T1  - High-resolution PVA along large environmental gradients to model the combined effects of climate change and land use timing
BT  - lessons from the large marsh grasshopper
JF  - Ecological modelling : international journal on ecological modelling and systems ecology
N2  - Both climate change and land use regimes affect the viability of populations, but they are often studied separately. Moreover, population viability analyses (PVAs) often ignore the effects of large environmental gradients and use temporal resolutions that are too coarse to take into account that different stages of a population's life cycle may be affected differently by climate change. Here, we present the High-resolution Large Environmental Gradient (HiLEG) model and apply it in a PVA with daily resolution based on daily climate projections for Northwest Germany. We used the large marsh grasshopper (LMG) as the target species and investigated (1) the effects of climate change on the viability and spatial distribution of the species, (2) the influence of the timing of grassland mowing on the species and (3) the interaction between the effects of climate change and grassland mowing. The stageand cohort-based model was run for the spatially differentiated environmental conditions temperature and soil moisture across the whole study region. We implemented three climate change scenarios and analyzed the population dynamics for four consecutive 20-year periods. Climate change alone would lead to an expansion of the regions suitable for the LMG, as warming accelerates development and due to reduced drought stress. However, in combination with land use, the timing of mowing was crucial, as this disturbance causes a high mortality rate in the aboveground life stages. Assuming the same date of mowing throughout the region, the impact on viability varied greatly between regions due to the different climate conditions. The regional negative effects of the mowing date can be divided into five phases: (1) In early spring, the populations were largely unaffected in all the regions; (2) between late spring and early summer, they were severely affected only in warm regions; (3) in summer, all the populations were severely affected so that they could hardly survive; (4) between late summer and early autumn, they were severely affected in cold regions; and (5) in autumn, the populations were equally affected across all regions. The duration and start of each phase differed slightly depending on the climate change scenario and simulation period, but overall, they showed the same pattern. Our model can be used to identify regions of concern and devise management recommendations. The model can be adapted to the life cycle of different target species, climate projections and disturbance regimes. We show with our adaption of the HiLEG model that high-resolution PVAs and applications on large environmental gradients can be reconciled to develop conservation strategies capable of dealing with multiple stressors.
KW  - Climate change
KW  - Land use
KW  - Population viability analysis
KW  - Stage-based model
KW  - High resolution
KW  - Environmental gradients
Y1  - 2020
U6  - https://doi.org/10.1016/j.ecolmodel.2020.109355
SN  - 0304-3800
VL  - 440
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Potente, Giacomo
A1  - Léveillé-Bourret, Étienne
A1  - Yousefi, Narjes
A1  - Choudhury, Rimjhim Roy
A1  - Keller, Barbara
A1  - Diop, Seydina Issa
A1  - Duijsings, Daniël
A1  - Pirovano, Walter
A1  - Lenhard, Michael
A1  - Szövényi, Péter
A1  - Conti, Elena
T1  - Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism
JF  - Molecular biology and evolution : MBE
N2  - Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?
KW  - genome architecture
KW  - supergene
KW  - heterostyly
KW  - evolutionary genomics
KW  - chromosome-scale genome assembly
KW  - primula
Y1  - 2022
U6  - https://doi.org/10.1093/molbev/msac035
SN  - 0737-4038
SN  - 1537-1719
VL  - 39
IS  - 2
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Lucena-Perez, María
A1  - Bazzicalupo, Enrico
A1  - Paijmans, Johanna
A1  - Kleinman-Ruiz, Daniel
A1  - Dalén, Love
A1  - Hofreiter, Michael
A1  - Delibes, Miguel
A1  - Clavero, Miguel
A1  - Godoy, José A.
T1  - Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe
JF  - Quaternary science reviews : the international multidisciplinary research and review journal
N2  - The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past.
Y1  - 2022
U6  - https://doi.org/10.1016/j.quascirev.2022.107518
SN  - 0277-3791
SN  - 1873-457X
VL  - 285
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Nwosu, Ebuka Canisius
A1  - Roeser, Patricia Angelika
A1  - Yang, Sizhong
A1  - Pinkerneil, Sylvia
A1  - Ganzert, Lars
A1  - Dittmann, Elke
A1  - Brauer, Achim
A1  - Wagner, Dirk
A1  - Liebner, Susanne
T1  - Species-level spatio-temporal dynamics of cyanobacteria in a hard-water temperate lake in the Southern Baltics
JF  - Frontiers in microbiology
N2  - Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p < 0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter-when the water column is mixed-picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes.
KW  - Cyanobium
KW  - picocyanobacteria diversity
KW  - amplicon sequencing
KW  - lake monitoring
KW  - ecological succession
KW  - lake stratification
KW  - psychrotolerant
Y1  - 2021
U6  - https://doi.org/10.3389/fmicb.2021.761259
SN  - 1664-302X
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Escalante, Ignacio
A1  - Dominguez, Marisol
A1  - Gomez-Ruiz, Daisy Alejandra
A1  - Machado, Glauco
T1  - Benefits and costs of mixed-species aggregations in Harvestmen (Arachnida: Opiliones)
JF  - Frontiers in ecology and evolution
N2  - Many animals form aggregations with individuals of the same species (single-species aggregations, SSA). Less frequently, individuals may also aggregate with individuals of other species (mixed-species aggregations, MSA). Although the benefits and costs of SSA have been intensively studied, the same is not true for MSA. Here, we first review the cases of MSA in harvestmen, an arachnid order in which the records of MSA are more frequent than other arthropod orders. We then propose several benefits and costs of MSA in harvestmen, and contrast them with those of SSA. Second, using field-gathered data we describe gregariousness in seven species of Prionostemma harvestmen from Costa Rica. These species form MSA, but individuals are also found solitarily or in SSA. We tested one possible benefit and one possible cost of gregariousness in Prionostemma harvestmen. Regarding the benefit, we hypothesized that individuals missing legs would be more exposed to predation than eight-legged individuals and thus they should be found preferentially in aggregations, where they would be more protected from predators. Our data, however, do not support this hypothesis. Regarding the cost, we hypothesized that gregariousness increases the chances of parasitism. We found no support for this hypothesis either because both mite prevalence and infestation intensity did not differ between solitary or aggregated individuals. Additionally, the type of aggregation (SSA or MSA) was not associated with the benefit or the cost we explored. This lack of effect may be explained by the fluid membership of the aggregations, as we found high turnover over time in the number of individuals and species composition of the aggregations. In conclusion, we hope our review and empirical data stimulate further studies on MSA, which remains one of the most elusive forms of group living in animals.
KW  - alarm signals
KW  - aggregation size
KW  - autotomy
KW  - chemical defenses
KW  - dilution
KW  - effect
KW  - ectoparasitism
KW  - group living
KW  - roosting site
Y1  - 2022
U6  - https://doi.org/10.3389/fevo.2021.766323
SN  - 2296-701X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
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  - Krumbholz, Julia
A1  - Ishida, Keishi
A1  - Baunach, Martin
A1  - Teikari, Jonna
A1  - Rose, Magdalena M.
A1  - Sasso, Severin
A1  - Hertweck, Christian
A1  - Dittmann, Elke
T1  - Deciphering chemical mediators regulating specialized metabolism in a symbiotic cyanobacterium
JF  - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker. International edition
N2  - Genomes of cyanobacteria feature a variety of cryptic biosynthetic pathways for complex natural products, but the peculiarities limiting the discovery and exploitation of the metabolic dark matter are not well understood. Here we describe the discovery of two cell density-dependent chemical mediators, nostoclide and nostovalerolactone, in the symbiotic model strain Nostoc punctiforme, and demonstrate their pronounced impact on the regulation of specialized metabolism. Through transcriptional, bioinformatic and labeling studies we assigned two adjacent biosynthetic gene clusters to the biosynthesis of the two polyketide mediators. Our findings provide insight into the orchestration of specialized metabolite production and give lessons for the genomic mining and high-titer production of cyanobacterial bioactive compounds.
KW  - Biosynthesis
KW  - Cyanobacteria
KW  - Genomic Mining
KW  - Quorum Sensing
KW  - Specialized
KW  - Metabolism
Y1  - 2022
U6  - https://doi.org/10.1002/anie.202204545
SN  - 1433-7851
SN  - 1521-3773
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Scheffler, Christiane
A1  - Bogin, Barry
A1  - Hermanussen, Michael
T1  - Catch-up growth is a better indicator of undernutrition than thresholds for stunting
JF  - Public health nutrition : PHN / The Nutrition Society
N2  - Objective: 
Stunting (height-for-age < −2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < −2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition.

Design: 
Cross-sectional study; breakpoint analysis.

Setting: 
Rural and urban regions of Indonesia and Guatemala – different socio-economic status (SES).

Participants:
1716 Indonesian children (6·0–13·2 years) and 3838 Guatemalan children (4·0–18·9 years) with up to 50 % stunted children.

Results: 
When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017.

