@misc{Matzk2016, type = {Master Thesis}, author = {Matzk, S{\"o}ren}, title = {Predictive analysis of metabolic and preventive patient data}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-406103}, school = {Universit{\"a}t Potsdam}, pages = {XI, 63}, year = {2016}, abstract = {Every day huge amounts of medical records are stored by means of hospitals' and medical offices' software. These data are generally unconsidered in research. In this work anonymized everyday medical records ascertained in a physician's office, cov- ering holistic internal medicine in combination with orthomolecular medicine, are analyzed. Due to the lack of cooperation by the provider of the medical practice software a selection of diagnoses and anthropometric parameters was extracted manually. Information about patients' treatment are not available in this study. Nevertheless, data mining approaches in- cluding machine learning techniques are used to enable research, prevention and monitoring of patients' course of treatment. The potential of these everyday medical data is demonstrated by investigating co-morbidity and pyroluria which is a metabolic dysfunction indicated by increased levels of hydroxy- hemopyrrolin-2-one (HPL). It points out that the metabolic syndrome forms a cluster of its components and cancer, as well as mental disorders are grouped with thyroid diseases including autoimmune thyroid diseases. In contrast to prevailing assumptions in which it was estimated that approximately 10 \% of the population show increased levels of HPL, in this analysis 84.9 \% of the tested patients have an increased concentration of HPL. Prevention is illustrated by using decision tree models to predict diseases. Evaluation of the obtained model for Hashimoto's disease yield an accuracy of 87.5 \%. The model generated for hypothyroidism (accuracy of 60.9 \%) reveals shortcomings due to missing information about the treatment. Dynamics in the biomolecular status of 20 patients who have visited the medical office at least one time a year between 2010 and 2014 for laboratory tests are visualized by STATIS, a consensus analysis based on an extension to principal component analysis. Thereby, one can obtain patterns which are predestinated for specific diseases as hypertension. This study demonstrates that these often overlooked everyday data are challenging due to its sparsity and heterogeneity but its analysis is a great possibility to do research on disease profiles of real patients.}, language = {de} } @misc{LiaimerJensenDittmannThuenemann2016, author = {Liaimer, Anton and Jensen, John B. and Dittmann-Th{\"u}nemann, Elke}, title = {A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L.}, series = {Frontiers in microbiology}, journal = {Frontiers in microbiology}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407179}, pages = {16}, year = {2016}, abstract = {Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.}, language = {en} } @misc{KrupinskiBozorgLarssonetal.2016, author = {Krupinski, Pawel and Bozorg, Behruz and Larsson, Andr{\´e} and Pietra, Stefano and Grebe, Markus and J{\"o}nsson, Henrik}, title = {A model analysis of mechanisms for radial microtubular patterns at root hair initiation sites}, series = {Frontiers in plant science}, journal = {Frontiers in plant science}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407181}, pages = {12}, year = {2016}, abstract = {Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.}, language = {en} } @misc{LukoszekFeistIgnatova2016, author = {Lukoszek, Radoslaw and Feist, Peter and Ignatova, Zoya}, title = {Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq}, series = {BMC plant biology}, journal = {BMC plant biology}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407262}, pages = {13}, year = {2016}, abstract = {Background: Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different levels of gene expression. Results: Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are likely candidates to play a role in regulating translation of those genes. Conclusions: Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids is maintained upon heat exposure.