@article{KnoxBrownRindfleischGuentheretal.2020, author = {Knox-Brown, Patrick and Rindfleisch, Tobias and G{\"u}nther, Anne and Balow, Kim and Bremer, Anne and Walther, Dirk and Miettinen, Markus S. and Hincha, Dirk K. and Thalhammer, Anja}, title = {Similar Yet Different}, series = {International Journal of Molecular Sciences}, volume = {21}, journal = {International Journal of Molecular Sciences}, number = {8}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms21082794}, pages = {25}, year = {2020}, abstract = {The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.}, language = {en} } @article{SinghDaniSharmaetal.2006, author = {Singh, Jasbir and Dani, Harinder M. and Sharma, Reeta and Steinberg, Pablo}, title = {Inhibition of the biosynthesis of SRP polypeptides and secretory proteins by aflatoxin B-1 can disrupt protein targeting}, series = {Cell biochemistry and function}, volume = {24}, journal = {Cell biochemistry and function}, publisher = {Wiley}, address = {Chichester}, issn = {0263-6484}, doi = {10.1027/cbf.1285}, pages = {507 -- 510}, year = {2006}, abstract = {Cell culture and western blotting studies revealed that aflatoxin B-1 (AFB(1)) inhibits the biosynthesis of two of the constituent polypeptides of signal recognition particle (SRP) (SRP54 and 72). SRP escorts polyribosomes carrying signal peptides from free form in the cytosol to the bound form on endoplasmic reticulum (ER) membrane during protein targeting. These effects of AFB(1) on SRP biosynthesis may inhibit the formation of functional SRP Our experiments have further shown that AFB(1) also inhibits the biosynthesis/translocation of a secretory protein, preprolactin, which fails to appear in the lumen of ER consequent to the treatment with this hepatocarcinogen. The results of the experiments presented in this article therefore enable us to infer for the first time that aflatoxin B-1 may inhibit the functioning of SRP as an escort and deplete the ER of polyribosomes for secretory protein synthesis. As these secretory proteins are important components of the plasma membrane, gap junctions and intercellular matrix, their absence from these locations could disturb cell to cell communication leading to tumorigenesis.}, language = {en} } @article{MaaresKeilKozaetal.2018, author = {Maares, Maria and Keil, Claudia and Koza, Jenny and Straubing, Sophia and Schwerdtle, Tanja and Haase, Hajo}, title = {In Vitro Studies on Zinc Binding and Buffering by Intestinal Mucins}, series = {International Journal of Molecular Sciences}, volume = {19}, journal = {International Journal of Molecular Sciences}, number = {9}, issn = {1422-0067}, doi = {10.3390/ijms19092662}, pages = {20}, year = {2018}, abstract = {The investigation of luminal factors influencing zinc availability and accessibility in the intestine is of great interest when analyzing parameters regulating intestinal zinc resorption. Of note, intestinal mucins were suggested to play a beneficial role in the luminal availability of zinc. Their exact zinc binding properties, however, remain unknown and the impact of these glycoproteins on human intestinal zinc resorption has not been investigated in detail. Thus, the aim of this study is to elucidate the impact of intestinal mucins on luminal uptake of zinc into enterocytes and its transfer into the blood. In the present study, in vitro zinc binding properties of mucins were analyzed using commercially available porcine mucins and secreted mucins of the goblet cell line HT-29-MTX. The molecular zinc binding capacity and average zinc binding affinity of these glycoproteins demonstrates that mucins contain multiple zinc-binding sites with biologically relevant affinity within one mucin molecule. Zinc uptake into the enterocyte cell line Caco-2 was impaired by zinc-depleted mucins. Yet this does not represent their form in the intestinal lumen in vivo under zinc adequate conditions. In fact, zinc-uptake studies into enterocytes in the presence of mucins with differing degree of zinc saturation revealed zinc buffering by these glycoproteins, indicating that mucin-bound zinc is still available for the cells. Finally, the impact of mucins on zinc resorption using three-dimensional cultures was studied comparing the zinc transfer of a Caco-2/HT-29-MTX co-culture and conventional Caco-2 monoculture. Here, the mucin secreting co-cultures yielded higher fractional zinc resorption and elevated zinc transport rates, suggesting that intestinal mucins facilitate the zinc uptake into enterocytes and act as a zinc delivery system for the intestinal epithelium.