@article{GuerreroRamirezCravenReichetal.2017, author = {Guerrero-Ramirez, Nathaly Rokssana and Craven, Dylan and Reich, Peter B. and Ewel, John J. and Isbell, Forest and Koricheva, Julia and Parrotta, John A. and Auge, Harald and Erickson, Heather E. and Forrester, David I. and Hector, Andy and Joshi, Jasmin Radha and Montagnini, Florencia and Palmborg, Cecilia and Piotto, Daniel and Potvin, Catherine and Roscher, Christiane and van Ruijven, Jasper and Tilman, David and Wilsey, Brian and Eisenhauer, Nico}, title = {Diversity-dependent temporal divergence of ecosystem functioning in experimental ecosystems}, series = {Nature ecology \& evolution}, volume = {1}, journal = {Nature ecology \& evolution}, number = {11}, publisher = {Nature Publ. Group}, address = {London}, issn = {2397-334X}, doi = {10.1038/s41559-017-0325-1}, pages = {1639 -- 1642}, year = {2017}, abstract = {The effects of biodiversity on ecosystem functioning generally increase over time, but the underlying processes remain unclear. Using 26 long-term grassland and forest experimental ecosystems, we demonstrate that biodiversity-ecosystem functioning relationships strengthen mainly by greater increases in functioning in high-diversity communities in grasslands and forests. In grasslands, biodiversity effects also strengthen due to decreases in functioning in low-diversity communities. Contrasting trends across grasslands are associated with differences in soil characteristics.}, language = {en} } @article{BerryRosaHowardetal.2017, author = {Berry, Scott and Rosa, Stefanie and Howard, Martin and Buhler, Marc and Dean, Caroline}, title = {Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression}, series = {Genes \& Development}, volume = {31}, journal = {Genes \& Development}, publisher = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, NY}, issn = {0890-9369}, doi = {10.1101/gad.305227.117}, pages = {2115 -- 2120}, year = {2017}, abstract = {Epigenetic maintenance of gene repression is essential for development. Polycomb complexes are central to this memory, but many aspects of the underlying mechanism remain unclear. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binds Polycomb-deposited H3K27me3 and is required for repression of many Polycomb target genes in Arabidopsis. Here we show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region. By independently perturbing the RNA-binding hinge region and H3K27me3 (trimethylation of histone H3 at Lys27) recognition, we found that both facilitate LHP1 localization and H3K27me3 maintenance. Disruption of the RNAbinding hinge region also prevented formation of subnuclear foci, structures potentially important for epigenetic repression.}, language = {en} } @article{EndesfelderWeicheltStraussetal.2017, author = {Endesfelder, Stefanie and Weichelt, Ulrike and Strauß, Evelyn and Schl{\"o}r, Anja and Sifringer, Marco and Scheuer, Till and B{\"u}hrer, Christoph and Schmitz, Thomas}, title = {Neuroprotection by caffeine in hyperoxia-induced neonatal brain injury}, series = {International journal of molecular sciences}, volume = {18}, journal = {International journal of molecular sciences}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms18010187}, pages = {24}, year = {2017}, abstract = {Sequelae of prematurity triggered by oxidative stress and free radical-mediated tissue damage have coined the term "oxygen radical disease of prematurity". Caffeine, a potent free radical scavenger and adenosine receptor antagonist, reduces rates of brain damage in preterm infants. In the present study, we investigated the effects of caffeine on oxidative stress markers, anti-oxidative response, inflammation, redox-sensitive transcription factors, apoptosis, and extracellular matrix following the induction of hyperoxia in neonatal rats. The brain of a rat pups at postnatal Day 6 (P6) corresponds to that of a human fetal brain at 28-32 weeks gestation and the neonatal rat is an ideal model in which to investigate effects of oxidative stress and neuroprotection of caffeine on the developing brain. Six-day-old Wistar rats were pre-treated with caffeine and exposed to 80\% oxygen for 24 and 48 h. Caffeine reduced oxidative stress marker (heme oxygenase-1, lipid peroxidation, hydrogen peroxide, and glutamate-cysteine ligase catalytic subunit (GCLC)), promoted anti-oxidative response (superoxide dismutase, peroxiredoxin 1, and sulfiredoxin 1), down-regulated pro-inflammatory cytokines, modulated redox-sensitive transcription factor expression (Nrf2/Keap1, and NFκB), reduced pro-apoptotic effectors (poly (ADP-ribose) polymerase-1 (PARP-1), apoptosis inducing factor (AIF), and caspase-3), and diminished extracellular matrix degeneration (matrix metalloproteinases (MMP) 2, and inhibitor of metalloproteinase (TIMP) 1/2). Our study affirms that caffeine is a pleiotropic neuroprotective drug in the developing brain due to its anti-oxidant, anti-inflammatory, and anti-apoptotic properties.