}, language = {en} } @article{FeoktistovaRoseProkopovicetal.2016, author = {Feoktistova, Natalia and Rose, J{\"u}rgen and Prokopovic, Vladimir Z. and Vikulina, Anna S. and Skirtach, Andre and Volodkin, Dmitry}, title = {Controlling the Vaterite CaCO3 Crystal Pores. Design of Tailor-Made Polymer Based Microcapsules by Hard Templating}, series = {Langmuir}, volume = {32}, journal = {Langmuir}, publisher = {American Chemical Society}, address = {Washington}, issn = {0743-7463}, doi = {10.1021/acs.langmuir.6b00717}, pages = {4229 -- 4238}, year = {2016}, abstract = {The spherical vaterite CaCO3 microcrystals are nowadays widely used as sacrificial templates for fabrication of various microcarriers made of biopolymers (e.g., proteins, nucleic acids, enzymes) due to porous structure and mild template elimination conditions. Here, we demonstrated for the first time that polymer microcarriers with tuned internal nanoarchitecture can be designed by employing the CaCO3 crystals of controlled porosity. The layer-by-layer deposition has been utilized to assemble shell-like (hollow) and matrix-like (filled) polymer capsules due to restricted and free polymer diffusion through the crystal pores, respectively. The crystal pore size in the range of few tens of nanometers can be adjusted without any additives by variation of the crystal preparation temperature in the range 745 degrees C. The temperature-mediated growth mechanism is explained by the Ostwald ripening of nanocrystallites forming the crystal secondary structure. Various techniques including SEM, AFM, CLSM, Raman microscopy, nitrogen adsorptiondesorption, and XRD have been employed for crystal and microcapsule analysis. A three-dimensional model is introduced to describe the crystal internal structure and predict the pore cutoff and available surface for the pore diffusing molecules. Inherent biocompatibility of CaCO3 and a possibility to scale the porosity in the size range of typical biomacromolecules make the CaCO3 crystals extremely attractive tools for template assisted designing tailor-made biopolymer-based architectures in 2D to 3D targeted at drug delivery and other bioapplications.}, language = {en} } @misc{ErdossyHorvathYarmanetal.2016, author = {Erdossy, Julia and Horvath, Viola and Yarman, Aysu and Scheller, Frieder W. and Gyurcsanyi, Robert E.}, title = {Electrosynthesized molecularly imprinted polymers for protein recognition}, series = {Trends in Analytical Chemistry}, volume = {79}, journal = {Trends in Analytical Chemistry}, publisher = {Elsevier}, address = {Oxford}, issn = {0165-9936}, doi = {10.1016/j.trac.2015.12.018}, pages = {179 -- 190}, year = {2016}, abstract = {Molecularly imprinted polymers (MIPs) for the recognition of proteins are expected to possess high affinity through the establishment of multiple interactions between the polymer matrix and the large number of functional groups of the target. However, while highly affine recognition sites need building blocks rich in complementary functionalities to their target, such units are likely to generate high levels of nonspecific binding. This paradox, that nature solved by evolution for biological receptors, needs to be addressed by the implementation of new concepts in molecular imprinting of proteins. Additionally, the structural variability, large size and incompatibility with a range of monomers made the development of protein MIPs to take a slow start. While the majority of MIP preparation methods are variants of chemical polymerization, the polymerization of electroactive functional monomers emerged as a particularly advantageous approach for chemical sensing application. Electropolymerization can be performed from aqueous solutions to preserve the natural conformation of the protein templates, with high spatial resolution and electrochemical control of the polymerization process. This review compiles the latest results, identifying major trends and providing an outlook on the perspectives of electrosynthesised protein-imprinted MIPs for chemical sensing. (C) 2016 Elsevier B.V. All rights reserved.}, language = {en} } @article{PinyouRuffPoelleretal.2016, author = {Pinyou, Piyanut and Ruff, Adrian and Poeller, Sascha and Alsaoub, Sabine and Leimk{\"u}hler, Silke and Wollenberger, Ursula and Schuhmann, Wolfgang}, title = {Wiring of the aldehyde oxidoreductase PaoABC to electrode surfaces via entrapment in low potential phenothiazine-modified redox polymers}, series = {Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society}, volume = {109}, journal = {Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society}, publisher = {Elsevier}, address = {Lausanne}, issn = {1567-5394}, doi = {10.1016/j.bioelechem.2015.12.005}, pages = {24 -- 30}, year = {2016}, abstract = {Phenothiazine-modified redox hydrogels were synthesized and used for the wiring of the aldehyde oxidoreductase PaoABC to electrode surfaces. The effects of the pH value and electrode surface modification on the biocatalytic activity of the layers were studied in the presence of vanillin as the substrate. The enzyme electrodes were successfully employed as bioanodes in vanillin/O-2 biofuel cells in combination with a high potential bilirubin oxidase biocathode. Open circuit voltages of around 700 mV could be obtained in a two compartment biofuel cell setup. Moreover, the use of a rather hydrophobic polymer with a high degree of crosslinking sites ensures the formation of stable polymer/enzyme films which were successfully used as bioanode in membrane-less biofuel cells. