TY - JOUR A1 - Aschenbrenner, Stefan A1 - Walz, Bernd T1 - Pleated septate junctions in leech photoreceptors : ultrastructure, arrangement of septa, gate and fence functions Y1 - 1998 ER - TY - JOUR A1 - Ast, Sandra A1 - Müller, Holger A1 - Flehr, Roman A1 - Klamroth, Tillmann A1 - Walz, Bernd A1 - Holdt, Hans-Jürgen T1 - High Na+ and K+-induced fluorescence enhancement of a pi-conjugated phenylaza-18-crown-6-triazol-substituted coumarin fluoroionophore JF - Chemical communications N2 - The new pi-conjugated 1,2,3-triazol-1,4-diyl fluoroionophore 1 generated via Cu(I) catalyzed [3 + 2] cycloaddition shows high fluorescence enhancement factors (FEF) in the presence of Na+ (FEF = 58) and K+ (FEF = 27) in MeCN and high selectivity towards K+ under simulated physiological conditions (160 mM K+ or Na+, respectively) with a FEF of 2.5 for K+. Y1 - 2011 U6 - https://doi.org/10.1039/c0cc04370b SN - 1359-7345 VL - 47 IS - 16 SP - 4685 EP - 4687 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Attermeyer, Katrin A1 - Grossart, Hans-Peter A1 - Flury, Sabine A1 - Premke, Katrin T1 - Bacterial processes and biogeochemical changes in the water body of kettle holes - mainly driven by autochthonous organic matter? JF - Aquatic sciences : research across boundaries N2 - Kettle holes are small inland waters formed from glacially-created depressions often situated in agricultural landscapes. Due to their high perimeter-to-area ratio facilitating a high aquatic-terrestrial coupling, kettle holes can accumulate high concentrations of organic carbon and nutrients, fueling microbial activities and turnover rates. Thus, they represent hotspots of carbon turnover in the landscape, but their bacterial activities and controlling factors have not been well investigated. Therefore, we aimed to assess the relative importance of various environmental factors on bacterial and biogeochemical processes in the water column of kettle holes and to disentangle their variations. In the water body of ten kettle holes in north-eastern Germany, we measured several physico-chemical and biological parameters such as carbon quantity and quality, as well as bacterial protein production (BP) and community respiration (CR) in spring, early summer and autumn 2014. Particulate organic matter served as an indicator of autochthonous production and represented an important parameter to explain variations in BP and CR. This notion is supported by qualitative absorbance indices of dissolved molecules in water samples and C: N ratios of the sediments, which demonstrate high fractions of autochthonous organic matter (OM) in the studied kettle holes. In contrast, dissolved chemical parameters were less important for bacterial activities although they revealed strong differences throughout the growing season. Pelagic bacterial activities and dynamics might thus be regulated by autochthonous OM in kettle holes implying a control of important biogeochemical processes by internal primary production rather than facilitated exchange with the terrestrial surrounding due to a high perimeter-to-area ratio. KW - Bacterial production KW - Carbon turnover KW - Growth efficiency KW - Ponds KW - Respiration KW - DOC quality KW - LC-OCD Y1 - 2017 U6 - https://doi.org/10.1007/s00027-017-0528-1 SN - 1015-1621 SN - 1420-9055 VL - 79 SP - 675 EP - 687 PB - Springer CY - Basel ER - TY - JOUR A1 - Attermeyer, Katrin A1 - Hornick, T. A1 - Kayler, Zachary A1 - Bahr, A. A1 - Zwirnmann, E. A1 - Grossart, Hans-Peter A1 - Premke, K. T1 - Enhanced bacterial decomposition with increasing addition of autochthonous to allochthonous carbon without any effect on bacterial community composition JF - Biogeosciences N2 - Dissolved organic carbon (DOC) concentrations - mainly of terrestrial origin - are increasing worldwide in inland waters. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. Our aim was to study bacterial carbon (C) turnover with respect to DOC quantity and chemical quality using both allochthonous and autochthonous DOC sources. We incubated a natural bacterial community with allochthonous C (C-13-labeled beech leachate) and increased concentrations and pulses (intermittent occurrence of organic matter input) of autochthonous C (phytoplankton lysate). We then determined bacterial C consumption, activities, and community composition together with the C flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and low-and high-molecular-weight substance fractions (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. Both DOC sources (allochthonous and autochthonous DOC) were metabolized at a high bacterial growth efficiency (BGE) around 50%. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption of up to 68% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substance (HS) fraction and an increase in bacterial biomass. Changes in DOC concentration and consumption in mixed treatments did not affect bacterial community composition (BCC), but BCC differed in single vs. mixed incubations. Our study highlights that DOC quantity affects bacterial C consumption but not BCC in nutrient-rich aquatic systems. BCC shifted when a mixture of allochthonous and autochthonous C was provided simultaneously to the bacterial community. Our results indicate that chemical quality rather than source of DOC per se (allochthonous vs. autochthonous) determines bacterial DOC turnover. Y1 - 2014 U6 - https://doi.org/10.5194/bg-11-1479-2014 SN - 1726-4170 SN - 1726-4189 VL - 11 IS - 6 SP - 1479 EP - 1489 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Attermeyer, Katrin A1 - Premke, Katrin A1 - Hornick, Thomas A1 - Hilt, Sabine A1 - Grossart, Hans-Peter T1 - Ecosystem-level studies of terrestrial carbon reveal contrasting bacterial metabolism in different aquatic habitats JF - Ecology : a publication of the Ecological Society of America N2 - In aquatic systems, terrestrial dissolved organic matter (t-DOM) is known to stimulate bacterial activities in the water column, but simultaneous effects of autumnal leaf input on water column and sediment microbial dynamics in littoral zones of lakes remain largely unknown. The study's objective was to determine the effects of leaf litter on bacterial metabolism in the littoral water and sediment, and subsequently, the consequences for carbon cycling and food web dynamics. Therefore, in late fall, we simultaneously measured water and sediment bacterial metabolism in the littoral zone of a temperate shallow lake after adding terrestrial particulate organic matter (t-POM), namely, maize leaves. To better evaluate bacterial production (BP) and community respiration (CR) in sediments, we incubated sediment cores with maize leaves of different quality (nonleached and leached) under controlled laboratory conditions. Additionally, to quantify the incorporated leaf carbon into microbial biomass, we determined carbon isotopic ratios of fatty acids from sediment and leaf-associated microbes from a laboratory experiment using C-13-enriched beech leaves. The concentrations of dissolved organic carbon (DOC) increased significantly in the lake after the addition of maize leaves, accompanied by a significant increase in water BP. In contrast, sediment BP declined after an initial peak, showing no positive response to t-POM addition. Sediment BP and CR were also not stimulated by t-POM in the laboratory experiment, either in short-term or in long-term incubations, except for a short increase in CR after 18 hours. However, this increase might have reflected the metabolism of leaf-associated microorganisms. We conclude that the leached t-DOM is actively incorporated into microbial biomass in the water column but that the settling leached t-POM (t-POML) does not enter the food web via sediment bacteria. Consequently, t-POML is either buried in the sediment or introduced into the aquatic food web via microorganisms (bacteria and fungi) directly associated with t-POML and via benthic macroinvertebrates by shredding of t-POML. The latter pathway represents a benthic shortcut which efficiently transfers t-POML to higher trophic levels. KW - bacterial production KW - carbon turnover KW - community respiration KW - leaf litter KW - phospholipid-derived fatty acid KW - PLFA KW - Schulzensee KW - Germany KW - sediments KW - shallow lakes KW - stable isotopes KW - terrestrial subsidies Y1 - 2013 U6 - https://doi.org/10.1890/13-0420.1 SN - 0012-9658 SN - 1939-9170 VL - 94 IS - 12 SP - 2754 EP - 2766 PB - Wiley CY - Washington ER - TY - JOUR A1 - Attermeyer, Katrin A1 - Tittel, Joerg A1 - Allgaier, Martin A1 - Frindte, Katharina A1 - Wurzbacher, Christian A1 - Hilt, Sabine A1 - Kamjunke, Norbert A1 - Grossart, Hans-Peter T1 - Effects of Light and Autochthonous Carbon Additions on Microbial Turnover of Allochthonous Organic Carbon and Community Composition JF - Microbial ecology N2 - The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties. KW - Bacterial growth efficiency KW - Continuous cultures KW - Carbon decomposition KW - Leaf litter KW - Photolysis Y1 - 2015 U6 - https://doi.org/10.1007/s00248-014-0549-4 SN - 0095-3628 SN - 1432-184X VL - 69 IS - 2 SP - 361 EP - 371 PB - Springer CY - New York ER - TY - JOUR A1 - Audisio, Paolo A1 - Cline, Andrew R. A1 - Solano, Emanuela A1 - Mancini, Emiliano A1 - Lamanna, Francesco A1 - Antonini, Gloria A1 - Trizzino, Marco T1 - A peculiar new genus and species of pollen-beetle (Coleoptera, Nitidulidae) from eastern Africa, with a molecular phylogeny of related Meligethinae JF - Systematics and biodiversity KW - new species KW - new genus KW - molecular analysis KW - pollen-beetles KW - host-plants KW - Asteraceae KW - Kenya KW - Tarchonanthopria freidbergi Y1 - 2014 U6 - https://doi.org/10.1080/14772000.2013.877539 SN - 1477-2000 SN - 1478-0933 VL - 12 IS - 1 SP - 77 EP - 91 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Autenrieth, Marijke A1 - Hartmann, Stefanie A1 - Lah, Ljerka A1 - Roos, Anna A1 - Dennis, Alice B. A1 - Tiedemann, Ralph T1 - High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) JF - Molecular ecology resources N2 - The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation. KW - cetaceans KW - genomics/proteomics KW - mammals KW - molecular evolution Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12932 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1469 EP - 1481 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Avcilar-Kucukgoze, Irem A1 - Bartholomäus, Alexander A1 - Varela, Juan A. Cordero A1 - Kaml, Robert Franz-Xaver A1 - Neubauer, Peter A1 - Budisa, Nediljko A1 - Ignatova, Zoya T1 - Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli JF - Nucleic acids research N2 - Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser). These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth. Y1 - 2016 U6 - https://doi.org/10.1093/nar/gkw697 SN - 0305-1048 SN - 1362-4962 VL - 44 SP - 8324 EP - 8334 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Averbeck, Christiane A1 - Apio, Ann A1 - Plath, Martin A1 - Wronski, Torsten T1 - Environmental parameters and anthropogenic effects predicting the spatial distribution of wild ungulates in the Akagera savannah ecosystem N2 - Savannah areas affected by human activities such as livestock keeping and agriculture are often characterized by shifts in landscape structuring, with a predominance of few(er) habitat types. This is typically accompanied by pronounced changes in the communities of ungulates. The aim of this study was to find out whether shifts in ungulate communities in Lake Mburo National Park (LMNP) are primarily predicted by an alteration in the composition of the preferred habitat types or if more complex interactions between habitat changes and the prevalence of ungulates occur. Monthly road counts were used to establish the number of eleven ungulate species in LMNP and adjacent unprotected Ankole Ranching Scheme. The common duiker (Sylvicapra grimmia campbelliae Gray, 1843) was found in more abundance in disturbed areas, while showing a significant change in habitat use. Common duiker tended to use the vegetation type otherwise used by the bushbuck (Tragelaphus scriptus dama Neumann, 1902). Our results support the claim that the occurrence of ungulates is not only directly affected by the availability of 'suitable' habitats, but behavioural plasticity and competitive exclusion also need to be considered. Y1 - 2009 UR - http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2028 U6 - https://doi.org/10.1111/j.1365-2028.2009.01076.x SN - 0141-6707 ER - TY - JOUR A1 - Averbeck, Christiane A1 - Apio, Ann A1 - Plath, Martin A1 - Wronski, Torsten T1 - Hunting differentially affects mixed-sex and bachelor-herds in a gregarious ungulate, the impala (Aepyceros melampus: Bovidae) N2 - We investigated herd-sizes and herd-compositions of Impala (Aepyceros melampus) inside a protected area [Lake Mburo National Park (LMNP) in western Uganda] and the unprotected adjacent ranchland [the Ankole Ranching Scheme (ARS)]. Impala experience intense hunting and poaching in the study area, and poaching is especially strong on the ARS. We found evidence for changes in overall group-sizes in both mixed-sex and pure bachelor herds between areas in and outside LMNP. Mixed-sex herds strongly decreased in size outside the National Park, but bachelor herds even slightly increased in size. While the group-composition of mixed-sex herds was very similar in areas in and outside LMNP, bachelor herds comprised more yearlings and subadult males on the ARS. Our study suggests that effects of hunting and other human nuisance may differ between herd types: mixed herds probably decrease in size because females are more strongly hunted. Around LMNP, impala are usually hunted using nets and spears, thereby increasing the hunters' chance of being injured. Poachers therefore prefer hornless females (and their calves), as it is less dangerous to handle net-caught females than males. As a result, males are less hunted, but increased vigilance and, therefore, reduced aggression among the members of a bachelor herd, may account for the observed increase in herd sizes and changes in group-compositions. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0141-6707 U6 - https://doi.org/10.1111/j.1365-2028.2009.01118.x SN - 0141-6707 ER - TY - JOUR A1 - Awan, Asad Bashir A1 - Schiebel, Juliane A1 - Boehm, Alexander A1 - Nitschke, Joerg A1 - Sarwar, Yasra A1 - Schierack, Peter A1 - Ali, Aamir T1 - Association of biofilm formation and cytotoxic potential with multidrug resistance in clinical isolates of pseudomonas aeruginosa JF - EXCLI Journal N2 - Multidrug resistant (MDR) Pseudomonas aeruginosa having strong biofilm potential and virulence factors are a serious threat for hospitalized patients having compromised immunity In this study, 34 P. aeruginosa isolates of human origin (17 MDR and 17 non-MDR clinical isolates) were checked for biofilm formation potential in enriched and minimal media. The biofilms were detected using crystal violet method and a modified software package of the automated VideoScan screening method. Cytotoxic potential of the isolates was also investigated on HepG2, LoVo and T24 cell lines using automated VideoScan technology. Pulse field gel electrophoresis revealed 10 PFGE types in MDR and 8 in non-MDR isolates. Although all isolates showed biofilm formation potential, strong biofilm formation was found more in enriched media than in minimal media. Eight MDR isolates showed strong biofilm potential in both enriched and minimal media by both detection methods. Strong direct correlation between crystal violet and VideoScan methods was observed in identifying strong biofilm forming isolates. High cytotoxic effect was observed by 4 isolates in all cell lines used while 6 other isolates showed high cytotoxic effect on T24 cell line only. Strong association of multidrug resistance was found with biofilm formation as strong biofilms were observed significantly higher in MDR isolates (p-value < 0.05) than non-MDR isolates. No significant association of cytotoxic potential with multidrug resistance or biofilm formation was found (p-value > 0.05). The MDR isolates showing significant cytotoxic effects and strong biofilm formation impose a serious threat for hospitalized patients with weak immune system. KW - Pseudomonas aeruginosa KW - multidrug resistance KW - biofilm KW - cytotoxicity KW - VideoScan technology Y1 - 2019 U6 - https://doi.org/10.17179/excli2018-1948 SN - 1611-2156 VL - 18 SP - 79 EP - 90 PB - Leibniz Research Centre for Working Environment and Human Factors CY - Dortmund ER - TY - JOUR A1 - Ayllon, Daniel A1 - Railsback, Steven Floyd A1 - Vincenzi, Simone A1 - Groeneveld, Juergen A1 - Almodoevar, Ana A1 - Grimm, Volker T1 - InSTREAM-Gen: Modelling eco-evolutionary dynamics of trout populations under anthropogenic environmental change JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Current rates of environmental change are exceeding the capacity of many populations to adapt to new conditions and thus avoid demographic collapse and ultimate extinction. In particular, cold-water freshwater fish species are predicted to experience strong selective pressure from climate change and a wide range of interacting anthropogenic stressors in the near future. To implement effective management and conservation measures, it is crucial to quantify the maximum rate of change that cold-water freshwater fish populations can withstand. Here, we present a spatially explicit eco-genetic individual-based model, inSTREAM-Gen, to predict the eco-evolutionary dynamics of stream-dwelling trout under anthropogenic environmental change. The model builds on a well-tested demographic model, which includes submodels of river dynamics, bioenergetics, and adaptive habitat selection, with a new genetic module that allows exploration of genetic and life-history adaptations to new environments. The genetic module models the transmission of two key traits, size at emergence and maturity size threshold. We parameterized the model for a brown trout (Salmo trutta L.) population at the warmest edge of its range to validate it and analyze its sensitivity to parameters under contrasting thermal profiles. To illustrate potential applications of the model, we analyzed the population's demographic and evolutionary dynamics under scenarios of (1) climate change-induced warming, and (2) warming plus flow reduction resulting from climate and land use change, compared to (3) a baseline of no environmental change. The model predicted severe declines in density and biomass under climate warming. These declines were lower than expected at range margins because of evolution towards smaller size at both emergence and maturation compared to the natural evolution under the baseline conditions. Despite stronger evolutionary responses, declining rates were substantially larger under the combined warming and flow reduction scenario, leading to a high probability of population extinction over contemporary time frames. Therefore, adaptive responses could not prevent extinction under high rates of environmental change. Our model demonstrates critical elements of next generation ecological modelling aiming at predictions in a changing world as it accounts for spatial and temporal resource heterogeneity, while merging individual behaviour and bioenergetics with microevolutionary adaptations. KW - Individual-based model KW - Eco-genetic modelling KW - Eco-evolution KW - Climate change KW - Brown trout KW - Next-generation modelling Y1 - 2016 U6 - https://doi.org/10.1016/j.ecolmodel.2015.07.026 SN - 0304-3800 SN - 1872-7026 VL - 326 SP - 36 EP - 53 PB - Elsevier CY - Amsterdam 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 - Azuma, Yusuke A1 - Kuekenshoener, Tim A1 - Ma, Guangyong A1 - Yasunaga, Jun-ichiro A1 - Imanishi, Miki A1 - Tanaka, Gen A1 - Nakase, Ikuhiko A1 - Maruno, Takahiro A1 - Kobayashi, Yuji A1 - Arndt, Katja Maren A1 - Matsuoka, Masao A1 - Futaki, Shiroh T1 - Controlling leucine-zipper partner recognition in cells through modification of a-g interactions JF - Chemical communications N2 - By focusing on the a-g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions. Y1 - 2014 U6 - https://doi.org/10.1039/c4cc00555d SN - 1359-7345 SN - 1364-548X VL - 50 IS - 48 SP - 6364 EP - 6367 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Babalola, Jonathan Oyebamiji A1 - Omorogie, Martins Osaigbovo A1 - Babarinde, Adesola Abiola A1 - Unuabonah, Emmanuel Iyayi A1 - Oninla, Vincent Olukayode T1 - OPTIMIZATION OF THE BIOSORPTION OF Cr3+, Cd2+ AND Pb2+ USING A NEW BIOWASTE: Zea mays SEED CHAFF JF - Environmental engineering and management journal N2 - This study highlights the potential use of yellow Zea mays seed chaff (YZMSC) biomass as a biosorbent for the removal of Cr3+, Cd2+ and Pb2+ ions from aqueous solutions. Fourier transformed Infrared analysis of the biomass suggests that YZMSC biomass is basically composed of cellulose and methyl cellulose. The biosorption capacities, q(max), of YZMSC biomass for Cr3+, Cd2+ and Pb2+ are 14.68, 121.95 and 384.62 mg/g respectively. Biosorption equilibrium was achieved at 20, 30 and 60 min for Cr3+, Cd2+ and Pb2+ respectively. YZMSC biomass was found to have higher biosorption capacity and overall kinetic rate of uptake for Pb2+ than for Cd2+ and Cr3+. However, Cr3+ had better initial kinetic rate of uptake by the biomass than Pb2+ and Cd2+. The Freundlich equilibrium isotherm model was found to describe equilibrium data better than Langmuir model suggesting that biosorption of these metal ions could be on more than one active site on the surface of YZMSC biomass. Kinetic study predicted the pseudo-second kinetic model as being able to better describe kinetic data obtained than either modified pseudo-first order or Bangham kinetic models. Biosorption of Cr3+, Cd2+ and Pb2+ onto YZMSC biomass was endothermic in nature with large positive entropy values. Biosorption of these metal ions onto YZMSC biomass was observed to be feasible and spontaneous above 283 K. Optimization of biomass weight for the removal of these metal ions suggest that 384 kg, 129 kg and 144 kg of YZMSC biomass is required for the removal of 95% of Cr3+, Cd2+ and Pb2+ metal ions respectively from 100 mg/L of metal ions in 10 tonnes of aqueous solutions. KW - biomass KW - biosorption KW - optimization KW - yellow Zea mays Y1 - 2016 SN - 1582-9596 SN - 1843-3707 VL - 15 SP - 1571 EP - 1580 PB - Gh. Asachi Universitatea Tehnică IaÅŸi CY - Iasi ER - TY - JOUR A1 - Bachmann, Jennifer A1 - Heimbach, Tabea A1 - Hassenrück, Christiane A1 - Kopprio, German A. A1 - Iversen, Morten Hvitfeldt A1 - Grossart, Hans-Peter A1 - Gärdes, Astrid T1 - Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System JF - Frontiers in microbiology N2 - Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; > 3.0 mu m) and free-living (FL; 0.2-3.0 mu m) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions. KW - prokaryotes KW - biodiversity KW - microbial ecology KW - alpha diversity KW - Bray Curtis dissimilarity KW - temperature KW - salinity KW - 16S rRNA Illumina amplicon sequencing Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.02836 SN - 1664-302X VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Badalyan, Artavazd A1 - Dierich, Marlen A1 - Stiba, Konstanze A1 - Schwuchow, Viola A1 - Leimkühler, Silke A1 - Wollenberger, Ulla T1 - Electrical wiring of the aldehyde oxidoreductase PaoABC with a polymer containing osmium redox centers BT - biosensors for benzaldehyde and GABA JF - Biosensors N2 - Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below −0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A “reagentless” biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10–150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer. KW - redox polymer KW - aldehyde oxidoreductase KW - ionic strength KW - benzaldehyde KW - GABA KW - biosensor Y1 - 2014 U6 - https://doi.org/10.3390/bios4040403 VL - 4 IS - 4 SP - 403 EP - 421 PB - MDPI CY - Basel ER - TY - JOUR A1 - Badalyan, Artavazd A1 - Neumann-Schaal, Meina A1 - Leimkühler, Silke A1 - Wollenberger, Ursula T1 - A Biosensor for aromatic aldehydes comprising the mediator dependent PaoABC-Aldehyde oxidoreductase JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - A novel aldehyde oxidoreductase (PaoABC) from Escherichia coli was utilized for the development of an oxygen insensitive biosensor for benzaldehyde. The enzyme was immobilized in polyvinyl alcohol and currents were measured for aldehyde oxidation with different one and two electron mediators with the highest sensitivity for benzaldehyde in the presence of hexacyanoferrate(III). The benzaldehyde biosensor was optimized with respect to mediator concentration, enzyme loading and pH using potassium hexacyanoferrate(III). The linear measuring range is between 0.5200 mu M benzaldehyde. In correspondence with the substrate selectivity of the enzyme in solution the biosensor revealed a preference for aromatic aldehydes and less effective conversion of aliphatic aldehydes. The biosensor is oxygen independent, which is a particularly attractive feature for application. The biosensor can be applied to detect contaminations with benzaldehyde in solvents such as benzyl alcohol, where traces of benzaldehyde in benzyl alcohol down to 0.0042?