Conclusions: 
Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting.
KW  - no threshold for stunting
KW  - catch-up growth
KW  - social-economic-political-emotional
KW  - (SEPE) factors
Y1  - 2020
U6  - https://doi.org/10.1017/S1368980020003067
SN  - 1475-2727
SN  - 1368-9800
VL  - 24
IS  - 1
SP  - 52
EP  - 61
PB  - Cambridge University Press
CY  - Cambridge ; New York, NY
ER  - 
TY  - JOUR
A1  - Horn, Juliane
A1  - Becher, Matthias A.
A1  - Johst, Karin
A1  - Kennedy, Peter J.
A1  - Osborne, Juliet L.
A1  - Radchuk, Viktoriia
A1  - Grimm, Volker
T1  - Honey bee colony performance affected by crop diversity and farmland structure
BT  - a modeling framework
JF  - Ecological applications
N2  - Forage availability has been suggested as one driver of the observed decline in honey bees. However, little is known about the effects of its spatiotemporal variation on colony success. We present a modeling framework for assessing honey bee colony viability in cropping systems. Based on two real farmland structures, we developed a landscape generator to design cropping systems varying in crop species identity, diversity, and relative abundance. The landscape scenarios generated were evaluated using the existing honey bee colony model BEEHAVE, which links foraging to in-hive dynamics. We thereby explored how different cropping systems determine spatiotemporal forage availability and, in turn, honey bee colony viability (e.g., time to extinction, TTE) and resilience (indicated by, e.g., brood mortality). To assess overall colony viability, we developed metrics,P(H)andP(P,)which quantified how much nectar and pollen provided by a cropping system per year was converted into a colony's adult worker population. Both crop species identity and diversity determined the temporal continuity in nectar and pollen supply and thus colony viability. Overall farmland structure and relative crop abundance were less important, but details mattered. For monocultures and for four-crop species systems composed of cereals, oilseed rape, maize, and sunflower,P(H)andP(P)were below the viability threshold. Such cropping systems showed frequent, badly timed, and prolonged forage gaps leading to detrimental cascading effects on life stages and in-hive work force, which critically reduced colony resilience. Four-crop systems composed of rye-grass-dandelion pasture, trefoil-grass pasture, sunflower, and phacelia ensured continuous nectar and pollen supply resulting in TTE > 5 yr, andP(H)(269.5 kg) andP(P)(108 kg) being above viability thresholds for 5 yr. Overall, trefoil-grass pasture, oilseed rape, buckwheat, and phacelia improved the temporal continuity in forage supply and colony's viability. Our results are hypothetical as they are obtained from simplified landscape settings, but they nevertheless match empirical observations, in particular the viability threshold. Our framework can be used to assess the effects of cropping systems on honey bee viability and to develop land-use strategies that help maintain pollination services by avoiding prolonged and badly timed forage gaps.
KW  - apis mellifera
KW  - BEEHAVE
KW  - colony viability
KW  - crop diversity
KW  - cropping system
KW  - decline
KW  - forage availability
KW  - forage gaps
KW  - honey bees
KW  - landscape generator
KW  - modeling
Y1  - 2020
U6  - https://doi.org/10.1002/eap.2216
SN  - 1939-5582
SN  - 1051-0761
VL  - 31
IS  - 1
SP  - 1
EP  - 22
PB  - Wiley Periodicals LLC
CY  - Washington DC
ER  - 
TY  - JOUR
A1  - Li, Chenzhi
A1  - Postl, Alexander K.
A1  - Böhmer, Thomas
A1  - Cao, Xianyong
A1  - Dolman, Andrew M.
A1  - Herzschuh, Ulrike
T1  - Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0)
JF  - Earth system science data : ESSD
N2  - We present a chronology framework named LegacyAge 1.0 containing harmonized chronologies for 2831 pollen records (downloaded from the Neotoma Paleoecology Database and the supplementary Asian datasets) together with their age control points and metadata in machine-readable data formats.  
All chronologies use the Bayesian framework implemented in Bacon version 2.5.3. Optimal parameter settings of priors (accumulation.shape, memory.strength, memory.mean, accumulation.rate, and thickness) were identified based on information in the original publication or iteratively after preliminary model inspection. 
The most common control points for the chronologies are radiocarbon dates (86.1 %), calibrated by the latest calibration curves (IntCal20 and SHCal20 for the terrestrial radiocarbon dates in the Northern Hemisphere and Southern Hemisphere and Marine20 for marine materials). 
The original publications were consulted when dealing with outliers and inconsistencies. Several major challenges when setting up the chronologies included the waterline issue (18.8% of records), reservoir effect (4.9 %), and sediment deposition discontinuity (4.4 %). 
Finally, we numerically compare the LegacyAge 1.0 chronologies to those published in the original publications and show that the reliability of the chronologies of 95.4% of records could be improved according to our assessment. 
Our chronology framework and revised chronologies provide the opportunity to make use of the ages and age uncertainties in synthesis studies of, for example, pollen-based vegetation and climate change. 
The LegacyAge 1.0 dataset, including metadata, datings, harmonized chronologies, and R code used, is openaccess and available at PANGAEA (https://doi.org/10.1594/PANGAEA.933132; Li et al., 2021) and Zenodo (https://doi.org/10.5281/zenodo.5815192; Li et al., 2022), respectively.
Y1  - 2022
U6  - https://doi.org/10.5194/essd-14-1331-2022
SN  - 1866-3508
SN  - 1866-3516
VL  - 14
IS  - 3
SP  - 1331
EP  - 1343
PB  - Copernics Publications
CY  - Katlenburg-Lindau
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  - Hampf, Anna
A1  - Nendel, Claas
A1  - Strey, Simone
A1  - Strey, Robert
T1  - Biotic yield losses in the Southern Amazon, Brazil
BT  - making use of smartphone-assisted plant disease diagnosis data
JF  - Frontiers in plant science : FPLS
N2  - Pathogens and animal pests (P&A) are a major threat to global food security as they directly affect the quantity and quality of food. The Southern Amazon, Brazil's largest domestic region for soybean, maize and cotton production, is particularly vulnerable to the outbreak of P&A due to its (sub)tropical climate and intensive farming systems. However, little is known about the spatial distribution of P&A and the related yield losses. Machine learning approaches for the automated recognition of plant diseases can help to overcome this research gap. The main objectives of this study are to (1) evaluate the performance of Convolutional Neural Networks (ConvNets) in classifying P&A, (2) map the spatial distribution of P&A in the Southern Amazon, and (3) quantify perceived yield and economic losses for the main soybean and maize P&A. The objectives were addressed by making use of data collected with the smartphone application Plantix. The core of the app's functioning is the automated recognition of plant diseases via ConvNets. Data on expected yield losses were gathered through a short survey included in an "expert" version of the application, which was distributed among agronomists. Between 2016 and 2020, Plantix users collected approximately 78,000 georeferenced P&A images in the Southern Amazon. The study results indicate a high performance of the trained ConvNets in classifying 420 different crop-disease combinations. Spatial distribution maps and expert-based yield loss estimates indicate that maize rust, bacterial stalk rot and the fall armyworm are among the most severe maize P&A, whereas soybean is mainly affected by P&A like anthracnose, downy mildew, frogeye leaf spot, stink bugs and brown spot. Perceived soybean and maize yield losses amount to 12 and 16%, respectively, resulting in annual yield losses of approximately 3.75 million tonnes for each crop and economic losses of US$2 billion for both crops together. The high level of accuracy of the trained ConvNets, when paired with widespread use from following a citizen-science approach, results in a data source that will shed new light on yield loss estimates, e.g., for the analysis of yield gaps and the development of measures to minimise them.
KW  - plant pathology
KW  - animal pests
KW  - pathogens
KW  - machine learning
KW  - digital
KW  - image processing
KW  - disease diagnosis
KW  - crowdsourcing
KW  - crop losses
Y1  - 2021
U6  - https://doi.org/10.3389/fpls.2021.621168
SN  - 1664-462X
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Irob, Katja
A1  - Blaum, Niels
A1  - Baldauf, Selina
A1  - Kerger, Leon
A1  - Strohbach, Ben
A1  - Kanduvarisa, Angelina
A1  - Lohmann, Dirk
A1  - Tietjen, Britta
T1  - Browsing herbivores improve the state and functioning of savannas
BT  - A model assessment of alternative land-use strategies
JF  - Ecology and evolution
N2  - Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle-dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land-use strategies on a Namibian savanna: grazer- versus browser-dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land-use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing-dominated land-use strategies, land-use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services.
KW  - browsing
KW  - ecohydrology
KW  - land use
KW  - plant community
KW  - savanna
KW  - wildlife
KW  - management
Y1  - 2022
U6  - https://doi.org/10.1002/ece3.8715
SN  - 2045-7758
VL  - 12
IS  - 3
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Ghafarian, Fatemeh
A1  - Wieland, Ralf
A1  - Lüttschwager, Dietmar
A1  - Nendel, Claas
T1  - Application of extreme gradient boosting and Shapley Additive explanations to predict temperature regimes inside forests from standard open-field meteorological data
JF  - Environmental modelling & software with environment data news
N2  - Forest microclimate can buffer biotic responses to summer heat waves, which are expected to become more extreme under climate warming. Prediction of forest microclimate is limited because meteorological observation standards seldom include situations inside forests. 
We use eXtreme Gradient Boosting - a Machine Learning technique - to predict the microclimate of forest sites in Brandenburg, Germany, using seasonal data comprising weather features. 
The analysis was amended by applying a SHapley Additive explanation to show the interaction effect of variables and individualised feature attributions. 
We evaluate model performance in comparison to artificial neural networks, random forest, support vector machine, and multi-linear regression. 
After implementing a feature selection, an ensemble approach was applied to combine individual models for each forest and improve robustness over a given single prediction model. 
The resulting model can be applied to translate climate change scenarios into temperatures inside forests to assess temperature-related ecosystem services provided by forests.
KW  - cooling effect
KW  - machine learning
KW  - ensemble method
KW  - ecosystem services
Y1  - 2022
U6  - https://doi.org/10.1016/j.envsoft.2022.105466
SN  - 1364-8152
SN  - 1873-6726
VL  - 156
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Caserta, Giorgio
A1  - Zhang, Xiaorong
A1  - Yarman, Aysu
A1  - Supala, Eszter
A1  - Wollenberger, Ulla
A1  - Gyurcsányi, Róbert  E.
A1  - Zebger, Ingo
A1  - Scheller, Frieder W.
T1  - Insights in electrosynthesis, target binding, and stability of peptide-imprinted polymer nanofilms
JF  - Electrochimica acta : the journal of the International Society of Electrochemistry (ISE)
N2  - Molecularly imprinted polymer (MIP) nanofilms have been successfully implemented for the recognition of different target molecules: however, the underlying mechanistic details remained vague. 
This paper provides new insights in the preparation and binding mechanism of electrosynthesized peptide-imprinted polymer nanofilms for selective recognition of the terminal pentapeptides of the beta-chains of human adult hemoglobin, HbA, and its glycated form HbA1c. 
To differentiate between peptides differing solely in a glucose adduct MIP nanofilms were prepared by a two-step hierarchical electrosynthesis that involves first the chemisorption of a cysteinyl derivative of the pentapeptide followed by electropolymerization of scopoletin. 
This approach was compared with a random single-step electrosynthesis using scopo-letin/pentapeptide mixtures. Electrochemical monitoring of the peptide binding to the MIP nanofilms by means of redox probe gating revealed a superior affinity of the hierarchical approach with a Kd value of 64.6 nM towards the related target. 
Changes in the electrosynthesized non-imprinted polymer and MIP nanofilms during chemical, electrochemical template removal and rebinding were substantiated in situ by monitoring the characteristic bands of both target peptides and polymer with surface enhanced infrared absorption spectroscopy. 
This rational approach led to MIPs with excellent selectivity and provided key mechanistic insights with respect to electrosynthesis, rebinding and stability of the formed MIPs.
KW  - SEIRA spectroelectrochemistry
KW  - peptide imprinting
KW  - electrosynthesis
KW  - MIP
KW  - glycated peptide
Y1  - 2021
U6  - https://doi.org/10.1016/j.electacta.2021.138236
SN  - 0013-4686
SN  - 1873-3859
VL  - 381
PB  - Elsevier
CY  - New York, NY [u.a.]
ER  - 
TY  - JOUR
A1  - Mitzscherling, Julia
A1  - MacLean, Joana
A1  - Lipus, Daniel
A1  - Bartholomäus, Alexander
A1  - Mangelsdorf, Kai
A1  - Lipski, André
A1  - Roddatis, Vladimir
A1  - Liebner, Susanne
A1  - Wagner, Dirk
T1  - Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste
JF  - International journal of systematic and evolutionary microbiology
N2  - Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. 
Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. 
The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. 
The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6%) and Nocardioides dubius KSL-104(T) (98.3%). 
The genomic DNA G+C content of strain NGK65(T) was 68.2%. 
Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. 
Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. 
The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)).
KW  - Nocardioides alcanivorans
KW  - hexadecane
KW  - plastic degradation
KW  - terrestrial
KW  - plastisphere
KW  - bacteria
Y1  - 2022
U6  - https://doi.org/10.1099/ijsem.0.005319
SN  - 1466-5026
SN  - 1466-5034
VL  - 72
IS  - 4
PB  - Microbiology Society
CY  - London
ER  - 
TY  - JOUR
A1  - Hilt, Sabine
A1  - Grossart, Hans-Peter
A1  - McGinnis, Daniel F.
A1  - Keppler, Frank
T1  - Potential role of submerged macrophytes for oxic methane production in aquatic ecosystems
JF  - Limnology and oceanography
N2  - Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems.
Y1  - 2022
U6  - https://doi.org/10.1002/lno.12095
SN  - 0024-3590
SN  - 1939-5590
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Yarman, Aysu
A1  - Kurbanoğlu, Sevinç
A1  - Zebger, Ingo
A1  - Scheller, Frieder W.
T1  - Simple and robust
BT  - the claims of protein sensing by molecularly imprinted polymers
JF  - Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers
N2  - A spectrum of 7562 publications on Molecularly Imprinted Polymers (MIPs) has been presented in literature within the last ten years (Scopus, September 7, 2020). Around 10 % of the papers published on MIPs describe the recognition of proteins. The straightforward synthesis of MIPs is a significant advantage as compared with the preparation of enzymes or antibodies. MIPs have been synthesized from only one up to six functional monomers while proteins are made up of 20 natural amino acids. Furthermore, they can be synthesized against structures of low immunogenicity and allow multi-analyte measurements via multi-target synthesis. Electrochemical methods allow simple polymer synthesis, removal of the template and readout. Among the different sensor configurations electrochemical MIP-sensors provide the broadest spectrum of protein analytes. The sensitivity of MIP-sensors is sufficiently high for biomarkers in the sub-nanomolar region, nevertheless the cross-reactivity of highly abundant proteins in human serum is still a challenge. MIPs for proteins offer innovative tools not only for clinical and environmental analysis, but also for bioimaging, therapy and protein engineering.
KW  - Molecularly imprinted polymer
KW  - Plastibodies
KW  - Functional scaffolds
KW  - Biomimetic sensors
KW  - Proteins
Y1  - 2021
U6  - https://doi.org/10.1016/j.snb.2020.129369
SN  - 0925-4005
SN  - 1873-3077
VL  - 330
PB  - Elsevier Science
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Tran, V. Phuong
A1  - Tamura, Yui
A1  - Pham, Van-Cuong
A1  - Elhussiny, Mohamed Z.
A1  - Han, Guofeng
A1  - Sur Chowdhury, Vishwajit
A1  - Furuse, Mitsuhiro
T1  - Neuropeptide Y modifies a part of diencephalic catecholamine but not indolamine metabolism in chicks depending on feeding status
JF  - Neuropeptides
N2  - The role of the monoaminergic system in the feeding behavior of neonatal chicks has been reported, but the functional relationship between the metabolism of monoamines and appetite-related neuropeptides is still unclear. This study aimed to investigate the changes in catecholamine and indolamine metabolism in response to the central action of neuropeptide Y (NPY) in different feeding statuses and the underlying mechanisms. In Experiment 1, the diencephalic concentrations of amino acids and monoamines following the intracerebroventricular (ICV) injection of NPY (375 pmol/10 mu l/chick), saline solution under ad libitum, and fasting conditions for 30 min were determined. Central NPY significantly decreased L-tyrosine concentration, the precursor of catecholamines under feeding condition, but not under fasting condition. Central NPY significantly increased dopamine metabolites, including 3,4-dihydroxyphenylacetic acid and homovanillic acid (HVA). The concentration of 3-methoxy-4-hydroxyphenylglycol was significantly reduced under feeding condition, but did not change under fasting condition by NPY. However, no effects of NPY on indolamine metabolism were found in either feeding status. Therefore, the mechanism of action of catecholamines with central NPY under feeding condition was elucidated in Experiment 2. Central NPY significantly attenuated diencephalic gene expression of catecholaminergic synthetic enzymes, such as tyrosine hydroxylase, L-aromatic amino acid decarboxylase, and GTP cyclohydrolase I after 30 min of feeding. In Experiment 3, co-injection of alpha-methyl-L-tyrosine, an inhibitor of tyrosine hydroxylase with NPY, moderately attenuated the orexigenic effect of NPY, accompanied by a significant positive correlation between food intake and HVA levels. In Experiment 4, there was a significant interaction between NPY and clorgyline, an inhibitor of monoamine oxidase A with ICV co-injection which implies that co-existence of NPY and clorgyline enhances the orexigenic effect of NPY. In conclusion, central NPY modifies a part of catecholamine metabolism, which is illustrated by the involvement of dopamine transmission and metabolism under feeding but not fasting conditions.
KW  - Neuropeptide Y
KW  - Feeding behavior