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @misc{LechonSanzPollmannetal.2016, author = {Lechon, Tamara and Sanz, Luis and Pollmann, Stephan and Sauer, Michael and Sandalio, Luisa and Lorenzo, Oscar}, title = {Nitric oxide modification of plant endocytosis and PIN1 localization}, series = {New biotechnology}, volume = {33}, journal = {New biotechnology}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1871-6784}, doi = {10.1016/j.nbt.2015.10.028}, pages = {424 -- 424}, year = {2016}, language = {en} } @article{HartmannSchrapersUteschetal.2016, author = {Hartmann, Tobias and Schrapers, Peer and Utesch, Tillmann and Nimtz, Manfred and Rippers, Yvonne and Dau, Holger and Mroginski, Maria Andrea and Haumann, Michael and Leimk{\"u}hler, Silke}, title = {The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C-H Bond Cleavage and Oxygen Atom Transfer Reactions}, series = {Biochemistry}, volume = {55}, journal = {Biochemistry}, publisher = {American Chemical Society}, address = {Washington}, issn = {0006-2960}, doi = {10.1021/acs.biochem.6b00002}, pages = {2381 -- 2389}, year = {2016}, abstract = {Formate dehydrogenases (FDHs) are capable of performing the reversible oxidation of formate and are enzymes of great interest for fuel cell applications and for the production of reduced carbon compounds as energy sources from CO2. Metal containing FDHs in general contain a highly conserved active site, comprising a molybdenum (or tungsten) center coordinated by two molybdopterin guanine dinucleotide molecules, a sulfido and a (seleno-)cysteine ligand, in addition to a histidine and arginine residue in the second coordination sphere. So far, the role of these amino acids in catalysis has not been studied in detail, because of the lack of suitable expression systems and the lability or oxygen sensitivity of the enzymes. Here, the roles of these active site residues is revealed using the Mo-containing FDH from Rhodobacter capsulatus. Our results show that the cysteine ligand at the Mo ion is displaced by the formate substrate during the reaction, the arginine has a direct role in substrate binding and stabilization, and the histidine elevates the pK(a) of the active site cysteine. We further found that in addition to reversible formate oxidation, the enzyme is further capable of reducing nitrate to nitrite. We propose a mechanistic scheme that combines both functionalities and provides important insights into the distinct mechanisms of C-H bond cleavage and oxygen atom transfer catalyzed by formate dehydrogenase.}, language = {en} } @article{SteinDoeringArjesFladungetal.2016, author = {Stein, F. and Doering-Arjes, P. and Fladung, Erik and Br{\"a}mick, Uwe and Bendall, B. and Schroeder, B.}, title = {Downstream Migration of the European Eel (Anguilla Anguilla) in the Elbe River, Germany: Movement Patterns and the Potential Impact of Environmental Factors}, series = {River Research and Applications}, volume = {32}, journal = {River Research and Applications}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1535-1459}, doi = {10.1002/rra.2881}, pages = {666 -- 676}, year = {2016}, abstract = {Recruitment of European eels (Anguilla anguilla) has declined to the extent that they have been added to the IUCN Red List of Threatened Species. Therefore, it is critical to ensure that eels complete their outward river migration in order to contribute to the available spawning stock. We conducted a 4-year (2007-2011) telemetry study to understand the migratory behaviour and potential impact of environmental factors on the eel during this critical life stage. Out of 399 female eels tagged with acoustic transmitters, only 28\% demonstrated clear downstream migratory behaviour. Fifty-five percent were detected exhibiting no downstream migration behaviour and 17\% were not detected at any monitoring station. Movement patterns of downstream-migrating (silver) eels were characterized by nocturnal activity and seasonal migration, with distinct peaks in autumn and spring. Migration was often discontinuous and exhibited phases of active locomotion and expanded stopovers. The most important determinants of movement activity were water temperature, cumulative precipitation and moonlight, although the significance varied by season and location in the river basin. Our results evidence a discontinuous, stepwise migration over an extended period. Furthermore, our findings indicate that migration success depends on holding duration prior to tagging and environmental predictors with varying importance depending on the season, as well as the locations of capture, tagging and release. Copyright (c) 2015 John Wiley \& Sons, Ltd.