}, language = {en} } @article{BhatMilicicThieulinPardoetal.2017, author = {Bhat, Javaid Y. and Milicic, Goran and Thieulin-Pardo, Gabriel and Bracher, Andreas and Maxwell, Andrew and Ciniawsky, Susanne and M{\"u}ller-Cajar, Oliver and Engen, John R. and Hartl, F. Ulrich and Wendler, Petra and Hayer-Hartl, Manajit}, title = {Mechanism of Enzyme Repair by the AAA(+) Chaperone Rubisco Activase}, series = {Molecular cell}, volume = {67}, journal = {Molecular cell}, publisher = {Cell Press}, address = {Cambridge}, issn = {1097-2765}, doi = {10.1016/j.molcel.2017.07.004}, pages = {744 -- 756}, year = {2017}, abstract = {How AAA(+) chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA(+) protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair.}, language = {en} } @article{HansenMeyerFerrarietal.2017, author = {Hansen, Bjoern Oest and Meyer, Etienne H. and Ferrari, Camilla and Vaid, Neha and Movahedi, Sara and Vandepoele, Klaas and Nikoloski, Zoran and Mutwil, Marek}, title = {Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana}, series = {New phytologist : international journal of plant science}, volume = {217}, journal = {New phytologist : international journal of plant science}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.14921}, pages = {1521 -- 1534}, year = {2017}, abstract = {Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists.}, language = {en} } @article{WeithoffTaubeBolius2017, author = {Weithoff, Guntram and Taube, Anne and Bolius, Sarah}, title = {The invasion success of the cyanobacterium Cylindrospermopsis raciborskii in experimental mesocosms}, series = {Aquatic Invasions}, volume = {12}, journal = {Aquatic Invasions}, publisher = {Regional Euro-Asian Biological Invasions centre-reabic}, address = {Helsinki}, issn = {1798-6540}, doi = {10.3391/ai.2017.12.3.07}, pages = {333 -- 341}, year = {2017}, abstract = {The potentially toxic, invasive cyanobacterium Cylindrospermopsis raciborskii, originating from sub-tropical regions, has spread into temperate climate zones in almost all continents. Potential factors in its success are temperature, light and nutrient levels. Grazing losses through zooplankton have been measured in the laboratory but are typically not regarded as a factor in (failed) invasion success. In some potentially suitable lakes, C. raciborskii has never been found, although it is present in water bodies close by. Therefore, we tested the invasive potential of three different isolates introduced into natural plankton communities using laboratory mesocosm experiments under three grazing levels: ambient zooplankton densities, removal of large species using 100 mu m mesh and a ca. doubling of large species. Three C. raciborskii isolates originating from the same geographic region (North-East Germany) were added separately to the four replicates of each treatment and kept in semi-continuous cultures for 21 days. Two isolates disappeared from the mesocosms and were also not viable in filtered lake water indicating that the lake water itself or the switch from culture medium to lake water led to the decay of the inoculated C. raciborskii. Only one out of the three isolates persisted in the plankton communities at a rather low level and only in the treatment without larger zooplankton. This result demonstrates that under potentially suitable environmental conditions, top-down control from zooplankton might hamper the establishment of C. raciborskii. Non-metric multidimensional scaling showed distinct variation in resident phytoplankton communities between the different grazing levels, thus differential grazing impact shaped the resident community in different ways allowing C. raciborskii only to invade under competitive (= low grazing pressure) conditions. Furthermore, even after invasion failure, the temporary presence of C. raciborskii influenced the phytoplankton community.}, language = {en} } @article{NietzscheGuerraAlseekhetal.2017, author = {Nietzsche, Madlen and Guerra, Tiziana and Alseekh, Saleh and Wiermer, Marcel and Sonnewald, Sophia and Fernie, Alisdair R. and B{\"o}rnke, Frederik}, title = {STOREKEEPER RELATED1/G-Element Binding Protein (STKR1) Interacts with Protein Kinase SnRK1}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {176}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.17.01461}, pages = {1773 -- 1792}, year = {2017}, abstract = {Sucrose nonfermenting related kinase1 (SnRK1) is a conserved energy sensor kinase that regulates cellular adaptation to energy deficit in plants. Activation of SnRK1 leads to the down-regulation of ATP-consuming biosynthetic processes and the stimulation of energy-generating catabolic reactions by transcriptional reprogramming and posttranslational modifications. Although considerable progress has been made during the last years in understanding the SnRK1 signaling pathway, many of its components remain unidentified. Here, we show that the catalytic alpha-subunits KIN10 and KIN11 of the Arabidopsis (Arabidopsis thaliana) SnRK1 complex interact with the STOREKEEPER RELATED1/G-Element Binding Protein (STKR1) inside the plant cell nucleus. Overexpression of STKR1 in transgenic Arabidopsis plants led to reduced growth, a delay in flowering, and strongly attenuated senescence. Metabolite profiling revealed that the transgenic lines exhausted their carbohydrates during the dark period to a greater extent than the wild type and accumulated a range of amino acids. At the global transcriptome level, genes affected by STKR1 overexpression were broadly associated with systemic acquired resistance, and transgenic plants showed enhanced resistance toward a virulent strain of the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2. We discuss a possible connection of STKR1 function, SnRK1 signaling, and plant immunity.