KW  - Neonatal chick
KW  - CNS
KW  - Catecholamines
Y1  - 2021
U6  - https://doi.org/10.1016/j.npep.2021.102169
SN  - 0143-4179
SN  - 1532-2785
VL  - 89
PB  - Elsevier
CY  - New York, NY
ER  - 
TY  - JOUR
A1  - Pan, Xuefeng
A1  - Sarhan, Radwan Mohamed
A1  - Kochovski, Zdravko
A1  - Chen, Guosong
A1  - Taubert, Andreas
A1  - Mei, Shilin
A1  - Lu, Yan
T1  - Template synthesis of dual-functional porous MoS2 nanoparticles with photothermal conversion and catalytic properties
JF  - Nanoscale
N2  - Advanced catalysis triggered by photothermal conversion effects has aroused increasing interest due to its huge potential in environmental purification. 
In this work, we developed a novel approach to the fast degradation of 4-nitrophenol (4-Nip) using porous MoS2 nanoparticles as catalysts, which integrate the intrinsic catalytic property of MoS2 with its photothermal conversion capability. 
Using assembled polystyrene-b-poly(2-vinylpyridine) block copolymers as soft templates, various MoS 2 particles were prepared, which exhibited tailored morphologies (e.g., pomegranate-like, hollow, and open porous structures). 
The photothermal conversion performance of these featured particles was compared under near-infrared (NIR) light irradiation. 
Intriguingly, when these porous MoS2 particles were further employed as catalysts for the reduction of 4-Nip, the reaction rate constant was increased by a factor of 1.5 under NIR illumination. 
We attribute this catalytic enhancement to the open porous architecture and light-to-heat conversion performance of the MoS2 particles. This contribution offers new opportunities for efficient photothermal-assisted catalysis.
Y1  - 2022
U6  - https://doi.org/10.1039/d2nr01040b
SN  - 2040-3372
VL  - 14
IS  - 18
SP  - 6888
EP  - 6901
PB  - RSC Publ. (Royal Society of Chemistry)
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Hagemann, Justus
A1  - Conejero, Carles
A1  - Stillfried, Milena
A1  - Mentaberre, Gregorio
A1  - Castillo-Contreras, Raquel
A1  - Fickel, Jörns
A1  - Lopez-Olvera, Jorge Ramón
T1  - Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain
JF  - The science of the total environment : an international journal for scientific research into the environment and its relationship with man
N2  - Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. 
However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. 
Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. 
The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. 
A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. 
This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. 
The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. 
Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. 
These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. 
The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.
KW  - gene flow
KW  - island population
KW  - population genetics
KW  - sus scrofa
KW  - synurbisation
KW  - urban ecology
Y1  - 2022
U6  - https://doi.org/10.1016/j.scitotenv.2022.155126
SN  - 0048-9697
SN  - 1879-1026
VL  - 833
PB  - Elsevier Science
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Ralevski, Alexandra
A1  - Apelt, Federico
A1  - Olas, Justyna Jadwiga
A1  - Müller-Röber, Bernd
A1  - Rugarli, Elena I.
A1  - Kragler, Friedrich
A1  - Horvath, Tamas L.
T1  - Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice
JF  - Cellular and molecular life sciences
N2  - Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.
KW  - Arabidopsis thaliana
KW  - Mitochondria
KW  - FMT
KW  - Hyponasty
KW  - Mice
KW  - CLUH;
KW  - Locomotion
Y1  - 2022
U6  - https://doi.org/10.1007/s00018-022-04382-3
SN  - 1420-682X
SN  - 1420-9071
VL  - 79
IS  - 6
PB  - Springer International Publishing AG
CY  - Cham (ZG)
ER  - 
TY  - JOUR
A1  - Witzel, Katja
A1  - Abu Risha, Marua
A1  - Albers, Philip
A1  - Börnke, Frederik
A1  - Hanschen, Franziska S.
T1  - Corrigendum : Identification and characterization of three epithiospecifier protein isoforms in Brassica oleracea / Witzel, Katja; Abu Risha, Marua; Albers, Philip; Börnke, Frederike; Hanschen, Franziska S. - Lausanne:  Frontiers Media, 2019. -  Frontiers in plant science : FPLS.  - 10 (2019) art. 1552. - doi: 10.3389/fpls.2019.01552
JF  - Frontiers in plant science : FPLS
KW  - epithionitrile
KW  - expression profile
KW  - functional complementation
KW  - glucosinolate hydrolysis
KW  - nitrile
KW  - specifier proteins
KW  - tissue
KW  - specificity
Y1  - 2020
U6  - https://doi.org/10.3389/fpls.2020.00523
SN  - 1664-462X
VL  - 11
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Schorn, Sina
A1  - Salman-Carvalho, Verena
A1  - Littmann, Sten
A1  - Ionescu, Danny
A1  - Grossart, Hans-Peter
A1  - Cypionka, Heribert
T1  - Cell architecture of the giant sulfur bacterium achromatium oxaliferum
BT  - Extra-cytoplasmic localization of calcium carbonate bodies
JF  - FEMS Microbiology Ecology
N2  - Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.
KW  - sulfur-bacteria
KW  - calcium carbonate inclusions
KW  - extra-cytoplasmic pockets
KW  - calcite
Y1  - 2019
U6  - https://doi.org/10.1093/femsec/fiz200
SN  - 1574-6941
VL  - 96
IS  - 2
SP  - 1
EP  - 8
PB  - Oxford University Press
CY  - Oxford
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  - Leins, Johannes A.
A1  - Grimm, Volker
A1  - Drechsler, Martin
T1  - Large-scale PVA modeling of insects in cultivated grasslands
BT  - the role of dispersal in mitigating the effects of management schedules under climate change
JF  - Ecology and evolution
N2  - In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60-year periods (2020-2079) on a fine temporal (daily) and high spatial (250 x 250 m(2)) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.
KW  - bilinear interpolation
KW  - climate change
KW  - dispersal success
KW  - land use
KW  - large marsh grasshopper
KW  - spatially explicit model
Y1  - 2022
U6  - https://doi.org/10.1002/ece3.9063
SN  - 2045-7758
VL  - 12
IS  - 7
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Ghafarian, Fatemeh
A1  - Wieland, Ralf
A1  - Nendel, Claas
T1  - Estimating the Evaporative Cooling Effect of Irrigation within and above Soybean Canopy
JF  - Water
N2  - Vegetation with an adequate supply of water might contribute to cooling the land surface around it through the latent heat flux of transpiration. This study investigates the potential estimation of evaporative cooling at plot scale, using soybean as example. Some of the plants' physiological parameters were monitored and sampled at weekly intervals. A physics-based model was then applied to estimate the irrigation-induced cooling effect within and above the canopy during the middle and late season of the soybean growth period. We then examined the results of the temperature changes at a temporal resolution of ten minutes between every two irrigation rounds. During the middle and late season of growth, the cooling effects caused by evapotranspiration within and above the canopy were, on average, 4.4 K and 2.9 K, respectively. We used quality indicators such as R-squared (R-2) and mean absolute error (MAE) to evaluate the performance of the model simulation. The performance of the model in this study was better above the canopy (R-2 = 0.98, MAE = 0.3 K) than below (R-2 = 0.87, MAE = 0.9 K) due to the predefined thermodynamic condition used to estimate evaporative cooling. Moreover, the study revealed that canopy cooling contributes to mitigating heat stress conditions during the middle and late seasons of crop growth.
KW  - canopy cooling effects
KW  - shading cooling
KW  - canopy-air temperature
KW  - energy
KW  - balance
KW  - the Penman-Monteith equation
Y1  - 2022
U6  - https://doi.org/10.3390/w14030319
SN  - 2073-4441
VL  - 14
IS  - 3
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Milles, Alexander Benedikt
A1  - Dammhahn, Melanie
A1  - Jeltsch, Florian
A1  - Schlägel, Ulrike
A1  - Grimm, Volker
T1  - Fluctuations in density-dependent selection drive the evolution of a pace-of-life syndrome within and between populations
JF  - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences
N2  - The pace-of-life syndrome (POLS) hypothesis posits that suites of traits are correlated along a slow-fast continuum owing to life history trade-offs. Despite widespread adoption, environmental conditions driving the emergence of POLS remain unclear. A recently proposed conceptual framework of POLS suggests that a slow-fast continuum should align to fluctuations in density-dependent selection. We tested three key predictions made by this framework with an ecoevolutionary agent-based population model. Selection acted on responsiveness (behavioral trait) to interpatch resource differences and the reproductive investment threshold (life history trait). Across environments with density fluctuations of different magnitudes, we observed the emergence of a common axis of trait covariation between and within populations (i.e., the evolution of a POLS). Slow-type (fast-type) populations with high (low) responsiveness and low (high) reproductive investment threshold were selected at high (low) population densities and less (more) intense and frequent density fluctuations. In support of the predictions, fast-type populations contained a higher degree of variation in traits and were associated with higher intrinsic reproductive rate (r(0)) and higher sensitivity to intraspecific competition (gamma), pointing to a universal trade-off. While our findings support that POLS aligns with density-dependent selection, we discuss possible mechanisms that may lead to alternative evolutionary pathways.
KW  - pace-of-life syndrome
KW  - density dependence
KW  - life history
KW  - trait
KW  - variation
KW  - model
KW  - personality
Y1  - 2022
U6  - https://doi.org/10.1086/718473
SN  - 0003-0147
SN  - 1537-5323
VL  - 199
IS  - 4
SP  - E124
EP  - E139
PB  - Univ. of Chicago Press
CY  - Chicago
ER  - 
TY  - JOUR
A1  - Masigol, Hossein
A1  - Khodaparast, Seyed Akbar
A1  - Mostowfizadeh-Ghalamfarsa, Reza
A1  - Rojas-Jimenez, Keilor
A1  - Woodhouse, Jason Nicholas
A1  - Neubauer, Darshan
A1  - Grossart, Hans-Peter
T1  - Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran
JF  - Aquatic Ecology
N2  - Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.
KW  - Achlya
KW  - Saprolegnia
KW  - aquatic ecosystems
KW  - carbon cycling
KW  - polymer degradation
KW  - Saprolegniaceae
KW  - Achlyaceae
Y1  - 2020
U6  - https://doi.org/10.1007/s10452-019-09745-w
SN  - 1573-5125
SN  - 1386-2588
VL  - 54
IS  - 1
SP  - 323
EP  - 336
PB  - Springer Science
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Stanke, Sandra
A1  - Wenger, Christian
A1  - Bier, Frank Fabian
A1  - Hölzel, Ralph
T1  - AC electrokinetic immobilization of influenza virus
JF  - Electrophoresis : microfluids & proteomics
N2  - The use of alternating current (AC) electrokinetic forces, like dielectrophoresis and AC electroosmosis, as a simple and fast method to immobilize sub-micrometer objects onto nanoelectrode arrays is presented. Due to its medical relevance, the influenza virus is chosen as a model organism. One of the outstanding features is that the immobilization of viral material to the electrodes can be achieved permanently, allowing subsequent handling independently from the electrical setup. Thus, by using merely electric fields, we demonstrate that the need of prior chemical surface modification could become obsolete. The accumulation of viral material over time is observed by fluorescence microscopy. The influences of side effects like electrothermal fluid flow, causing a fluid motion above the electrodes and causing an intensity gradient within the electrode array, are discussed. Due to the improved resolution by combining fluorescence microscopy with deconvolution, it is shown that the viral material is mainly drawn to the electrode edge and to a lesser extent to the electrode surface. Finally, areas of application for this functionalization technique are presented.
KW  - AC electrokinetics
KW  - AC electroosmosis
KW  - dielectrophoresis
KW  - influenza virus
KW  - nanoelectrodes
Y1  - 2022
U6  - https://doi.org/10.1002/elps.202100324
SN  - 0173-0835
SN  - 1522-2683
VL  - 43
IS  - 12
SP  - 1309
EP  - 1321
PB  - Wiley-Blackwell
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Tong, Hao
A1  - Nankar, Amol N.
A1  - Liu, Jintao
A1  - Todorova, Velichka
A1  - Ganeva, Daniela
A1  - Grozeva, Stanislava
A1  - Tringovska, Ivanka
A1  - Pasev, Gancho
A1  - Radeva-Ivanova, Vesela
A1  - Gechev, Tsanko
A1  - Kostova, Dimitrina
A1  - Nikoloski, Zoran
T1  - Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits
JF  - Horticulture research
N2  - Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.
Y1  - 2022
U6  - https://doi.org/10.1093/hr/uhac072
SN  - 2052-7276
VL  - 9
PB  - Oxford Univ. Press
CY  - Cary
ER  - 
TY  - JOUR
A1  - Moradian, Hanieh
A1  - Roch, Toralf
A1  - Lendlein, Andreas
A1  - Gossen, Manfred
T1  - mRNA transfection-induced activation of primary human monocytes and macrophages
BT  - Dependence on carrier system and nucleotide modifcation
JF  - Scientific reports
N2  - Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications.
KW  - sirna transfection
KW  - mediated delivery
KW  - gene delivery
KW  - efficient
KW  - immunogenicity
KW  - lipoplexes
KW  - cells
KW  - therapeutics
KW  - polarization
KW  - pathways
Y1  - 2020
U6  - https://doi.org/10.1038/s41598-020-60506-4
SN  - 2045-2322
VL  - 10
IS  - 1
SP  - 1
EP  - 15
PB  - Springer Nature
CY  - London
ER  - 
TY  - JOUR
A1  - Obbard, Darren J.
A1  - Shi, Mang
A1  - Roberts, Katherine E.
A1  - Longdon, Ben
A1  - Dennis, Alice B.
T1  - A new lineage of segmented RNA viruses infecting animals
JF  - Virus Evolution
N2  - Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
KW  - metagenome
KW  - RNA virus
KW  - dark virus
KW  - arthropod
KW  - RNA interference
Y1  - 2020
U6  - https://doi.org/10.1093/ve/vez061
SN  - 2057-1577
VL  - 6
IS  - 1
SP  - 1
EP  - 10
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Zwaag, Jelle
A1  - Horst, Rob ter
A1  - Blaženović, Ivana
A1  - Stößel, Daniel
A1  - Ratter, Jacqueline
A1  - Worseck, Josephine M.
A1  - Schauer, Nicolas
A1  - Stienstra, Rinke
A1  - Netea, Mihai G.
A1  - Jahn, Dieter
A1  - Pickkers, Peter
A1  - Kox, Matthijs
T1  - Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system
JF  - Metabolites
N2  - We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects.
KW  - metabolomics
KW  - LPS
KW  - endotoxin
KW  - pyruvate
KW  - lactate
KW  - cytokines
KW  - inflammation
KW  - human endotoxemia
KW  - cori cycle
KW  - warburg effect
Y1  - 2020
U6  - https://doi.org/10.3390/metabo10040148
SN  - 2218-1989
VL  - 10
IS  - 4
SP  - 1
EP  - 18
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Amen, Rahma
A1  - Nagel, Rebecca
A1  - Hedt, Maximilian
A1  - Kirschbaum, Frank
A1  - Tiedemann, Ralph
T1  - Morphological differentiation in African weakly electric fish (genus Campylomormyrus) relates to substrate preferences
JF  - Evolutionary Ecology
N2  - Under an ecological speciation scenario, the radiation of African weakly electric fish (genus Campylomormyrus) is caused by an adaptation to different food sources, associated with diversification of the electric organ discharge (EOD). This study experimentally investigates a phenotype-environment correlation to further support this scenario. Our behavioural experiments showed that three sympatric Campylomormyrus species with significantly divergent snout morphology differentially react to variation in substrate structure. While the short snout species (C. tamandua) exhibits preference to sandy substrate, the long snout species (C. rhynchophorus) significantly prefers a stone substrate for feeding. A third species with intermediate snout size (C. compressirostris) does not exhibit any substrate preference. This preference is matched with the observation that long-snouted specimens probe deeper into the stone substrate, presumably enabling them to reach prey more distant to the substrate surface. These findings suggest that the diverse feeding apparatus in the genus Campylomormyrus may have evolved in adaptation to specific microhabitats, i.e., substrate structures where these fish forage. Whether the parallel divergence in EOD is functionally related to this adaptation or solely serves as a prezygotic isolation mechanism remains to be elucidated.
KW  - ecological speciation
KW  - feeding behaviour
KW  - electric fish
KW  - trophic apparatus
KW  - evolutionary ecology
Y1  - 2020
U6  - https://doi.org/10.1007/s10682-020-10043-3
SN  - 0269-7653
SN  - 1573-8477
VL  - 34
IS  - 3
SP  - 427
EP  - 437
PB  - Springer Science
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Sabrowski, Wiebke
A1  - Dreymann, Nico
A1  - Möller, Anja
A1  - Czepluch, Denise
A1  - Albani, Patricia P.
A1  - Theodoridis, Dimitrios
A1  - Menger, Marcus M.
T1  - The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer
JF  - Scientific reports
N2  - The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ss-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ss-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ss-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ss-lactamase 1 expressing Enterobacteriaceae.
Y1  - 2022
U6  - https://doi.org/10.1038/s41598-022-12062-2
SN  - 2045-2322
VL  - 12
IS  - 1
PB  - Macmillan Publishers Limited, part of Springer Nature
CY  - London
ER  - 
TY  - JOUR
A1  - Moreno-Romero, Jordi
A1  - Probst, Aline V.
A1  - Trindade, Inês
A1  - Kalyanikrishna, 
A1  - Engelhorn, Julia
A1  - Farrona, Sara
T1  - Looking At the Past and Heading to the Future
BT  - Meeting Summary of the 6th European Workshop on Plant Chromatin 2019 in Cologne, Germany
JF  - Frontiers in Plant Science
N2  - In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop.
KW  - EWPC2019
KW  - chromatin
KW  - epigenetics
KW  - transcription
KW  - nucleus
Y1  - 2020
U6  - https://doi.org/10.3389/fpls.2019.01795
SN  - 1664-462X
VL  - 10
IS  - 1795
SP  - 1
EP  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Cao, Xianyong
A1  - Tian, Fang
A1  - Andreev, Andrei
A1  - Anderson, Patricia M.
A1  - Lozhkin, Anatoly V.
A1  - Bezrukova, Elena
A1  - Ni, Jian
A1  - Rudaya, Natalia
A1  - Stobbe, Astrid
A1  - Wieczorek, Mareike
A1  - Herzschuh, Ulrike
T1  - A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr
JF  - Earth System Science Data
N2  - Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 % of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 % were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 %) and lake sediments (33 %). Most of the records (83 %) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa.
KW  - Late Quaternary vegetation
KW  - Holocene environmental history
KW  - eastern continental Asia
KW  - plant macrofossil data
KW  - late pleistocene
KW  - paleoenvironmental records
KW  - Verkhoyansk mountains
KW  - climate dynamics
KW  - glacial maximum
KW  - Northern Asia
Y1  - 2020
U6  - https://doi.org/10.5194/essd-12-119-2020
SN  - 1866-3508
SN  - 1866-3516
VL  - 12
IS  - 1
SP  - 119
EP  - 135
PB  - Copernics Publications
CY  - Katlenburg-Lindau
ER  - 
TY  - JOUR
A1  - Kaech, Heidi
A1  - Dennis, Alice B.
A1  - Vorburger, Christoph
T1  - Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa
JF  - BMC genomics
N2  - Background
Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly.