}, language = {en} } @article{vandeWeijerBijleveldHuschek2016, author = {van de Weijer, Steve and Bijleveld, Catrien and Huschek, Doreen}, title = {Offending and mortality}, series = {Advances in life course research}, volume = {28}, journal = {Advances in life course research}, publisher = {Elsevier}, address = {Oxford}, issn = {1569-4909}, doi = {10.1016/j.alcr.2015.11.004}, pages = {91 -- 99}, year = {2016}, abstract = {Background: Previous research has shown that offenders are at increased risk to die prematurely, but the etiology of this association is still unknown. Moreover, most previous studies use relatively short follow-up periods and do not take into account variation within the offender population with respect to frequency, timing and types of offenses. Method: Using conviction data for a number of families at high-risk of offending born on average in 1932, we study mortality in both offenders and non-offenders, from a similar socio-economic background, until 2007. We condition on life expectancy of the parents, age, gender, year of birth and marital status. We investigate associations between mortality and offending for different types of offenses: violent offenses, property offenses, weapons offenses, drugs offenses and driving under influence. Results: In general, offending sample members were not significantly more likely to have died than non offending sample members. Compared to the general population, however, both the offending and non offending sample members were at increased risk to die. Sample members who were convicted for driving under the influence of alcohol or weapons offenses were at increased risk to die prematurely compared to non-offending sample members. Conclusions: The relationship between offending in general and mortality is largely spurious. Limitations: The use of official conviction data might have influenced the results. (C) 2015 Elsevier Ltd. All rights reserved.}, language = {en} } @article{FerTietjenJeltsch2016, author = {Fer, Istem and Tietjen, Britta and Jeltsch, Florian}, title = {High-resolution modelling closes the gap between data and model simulations for Mid-Holocene and present-day biomes of East Africa}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {444}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2015.12.001}, pages = {144 -- 151}, year = {2016}, abstract = {East Africa hosts a striking diversity of terrestrial ecosystems, which vary both in space and time due to complex regional topography and a dynamic climate. The structure and functioning of these ecosystems under this environmental setting can be studied with dynamic vegetation models (DVMs) in a spatially explicit way. Yet, regional applications of DVMs to East Africa are rare and a comprehensive validation of such applications is missing. Here, we simulated the present-day and mid-Holocene vegetation of East Africa with the DVM, LPJ-GUESS and we conducted an exhaustive comparison of model outputs with maps of potential modern vegetation distribution, and with pollen records of local change through time. Overall, the model was able to reproduce the observed spatial patterns of East African vegetation. To see whether running the model at higher spatial resolutions (10\&\#8242; × 10\&\#8242;) contribute to resolve the vegetation distribution better and have a better comparison scale with the observational data (i.e. pollen data), we run the model with coarser spatial resolution (0.5° × 0.5°) for the present-day as well. Both the area- and point-wise comparison showed that a higher spatial resolution allows to better describe spatial vegetation changes induced by the complex topography of East Africa. Our analysis of the difference between modelled mid-Holocene and modern-day vegetation showed that whether a biome shifts to another is best explained by both the amount of change in precipitation it experiences and the amount of precipitation it received originally. We also confirmed that tropical forest biomes were more sensitive to a decrease in precipitation compared to woodland and savanna biomes and that Holocene vegetation changes in East Africa were driven not only by changes in annual precipitation but also by changes in its seasonality.