}, language = {en} } @article{ColomaGaedkeSivonenetal.2019, author = {Coloma, Sebastian and Gaedke, Ursula and Sivonen, Kaarina and Hiltunen, Teppo}, title = {Frequency of virus-resistant hosts determines experimental community dynamics}, series = {Ecology : a publication of the Ecological Society of America}, volume = {100}, journal = {Ecology : a publication of the Ecological Society of America}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0012-9658}, doi = {10.1002/ecy.2554}, pages = {10}, year = {2019}, abstract = {Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics, and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics of the evolution of phage resistance in bloom forming cyanobacterial populations are still poorly studied. Here, we examined the effect of different frequencies of a phage-resistant genotype within a filamentous nitrogen-fixing Nodularia spumigena population on an experimental plankton community. Three Nodularia populations with different initial frequencies (0\%, 5\%, and 50\%) of phage-resistant genotypes were inoculated in separate treatments with the phage 2AV2, the green alga Chlorella vulgaris, and the rotifer Brachionus plicatilis, which formed the experimental plankton community subjected to either nitrogen-limited or nitrogen-rich conditions. We found that the frequency of the phage-resistant Nodularia genotype determined experimental community dynamics. Cyanobacterial populations with a high frequency (50\%) of the phage-resistant genotype dominated the cultures despite the presence of phages, retaining most of the intracellular nitrogen in the plankton community. In contrast, populations with low frequencies (0\% and 5\%) of the phage-resistant genotype were lysed and reduced to extinction by the phage, transferring the intracellular nitrogen held by Nodularia to Chlorella and rotifers, and allowing Chlorella to dominate the communities and rotifers to survive. This study shows that even though phages represent minuscule biomass, they can have key effects on community composition and eco-evolutionary feedbacks in plankton communities.}, language = {en} } @article{RyoJeschkeRilligetal.2020, author = {Ryo, Masahiro and Jeschke, Jonathan M. and Rillig, Matthias C. and Heger, Tina}, title = {Machine learning with the hierarchy-of-hypotheses (HoH) approach discovers novel pattern in studies on biological invasions}, series = {Research synthesis methods}, volume = {11}, journal = {Research synthesis methods}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1759-2879}, doi = {10.1002/jrsm.1363}, pages = {66 -- 73}, year = {2020}, abstract = {Research synthesis on simple yet general hypotheses and ideas is challenging in scientific disciplines studying highly context-dependent systems such as medical, social, and biological sciences. This study shows that machine learning, equation-free statistical modeling of artificial intelligence, is a promising synthesis tool for discovering novel patterns and the source of controversy in a general hypothesis. We apply a decision tree algorithm, assuming that evidence from various contexts can be adequately integrated in a hierarchically nested structure. As a case study, we analyzed 163 articles that studied a prominent hypothesis in invasion biology, the enemy release hypothesis. We explored if any of the nine attributes that classify each study can differentiate conclusions as classification problem. Results corroborated that machine learning can be useful for research synthesis, as the algorithm could detect patterns that had been already focused in previous narrative reviews. Compared with the previous synthesis study that assessed the same evidence collection based on experts' judgement, the algorithm has newly proposed that the studies focusing on Asian regions mostly supported the hypothesis, suggesting that more detailed investigations in these regions can enhance our understanding of the hypothesis. We suggest that machine learning algorithms can be a promising synthesis tool especially where studies (a) reformulate a general hypothesis from different perspectives, (b) use different methods or variables, or (c) report insufficient information for conducting meta-analyses.}, language = {en} } @article{SchaubKlaassenBoutenetal.2020, author = {Schaub, Tonio and Klaassen, Raymond H. G. and Bouten, Willem and Schlaich, Almut E. and Koks, Ben J.