Results
We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402.

Conclusions
Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola.
KW  - Aphis fabae
KW  - Buchnera
KW  - Cost of resistance
KW  - Hamiltonella
KW  - Host-symbiont interaction
KW  - RNA-Seq
KW  - Symbiosis
Y1  - 2021
U6  - https://doi.org/10.1186/s12864-021-07742-8
SN  - 1471-2164
VL  - 22
IS  - 1
PB  - BioMed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Fichtner, Franziska
A1  - Olas, Justyna Jadwiga
A1  - Feil, Regina
A1  - Watanabe, Mutsumi
A1  - Krause, Ursula
A1  - Hoefgen, Rainer
A1  - Stitt, Mark
A1  - Lunn, John Edward
T1  - Functional features of Trehalose-6-Phosphate Synthase 1
BT  - an essential enzyme in Arabidopsis
JF  - The Plant Cell
N2  - Tre6P synthesis by TPS1 is essential for embryogenesis and postembryonic growth in Arabidopsis, and appropriate Suc signaling by Tre6P is dependent on the noncatalytic domains of TPS1. In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P.
KW  - cyanobacterial sucrose-phosphatase
KW  - trehalose 6-phosphate
KW  - vegetative growth
KW  - crystal-structure
KW  - gene-expression
KW  - thaliana
KW  - metabolism
KW  - phosphorylation
KW  - reveals
KW  - proteins
Y1  - 2020
U6  - https://doi.org/10.1105/tpc.19.00837
SN  - 0032-0781
SN  - 1471-9053
VL  - 32
IS  - 6
SP  - 1949
EP  - 1972
PB  - Oxford University Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Weise, Hanna
A1  - Auge, Harald
A1  - Baessler, Cornelia
A1  - Bärlund, Ilona
A1  - Bennett, Elena M.
A1  - Berger, Uta
A1  - Bohn, Friedrich
A1  - Bonn, Aletta
A1  - Borchardt, Dietrich
A1  - Brand, Fridolin
A1  - Jeltsch, Florian
A1  - Joshi, Jasmin Radha
A1  - Grimm, Volker
T1  - Resilience trinity
BT  - safeguarding ecosystem functioning and services across three different time horizons and decision contexts
JF  - Oikos
N2  - Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.
KW  - concepts
KW  - ecosystems
KW  - ecosystem services provisioning
KW  - management
KW  - resilience
Y1  - 2020
U6  - https://doi.org/10.1111/oik.07213
SN  - 0030-1299
SN  - 1600-0706
VL  - 129
IS  - 4
SP  - 445
EP  - 456
PB  - Wiley-Blackwell
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Korniienko, Yevheniia
A1  - Nguyen, Linh
A1  - Baumgartner, Stephanie
A1  - Vater, Marianne
A1  - Tiedemann, Ralph
A1  - Kirschbaum, Frank
T1  - Correction to: Intragenus F1-hybrids of African weakly electric fish (Mormyridae: Campylomormyrus tamandua male x C. compressirostris female) are fertile (vol 206, pg 571, 2020)
JF  - Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology
Y1  - 2021
U6  - https://doi.org/10.1007/s00359-021-01513-2
SN  - 0340-7594
SN  - 1432-1351
VL  - 207
IS  - 6
SP  - 773
EP  - 773
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Haueis, Lisa
A1  - Stech, Marlitt
A1  - Kubick, Stefan
T1  - A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies
JF  - Frontiers in Bioengineering and Biotechnology
N2  - Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, similar to 15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.
KW  - cell-free protein synthesis
KW  - In vitro transcription
KW  - translation
KW  - nanobody
KW  - VHH
KW  - camelid
KW  - CHO cell lysate
Y1  - 2022
U6  - https://doi.org/10.3389/fbioe.2022.896763
SN  - 2296-4185
VL  - 10
PB  - Frontiers Media
CY  - Lausanne
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  - 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  - Angeleska, Angela
A1  - Omranian, Sara
A1  - Nikoloski, Zoran
T1  - Coherent network partitions
BT  - Characterizations with cographs and prime graphs
JF  - Theoretical computer science : the journal of the EATCS
N2  - We continue to study coherent partitions of graphs whereby the vertex set is partitioned into subsets that induce biclique spanned subgraphs. The problem of identifying the minimum number of edges to obtain biclique spanned connected components (CNP), called the coherence number, is NP-hard even on bipartite graphs. Here, we propose a graph transformation geared towards obtaining an O (log n)-approximation algorithm for the CNP on a bipartite graph with n vertices. The transformation is inspired by a new characterization of biclique spanned subgraphs. In addition, we study coherent partitions on prime graphs, and show that finding coherent partitions reduces to the problem of finding coherent partitions in a prime graph. Therefore, these results provide future directions for approximation algorithms for the coherence number of a given graph.
KW  - Graph partitions
KW  - Network clustering
KW  - Cographs
KW  - Coherent partition
KW  - Prime graphs
Y1  - 2021
U6  - https://doi.org/10.1016/j.tcs.2021.10.002
SN  - 0304-3975
VL  - 894
SP  - 3
EP  - 11
PB  - Elsevier
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Andersson, Matilda L.
A1  - Scharnweber, Inga Kristin
A1  - Eklöv, Peter
T1  - The interaction between metabolic rate, habitat choice, and resource use in a polymorphic freshwater species
JF  - Ecology and evolution
N2  - Resource polymorphism is common across taxa and can result in alternate ecotypes with specific morphologies, feeding modes, and behaviors that increase performance in a specific habitat. This can result in high intraspecific variation in the expression of specific traits and the extent to which these traits are correlated within a single population. Although metabolic rate influences resource acquisition and the overall pace of life of individuals it is not clear how metabolic rate interacts with the larger suite of traits to ultimately determine individual fitness. We examined the relationship between metabolic rates and the major differences (habitat use, morphology, and resource use) between littoral and pelagic ecotypes of European perch (Perca fluviatilis) from a single lake in Central Sweden. Standard metabolic rate (SMR) was significantly higher in pelagic perch but did not correlate with resource use or morphology. Maximum metabolic rate (MMR) was not correlated with any of our explanatory variables or with SMR. Aerobic scope (AS) showed the same pattern as SMR, differing across habitats, but contrary to expectations, was lower in pelagic perch. This study helps to establish a framework for future experiments further exploring the drivers of intraspecific differences in metabolism. In addition, since metabolic rates scale with temperature and determine predator energy requirements, our observed differences in SMR across habitats will help determine ecotype-specific vulnerabilities to climate change and differences in top-down predation pressure across habitats.
KW  - intraspecific variation
KW  - metabolic rate
KW  - morphometrics
KW  - Perca
KW  - fluviatilis
KW  - plasticity
KW  - resource use
KW  - respirometry
KW  - stable isotopes
Y1  - 2022
U6  - https://doi.org/10.1002/ece3.9129
SN  - 2045-7758
VL  - 12
IS  - 8
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Yan, Jiawei
A1  - Frøkjær, Emil Egede
A1  - Engelbrekt, Christian
A1  - Leimkühler, Silke
A1  - Ulstrup, Jens
A1  - Wollenberger, Ulla
A1  - Xiao, Xinxin
A1  - Zhang, Jingdong
T1  - Voltammetry and single-molecule in situ scanning tunnelling microscopy of the redox metalloenzyme human sulfite oxidase
JF  - ChemElectroChem
N2  - Human sulfite oxidase (hSO) is a homodimeric two-domain enzyme central in the biological sulfur cycle. A pyranopterin molybdenum cofactor (Moco) is the catalytic site and a heme b(5) group located in the N-terminal domain. The two domains are connected by a flexible linker region. Electrons produced at the Moco in sulfite oxidation, are relayed via heme b(5) to electron acceptors or an electrode surface. Inter-domain conformational changes between an open and a closed enzyme conformation, allowing "gated" electron transfer has been suggested. We first recorded cyclic voltammetry (CV) of hSO on single-crystal Au(111)-electrode surfaces modified by self-assembled monolayers (SAMs) both of a short rigid thiol, cysteamine and of a longer structurally flexible thiol, omega-amino-octanethiol (AOT). hSO on cysteamine SAMs displays a well-defined pair of voltammetric peaks around -0.207 V vs. SCE in the absence of sulfite substrate, but no electrocatalysis. hSO on AOT SAMs displays well-defined electrocatalysis, but only "fair" quality voltammetry in the absence of sulfite. We recorded next in situ scanning tunnelling spectroscopy (STS) of hSO on AOT modified Au(111)-electrodes, disclosing, a 2-5 % surface coverage of strong molecular scale contrasts, assigned to single hSO molecules, notably with no contrast difference in the absence and presence of sulfite. In situ STS corroborated this observation with a sigmoidal tunnelling current/overpotential correlation.
KW  - cyclic voltammetry
KW  - human sulfite oxidase
KW  - in  situ scanning
KW  - tunnelling spectroscopy
KW  - self-assembled molecular monolayers
KW  - single-crystal gold electrodes
Y1  - 2021
U6  - https://doi.org/10.1002/celc.202001258
SN  - 2196-0216
VL  - 8
IS  - 1
SP  - 164
EP  - 171
PB  - Wiley-VCH
CY  - Weinheim
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  - Scheffler, Christiane
A1  - Hermanussen, Michael
T1  - Reply to the letter titled:  "Pathologizing normal height or identifying chronic malnutrition: Public health concerns of calling stunting normal" / by Nafis Faizi,  Mohd Yasir Zubair and Fazeelah Tasleem'. -  New York, NY [u.a.] : Wiley Interscience. - 2022. - (American Journal of Human Biology : the Official Journal of the Human Biology Council, 16 Feb 2022. - 34(2022) 5 ). - https://doi.org/10.1002/ajhb.23735
JF  - American journal of human biology : the official journal of the Human Biology Association
Y1  - 2022
U6  - https://doi.org/10.1002/ajhb.23741
SN  - 1520-6300
VL  - 34
IS  - 5
PB  - Wiley Interscience
CY  - New York, NY [u.a.]
ER  - 
TY  - JOUR
A1  - Berg-Mohnicke, Michael
A1  - Nendel, Claas
T1  - A case for object capabilities as the foundation of a distributed environmental model and simulation infrastructure
JF  - Environmental modelling & software with environment data news
N2  - With the advent of increasingly powerful computational architectures, scientists use these possibilities to create simulations of ever-increasing size and complexity. Large-scale simulations of environmental systems require huge amounts of resources. Managing these in an operational way becomes increasingly complex and difficult to handle for individual scientists. State-of-the-art simulation infrastructures usually provide the necessary re-sources in a centralised setup, which often results in an all-or-nothing choice for the user. Here, we outline an alternative approach to handling this complexity, while rendering the use of high-performance hardware and large datasets still possible. It retains a number of desirable properties: (i) a decentralised structure, (ii) easy sharing of resources to promote collaboration and (iii) secure access to everything, including natural delegation of authority across levels and system boundaries. We show that the object capability paradigm will cover these issues, and present the first steps towards developing a simulation infrastructure based on these principles.
KW  - Cap'n proto
KW  - Scientific collaboration
KW  - Co -development
KW  - Communication
KW  - protocol
KW  - Object capability
Y1  - 2022
U6  - https://doi.org/10.1016/j.envsoft.2022.105471
SN  - 1364-8152
SN  - 1873-6726
VL  - 156
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Çabuk, Uğur
A1  - Ünlü, Ercan Selçuk
T1  - A combined de novo assembly approach increases the quality of prokaryotic draft genomes
JF  - Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology
N2  - Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.
KW  - De novo assembly
KW  - Prokaryotes
KW  - Bacteria
KW  - NGS
KW  - Short reads
KW  - Draft genome
Y1  - 2022
U6  - https://doi.org/10.1007/s12223-022-00980-7
SN  - 0015-5632
SN  - 1874-9356
VL  - 67
SP  - 801
EP  - 810
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Olimi, Expedito
A1  - Kusstatscher, Peter
A1  - Wicaksono, Wisnu Adi
A1  - Abdelfattah, Ahmed
A1  - Cernava, Tomislav
A1  - Berg, Gabriele
T1  - Insights into the microbiome assembly during different growth stages and storage of strawberry plants
JF  - Environmental microbiome
N2  - Background: Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. <br /> Results: Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10(7)-10(10) marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. <br /> Conclusion: Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.
KW  - Fragaria x ananassa
KW  - Microbiome assembly
KW  - Fruit pathogens
KW  - Bacterial
KW  - communities
KW  - Fungal communities
KW  - Amplicon sequencing
KW  - CLSM
Y1  - 2022
U6  - https://doi.org/10.1186/s40793-022-00415-3
SN  - 2524-6372
VL  - 17
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Scheffler, Christiane
A1  - Hermanussen, Michael
A1  - Rogol, Alan D.
T1  - Stunting
BT  - historical lessons that catch-up growth tells us for mapping growth restoration
JF  - Archives of disease in childhood : a peer review journal for health professionals and researchers covering conception to adolescence
Y1  - 2020
U6  - https://doi.org/10.1136/archdischild-2020-319240
SN  - 0003-9888
SN  - 1468-2044
VL  - 106
IS  - 8
SP  - 819
EP  - 820
PB  - BMJ Publishing Group
CY  - London
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  - Weyrich, Alexandra
A1  - Guerrero-Altamirano, Tania P.
A1  - Yasar, Selma
A1  - Czirjak, Gábor-Árpád
A1  - Wachter, Bettina
A1  - Fickel, Jörns
T1  - First Steps towards the development of epigenetic biomarkers in female cheetahs (Acinonyx jubatus)
JF  - Life : open access journal