}, language = {en} } @article{OrawetzMalinovaOrzechowskietal.2016, author = {Orawetz, Tom and Malinova, Irina and Orzechowski, Slawomir and Fettke, J{\"o}rg}, title = {Reduction of the plastidial phosphorylase in potato (Solanum tuberosum L.) reveals impact on storage starch structure during growth at low temperature}, series = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, volume = {100}, journal = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, publisher = {Elsevier}, address = {Paris}, issn = {0981-9428}, doi = {10.1016/j.plaphy.2016.01.013}, pages = {141 -- 149}, year = {2016}, abstract = {Tubers of potato (Solanum tuberosum L.), one of the most important crops, are a prominent example for an efficient production of storage starch. Nevertheless, the synthesis of this storage starch is not completely understood. The plastidial phosphorylase (Phol; EC 2.4.11) catalyzes the reversible transfer of glucosyl residues from glucose-1-phosphate to the non-reducing end of alpha-glucans with the release of orthophosphate. Thus, the enzyme is in principle able to act during starch synthesis. However, so far under normal growth conditions no alterations in tuber starch metabolism were observed. Based on analyses of other species and also from in vitro experiments with potato tuber slices it was supposed, that Phol has a stronger impact on starch metabolism, when plants grow under low temperature conditions. Therefore, we analyzed the starch content, granule size, as well as the internal structure of starch granules isolated from potato plants grown under low temperatures. Besides wild type, transgenic potato plants with a strong reduction in the Phol activity were analyzed. No significant alterations in starch content and granule size were detected. In contrast, when plants were cultivated at low temperatures the chain length distributions of the starch granules were altered. Thus, the granules contained more short glucan chains. That was not observed in the transgenic plants, revealing that Pho1 in wild type is involved in the formation of the short glucan chains, at least at low temperatures. (C) 2016 Elsevier Masson SAS. All rights reserved.}, language = {en} } @article{PfestorfKoernerSonnemannetal.2016, author = {Pfestorf, Hans and K{\"o}rner, Katrin and Sonnemann, Ilja and Wurst, Susanne and Jeltsch, Florian}, title = {Coupling experimental data with individual-based modelling reveals differential effects of root herbivory on grassland plant co-existence along a resource gradient}, series = {Journal of vegetation science}, volume = {27}, journal = {Journal of vegetation science}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1100-9233}, doi = {10.1111/jvs.12357}, pages = {269 -- 282}, year = {2016}, abstract = {QuestionThe empirical evidence of root herbivory effects on plant community composition and co-existence is contradictory. This originates from difficulties connected to below-ground research and confinement of experimental studies to a small range of environmental conditions. Here we suggest coupling experimental data with an individual-based model to overcome the limitations inherent in either approach. To demonstrate this, we investigated the consequences of root herbivory, as experimentally observed on individual plants, on plant competition and co-existence in a population and community context under different root herbivory intensities (RHI), fluctuating and constant root herbivore activity and grazing along a resource gradient. LocationBerlin, Germany, glasshouse; Potsdam, Germany, high performance cluster computer. MethodsThe well-established community model IBC-Grass was adapted to allow for a flexible species parameterization and to include annual species. Experimentally observed root herbivory effects on performance of eight common grassland plant species were incorporated into the model by altering plant growth rates. We then determined root herbivore effects on plant populations, competitive hierarchy and consequences for co-existence and community diversity. ResultsRoot herbivory reduced individual biomass, but temporal fluctuation allowed for compensation of herbivore effects. Reducing resource availability strongly shifted competitive hierarchies, with, however, more similar hierarchies along the gradient under root herbivory, pointing to reduced ecological species differences. Consequently, negative effects on co-existence and diversity prevailed, with the