% can be detected. KW - Aldehyde oxidoreductase KW - Benzaldehyde KW - Biosensor KW - Aromatic aldehydes KW - Molybdenum cofactor Y1 - 2013 U6 - https://doi.org/10.1002/elan.201200362 SN - 1040-0397 VL - 25 IS - 1 SP - 101 EP - 108 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Badalyan, Artavazd A1 - Yoga, Etienne Galemou A1 - Schwuchow, Viola A1 - Pöller, Sascha A1 - Schuhmann, Wolfgang A1 - Leimkühler, Silke A1 - Wollenberger, Ursula T1 - Analysis of the interaction of the molybdenum hydroxylase PaoABC from Escherichia coli with positively and negatively charged metal complexes JF - Electrochemistry communications : an international journal dedicated to rapid publications in electrochemistry N2 - An unusual behavior of the periplasmic aldehyde oxidoreductase (PaoABC) from Escherichia coil has been observed from electrochemical investigations of the enzyme catalyzed oxidation of aromatic aldehydes with different mediators under different conditions of ionic strength. The enzyme has similarity to other molybdoenzymes of the xanthine oxidase family, but the catalytic behavior turned out to be very different. Under steady state conditions the turnover of PaoABC is maximal at pH 4 for the negatively charged ferricyanide and at pH 9 for a positively charged osmium complex. Stopped-flow kinetic measurements of the catalytic half reaction showed that oxidation of benzaldehyde proceeds also above pH 7. Thus, benzaldehyde oxidation can proceed under acidic and basic conditions using this enzyme, a property which has not been described before for molybdenum hydroxylases. It is also suggested that the electron transfer with artificial electron acceptors and PaoABC can proceed at different protein sites and depends on the nature of the electron acceptor in addition to the ionic strength. (C) 2013 Elsevier B.V. All rights reserved. KW - Electron transfer KW - Multi-cofactor enzymes KW - Molybdoenzymes KW - Aldehyde oxidoreductase Y1 - 2013 U6 - https://doi.org/10.1016/j.elecom.2013.09.017 SN - 1388-2481 SN - 1873-1902 VL - 37 SP - 5 EP - 7 PB - Elsevier CY - New York ER - TY - JOUR A1 - Bader, Denise A1 - Klier, Dennis Tobias A1 - Hettrich, C. A1 - Bier, Frank Fabian A1 - Wessig, Pablo T1 - Detecting carbohydrate-lectin interactions using a fluorescent probe based on DBD dyes JF - Analytical methods : advancing methods and applications N2 - Herein we present an efficient synthesis of a biomimetic probe with modular construction that can be specifically bound by the mannose binding FimH protein - a surface adhesion protein of E. coli bacteria. The synthesis combines the new and interesting DBD dye with the carbohydrate ligand mannose via a Click reaction. We demonstrate the binding to E. coli bacteria over a large concentration range and also present some special characteristics of those molecules that are of particular interest for the application as a biosensor. In particular, the mix-and-measure ability and the very good photo-stability should be highlighted here. Y1 - 2016 U6 - https://doi.org/10.1039/c5ay02991k SN - 1759-9660 SN - 1759-9679 VL - 8 SP - 1235 EP - 1238 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Baeten, Lander A1 - Warton, David I. A1 - Van Calster, Hans A1 - De Frenne, Pieter A1 - Verstraeten, Gorik A1 - Bonte, Dries A1 - Bernhardt-Römermann, Markus A1 - Cornelis, Johnny A1 - Decocq, Guillaume A1 - Eriksson, Ove A1 - Hedl, Radim A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Hommel, Patrick A1 - Kirby, Keith J. A1 - Naaf, Tobias A1 - Petrik, Petr A1 - Walther, Gian-Reto A1 - Wulf, Monica A1 - Verheyen, Kris T1 - A model-based approach to studying changes in compositional heterogeneity JF - Methods in ecology and evolution : an official journal of the British Ecological Society Y1 - 2014 SN - 2041-210X SN - 2041-2096 VL - 5 IS - 2 SP - 156 EP - 164 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Baeumner, Antje J. A1 - Gauglitz, Guenter A1 - Scheller, Frieder W. T1 - Focus on bioanalysis N2 - Editoria Y1 - 2010 UR - http://www.springerlink.com/content/100417 U6 - https://doi.org/10.1007/s00216-010-4203-9 SN - 1618-2642 ER - TY - JOUR A1 - Bailleul, Frederic A1 - Grimm, Volker A1 - Chion, Clement A1 - Hammill, Mike T1 - Modeling implications of food resource aggregation on animal migration phenology JF - Ecology and evolution N2 - The distribution of poikilotherms is determined by the thermal structure of the marine environment that they are exposed to. Recent research has indicated that changes in migration phenology of beluga whales in the Arctic are triggered by changes in the thermal structure of the marine environment in their summering area. If sea temperatures reflect the spatial distribution of food resources, then changes in the thermal regime will affect how homogeneous or clumped food is distributed. We explore, by individual-based modelling, the hypothesis that changes in migration phenology are not necessarily or exclusively triggered by changes in food abundance, but also by changes in the spatial aggregation of food. We found that the level of food aggregation can significantly affect the relationship between the timing of the start of migration to the winter grounds and the total prey capture of individuals. Our approach strongly indicates that changes in the spatial distribution of food resources should be considered for understanding and quantitatively predicting changes in the phenology of animal migration. KW - Animal migration KW - food structuring KW - global change KW - individual-based model KW - polar environment Y1 - 2013 U6 - https://doi.org/10.1002/ece3.656 SN - 2045-7758 VL - 3 IS - 8 SP - 2535 EP - 2546 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Balazadeh, Salma A1 - Jaspert, Nils A1 - Arif, Muhammad A1 - Müller-Röber, Bernd A1 - Maurino, Veronica G. T1 - Expression of ROS-responsive genes and transcription factors after metabolic formation of H2O2 in chloroplasts JF - Frontiers in plant science N2 - Glycolate oxidase (GO) catalyses the oxidation of glycolate to glyoxylate, thereby consuming O-2 and producing H2O2. In this work, Arabidopsis thaliana plants expressing GO in the chloroplasts (GO plants) were used to assess the expressional behavior of reactive oxygen species (ROS)-responsive genes and transcription factors (TFs) after metabolic induction of H2O2 formation in chloroplasts. In this organelle, GO uses the glycolate derived from the oxygenase activity of RubisCO. Here, to identify genes responding to an abrupt production of H2O2 in chloroplasts we used quantitative real-time PCR (qRT-PCR) to test the expression of 187 ROS-responsive genes and 1880 TFs after transferring GO and wild-type (WT) plants grown at high CO2 levels to ambient CO2 concentration. Our data revealed coordinated expression changes of genes of specific functional networks 0.5 h after metabolic induction of H2O2 production in GO plants, including the induction of indole glucosinolate and camalexin biosynthesis genes. Comparative analysis using available microarray data suggests that signals for the induction of these genes through H2O2 may originate in the chloroplast. The TF profiling indicated an up-regulation in GO plants of a group of genes involved in the regulation of proanthocyanidin and anthocyanin biosynthesis. Moreover, the upregulation of expression of IF and IF interacting proteins affecting development (e.g., cell division, stem branching, flowering time, flower development) would impact growth and reproductive capacity, resulting in altered development under conditions that promote the formation of H2O2. KW - glycolate oxidase KW - H2O2 KW - ROS-responsive genes KW - transcription factors Y1 - 2012 U6 - https://doi.org/10.3389/fpls.2012.00234 SN - 1664-462X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Balazadeh, Salma A1 - Kwasniewski, Miroslaw A1 - Caldana, Camila A1 - Mehrnia, Mohammad A1 - Zanor, Maria Ines A1 - Xue, Gang-Ping A1 - Müller-Röber, Bernd T1 - ORS1, an H2O2-Responsive NAC Transcription Factor, Controls Senescence in Arabidopsis thaliana JF - Molecular plant N2 - We report here that ORS1, a previously uncharacterized member of the NAC transcription factor family, controls leaf senescence in Arabidopsis thaliana. Overexpression of ORS1 accelerates senescence in transgenic plants, whereas its inhibition delays it. Genes acting downstream of