N2  - Free-ranging cheetahs (Acinonyx jubatus) are generally healthy, whereas cheetahs under human care, such as those in zoological gardens, suffer from ill-defined infectious and degenerative pathologies. These differences are only partially explained by husbandry management programs because both groups share low genetic diversity. However, mounting evidence suggests that physiological differences between populations in different environments can be tracked down to differences in epigenetic signatures. Here, we identified differentially methylated regions (DMRs) between free-ranging cheetahs and conspecifics in zoological gardens and prospect putative links to pathways relevant to immunity, energy balance and homeostasis. Comparing epigenomic DNA methylation profiles obtained from peripheral blood mononuclear cells (PBMCs) from eight free-ranging female cheetahs from Namibia and seven female cheetahs living in zoological gardens within Europe, we identified DMRs of which 22 were hypermethylated and 23 hypomethylated. Hypermethylated regions in cheetahs under human care were located in the promoter region of a gene involved in host-pathogen interactions (KLC1) and in an intron of a transcription factor relevant for the development of pancreatic beta-cells, liver, and kidney (GLIS3). The most canonical mechanism of DNA methylation in promoter regions is assumed to repress gene transcription. Taken together, this could indicate that hypermethylation at the promoter region of KLC1 is involved in the reduced immunity in cheetahs under human care. This approach can be generalized to characterize DNA methylation profiles in larger cheetah populations under human care with a more granular longitudinal data collection, which, in the future, could be used to monitor the early onset of pathologies, and ultimately translate into the development of biomarkers with prophylactic and/or therapeutic potential.
KW  - animals under human care
KW  - captivity
KW  - carnivore
KW  - DNA methylation;
KW  - felidae
KW  - free-ranging
KW  - wildlife
Y1  - 2022
U6  - https://doi.org/10.3390/life12060920
SN  - 2075-1729
VL  - 12
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Lischeid, Gunnar
A1  - Webber, Heidi
A1  - Sommer, Michael
A1  - Nendel, Claas
A1  - Ewert, Frank
T1  - Machine learning in crop yield modelling
BT  - A powerful tool, but no surrogate for science
JF  - Agricultural and forest meteorology
N2  - Provisioning a sufficient stable source of food requires sound knowledge about current and upcoming threats to agricultural production. To that end machine learning approaches were used to identify the prevailing climatic and soil hydrological drivers of spatial and temporal yield variability of four crops, comprising 40 years yield data each from 351 counties in Germany. Effects of progress in agricultural management and breeding were subtracted from the data prior the machine learning modelling by fitting smooth non-linear trends to the 95th percentiles of observed yield data. An extensive feature selection approach was followed then to identify the most relevant predictors out of a large set of candidate predictors, comprising various soil and meteorological data. Particular emphasis was placed on studying the uniqueness of identified key predictors. Random Forest and Support Vector Machine models yielded similar although not identical results, capturing between 50% and 70% of the spatial and temporal variance of silage maize, winter barley, winter rapeseed and winter wheat yield. Equally good performance could be achieved with different sets of predictors. Thus identification of the most reliable models could not be based on the outcome of the model study only but required expert's judgement. Relationships between drivers and response often exhibited optimum curves, especially for summer air temperature and precipitation. In contrast, soil moisture clearly proved less relevant compared to meteorological drivers. In view of the expected climate change both excess precipitation and the excess heat effect deserve more attention in breeding as well as in crop modelling.
KW  - Crop modelling
KW  - Machine learning
KW  - Random forests
KW  - Support vector
KW  - machine
KW  - Feature selection
KW  - Equivocality
Y1  - 2021
U6  - https://doi.org/10.1016/j.agrformet.2021.108698
SN  - 0168-1923
SN  - 1873-2240
VL  - 312
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Agarwal, Saloni
A1  - Warmt, Christian
A1  - Henkel, Jörg
A1  - Schrick, Livia
A1  - Nitsche, Andreas
A1  - Bier, Frank Fabian
T1  - Lateral flow-based nucleic acid detection of SARS-CoV-2 using enzymatic incorporation of biotin-labeled dUTP for POCT use
JF  - Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica
N2  - The degree of detrimental effects inflicted on mankind by the COVID-19 pandemic increased the need to develop ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable) POCT (point of care testing) to overcome the current and any future pandemics. Much effort in research and development is currently advancing the progress to overcome the diagnostic pressure built up by emerging new pathogens. LAMP (loop-mediated isothermal amplification) is a well-researched isothermal technique for specific nucleic acid amplification which can be combined with a highly sensitive immunochromatographic readout via lateral flow assays (LFA). Here we discuss LAMP-LFA robustness, sensitivity, and specificity for SARS-CoV-2 N-gene detection in cDNA and clinical swab-extracted RNA samples. The LFA readout is designed to produce highly specific results by incorporation of biotin and FITC labels to 11-dUTP and LF (loop forming forward) primer, respectively. The LAMP-LFA assay was established using cDNA for N-gene with an accuracy of 95.65%. To validate the study, 82 SARS-CoV-2-positive RNA samples were tested. Reverse transcriptase (RT)-LAMP-LFA was positive for the RNA samples with an accuracy of 81.66%; SARS-CoV-2 viral RNA was detected by RT-LAMP-LFA for as low as CT-33. Our method reduced the detection time to 15 min and indicates therefore that RT-LAMP in combination with LFA represents a promising nucleic acid biosensing POCT platform that combines with smartphone based semi-quantitative data analysis.
KW  - Point of care testing (POCT)
KW  - Lateral flow assay (LFA)
KW  - COVID-19
KW  - Reverse transcription loop-mediated isothermal amplification (RT-LAMP);
KW  - SARS-CoV-2 N-gene
Y1  - 2022
U6  - https://doi.org/10.1007/s00216-022-03880-4
SN  - 1618-2642
SN  - 1618-2650
VL  - 414
IS  - 10
SP  - 3177
EP  - 3186
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Laun, Konstantin
A1  - Duffus, Benjamin R.
A1  - Wahlefeld, Stefan
A1  - Katz, Sagie
A1  - Belger, Dennis Heinz
A1  - Hildebrandt, Peter
A1  - Mroginski, Maria Andrea
A1  - Leimkühler, Silke
A1  - Zebger, Ingo
T1  - Infrared spectroscopy flucidates the inhibitor binding sites in a metal-dependent formate dehydrogenase
JF  - Chemistry - a European journal
N2  - Biological carbon dioxide (CO2) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.
KW  - CO2 reduction
KW  - DFT
KW  - formate oxidation
KW  - inhibition kinetics
KW  - IR
KW  - spectroscopy
KW  - molybdoenzyme
Y1  - 2022
U6  - https://doi.org/10.1002/chem.202201091
SN  - 0947-6539
SN  - 1521-3765
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Gryzik, Stefanie
A1  - Hoang, Yen
A1  - Lischke, Timo
A1  - Mohr, Elodie
A1  - Venzke, Melanie
A1  - Kadner, Isabelle
A1  - Pötzsch, Josephine
A1  - Groth, Detlef
A1  - Radbruch, Andreas
A1  - Hutloff, Andreas
A1  - Baumgrass, Ria
T1  - Identification of a super-functional Tfh-like subpopulation in murine lupus by pattern perception
JF  - eLife
N2  - Dysregulated cytokine expression by T cells plays a pivotal role in the pathogenesis of autoimmune diseases. However, the identification of the corresponding pathogenic subpopulations is a challenge, since a distinction between physiological variation and a new quality in the expression of protein markers requires combinatorial evaluation. Here, we were able to identify a super-functional follicular helper T cell (Tfh)-like subpopulation in lupus-prone NZBxW mice with our binning approach "pattern recognition of immune cells (PRI)". PRI uncovered a subpopulation of IL-21(+) IFN-gamma(high) PD-1(low) CD40L(high) CXCR5(-) Bcl-6(-) T cells specifically expanded in diseased mice. In addition, these cells express high levels of TNF-alpha and IL-2, and provide B cell help for IgG production in an IL-21 and CD40L dependent manner. This super-functional T cell subset might be a superior driver of autoimmune processes due to a polyfunctional and high cytokine expression combined with Tfh-like properties.
Y1  - 2020
U6  - https://doi.org/10.7554/eLife.53226
SN  - 2050-084X
VL  - 9
PB  - eLife Sciences Publications
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Cordeiro, Andre M.
A1  - Andrade, Luis
A1  - Monteiro, Catarina C.
A1  - Leitao, Guilherme
A1  - Wigge, Philip Anthony
A1  - Saibo, Nelson J. M.
T1  - Phytochrome-interacting factors
BT  - a promising tool to improve crop productivity
JF  - Journal of experimental botany
N2  - Review exploring the regulation of PHYTOCHROME-INTERACTING FACTORS by light, their role in abiotic stress tolerance and plant architecture, and their influence on crop productivity. 
Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.
KW  - Cold
KW  - drought
KW  - grain size
KW  - heat
KW  - light signaling
KW  - phytochrome
KW  - PIF
KW  - plant architecture
KW  - plant breeding
KW  - plant yield
KW  - salinity
Y1  - 2022
U6  - https://doi.org/10.1093/jxb/erac142
SN  - 0022-0957
SN  - 1460-2431
VL  - 73
IS  - 12
SP  - 3881
EP  - 3897
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Aichner, Bernhard
A1  - Dubbert, David
A1  - Kiel, Christine
A1  - Kohnert, Katrin
A1  - Ogashawara, Igor
A1  - Jechow, Andreas
A1  - Harpenslager, Sarah-Faye
A1  - Hölker, Franz
A1  - Nejstgaard, Jens Christian
A1  - Grossart, Hans-Peter
A1  - Singer, Gabriel
A1  - Wollrab, Sabine
A1  - Berger, Stella Angela
T1  - Spatial and seasonal patterns of water isotopes in northeastern German lakes
JF  - Earth system science data : ESSD
N2  - Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.
Y1  - 2022
U6  - https://doi.org/10.5194/essd-14-1857-2022
SN  - 1866-3508
SN  - 1866-3516
VL  - 14
IS  - 4
SP  - 1857
EP  - 1867
PB  - Copernicus
CY  - Göttingen
ER  - 
TY  - JOUR
A1  - Prüfer, Mareike
A1  - Wenger, Christian
A1  - Bier, Frank Fabian
A1  - Laux, Eva-Maria
A1  - Hölzel, Ralph
T1  - Activity of AC electrokinetically immobilized horseradish peroxidase
JF  - Electrophoresis : microfluidics, nanoanalysis & proteomics
N2  - Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H2O2 to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.
KW  - AC electrokinetics
KW  - dielectrophoresis
KW  - enzyme activity
KW  - immobilization;
KW  - nanoelectrodes
Y1  - 2022
U6  - https://doi.org/10.1002/elps.202200073
SN  - 0173-0835
SN  - 1522-2683
SP  - 1920
EP  - 1933
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Kiemel, Katrin
A1  - De Cahsan, Binia
A1  - Paraskevopoulou, Sofia
A1  - Weithoff, Guntram
A1  - Tiedemann, Ralph
T1  - Mitochondrial genomes of the freshwater monogonont rotifer Brachionus fernandoi and of two additional B. calyciflorus sensu stricto lineages from Germany and the USA (Rotifera, Brachionidae)
JF  - Mitochondrial DNA. Part B-Resources
N2  - The Brachionus calyciflorus species complex was recently subdivided into four species, but genetic resources to resolve phylogenetic relationships within this complex are still lacking. We provide two complete mitochondrial (mt) genomes from B. calyciflorus sensu stricto (Germany, USA) and the mt coding sequences (cds) from a German B. fernandoi. Phylogenetic analysis placed our B. calyciflorus sensu stricto strains close to the published genomes of B. calyciflorus, forming the putative sister species to B. fernandoi. Global representatives of B. calyciflorus sensu stricto (i.e. Europe, USA, and China) are genetically closer related to each other than to B. fernandoi (average pairwise nucleotide diversity 0.079 intraspecific vs. 0.254 interspecific).
KW  - Mitogenome
KW  - cryptic species
KW  - Brachionus calyciflorus s
KW  - Brachionus
KW  - fernandoi
KW  - monogonont rotifer
Y1  - 2022
U6  - https://doi.org/10.1080/23802359.2022.2060765
SN  - 2380-2359
VL  - 7
IS  - 4
SP  - 646
EP  - 648
PB  - Routledge, Taylor & Francis Group
CY  - Abingdon
ER  - 
TY  - JOUR
A1  - Kernecker, Maria
A1  - Fienitz, Meike
A1  - Nendel, Claas
A1  - Paetzig, Marlene
A1  - Walzl, Karin Pirhofer
A1  - Raatz, Larissa
A1  - Schmidt, Martin
A1  - Wulf, Monika
A1  - Zscheischler, Jana
T1  - Transition zones across agricultural field boundaries for integrated landscape research and management of biodiversity and yields
JF  - Ecological solutions and evidence
N2  - Biodiversity conservation and agricultural production have been largely framed as separate goals for landscapes in the discourse on land use. Although there is an increasing tendency to move away from this dichotomy in theory, the tendency is perpetuated by the spatially explicit approaches used in research and management practice. Transition zones (TZ) have previously been defined as areas where two adjacent fields or patches interact, and so they occur abundantly throughout agricultural landscapes. Biodiversity patterns in TZ have been extensively studied, but their relationship to yield patterns and social-ecological dimensions has been largely neglected. Focusing on European, temperate agricultural landscapes, we outline three areas of research and management that together demonstrate how TZ might be used to facilitate an integrated landscape approach: (i) plant and animal species' use and response to boundaries and the resulting effects on yield, for a deeper understanding of how landscape structure shapes quantity and quality of TZ; (ii) local knowledge on field or patch-level management and its interactions with biodiversity and yield in TZ, and (iii) conflict prevention and collaborative management across land-use boundaries.
KW  - ecotones
KW  - field boundaries
KW  - functional traits
KW  - landscape complexity;
KW  - land-use conflicts
KW  - local knowledge
KW  - spillovers
Y1  - 2022
U6  - https://doi.org/10.1002/2688-8319.12122
SN  - 2688-8319
VL  - 3
IS  - 1
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Palma-Vera, Sergio E.
A1  - Reyer, Henry
A1  - Langhammer, Martina
A1  - Reinsch, Norbert
A1  - Derezanin, Lorena
A1  - Fickel, Jörns
A1  - Qanbari, Saber
A1  - Weitzel, Joachim M.
A1  - Franzenburg, Soeren
A1  - Hemmrich-Stanisak, Georg
A1  - Schön, Jennifer
T1  - Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits
JF  - BMC Biology
N2  - Background
Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits. 