exception of a few positive effects on co-existence of selected species pairs. Temporal fluctuation alleviated but did not remove negative root herbivore effects, despite of the stronger influence of intra- compared to interspecific competition. Grazing in general augmented co-existence. Most interestingly, grazing interacted with RHI and resource availability by promoting positive effects of root herbivory. ConclusionsThrough integrating experimental data on the scale of individual plants with a simulation model we verified that root herbivory could affect plant competition with consequences for species co-existence. Our approach demonstrates the benefit that accrues when empirical and modelling approaches are brought more closely together, and that gathering data on distinct processes and under specific conditions, combined with appropriate models, can be used to answer challenging research questions in a more general way.}, language = {en} } @article{JargoschKroegerGralinskaetal.2016, author = {Jargosch, M. and Kroeger, S. and Gralinska, E. and Klotz, Ulrike and Fang, Z. and Chen, W. and Leser, U. and Selbig, Joachim and Groth, Detlef and Baumgrass, Ria}, title = {Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions}, series = {Genetics and molecular research}, volume = {15}, journal = {Genetics and molecular research}, publisher = {FUNPEC}, address = {Ribeirao Preto}, issn = {1676-5680}, doi = {10.4238/gmr.15028493}, pages = {17}, year = {2016}, abstract = {Data integration has become a useful strategy for uncovering new insights into complex biological networks. We studied whether this approach can help to delineate the signal transducer and activator of transcription 6 (STAT6)-mediated transcriptional network driving T helper (Th) 2 cell fate decisions. To this end, we performed an integrative analysis of publicly available RNA-seq data of Stat6-knockout mouse studies together with STAT6 ChIP-seq data and our own gene expression time series data during Th2 cell differentiation. We focused on transcription factors (TFs), cytokines, and cytokine receptors and delineated 59 positively and 41 negatively STAT6-regulated genes, which were used to construct a transcriptional network around STAT6. The network illustrates that important and well-known TFs for Th2 cell differentiation are positively regulated by STAT6 and act either as activators for Th2 cells (e.g., Gata3, Atf3, Satb1, Nfil3, Maf, and Pparg) or as suppressors for other Th cell subpopulations such as Th1 (e.g., Ar), Th17 (e.g., Etv6), or iTreg (e.g., Stat3 and Hifla) cells. Moreover, our approach reveals 11 TFs (e.g., Atf5, Creb3l2, and Asb2) with unknown functions in Th cell differentiation. This fact together with the observed enrichment of asthma risk genes among those regulated by STAT6 underlines the potential value of the data integration strategy used here. Thus, our results clearly support the opinion that data integration is a useful tool to delineate complex physiological processes.}, language = {en} } @article{UdDinRaufGhafooretal.2016, author = {Ud-Din, Aziz and Rauf, Mamoona and Ghafoor, S. and Khattak, M. N. K. and Hameed, M. W. and Shah, H. and Jan, S. and Muhammad, K. and Rehman, A. and Inamullah,}, title = {Efficient use of artificial micro-RNA to downregulate the expression of genes at the post-transcriptional level in Arabidopsis thaliana}, series = {Genetics and molecular research}, volume = {15}, journal = {Genetics and molecular research}, publisher = {FUNPEC}, address = {Ribeirao Preto}, issn = {1676-5680}, doi = {10.4238/gmr.15027439}, pages = {11}, year = {2016}, abstract = {Micro-RNAs are cellular components regulating gene expression at the post-transcription level. In the present study, artificial micro-RNAs were used to decrease the transcript level of two genes, AtExpA8 (encoding an expansin) and AHL25 (encoding an AT-hook motif nuclear localized protein) in Arabidopsis thaliana. The backbone of the Arabidopsis endogenous MIR319a micro-RNA was used in a site-directed mutagenesis approach for the generation of artificial micro-RNAs targeting two genes. The recombinant cassettes were expressed under the control of the CaMV 35S promoter in individual A. thaliana plants. Transgenic lines of the third generation were tested by isolating total RNA and by subsequent cDNA synthesis using oligo-dT18 primers and mRNAs as templates. The expression of the two target genes was checked through quantitative realtime polymerase chain reaction to confirm reduced transcript levels for AtExpA8 and AHL25. Downregulation of AtExpA8 resulted in the formation of short hypocotyls compared with those of the wild-type control in response to low pH and high salt concentration. This technology could be used to prevent the expression of exogenous and invading genes posing a threat to the normal cellular physiology of the host plant.