}, language = {en} } @article{Schmidt2017, author = {Schmidt, Marco F.}, title = {miRNA Targeting Drugs}, series = {Drug Target miRNA: Methods and Protocols}, volume = {1517}, journal = {Drug Target miRNA: Methods and Protocols}, publisher = {Springer}, address = {New York}, isbn = {978-1-4939-6563-2}, issn = {1064-3745}, doi = {10.1007/978-1-4939-6563-2_1}, pages = {3 -- 22}, year = {2017}, abstract = {Only 20 years after the discovery of small non-coding, single-stranded ribonucleic acids, so-called microRNAs (miRNAs), as post-transcriptional gene regulators, the first miRNA-targeting drug Miravirsen for the treatment of hepatitis C has been successfully tested in clinical Phase II trials. Addressing miRNAs as drug targets may enable the cure, or at least the treatment of diseases, which presently seems impossible. However, due to miRNAs' chemical structure, generation of potential drug molecules with necessary pharmacokinetic properties is still challenging and requires a re-thinking of the drug discovery process. Therefore, this chapter highlights the potential of miRNAs as drug targets, discusses the challenges, and tries to give a complete overview of recent strategies in miRNA drug discovery.}, language = {en} } @article{PospisilCzernitzkiScheffler2017, author = {Pospisil, Christina and Czernitzki, Anna-Franziska and Scheffler, Christiane}, title = {No association between nutrition and body height in German kindergarten children}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {74}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {3}, publisher = {Schweizerbart}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2017/0704}, pages = {199 -- 202}, year = {2017}, abstract = {Anthropologists all over the world are discussing influences on individual height including quantity and quality of nutrition. To examine whether a relationship between nutritional components and height can be found this pilot study has been developed. The research samples consisted of 44 children (age 3-6 years) attending two different kindergartens in Germany. Height measurements were taken for each child. Furthermore the parents had to fill out a 24-hour questionnaire to document their children's eating habits during the weekend. In order to standardize the measured height values z-scores were calculated with reference to the average height of the overall cohort. The results of correlation analysis indicate that height is not significantly related to any of the main nutritional components as protein (r = -0.148), carbohydrates (r = 0.126), fat (r = 0.107), fibre (r = -0.289), vitamin (r = 0.050), calcium (r = 0.110), potassium (r = 0.189) and overall calorie intake (r = 0.302). In conclusion, it can be stated that the quality of nutrition may not have a strong influence on individual height. However, due to the small sample size further research should be provided with a larger cohort of children to verify the present results.}, language = {en} } @article{CzernitzkiPospisilMusaleketal.2017, author = {Czernitzki, Anna-Franziska and Pospisil, Christina and Musalek, Martin and Mumm, Rebekka and Scheffler, Christiane}, title = {Analysis of longitudinal data of height z-scores in kindergarten children}, series = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, volume = {74}, journal = {Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft f{\"u}r Anthropologie}, number = {2}, publisher = {Schweizerbart science publishers}, address = {Stuttgart}, issn = {0003-5548}, doi = {10.1127/anthranz/2017/0708}, pages = {109 -- 112}, year = {2017}, abstract = {Changes in body height throughout extended historic periods are very complex and dynamic processes. Thispilot study aimed to investigate the pattern of longitudinal height z-scores changes in children before and after entering kindergarten. In summer 2016, we measured height and weight of 32 children from 4 groups of two kindergartens aged 3-6 years. All ages were centered according to the age of entry into the kindergarten. For each child we determined mean z-scores for height before and after entering the kindergarten, and assessed the variances for each kindergarten group. Twenty-two children targeted in height z-scores towards average height of their respective kindergarten group, 10 children did not. Due to the small numbers, the convergence in height variance however, remained insignificant (chi-squared independence test, p = 0.127). Additional studies with larger sample sizes are needed to confirm this pilot study.}, language = {en} }