Results
Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits. 

Conclusions
The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.
KW  - Mouse
KW  - Fertility
KW  - Body mass
KW  - Endurance
KW  - Selective breeding
KW  - Genetic
KW  - drift
KW  - Bottleneck
KW  - Whole genome sequencing
KW  - Single-nucleotide
KW  - polymorphism
KW  - Structural variation
Y1  - 2022
U6  - https://doi.org/10.1186/s12915-022-01248-9
SN  - 1741-7007
VL  - 20
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Wiebke, Ullmann
T1  - Warum hat Bayern mehr Feldhasen als Brandenburg?
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 46
EP  - 47
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Teckentrup, Lisa
T1  - Gefahr an jeder Ecke
BT  - wie die Landschaftsstruktur die Verteilung von Beutetieren beeinflusst
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 54
EP  - 55
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Schäfer, Merlin
T1  - Mut macht einsam
BT  - der Einfluss von Persönlichkeit auf das Zusammenleben von Tieren
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 52
EP  - 53
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Kowalski, Gabriele Joanna
T1  - Auf dem Sprung
BT  - wie bewegen sich Tiere durch die Landschaft?
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 41
EP  - 42
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Raatz, Larissa
T1  - Wirtschaften in einer reich strukturierten Landschaft - geht das ?
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 32
EP  - 33
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Lozada Gobilard, Sissi Donna
T1  - Können auch Pflanzen zwischen den Söllen "wandern"
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 30
EP  - 31
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Litwin, Magdalena
A1  - Colangeli, Pierluigi
T1  - Wie und wohin reisen Wasserflöhe?
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 28
EP  - 29
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Maaß, Stefanie
T1  - Blick in die Zukunft
BT  - wie werden sich Pflanzengemeinschaften in Brandenburg verändern?
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 24
EP  - 25
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Weiß, Lina
A1  - Wulff, Monika
T1  - Veränderung der Landnutzung in der nord-westlichen Uckermark von 1780 bis heute
JF  - Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Y1  - 2019
SP  - 20
EP  - 21
PB  - oerding print GmbH
CY  - Braunschweig
ER  - 
TY  - JOUR
A1  - Bapolisi, Alain Murhimalika
A1  - Kielb, Patrycja
A1  - Bekir, Marek
A1  - Lehnen, Anne-Catherine
A1  - Radon, Christin
A1  - Laroque, Sophie
A1  - Wendler, Petra
A1  - Müller-Werkmeister, Henrike
A1  - Hartlieb, Matthias
T1  - Antimicrobial polymers of linear and bottlebrush architecture
BT  - Probing the membrane interaction and physicochemical properties
JF  - Macromolecular rapid communications : publishing the newsletters of the European Polymer Federation
N2  - Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focus on random linear copolymers, the development of APs with advanced architectures proves to be more potent. It is recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using various spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive, and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking Escheria coli membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.
KW  - antimicrobial polymers
KW  - bottlebrush copolymers
KW  - liposomes
KW  - membrane
KW  - interactions
KW  - quartz crystal microbalance
Y1  - 2022
U6  - https://doi.org/10.1002/marc.202200288
SN  - 1521-3927
SN  - 1022-1336
VL  - 43
IS  - 19
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Azcorra, Hugo
A1  - Dickinson, Federico
A1  - Mendez-Dominguez, Nina
A1  - Mumm, Rebekka
A1  - Valentín, Graciela
T1  - Development of birthweight and length for gestational age and sex references in Yucatan, Mexico
JF  - American journal of human biology : the official journal of the Human Biology Council
N2  - Objective To develop sex- and gestational age specific reference percentiles and curves for birth weight and length for Yucatec neonates using data from birth registers of infants born during 2015-2019. Material and methods Observational, descriptive, epidemiologic study in a 5-year period including every registered birth in the state of Yucatan, Mexico using birth registries. A total of 158 432 live, physically healthy singletons (76 442 females and 81 990 males) between 25 and 42 weeks of gestation were included in the analysis. We used the LMS method to construct smoothed reference centiles (3rd, 10th, 25th, 50th, 75th, 95th, and 97th) and curves for males and females separately. Results Mean maternal age was 26 (SD = 6.22) years. Fifty-two percent of births occurred by vaginal delivery, 37% were firstborn and similar proportions were second (33%) and third or more (30%) born. 5.5% of newborns included in the references corresponds to neonates born before 37 weeks of gestation (5.9% boys and 5.1% girls). In both sexes, the percentage of infants with a birthweight less than 2500 g was 6.7%. The birthweight at the 50th percentile for males and females at 40 weeks of gestation in this cohort was 3256 and 3167 g, respectively, and the corresponding values for birth length were 50.23 and 49.84 cm (mean differences between sexes: 89 g and 0.40 cm, respectively). Conclusion The reference percentile and curves developed in this study are useful for research purposes and can help health practitioners to assess the biological status of infants born in Yucatan.
Y1  - 2022
U6  - https://doi.org/10.1002/ajhb.23732
SN  - 1042-0533
SN  - 1520-6300
VL  - 34
IS  - 6
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Ehrlich, Elias
A1  - Thygesen, Uffe Høgsbro
A1  - Kiørboe, Thomas
T1  - Evolution of toxins as a public good in phytoplankton
JF  - Proceedings of the Royal Society of London : B, Biological sciences
N2  - Toxic phytoplankton blooms have increased in many waterbodies worldwide with well-known negative impacts on human health, fisheries and ecosystems. However, why and how phytoplankton evolved toxin production is still a puzzling question, given that the producer that pays the costs often shares the benefit with other competing algae and thus provides toxins as a 'public good' (e.g. damaging a common competitor or predator). Furthermore, blooming phytoplankton species often show a high intraspecific variation in toxicity and we lack an understanding of what drives the dynamics of coexisting toxic and non-toxic genotypes. Here, by using an individual-based two-dimensional model, we show that small-scale patchiness of phytoplankton strains caused by demography can explain toxin evolution in phytoplankton with low motility and the maintenance of genetic diversity within their blooms. This patchiness vanishes for phytoplankton with high diffusive motility, suggesting different evolutionary pathways for different phytoplankton groups. In conclusion, our study reveals that small-scale spatial heterogeneity, generated by cell division and counteracted by diffusive cell motility and turbulence, can crucially affect toxin evolution and eco-evolutionary dynamics in toxic phytoplankton species. This contributes to a better understanding of conditions favouring toxin production and the evolution of public goods in asexually reproducing organisms in general.
KW  - toxic algal blooms
KW  - evolution of cooperation
KW  - coexistence
KW  - patchiness in
KW  - phytoplankton
KW  - eco-evolutionary feedback
KW  - spatial pattern formation
Y1  - 2022
U6  - https://doi.org/10.1098/rspb.2022.0393
SN  - 0962-8452
SN  - 1471-2954
VL  - 289
IS  - 1977
PB  - Royal Society
CY  - London
ER  - 
TY  - JOUR
A1  - Eccard, Jana
A1  - Mendes Ferreira, Clara
A1  - Peredo Arce, Andres
A1  - Dammhahn, Melanie
T1  - Top-down effects of foraging decisions on local, landscape and regional biodiversity of resources (DivGUD)
JF  - Ecology letters
N2  - Foraging by consumers acts as a biotic filtering mechanism for biodiversity at the trophic level of resources. Variation in foraging behaviour has cascading effects on abundance, diversity, and functional trait composition of the community of resource species. Here we propose diversity at giving-up density (DivGUD), i.e. when foragers quit exploiting a patch, as a novel concept and simple measure quantifying cascading effects at multiple spatial scales. In experimental landscapes with an assemblage of plant seeds, patch residency of wild rodents decreased local alpha-DivGUD (via elevated mortality of species with large seeds) and regional gamma-DivGUD, while dissimilarity among patches in a landscape (beta-DivGUD) increased. By linking theories of adaptive foraging behaviour with community ecology, DivGUD allows to investigate cascading indirect predation effects, e.g. the ecology-of-fear framework, feedbacks between functional trait composition of resource species and consumer communities, and effects of inter-individual differences among foragers on the biodiversity of resource communities.
KW  - biodiversity
KW  - cascading effects
KW  - foraging behaviour
KW  - functional traits
KW  - giving-up density
KW  - landscape of fear
KW  - optimal foraging
KW  - patch use
Y1  - 2022
U6  - https://doi.org/10.1111/ele.13901
SN  - 1461-0248
VL  - 25
IS  - 1
SP  - 3
EP  - 16
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Perrella, Giorgio
A1  - Bäurle, Isabel
A1  - van Zanten, Martijn
T1  - Epigenetic regulation of thermomorphogenesis and heat stress tolerance
JF  - New phytologist : international journal of plant science
N2  - Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.
KW  - chromatin remodelling
KW  - elevated temperature
KW  - epigenetics
KW  - heat stress
KW  - histone modification
KW  - memory
KW  - temperature response
KW  - thermomorphogenesis
Y1  - 2022
U6  - https://doi.org/10.1111/nph.17970
SN  - 0028-646X
SN  - 1469-8137
VL  - 234
IS  - 4
SP  - 1144
EP  - 1160
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Berg, Gabriele
A1  - Cernava, Tomislav
T1  - The plant microbiota signature of the Anthropocene as a challenge for microbiome research
JF  - Microbiome
N2  - Background: 
One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.