}, language = {en} } @article{KruseSteinBachingerGottwaldetal.2016, author = {Kruse, Michaela and Stein-Bachinger, Karin and Gottwald, Frank and Schmidt, Elisabeth and Heinken, Thilo}, title = {Influence of grassland management on the biodiversity of plants and butterflies on organic suckler cow farms}, series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, volume = {37}, journal = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft}, publisher = {Floristisch-Soziologische Arbeitsgemeinschaft}, address = {G{\"o}ttingen}, issn = {0722-494X}, doi = {10.14471/2016.56.006}, pages = {97 -- 119}, year = {2016}, abstract = {The intensification of agricultural practices has led to a severe decrease in grassland biodiversity. Although there is strong evidence that organic farming can reduce the negative impacts of land use, knowledge regarding the most beneficial management system for species richness on organic grasslands is still scarce. This study examines differences in the biodiversity of plants and butterflies on rotationally and continuously grazed pastures as well as on meadows cut twice per year on two large organic suckler cow farms in NE Germany. Vegetation and flower abundance, as factors likely to influence butterfly abundance and diversity, were compared and used to explain the differences. The data attained by vegetation assessments and monthly transect inspections from May to August were analyzed using descriptive statistics and nonparametric methods. The abiotic site conditions of the studied plots had more influence on plant species numbers than the management method. Dry and nutrient-poor areas (mainly poor types of Cynosurion) and undrained wet fens (Calthion) were important for phytodiversity, measured by the absolute number of species, indicator species for ecologically valuable grasslands and the Shannon Index. Meadows tended to have more indicator species than pastures, where small-scale special sites such as wet depressions were crucial for plant diversity. Butterfly diversity was very low, and 90\% of the recorded butterflies were individuals of the generalist species Pieris napi. Butterfly abundance depended mainly on occurrence of specific habitat types and specific larval host plants. Supply of flowers was crucial only in certain time periods. Differences in butterfly abundance between the management systems could be explained by the site conditions of the studied grasslands. We conclude that meadows are more favorable to support ecologically valuable plant species; however, their extension is contradictory to the organic farming method of suckler cows maintained outside of stables. Rotationally grazed pastures could be a compromise that would enhance the temporal heterogeneity of flower abundance and vegetation structure. The plant diversity on pastures should be improved by less intensive grazing on special sites and plant species enrichment by means of hay transfer. For enhancing butterfly diversity we suggest to reduce land use intensity especially on poor soils. Considering the economic perspective of the farms, small parts of the agricultural area could be sufficient if connectivity to other suitable habitats is assured. Flower abundance and diversity of larval host plants could be promoted by high diversity of farming practices as well as preserving small uncut strips of meadows.}, language = {en} } @article{MaoNakamuraViottietal.2016, author = {Mao, Hailiang and Nakamura, Moritaka and Viotti, Corrado and Grebe, Markus}, title = {A Framework for Lateral Membrane Trafficking and Polar Tethering of the PEN3 ATP-Binding Cassette Transporter}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {172}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.16.01252}, pages = {2245 -- 2260}, year = {2016}, abstract = {The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity.}, language = {en} } @article{ReineckeWulfBaetenetal.2016, author = {Reinecke, J. and Wulf, M. and Baeten, Lander and Brunet, J. and Decocq, G. and De Frenne, G. and Diekmann, M. and Graae, B. J. and Heinken, Thilo and Hermy, M. and Jamoneau, A. and Lenoir, J. and Plue, J. and Orczewska, A. and Van Calster, H. and Verheyen, Kris and Naaf, T.