}, title = {Collision risk of Montagu's Harriers Circus pygargus with wind turbines derived from high-resolution GPS tracking}, series = {Ibis : the international journal of avian science ; the journal of the British Ornithologists' Union}, volume = {162}, journal = {Ibis : the international journal of avian science ; the journal of the British Ornithologists' Union}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {0019-1019}, doi = {10.1111/ibi.12788}, pages = {520 -- 534}, year = {2020}, abstract = {Flight behaviour characteristics such as flight altitude and avoidance behaviour determine the species-specific collision risk of birds with wind turbines. However, traditional observational methods exhibit limited positional accuracy. High-resolution GPS telemetry represents a promising method to overcome this drawback. In this study, we used three-dimensional GPS tracking data including high-accuracy tracks recorded at 3-s intervals to investigate the collision risk of breeding male Montagu's Harriers Circus pygargus in the Dutch-German border region. Avoidance of wind turbines was quantified by a novel approach comparing observed flights to a null model of random flight behaviour. On average, Montagu's Harriers spent as much as 8.2 h per day in flight. Most flights were at low altitude, with only 7.1\% within the average rotor height range (RHR; 45-125 m). Montagu's Harriers showed significant avoidance behaviour, approaching turbines less often than expected, particularly when flying within the RHR (avoidance rate of 93.5\%). For the present state, with wind farms situated on the fringes of the regional nesting range, collision risk models based on our new insights on flight behaviour indicated 0.6-2.0 yearly collisions of adult males (as compared with a population size of c. 40 pairs). However, the erection of a new wind farm inside the core breeding area could markedly increase mortality (up to 9.7 yearly collisions). If repowering of the wind farms was carried out using low-reaching modern turbines (RHR 36-150 m), mortality would more than double, whereas it would stay approximately constant if higher turbines (RHR 86-200 m) were used. Our study demonstrates the great potential of high-resolution GPS tracking for collision risk assessments. The resulting information on collision-related flight behaviour allows for performing detailed scenario analyses on wind farm siting and turbine design, in contrast to current environmental assessment practices. With regard to Montagu's Harriers, we conclude that although the deployment of higher wind turbines represents an opportunity to reduce collision risk for this species, precluding wind energy developments in core breeding areas remains the most important mitigation measure.}, language = {en} } @article{VoigtSchollBaueretal.2020, author = {Voigt, Christian and Scholl, Julia M. and Bauer, Juliane and Teige, Tobias and Yovel, Yossi and Kramer-Schadt, Stephanie and Gras, Pierre}, title = {Movement responses of common noctule bats to the illuminated urban landscape}, series = {Landscape ecology}, volume = {35}, journal = {Landscape ecology}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2973}, doi = {10.1007/s10980-019-00942-4}, pages = {189 -- 201}, year = {2020}, abstract = {Context Cities are a challenging habitat for obligate nocturnal mammals because of the ubiquitous use of artificial light at night (ALAN). How nocturnal animals move in an urban landscape, particularly in response to ALAN is largely unknown. Objectives We studied the movement responses, foraging and commuting, of common noctules (Nyctalus noctula) to urban landscape features in general and ALAN in particular. Methods We equipped 20 bats with miniaturized GPS loggers in the Berlin metropolitan area and related spatial positions of bats to anthropogenic and natural landscape features and levels of ALAN. Results Common noctules foraged close to ALAN only next to bodies of water or well vegetated areas, probably to exploit swarms of insects lured by street lights. In contrast, they avoided illuminated roads, irrespective of vegetation cover nearby. Predictive maps identified most of the metropolitan area as non-favoured by this species because of high levels of impervious surfaces and ALAN. Dark corridors were used by common noctules for commuting and thus likely improved the permeability of the city landscape. Conclusions We conclude that the spatial use of common noctules, previously considered to be more tolerant to light than other bats, is largely constrained by ALAN. Our study is the first individual-based GPS tracking study to show sensitive responses of nocturnal wildlife to light pollution. Approaches to protect urban biodiversity need to include ALAN to safeguard the larger network of dark habitats for bats and other nocturnal species in cities.