Results: 
Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies. 

Conclusions: 
Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health.
Y1  - 2022
U6  - https://doi.org/10.1186/s40168-021-01224-5
SN  - 2049-2618
VL  - 10
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Stripp, Sven T.
A1  - Duffus, Benjamin R.
A1  - Fourmond, Vincent
A1  - Leger, Christophe
A1  - Leimkühler, Silke
A1  - Hirota, Shun
A1  - Hu, Yilin
A1  - Jasniewski, Andrew
A1  - Ogata, Hideaki
A1  - Ribbe, Markus W.
T1  - Second and outer coordination sphere effects in nitrogenase, hydrogenase, formate dehydrogenase, and CO dehydrogenase
JF  - Chemical reviews : CR
N2  - Gases like H-2, N-2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N-2, CO2, and CO and the production of H-2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N-2 fixation by nitrogenase and H-2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
Y1  - 2022
U6  - https://doi.org/10.1021/acs.chemrev.1c00914
SN  - 0009-2665
SN  - 1520-6890
VL  - 122
IS  - 14
SP  - 11900
EP  - 11973
PB  - American Chemical Society
CY  - Washington, DC
ER  - 
TY  - JOUR
A1  - Delker, Carolin
A1  - Quint, Marcel
A1  - Wigge, Philip Anthony
T1  - Recent advances in understanding thermomorphogenesis signaling
JF  - Current opinion in plant biology
N2  - Plants show remarkable phenotypic plasticity and are able to adjust their morphology and development to diverse environmental stimuli. Morphological acclimation responses to elevated ambient temperatures are collectively termed thermomorphogenesis. In Arabidopsis thaliana, morphological changes are coordinated to a large extent by the transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), which in turn is regulated by several thermosensing mechanisms and modulators. Here, we review recent advances in the identification of factors that regulate thermomorphogenesis of Arabidopsis seedlings by affecting PIF4 expression and PIF4 activity. We summarize newly identified thermosensing mechanisms and highlight work on the emerging topic of organ- and tissue-specificity in the regulation of thermomorphogenesis.
Y1  - 2022
U6  - https://doi.org/10.1016/j.pbi.2022.102231
SN  - 1369-5266
SN  - 1879-0356
VL  - 68
PB  - Elsevier
CY  - London
ER  - 
TY  - JOUR
A1  - Ristow, Michael
A1  - Panitsa, Maria
A1  - Meyer, Stefan
A1  - Bergmeier, Erwin
T1  - Factors of detection deficits in vascular plant inventories - an island case study
JF  - Diversity
N2  - The degree of completeness of large-scale floristic inventories is often difficult to judge. We compared prior vascular plant species inventories of the Mediterranean island of Limnos (North Aegean, Greece) with 231 recent records from 2016-2021. Together with the recent records, the known number of vascular plant species on the island is 960 native taxa, 63 established neophytes, and 27 species of as yet casual status for a total of 1050 taxa. We looked at a number of traits (plant family, size, flower color, perceptibility, habitat, reproduction period, rarity, and status) to investigate whether they were overrepresented in the dataset of the newly found taxa. Overrepresentation was found in some plant families (e.g., Poaceae and Chenopodiaceae) and for traits such as hydrophytic life form, unobtrusive flower color, coastal as well as agricultural and ruderal habitats, and late (summer/autumn) reproduction period. Apart from the well-known fact of esthetic bias, we found evidence for ecological and perceptibility biases. Plant species inventories based on prior piecemeal collated data should focus on regionally specific species groups and underrepresented and rare habitats.
KW  - Aegean flora
KW  - floristic survey
KW  - Mediterranean island
KW  - perceptibility
KW  - habitat
KW  - plant traits
KW  - rarity
Y1  - 2022
U6  - https://doi.org/10.3390/d14040303
SN  - 1424-2818
VL  - 14
IS  - 4
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Scharf, Christina
A1  - Weinelt, Ferdinand Anton
A1  - Schroeder, Ines
A1  - Paal, Michael
A1  - Weigand, Michael
A1  - Zoller, Michael
A1  - Irlbeck, Michael
A1  - Kloft, Charlotte
A1  - Briegel, Josef
A1  - Liebchen, Uwe
T1  - Does the cytokine adsorber CytoSorb (R) reduce vancomycin exposure in critically ill patients with sepsis or septic shock?
BT  - a prospective observational study
JF  - Annals of intensive care
N2  - Background: 
Hemadsorption of cytokines is used in critically ill patients with sepsis or septic shock. Concerns have been raised that the cytokine adsorber CytoSorb (R) unintentionally adsorbs vancomycin. This study aimed to quantify vancomycin elimination by CytoSorb (R) . 

Methods: 
Critically ill patients with sepsis or septic shock receiving continuous renal replacement therapy and CytoSorb (R) treatment during a prospective observational study were included in the analysis. Vancomycin pharmacokinetics was characterized using population pharmacokinetic modeling. Adsorption of vancomycin by the CytoSorb (R) was investigated as linear or saturable process. The final model was used to derive dosing recommendations based on stochastic simulations. 