}, title = {Acido- and neutrophilic temperate forest plants display distinct shifts in ecological pH niche across north-western Europe}, series = {Ecography : pattern and diversity in ecology ; research papers forum}, volume = {39}, journal = {Ecography : pattern and diversity in ecology ; research papers forum}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0906-7590}, doi = {10.1111/ecog.02051}, pages = {1164 -- 1175}, year = {2016}, abstract = {Ecological niches of organisms vary across geographical space, but niche shift patterns between regions and the underlying mechanisms remain largely unexplored. We studied shifts in the pH niche of 42 temperate forest plant species across a latitudinal gradient from northern France to boreo-nemoral Sweden. We asked 1) whether species restrict their niches with increasing latitude as they reach their northern range margin (environmental constraints); 2) whether species expand their niches with increasing latitude as regional plant species richness decreases (competitive release); and 3) whether species shift their niche position toward more acidic sites with increasing latitude as the relative proportion of acidic soils increases (local adaptation). Based on 1458 vegetation plots and corresponding soil pH values, we modelled species response curves using Huisman-Olff-Fresco models. Four niche measures (width, position, left and right border) were compared among regions by randomization tests. We found that with increasing latitude, neutrophilic species tended to retreat from acidic sites, indicating that these species retreat to more favorable sites when approaching their range margin. Alternatively, these species might benefit from enhanced nitrogen deposition on formerly nutrient-poor, acidic sites in southern regions or lag behind in post-glacial recolonization of potential habitats in northern regions. Most acidophilic species extended their niche toward more base-rich sites with increasing latitude, indicating competitive release from neutrophilic species. Alternatively, acidophilic species might benefit from optimal climatic conditions in the north where some have their core distribution area. Shifts in the niche position suggested that local adaptation is of minor importance. We conclude that shifts in the pH niche of temperate forest plants are the rule, but the directions of the niche shifts and possible explanations vary. Our study demonstrates that differentiating between acidophilic and neutrophilic species is crucial to identify general patterns and underlying mechanisms.}, language = {en} } @article{ProcterCottrellWattsetal.2016, author = {Procter, Duncan S. and Cottrell, Joan E. and Watts, Kevin and Hofreiter, Michael and Robinson, Elva J. H.}, title = {Does cooperation mean kinship between spatially discrete ant nests?}, series = {Ecology and evolution}, volume = {6}, journal = {Ecology and evolution}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.2590}, pages = {8846 -- 8856}, year = {2016}, abstract = {Eusociality is one of the most complex forms of social organization, characterized by cooperative and reproductive units termed colonies. Altruistic behavior of workers within colonies is explained by inclusive fitness, with indirect fitness benefits accrued by helping kin. Members of a social insect colony are expected to be more closely related to one another than they are to other conspecifics. In many social insects, the colony can extend to multiple socially connected but spatially separate nests (polydomy). Social connections, such as trails between nests, promote cooperation and resource exchange, and we predict that workers from socially connected nests will have higher internest relatedness than those from socially unconnected, and noncooperating, nests. We measure social connections, resource exchange, and internest genetic relatedness in the polydomous wood ant Formica lugubris to test whether (1) socially connected but spatially separate nests cooperate, and (2) high internest relatedness is the underlying driver of this cooperation. Our results show that socially connected nests exhibit movement of workers and resources, which suggests they do cooperate, whereas unconnected nests do not. However, we find no difference in internest genetic relatedness between socially connected and unconnected nest pairs, both show high kinship. Our results suggest that neighboring pairs of connected nests show a social and cooperative distinction, but no genetic distinction. We hypothesize that the loss of a social connection may initiate ecological divergence within colonies. Genetic divergence between neighboring nests may build up only later, as a consequence rather than a cause of colony separation.}, language = {en} }