}, language = {en} } @article{FrancoObregonCambriaGreutertetal.2018, author = {Franco-Obregon, Alfredo and Cambria, Elena and Greutert, Helen and Wernas, Timon and Hitzl, Wolfgang and Egli, Marcel and Sekiguchi, Miho and Boos, Norbert and Hausmann, Oliver and Ferguson, Stephen J. and Kobayashi, Hiroshi and W{\"u}rtz-Kozak, Karin}, title = {TRPC6 in simulated microgravity of intervertebral disc cells}, series = {European Spine Journal}, volume = {27}, journal = {European Spine Journal}, number = {10}, publisher = {Springer}, address = {New York}, issn = {0940-6719}, doi = {10.1007/s00586-018-5688-8}, pages = {2621 -- 2630}, year = {2018}, abstract = {Purpose Prolonged bed rest and microgravity in space cause intervertebral disc (IVD) degeneration. However, the underlying molecular mechanisms are not completely understood. Transient receptor potential canonical (TRPC) channels are implicated in mechanosensing of several tissues, but are poorly explored in IVDs. Methods Primary human IVD cells from surgical biopsies composed of both annulus fibrosus and nucleus pulposus (passage 1-2) were exposed to simulated microgravity and to the TRPC channel inhibitor SKF-96365 (SKF) for up to 5days. Proliferative capacity, cell cycle distribution, senescence and TRPC channel expression were analyzed. Results Both simulated microgravity and TRPC channel antagonism reduced the proliferative capacity of IVD cells and induced senescence. While significant changes in cell cycle distributions (reduction in G1 and accumulation in G2/M) were observed upon SKF treatment, the effect was small upon 3days of simulated microgravity. Finally, downregulation of TRPC6 was shown under simulated microgravity. Conclusions Simulated microgravity and TRPC channel inhibition both led to reduced proliferation and increased senescence. Furthermore, simulated microgravity reduced TRPC6 expression. IVD cell senescence and mechanotransduction may hence potentially be regulated by TRPC6 expression. This study thus reveals promising targets for future studies.}, language = {en} } @article{AmbarliMenguellueoğluFickeletal.2018, author = {Ambarli, H{\"u}seyin and Meng{\"u}ll{\"u}oğlu, Deniz and Fickel, J{\"o}rns and F{\"o}rster, Daniel W.}, title = {Hotel AMANO Grand Central of brown bears in southwest Asia}, series = {PeerJ}, volume = {6}, journal = {PeerJ}, publisher = {PeerJ Inc.}, address = {London}, issn = {2167-8359}, doi = {10.7717/peerj.5660}, pages = {18}, year = {2018}, abstract = {Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kackar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroduction in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus.}, language = {en} } @article{GoetzNaherFettkeetal.2018, author = {G{\"o}tz, Klaus-Peter and Naher, Jobadatun and Fettke, J{\"o}rg and Chmielewski, Frank M.}, title = {Changes of proteins during dormancy and bud development of sweet cherry (Prunus avium L.)}, series = {Scientia horticulturae : an international journal sponsored by the International Society for Horticultural Science}, volume = {239}, journal = {Scientia horticulturae : an international journal sponsored by the International Society for Horticultural Science}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-4238}, doi = {10.1016/j.scienta.2018.05.016}, pages = {41 -- 49}, year = {2018}, abstract = {Trees control the flowering processes in response to both environmental and endogenous (mechanisms at cellular/tissue level) conditions. Dormancy of flower buds is characterized by the reduction of growth and the enhancement of frost and desiccation resistance. The release of endodormancy and the beginning of ontogenetic development, as two important dates for developing reliable phenological models, escape from any visible signs. Thus, we identified - to our knowledge as first - relevant proteins in sweet cherry buds occurring during these phenological phases at high time resolution in three seasons (2012/13-2014/15) under natural conditions in Northeast Germany. The protein content of buds from the first week of October to leaf fall, from leaf fall to the end of endodormancy (t1), from t1 to the beginning of ontogenetic development (t1*), and from t1* until swollen bud, was comparable in each of the seasons. The increase of the protein content began after swollen bud and markedly differences occurred at side green, green tip, tight and open cluster. SDS gel electrophoresis followed by peptide mass fingerprinting accomplished by MALDI-TOF MS was applied for protein identification. 'Volume intensity' has been used to demonstrate the pattern and changes of proteins. None of the analysed proteins like for cell proliferation/differentiation (Phytosulfokines 3), carbon fixation (Rubisco), and defense against pathogenes (Major allergen Pru sv 1) indicates the date of endodormancy release or the beginning of the (invisible) ontogenetic development. The stages around green tip, tight, and open cluster resulted in markedly increase of the volume intensity of the protein for cell proliferation/differentiation and the carbon fixation, whereas the volume intensity of a protein for defense against pathogens markedly decreased. The pattern and changes of the volume intensity of neoxanthin synthase (NXS) in sweet cherry buds followed the increasing demand during endo- and ecodormancy to produce neoxanthin, which is a prominent member of the group of reactive oxygen species (ROS) scavengers.}, language = {en} }