Results:
20 CytoSorb (R) treatments in 7 patients (160 serum samples/24 during CytoSorb (R)-treatment, all continuous infusion) were included in the study. A classical one-compartment model, including effluent flow rate of the continuous hemodialysis as linear covariate on clearance, best described the measured concentrations (without CytoSorb (R)). Significant adsorption with a linear decrease during CytoSorb (R) treatment was identified (p <0.0001) and revealed a maximum increase in vancomycin clearance of 291% (initially after CytoSorb (R) installation) and a maximum adsorption capacity of 572 mg. For a representative patient of our cohort a reduction of the area under the curve (AUC) by 93 mg/L*24 h during CytoSorb (R) treatment was observed. The additional administration of 500 mg vancomycin over 2 h during CytoSorb (R) attenuated the effect and revealed a negligible reduction of the AUC by 4 mg/L*24h.

Conclusion: 
We recommend the infusion of 500 mg vancomycin over 2 h during CytoSorb (R) treatment to avoid subtherapeutic concentrations.
KW  - Vancomycin
KW  - Critically ill patients
KW  - CytoSorb (R)
KW  - Sepsis;
KW  - Pharmacokinetics
KW  - Adsorption
Y1  - 2022
U6  - https://doi.org/10.1186/s13613-022-01017-5
SN  - 2110-5820
VL  - 12
IS  - 1
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Kindermann, Liana
A1  - Dobler, Magnus
A1  - Niedeggen, Daniela
A1  - Linstädter, Anja
T1  - A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems
JF  - Ecological indicators : integrating monitoring, assessment and management
N2  - Almost one third of global drylands are open forests and savannas, which are typically shaped by frequent natural disturbances such as wildfire and herbivory. Studies on ecosystem functions and services of woody vegetation require robust estimates of aboveground biomass (AGB). However, most methods have been developed for comparatively undisturbed forest ecosystems. As they are not tailored to accurately quantify AGB of small and irregular growth forms, their application on these growth forms may lead to unreliable or even biased AGB estimates in disturbance-prone dryland ecosystems. Moreover, these methods cannot quantify AGB losses caused by disturbance agents. Here we propose a methodology to estimate individual-and stand-level woody AGB in disturbance-prone ecosystems. It consists of flexible field sampling routines and estimation workflows for six growth classes, delineated by size and damage criteria. It also comprises a detailed damage assessment, harnessing the ecological archive of woody growth for past disturbances. 

Based on large inventories collected along steep gradients of elephant disturbances in African dryland ecosystems, we compared the AGB estimates generated with our proposed method against estimates from a less adapted forest inventory method. We evaluated the necessary stepwise procedures of method adaptation and analyzed each step's effect on stand-level AGB estimation. We further explored additional advantages of our proposed method with regard to disturbance impact quantification. Results indicate that a majority of growth forms and individuals in savanna vegetation could only be assessed if methods of AGB estimation were adapted to the conditions of a disturbance-prone ecosystem. Furthermore, our damage assessment demonstrated that one third to half of all woody AGB was lost to disturbances. Consequently, less adapted methods may be insufficient and are likely to render inaccurate AGB estimations.

Our proposed method has the potential to accurately quantify woody AGB in disturbance-prone ecosystems, as well as AGB losses. Our method is more time consuming than conventional allometric approaches, yet it can cover sufficient areas within reasonable timespans, and can also be easily adapted to alternative sampling schemes.
KW  - Damage assessment
KW  - Disturbance impacts
KW  - Tree growth classes
KW  - Method
KW  - comparison
KW  - Flexible sampling strategy
KW  - Tree allometry
KW  - Woody
KW  - aboveground biomass
Y1  - 2021
U6  - https://doi.org/10.1016/j.ecolind.2021.108466
SN  - 1470-160X
SN  - 1872-7034
VL  - 135
PB  - Elsevier
CY  - Amsterdam
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  - 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  - Voigt, Christian C.
A1  - Kaiser, Klara
A1  - Look, Samantha
A1  - Scharnweber, Inga Kristin
A1  - Scholz, Carolin
T1  - Wind turbines without curtailment produce large numbers of bat fatalities throughout their lifetime
BT  - a call against ignorance and neglect
JF  - Global ecology and conservation
N2  - Bats are protected by national and international legislation in European countries, yet many species, particularly migratory aerial insectivores, collide with wind turbines which counteracts conservation efforts. Within the European Union it is legally required to curtail the operation of wind turbines at periods of high bat activity, yet this is not practiced at old wind turbines. Based on data from the national carcass repository in Germany and from our own carcass searches at a wind park with three turbines west of Berlin, we evaluated the magnitude of bat casualties at old, potentially poor-sited wind turbines operating without curtailment. We report 88 documented bat carcasses collected by various searchers over the 20-year operation period of this wind park from 2001 to 2021. Common noctule bats (Nyctalus noctula) and common pipistrelles (Pipistrellus pipistrellus) were most often found dead at these turbines. Our search campaign in August and September 2021 yielded a total of 18 carcasses. We estimated that at least 209 bats were likely killed during our field survey, yielding more than 70 casualties/wind turbine or 39 casualties/ MW in two months. Since our campaign covered only part of the migration season, we consider this value as an underestimate. The 20-year period of the wind park emphasises the substantial impact old turbines may have on bat individuals and populations when operating without curtailments. We call for reconsidering the operation procedures of old wind turbines to stop the continuous loss of bats in Germany and other countries where turbine curtailments are even less practiced than in Germany.
KW  - green-green dilemma
KW  - wind energy bat conflict
KW  - wildlife casualties
Y1  - 2022
U6  - https://doi.org/10.1016/j.gecco.2022.e02149
SN  - 2351-9894
VL  - 37
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Pohle, Lara
A1  - Hosoya, Georg
A1  - Pohle, Jennifer
A1  - Meyer-Jenßen, Lars
T1  - The relationship between early childhood teachers' instructional quality and children's mathematics development
JF  - Learning and instruction : the journal of the European Association for Research on Learning and Instruction
N2  - This study examined how early childhood (EC) teachers' instructional quality predicted children's development in mathematics across two measurement occasions. Therefore, EC teachers' (n = 25) instructional quality was assessed using one standardized observation instrument covering both domain-specific and general aspects of instructional quality. Additionally, data on children's (n = 208) outcome in early number skills was collected applying a standardized test. Multilevel structural equation modeling was used accounting for nested data. Children's age and the average size of preschool groups were controlled for. Results revealed that EC teachers' instructional quality predicted children's development but was not associated with their initial achievement. The findings suggest that instruments covering domain-specific and general aspects might be helpful in order to measure EC teachers' instructional quality in mathematics and predict children's learning growth. Understanding the mechanisms between instructional quality and children's development may help EC teachers to enhance their math teaching in practice.
KW  - Early childhood education
KW  - Early childhood teachers
KW  - Instructional
KW  - quality
KW  - Early mathematics development
Y1  - 2022
U6  - https://doi.org/10.1016/j.learninstruc.2022.101636
SN  - 0959-4752
SN  - 1873-3263
VL  - 82
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Zhang, Xiaorong
A1  - Caserta, Giorgio
A1  - Yarman, Aysu
A1  - Supala, Eszter
A1  - Tadjoung Waffo, Armel Franklin
A1  - Wollenberger, Ulla
A1  - Gyurcsanyi, Robert E.
A1  - Zebger, Ingo
A1  - Scheller, Frieder W.
T1  - "Out of Pocket" protein binding
BT  - a dilemma of epitope imprinted polymers revealed for human hemoglobin
JF  - Chemosensors
N2  - The epitope imprinting approach applies exposed peptides as templates to synthesize Molecularly Imprinted Polymers (MIPs) for the recognition of the parent protein. While generally the template protein binding to such MIPs is considered to occur via the epitope-shaped cavities, unspecific interactions of the analyte with non-imprinted polymer as well as the detection method used may add to the complexity and interpretation of the target rebinding. To get new insights on the effects governing the rebinding of analytes, we electrosynthesized two epitope-imprinted polymers using the N-terminal pentapeptide VHLTP-amide of human hemoglobin (HbA) as the template. MIPs were prepared either by single-step electrosynthesis of scopoletin/pentapeptide mixtures or electropolymerization was performed after chemisorption of the cysteine extended VHLTP peptide. Rebinding of the target peptide and the parent HbA protein to the MIP nanofilms was quantified by square wave voltammetry using a redox probe gating, surface enhanced infrared absorption spectroscopy, and atomic force microscopy. While binding of the pentapeptide shows large influence of the amino acid sequence, all three methods revealed strong non-specific binding of HbA to both polyscopoletin-based MIPs with even higher affinities than the target peptides.
KW  - Molecularly Imprinted Polymers
KW  - epitope imprinting
KW  - non-specific
KW  - binding
KW  - redox gating
KW  - SEIRA spectroelectrochemistry
Y1  - 2021
U6  - https://doi.org/10.3390/chemosensors9060128
SN  - 2227-9040
VL  - 9
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Andrade, Luis
A1  - Lu, Yunlong
A1  - Cordeiro, Andre
A1  - Costa, João M. F.
A1  - Wigge, Philip Anthony
A1  - Saibo, Nelson J. M.
A1  - Jaeger, Katja E.
T1  - The evening complex integrates photoperiod signals to control flowering in rice
JF  - Proceedings of the National Academy of Sciences of the United States of America : PNAS
N2  - Plants use photoperiodism to activate flowering in response to a particular daylength. In rice, flowering is accelerated in short-day conditions, and even a brief exposure to light during the dark period (night-break) is sufficient to delay flowering. Although many of the genes involved in controlling flowering in rice have been uncovered, how the long- and short-day flowering pathways are integrated, and the mechanism of photoperiod perception is not understood. While many of the signaling components controlling photoperiod-activated flowering are conserved between Arabidopsis and rice, flowering in these two systems is activated by opposite photoperiods. Here we establish that photoperiodism in rice is controlled by the evening complex (EC). We show that mutants in the EC genes LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) paralogs abolish rice flowering. We also show that the EC directly binds and suppresses the expression of flowering repressors, including PRR37 and Ghd7. We further demonstrate that light acts via phyB to cause a rapid and sustained posttranslational modification of ELF3-1. Our results suggest a mechanism by which the EC is able to control both long- and short-day flowering pathways.
KW  - rice
KW  - flowering
KW  - ELF3
KW  - LUX
KW  - Evening Complex
Y1  - 2022
U6  - https://doi.org/10.1073/pnas.2122582119
SN  - 0027-8424
SN  - 1091-6490
VL  - 119
IS  - 26
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Yuan, Junxia
A1  - Sheng, Guilian
A1  - Preick, Michaela
A1  - Sun, Boyang
A1  - Hou, Xindong
A1  - Chen, Shungang
A1  - Taron, Ulrike Helene
A1  - Barlow, Axel
A1  - Wang, Linying
A1  - Hu, Jiaming
A1  - Deng, Tao
A1  - Lai, Xulong
A1  - Hofreiter, Michael
T1  - Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade
JF  - Quaternary science reviews : the international multidisciplinary research and review journal
N2  - There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86-1.24 Ma), and the two Old World lineages (I & II) split at 0.88 Ma (95% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species.
KW  - Equus dalianensis
KW  - Equus przewalskii
KW  - Pleistocene caballine horses
KW  - ancient DNA
KW  - phylogenetic relationship
KW  - divergence time
Y1  - 2020
U6  - https://doi.org/10.1016/j.quascirev.2020.106691
SN  - 0277-3791
VL  - 250
PB  - Elsevier
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Botero, David
A1  - Monk, Jonathan
A1  - Rodriguez Cubillos, Maria Juliana
A1  - Rodriguez Cubillos, Andres Eduardo
A1  - Restrepo, Mariana
A1  - Bernal-Galeano, Vivian
A1  - Reyes, Alejandro
A1  - Gonzalez Barrios, Andres
A1  - Palsson, Bernhard O.
A1  - Restrepo, Silvia
A1  - Bernal, Adriana
T1  - Genome-scale metabolic model of Xanthomonas phaseoli pv. manihotis
BT  - an approach to elucidate pathogenicity at the metabolic level
JF  - Frontiers in genetics
N2  - Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)(+) balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species.
KW  - Xanthomonas
KW  - Xpm
KW  - cassava bacterial blight
KW  - genome-scale metabolic
KW  - model
KW  - quorum sensing
Y1  - 2020
U6  - https://doi.org/10.3389/fgene.2020.00837
SN  - 1664-8021
VL  - 11
PB  - Frontiers Media
CY  - Lausanne
ER  -