ORS1 were identified by global expression analysis using transgenic plants producing dexamethasone-inducible ORS1-GR fusion protein. Of the 42 up-regulated genes, 30 (similar to 70%) were previously shown to be up-regulated during age-dependent senescence. We also observed that 32 (similar to 76%) of the ORS1-dependent genes were induced by long-term (4 d), but not short-term (6 h) salinity stress (150 mM NaCl). Furthermore, expression of 16 and 24 genes, respectively, was induced after 1 and 5 h of treatment with hydrogen peroxide (H2O2), a reactive oxygen species known to accumulate during salinity stress. ORS1 itself was found to be rapidly and strongly induced by H2O2 treatment in both leaves and roots. Using in vitro binding site selection, we determined the preferred binding motif of ORS1 and found it to be present in half of the ORS1-dependent genes. ORS1 is a paralog of ORE1/ANAC092/AtNAC2, a previously reported regulator of leaf senescence. Phylogenetic footprinting revealed evolutionary conservation of the ORS1 and ORE1 promoter sequences in different Brassicaceae species, indicating strong positive selection acting on both genes. We conclude that ORS1, similarly to ORE1, triggers expression of senescence-associated genes through a regulatory network that may involve cross-talk with salt- and H2O2-dependent signaling pathways. KW - NAC transcription factor KW - leaf senescence KW - gene expression KW - gene regulatory network KW - hydrogen peroxide Y1 - 2011 U6 - https://doi.org/10.1093/mp/ssq080 SN - 1674-2052 VL - 4 IS - 2 SP - 346 EP - 360 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Balazadeh, Salma A1 - Schildhauer, Joerg A1 - Araujo, Wagner L. A1 - Munne-Bosch, Sergi A1 - Fernie, Alisdair R. A1 - Proost, Sebastian A1 - Humbeck, Klaus A1 - Müller-Röber, Bernd T1 - Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences JF - Journal of experimental botany N2 - Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated. KW - Arabidopsis KW - gene expression KW - metabolomics KW - nitrogen limitation KW - senescence KW - transcriptome Y1 - 2014 U6 - https://doi.org/10.1093/jxb/eru119 SN - 0022-0957 SN - 1460-2431 VL - 65 IS - 14 SP - 3975 EP - 3992 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Balazadeh, Salma A1 - Siddiqui, Hamad A1 - Allu, Annapurna Devi A1 - Matallana-Ramirez, Lilian Paola A1 - Caldana, Camila A1 - Mehrnia, Mohammad A1 - Zanor, Maria-Inés A1 - Koehler, Barbara A1 - Müller-Röber, Bernd T1 - A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence N2 - P>The onset and progression of senescence are under genetic and environmental control. The Arabidopsis thaliana NAC transcription factor ANAC092 (also called AtNAC2 and ORE1) has recently been shown to control age-dependent senescence, but its mode of action has not been analysed yet. To explore the regulatory network administered by ANAC092 we performed microarray-based expression profiling using estradiol-inducible ANAC092 overexpression lines. Approximately 46% of the 170 genes up-regulated upon ANAC092 induction are known senescence-associated genes, suggesting that the NAC factor exerts its role in senescence through a regulatory network that includes many of the genes previously reported to be senescence regulated. We selected 39 candidate genes and confirmed their time-dependent response to enhanced ANAC092 expression by quantitative RT-PCR. We also found that the majority of them (24 genes) are up-regulated by salt stress, a major promoter of plant senescence, in a manner similar to that of ANAC092, which itself is salt responsive. Furthermore, 24 genes like ANAC092 turned out to be stage-dependently expressed during seed growth with low expression at early and elevated expression at late stages of seed development. Disruption of ANAC092 increased the rate of seed germination under saline conditions, whereas the opposite occurred in respective overexpression plants. We also detected a delay of salinity-induced chlorophyll loss in detached anac092-1 mutant leaves. Promoter-reporter (GUS) studies revealed transcriptional control of ANAC092 expression during leaf and flower ageing and in response to salt stress. We conclude that ANAC092 exerts its functions during senescence and seed germination through partly overlapping target gene sets. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0960-7412 U6 - https://doi.org/10.1111/j.1365-313X.2010.04151.x SN - 0960-7412 ER - TY - JOUR A1 - Balint, Miklos A1 - Marton, Orsolya A1 - Schatz, Marlene A1 - Düring, Rolf-Alexander A1 - Grossart, Hans-Peter T1 - Proper experimental design requires randomization/balancing of molecular ecology experiments JF - Ecology and evolution N2 - Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results. KW - batch effect KW - bias KW - DNA extraction KW - environmental DNA KW - laboratory practice KW - lake community KW - metabarcoding KW - nondemonic intrusions KW - PCR KW - sediment Y1 - 2018 U6 - https://doi.org/10.1002/ece3.3687 SN - 2045-7758 VL - 8 IS - 3 SP - 1786 EP - 1793 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Ball, Steven G. A1 - Liénard, Luc A1 - Wattebled, Fabrice A1 - Steup, Martin A1 - Hicks, Glenn A1 - d'Hulst, Christophe T1 - Defining the functions of maltodextrin active enzymes in starch metabolism in the unicellular alga Chlamydomonas reinhardtii Y1 - 2003 ER - TY - JOUR A1 - Banerjee, Pallavi A1 - Lipowsky, Reinhard A1 - Santer, Mark T1 - Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein JF - Journal of Chemical Theory and Computation N2 - Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models. KW - Martini force-field KW - osmotic-pressure KW - potential-functions KW - aqueous-solution KW - dynamics KW - coefficient KW - simulation KW - trypanosoma KW - transition KW - parameters Y1 - 2020 U6 - https://doi.org/10.1021/acs.jctc.0c00056 SN - 1549-9626 SN - 1549-9618 VL - 16 IS - 6 PB - ACS Publications CY - Washington DC ER - TY - JOUR A1 - Banks, Jo Ann A1 - Nishiyama, Tomoaki A1 - Hasebe, Mitsuyasu A1 - Bowman, John L. A1 - Gribskov, Michael A1 - dePamphilis, Claude A1 - Albert, Victor A. A1 - Aono, Naoki A1 - Aoyama, Tsuyoshi A1 - Ambrose, Barbara A. A1 - Ashton, Neil W. A1 - Axtell, Michael J. A1 - Barker, Elizabeth A1 - Barker, Michael S. A1 - Bennetzen, Jeffrey L. A1 - Bonawitz, Nicholas D. A1 - Chapple, Clint A1 - Cheng, Chaoyang A1 - Correa, Luiz Gustavo Guedes A1 - Dacre, Michael A1 - DeBarry, Jeremy A1 - Dreyer, Ingo A1 - Elias, Marek A1 - Engstrom, Eric M. A1 - Estelle, Mark A1 - Feng, Liang A1 - Finet, Cedric A1 - Floyd, Sandra K. A1 - Frommer, Wolf B. A1 - Fujita, Tomomichi A1 - Gramzow, Lydia A1 - Gutensohn, Michael A1 - Harholt, Jesper A1 - Hattori, Mitsuru A1 - Heyl, Alexander A1 - Hirai, Tadayoshi A1 - Hiwatashi, Yuji A1 - Ishikawa, Masaki A1 - Iwata, Mineko A1 - Karol, Kenneth G. A1 - Koehler, Barbara A1 - Kolukisaoglu, Uener A1 - Kubo, Minoru A1 - Kurata, Tetsuya A1 - Lalonde, Sylvie A1 - Li, Kejie A1 - Li, Ying A1 - Litt, Amy A1 - Lyons, Eric A1 - Manning, Gerard A1 - Maruyama, Takeshi A1 - Michael, Todd P. A1 - Mikami, Koji A1 - Miyazaki, Saori A1 - Morinaga, Shin-ichi A1 - Murata, Takashi A1 - Müller-Röber, Bernd A1 - Nelson, David R. A1 - Obara, Mari A1 - Oguri, Yasuko A1 - Olmstead, Richard G. A1 - Onodera, Naoko A1 - Petersen, Bent Larsen A1 - Pils, Birgit A1 - Prigge, Michael A1 - Rensing, Stefan A. A1 - Mauricio Riano-Pachon, Diego A1 - Roberts, Alison W. A1 - Sato, Yoshikatsu A1 - Scheller, Henrik Vibe A1 - Schulz, Burkhard A1 - Schulz, Christian A1 - Shakirov, Eugene V. A1 - Shibagaki, Nakako A1 - Shinohara, Naoki A1 - Shippen, Dorothy E. A1 - Sorensen, Iben A1 - Sotooka, Ryo A1 - Sugimoto, Nagisa A1 - Sugita, Mamoru A1 - Sumikawa, Naomi A1 - Tanurdzic, Milos A1 - Theissen, Guenter A1 - Ulvskov, Peter A1 - Wakazuki, Sachiko A1 - Weng, Jing-Ke A1 - Willats, William W. G. T. A1 - Wipf, Daniel A1 - Wolf, Paul G. A1 - Yang, Lixing A1 - Zimmer, Andreas D. A1 - Zhu, Qihui A1 - Mitros, Therese A1 - Hellsten, Uffe A1 - Loque, Dominique A1 - Otillar, Robert A1 - Salamov, Asaf A1 - Schmutz, Jeremy A1 - Shapiro, Harris A1 - Lindquist, Erika A1 - Lucas, Susan A1 - Rokhsar, Daniel A1 - Grigoriev, Igor V. T1 - The selaginella genome identifies genetic changes associated with the evolution of vascular plants JF - Science N2 - Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes. Y1 - 2011 U6 - https://doi.org/10.1126/science.1203810 SN - 0036-8075 VL - 332 IS - 6032 SP - 960 EP - 963 PB - American Assoc. for the Advancement of Science CY - Washington 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 - Baral, Hans Otto A1 - Rönsch, Peter A1 - Richter, Udo A1 - Urban, Alexander A1 - Kruse, Julia A1 - Bemmann, Martin A1 - Kummer, Volker A1 - Javier Valencia, Francisco A1 - Huth, Wolfgang T1 - Schroeteria decaisneana, S. poeltii, and Ciboria ploettneriana (Sclerotiniaceae, Helotiales, Ascomycota), three parasites on Veronica seeds BT - first report of teleomorphs in Schroeteria JF - Mycological progress : international journal of the German Mycological Society N2 - Ciboria ploettneriana, Schroeteria decaisneana, and S. poeltii produce morphologically very similar apothecia emerging from fallen stromatized seeds of Veronica spp., the former two on V. hederifolia agg. in temperate central Europe and S. poeltii on V. cymbalaria in mediterranean southern Europe. They are described and illustrated in detail based on fresh collections or moist chamber cultures of infected seeds. A key is provided to differentiate the three species from their teleomorphs. For the first time, connections between two teleomorphs and two Schroeteria anamorphs are reported. Members of the anamorph-typified genus Schroeteria are known as host-specific plant parasites that infect seeds of different Veronica spp. In earlier times, they were classified in the Ustilaginales (Basidiomycota), but since more than 30 years, they are referred to as false smut fungi producing smut-like chlamydospores, based on light microscopic and ultrastructural studies which referred them to the Sclerotiniaceae (Helotiales). During the present study, rDNA sequences were obtained for the first time from chlamydospores of Schroeteria bornmuelleri (on V. rubrifolia), S. decaisneana (on V. hederifolia), S. delastrina (generic type, on V. arvensis), and S. poeltii (on V. cymbalaria) and from apothecia of C. ploettneriana, S. decaisneana, and S. poeltii. As a result, the anamorph-teleomorph connection could be established for S. decaisneana and S. poeltii by a 100% ITS similarity, whereas C. ploettneriana could not be connected to a smut-like anamorph. Ciboria ploettneriana in the here-redefined sense clustered in our combined phylogenetic analyses of ITS and LSU in relationship of Sclerotinia s.l., Botrytis, and Myriosclerotinia rather than Ciboria, but its placement was not supported. Its affiliation in Ciboria was retained until a better solution is found. Also Schroeteria poeltii clustered unresolved in this relationship but with a much higher molecular distance. The remaining three Schroeteria spp. formed a strongly supported monophyletic group, here referred to as "Schroeteria core clade", which clustered with medium to high support as a sister clade of Monilinia jezoensis, a member of the Monilinia alpina group of section Disjunctoriae. We observed ITS distances of 5-6.3% among members of the Schroeteria core clade, but 13.8-14.7% between this clade and S. poeltii, which appears to be correlated with the deviating chlamydospore morphology of S. poeltii. Despite its apparent paraphyly, Schroeteria is accepted here in a wide sense as a genus distinct from Monilinia, particularly because of its very special anamorphs. A comparable heterogeneity in rDNA analyses was observed in Monilinia and other genera of Sclerotiniaceae. Such apparent heterogeneity should be met with skepticism, however, because the inclusion of protein-coding genes in phylogenetic analyses resulted in a monophyletic genus Monilinia. More sclerotiniaceous taxa should be analysed for protein-coding genes in the future, including Schroeteria. Four syntype specimens of Ciboria ploettneriana in B were reexamined in the present study, revealing a mixture of the two species growing on V. hederifolia agg. Based on its larger ascospores in comparison with S. decaisneana, a lectotype is proposed for C. ploettneriana. KW - anamorph-teleomorph connection KW - plant parasite KW - false smut fungi KW - seed KW - infection KW - Veronica hederifolia KW - Veronica cymbalaria Y1 - 2022 U6 - https://doi.org/10.1007/s11557-021-01742-4 SN - 1617-416X SN - 1861-8952 VL - 21 IS - 1 SP - 359 EP - 407 PB - Springer CY - Berlin ; Heidelberg ER - TY - JOUR A1 - Barbier, Guillaume A1 - Oesterhelt, Christine A1 - Larson, Matthew D. A1 - Halgren, Robert G. A1 - Wilkerson, Curtis A1 - Garavito, Michael R. A1 - Benning, Christoph A1 - Weber, Andreas P. M. T1 - Comparative genomics of two closely related unicellular thermo-acidophilic red algae, Galdieria sulphuraria and Cyanidioschyzon merolae, reveals the molecular basis of the metabolic flexibility of Galdieria sulphuraria and sigant differences in carbohydrate metabolism of both algae N2 - Unicellular algae serve as models for the study and discovery of metabolic pathways, for the functional dissection of cell biological processes such as organellar division and cell motility, and for the identification of novel genes and gene functions. The recent completion of several algal genome sequences and expressed sequence tag collections and the establishment of nuclear and organellar transformation methods has opened the way for functional genomics approaches using algal model systems. The thermo-acidophilic unicellular red alga Galdieria sulphuraria represents a particularly interesting species for a genomics approach owing to its extraordinary metabolic versatility such as heterotrophic and mixotrophic growth on more than 50 different carbon sources and its adaptation to hot acidic environments. However, the ab initio prediction of genes required for unknown metabolic pathways from genome sequences is not trivial. A compelling strategy for gene identification is the comparison of similarly sized genomes of related organisms with different physiologies. Using this approach, candidate genes were identified that are critical to the metabolic versatility of Galdieria. Expressed sequence tags and high-throughput genomic sequence reads covering >70% of the G. sulphuraria genome were compared to the genome of the unicellular, obligate photoautotrophic red alga Cyanidioschyzon merolae. More than 30% of the Galdieria sequences did not relate to any of the Cyandioschyzon genes. A closer inspection of these sequences revealed a large number of membrane transporters and enzymes of carbohydrate metabolism that are unique to Galdieria. Based on these data, it is proposed that genes involved in the uptake of reduced carbon compounds and enzymes involved in their metabolism are crucial to the metabolic flexibility of G. sulphuraria Y1 - 2005 ER - TY - JOUR A1 - Barbirz, Stefanie A1 - Becker, Marion A1 - Freiberg, Alexander A1 - Seckler, Robert T1 - Phage tailspike proteins with beta-solenoid fold as thermostable carbohydrate binding materials N2 - We have investigated the stability of three tailspike proteins (TSPs) from bacteriophages Sf6, P22, and HK620. Tailspikes are rod-like homotrimers with comparable beta-solenoid folds and similarly high kinetic stability in spite of different amino acid sequences. As tailspikes bind polysaccharides to recognize the bacterial host cell, their stability is required for maintenance of bacteriophage infectivity under harsh extracellular conditions. They resist denaturation by SDS at ambient temperature and their unfolding is slow even in 6 m guanidinium hydrochloride (GdmHCl). This makes them interesting candidates for very stable carbohydrate binding protein materials. Y1 - 2009 UR - http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291616-5195 U6 - https://doi.org/10.1002/mabi.200800278 SN - 1616-5187 ER - TY - JOUR A1 - Barbirz, Stefanie A1 - Müller, Jürgen J. A1 - Uetrecht, Charlotte A1 - Clark, Alvin J. A1 - Heinemann, Udo A1 - Seckler, Robert T1 - Crystal structure of Escherichia coli phage HK620 tailspike : podoviral tailspike endoglycosidase modules are evolutionarily related N2 - Bacteriophage HK620 infects Escherichia coli H and is closely related to Shigella phage Sf6 and Salmonella phage P22. All three Podoviridae recognize and cleave their respective host cell receptor polysaccharide by homotrimeric tailspike proteins. The three proteins exhibit high sequence identity in the 110 residues of their N-terminal particle- binding domains, but no apparent sequence similarity in their major, receptor-binding parts. We have biochemically characterized the receptor-binding part of HK620 tailspike and determined its crystal structure to 1.38 Å resolution. Its major domain is a right-handed parallel ;-helix, as in Sf6 and P22 tailspikes. HK620 tailspike has endo-N- acetylglucosaminidase activity and produces hexasaccharides of an O18A1-type O-antigen. As indicated by the structure of a hexasaccharide complex determined at 1.6 Å resolution, the endoglycosidase-active sites are located intramolecularly, as in P22, and not between subunits, as in Sf6 tailspike. In contrast, the extreme C-terminal domain of HK620 tailspike forms a ;-sandwich, as in Sf6 and unlike P22 tailspike. Despite the different folds, structure-based sequence alignments of the C-termini reveal motifs conserved between the three proteins. We propose that the tailspike genes of P22, Sf6 and HK620 have a common precursor and are not mosaics of unrelated gene fragments. Y1 - 2008 UR - http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2008.06311.x/pdf SN - 0950-382X ER - TY - JOUR A1 - Barchewitz, Tino A1 - Guljamow, Arthur A1 - Meißner, Sven A1 - Timm, Stefan A1 - Henneberg, Manja A1 - Baumann, Otto A1 - Hagemann, Martin A1 - Dittmann, Elke T1 - Non-canonical localization of RubisCO under high-light conditions in the toxic cyanobacterium Microcystis aeruginosa PCC7806 JF - Environmental microbiology N2 - The frequent production of the hepatotoxin microcystin (MC) and its impact on the lifestyle of bloom-forming cyanobacteria are poorly understood. Here, we report that MC interferes with the assembly and the subcellular localization of RubisCO, in Microcystis aeruginosa PCC7806. Immunofluorescence, electron microscopic and cellular fractionation studies revealed a pronounced heterogeneity in the subcellular localization of RubisCO. At high cell density, RubisCO particles are largely separate from carboxysomes in M. aeruginosa and relocate to the cytoplasmic membrane under high-light conditions. We hypothesize that the binding of MC to RubisCO promotes its membrane association and enables an extreme versatility of the enzyme. Steady-state levels of the RubisCO CO2 fixation product 3-phosphoglycerate are significantly higher in the MC-producing wild type. We also detected noticeable amounts of the RubisCO oxygenase reaction product secreted into the medium that may support the mutual interaction of M. aeruginosa with its heterotrophic microbial community. Y1 - 2019 U6 - https://doi.org/10.1111/1462-2920.14837 SN - 1462-2912 SN - 1462-2920 VL - 21 IS - 12 SP - 4836 EP - 4851 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Bareither, Nils A1 - Scheffel, Andre A1 - Metz, Johannes T1 - Distribution of polyploid plants in the common annual Brachypodium distachyon (s.l.) in Israel is not linearly correlated with aridity JF - Israel Journal of Plant Sciences N2 - The ecological benefits of polyploidy are intensely debated. Some authors argue that plants with duplicated chromosome sets (polyploids) are more stress- resistant and superior colonizers and may thus outnumber their low ploidy conspecifics in more extreme habitats. Brachypodium distachyon (sensu lato), for example, a common annual grass in Israel and the entire Mediterranean basin, comprises three cytotypes of differing chromosome numbers that were recently proposed as distinct species. It was suggested that increased aridity increases the occurrence of its polyploid cytotype. Here, we tested at two spatial scales whether polyploid plants of B. distachyon s. l. are more frequently found in drier habitats in Israel. We collected a total of 430 specimens (i) along a largescale climatic gradient with 15 thoroughly selected sites (spanning 114- 954 mm annual rainfall), and (ii) from corresponding Northern (more mesic) and Southern (more arid) hill slopes to assess the micro- climatic difference between contrasting exposures. Cytotypes were then determined via flow cytometry. Polyploid plants comprised 90% of all specimens and their proportion ranged between 0% and 100% per site. However, this proportion was not correlated with aridity along the large- scale gradient, nor were polyploids more frequently found on Southern exposures. Our results show for both spatial scales that increasing aridity is not the principal driver for the distribution of polyploids in B. distachyon s. l. in Israel. Notably, though, diploid plants were restricted essentially to four intermediate sites, while polyploids dominated the most arid and the most mesic sites. This, to some degree, clustered pattern suggests that the distribution of cytotypes is not entirely random and calls for future studies to assess further potential drivers. KW - Aridity KW - Brachypodium distachyon KW - Brachypodium hybridum KW - Brachypodium stacei KW - cytotype KW - exposition KW - Israel KW - Mediterranean grass species KW - polyploidization KW - rainfall gradient KW - slope aspect Y1 - 2017 SN - 0792-9978 SN - 2223-8980 VL - 64 SP - 83 EP - 92 PB - Taylor & Francis CY - London ER - TY - JOUR A1 - Barlow, Axel A1 - Cahill, James A. A1 - Hartmann, Stefanie A1 - Theunert, Christoph A1 - Xenikoudakis, Georgios A1 - Gonzalez-Fortes, Gloria M. A1 - Paijmans, Johanna L. A. A1 - Rabeder, Gernot A1 - Frischauf, Christine A1 - Garcia-Vazquez, Ana A1 - Murtskhvaladze, Marine A1 - Saarma, Urmas A1 - Anijalg, Peeter A1 - Skrbinsek, Tomaz A1 - Bertorelle, Giorgio A1 - Gasparian, Boris A1 - Bar-Oz, Guy A1 - Pinhasi, Ron A1 - Slatkin, Montgomery A1 - Dalen, Love A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Partial genomic survival of cave bears in living brown bears JF - Nature Ecology & Evolution N2 - Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species. Y1 - 2018 U6 - https://doi.org/10.1038/s41559-018-0654-8 SN - 2397-334X VL - 2 IS - 10 SP - 1563 EP - 1570 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Barlow, Axel A1 - Hartmann, Stefanie A1 - Gonzalez, Javier A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. T1 - Consensify BT - a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates JF - Genes / Molecular Diversity Preservation International N2 - A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes. KW - palaeogenomics KW - ancient DNA KW - sequencing error KW - error reduction KW - D statistics KW - bioinformatics Y1 - 2020 U6 - https://doi.org/10.3390/genes11010050 SN - 2073-4425 VL - 11 IS - 1 PB - MDPI CY - Basel ER - TY - JOUR A1 - Barnett, Ross A1 - Westbury, Michael V. A1 - Sandoval-Velasco, Marcela A1 - Vieira, Filipe Garrett A1 - Jeon, Sungwon A1 - Zazula, Grant A1 - Martin, Michael D. A1 - Ho, Simon Y. W. A1 - Mather, Niklas A1 - Gopalakrishnan, Shyam A1 - Ramos-Madrigal, Jazmin A1 - de Manuel, Marc A1 - Zepeda-Mendoza, M. Lisandra A1 - Antunes, Agostinho A1 - Baez, Aldo Carmona A1 - De Cahsan, Binia A1 - Larson, Greger A1 - O'Brien, Stephen J. A1 - Eizirik, Eduardo A1 - Johnson, Warren E. A1 - Koepfli, Klaus-Peter A1 - Wilting, Andreas A1 - Fickel, Jörns A1 - Dalen, Love A1 - Lorenzen, Eline D. A1 - Marques-Bonet, Tomas A1 - Hansen, Anders J. A1 - Zhang, Guojie A1 - Bhak, Jong A1 - Yamaguchi, Nobuyuki A1 - Gilbert, M. Thomas P. T1 - Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat BT - Homotherium latidens JF - Current biology N2 - Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a -7x nuclear genome and a similar to 38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (similar to 22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage. Y1 - 2020 U6 - https://doi.org/10.1016/j.cub.2020.09.051 SN - 0960-9822 SN - 1879-0445 VL - 30 IS - 24 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Bartel, Manuela A1 - Hartmann, Stefanie A1 - Lehmann, Karola A1 - Postel, Kai A1 - Quesada, Humberto A1 - Philipp, Eva E. R. A1 - Heilmann, Katja A1 - Micheel, Burkhard A1 - Stuckas, Heiko T1 - Identification of sperm proteins as candidate biomarkers for the analysis of reproductive isolation in Mytilus: a case study for the enkurin locus JF - Marine biology : international journal on life in oceans and coastal waters N2 - Sperm proteins of the marine sessile mussels of the Mytilus edulis species complex are models to investigate reproductive isolation and speciation. This study aimed at identifying sperm proteins and their corresponding genes. This was aided by the use of monoclonal antibodies that preferentially bind to yet unknown sperm molecules. By identifying their target molecules, this approach identified proteins with relevance to Mytilus sperm function. This procedure identified 16 proteins, for example, enkurin, laminin, porin and heat shock proteins. The potential use of these proteins as genetic markers to study reproductive isolation is exemplified by analysing the enkurin locus. Enkurin evolution is driven by purifying selection, the locus displays high levels of intraspecific variation and species-specific alleles group in distinct phylogenetic clusters. These findings characterize enkurin as informative candidate biomarker for analyses of clinal variation and differential introgression in hybrid zones, for example, to understand determinants of reproductive isolation in Baltic Mytilus populations. Y1 - 2012 U6 - https://doi.org/10.1007/s00227-012-2005-7 SN - 0025-3162 VL - 159 IS - 10 SP - 2195 EP - 2207 PB - Springer CY - New York ER - TY - JOUR A1 - Bartholomäus, Alexander A1 - Fedyunin, Ivan A1 - Feist, Peter A1 - Sin, Celine A1 - Zhang, Gong A1 - Valleriani, Angelo A1 - Ignatova, Zoya T1 - Bacteria differently regulate mRNA abundance to specifically respond to various stresses JF - Geology N2 - Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up-and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs. KW - transcription KW - translation KW - deep sequencing KW - Escherichia coli KW - copy numbers Y1 - 2016 U6 - https://doi.org/10.1098/rsta.2015.0069 SN - 1364-503X SN - 1471-2962 VL - 374 PB - Royal Society CY - London ER - TY - JOUR A1 - Basel, Nicolai A1 - Harms, Ute A1 - Prechtl, Helmut T1 - Analysis of students' arguments on evolutionary theory JF - Journal of biological education N2 - A qualitative exploratory study was conducted to reveal students' argumentation skills in the context of the topic of evolution. Transcripts from problem-centred interviews on secondary students' beliefs about evolutionary processes of adaptation were analysed using a content analysis approach. For this purpose two categorical systems were deductively developed: one addressing the complexity of students' arguments, the other focusing on students' use of argumentation schemes. Subsequently, the categorical systems were inductively elaborated upon the basis of the analysed material showing a satisfactory inter-rater reliability. Regarding the arguments' complexity, students produced mainly single claims or claims with a single justification consisting of either data or warrants. With regard to argumentation schemes students drew their arguments mainly using causal schemes, analogies, or illustrative examples. Results are discussed in light of possible implications for teaching evolutionary theory using classroom argumentation. KW - evolutionary theory KW - reasoning KW - argumentation KW - argumentation schemes Y1 - 2013 U6 - https://doi.org/10.1080/00219266.2013.799078 SN - 0021-9266 SN - 2157-6009 VL - 47 IS - 4 SP - 192 EP - 199 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Basel, Nicolai A1 - Harms, Ute A1 - Prechtl, Helmut A1 - Weiss, Thomas A1 - Rothgangel, Martin T1 - Students' arguments on the science and religion issue: the example of evolutionary theory and Genesis JF - Journal of biological education N2 - Treating creationism as a controversial topic within the science and religion issue in the science classroom has been widely discussed in the recent literature. Some researchers have proposed that this topic is best addressed by focusing on sociocognitive conflict. To prepare new learning opportunities for this approach, it is necessary to know the concrete arguments that students use in their discussions on this issue. Therefore, this study aimed to provide a systematic description of these arguments. For this purpose, upper secondary students (N=43) argued for either the acceptance of evolutionary theory or faith in Genesis in a written speech. The study was conducted during their regular biology and religious education classes. Generated arguments were analysed by qualitative content analysis. Three dimensions of the arguments were described: the content (science or religion), the valuation of the argument (positive or negative), and whether the argument consisted of a descriptive or normative argumentation. The results indicate that students found it easier to generate arguments about the scientific side of the issue; however, these arguments were negatively constructed. The results are discussed with regard to implications for educational approaches for teaching controversial issues at the high-school level. KW - evolutionary theory KW - argumentation KW - science KW - religion issue KW - controversial issues Y1 - 2014 U6 - https://doi.org/10.1080/00219266.2013.849286 SN - 0021-9266 SN - 2157-6009 VL - 48 IS - 4 SP - 179 EP - 187 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Basler, Georg A1 - Ebenhoeh, Oliver A1 - Selbig, Joachim A1 - Nikoloski, Zoran T1 - Mass-balanced randomization of metabolic networks JF - Bioinformatics N2 - Motivation: Network-centered studies in systems biology attempt to integrate the topological properties of biological networks with experimental data in order to make predictions and posit hypotheses. For any topology-based prediction, it is necessary to first assess the significance of the analyzed property in a biologically meaningful context. Therefore, devising network null models, carefully tailored to the topological and biochemical constraints imposed on the network, remains an important computational problem. Results: We first review the shortcomings of the existing generic sampling scheme-switch randomization-and explain its unsuitability for application to metabolic networks. We then devise a novel polynomial-time algorithm for randomizing metabolic networks under the (bio)chemical constraint of mass balance. The tractability of our method follows from the concept of mass equivalence classes, defined on the representation of compounds in the vector space over chemical elements. We finally demonstrate the uniformity of the proposed method on seven genome-scale metabolic networks, and empirically validate the theoretical findings. The proposed method allows a biologically meaningful estimation of significance for metabolic network properties. Y1 - 2011 U6 - https://doi.org/10.1093/bioinformatics/btr145 SN - 1367-4803 VL - 27 IS - 10 SP - 1397 EP - 1403 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Basler, Georg A1 - Grimbs, Sergio A1 - Ebenhöh, Oliver A1 - Selbig, Joachim A1 - Nikoloski, Zoran T1 - Evolutionary significance of metabolic network properties JF - Interface : journal of the Royal Society N2 - Complex networks have been successfully employed to represent different levels of biological systems, ranging from gene regulation to protein-protein interactions and metabolism. Network-based research has mainly focused on identifying unifying structural properties, such as small average path length, large clustering coefficient, heavy-tail degree distribution and hierarchical organization, viewed as requirements for efficient and robust system architectures. However, for biological networks, it is unclear to what extent these properties reflect the evolutionary history of the represented systems. Here, we show that the salient structural properties of six metabolic networks from all kingdoms of life may be inherently related to the evolution and functional organization of metabolism by employing network randomization under mass balance constraints. Contrary to the results from the common Markov-chain switching algorithm, our findings suggest the evolutionary importance of the small-world hypothesis as a fundamental design principle of complex networks. The approach may help us to determine the biologically meaningful properties that result from evolutionary pressure imposed on metabolism, such as the global impact of local reaction knockouts. Moreover, the approach can be applied to test to what extent novel structural properties can be used to draw biologically meaningful hypothesis or predictions from structure alone. KW - metabolic networks KW - significance KW - randomization KW - null model KW - centrality Y1 - 2012 U6 - https://doi.org/10.1098/rsif.2011.0652 SN - 1742-5689 VL - 9 IS - 71 SP - 1168 EP - 1176 PB - Royal Society CY - London ER - TY - JOUR A1 - Basler, Georg A1 - Grimbs, Sergio A1 - Nikoloski, Zoran T1 - Optimizing metabolic pathways by screening for feasible synthetic reactions JF - Biosystems : journal of biological and information processing sciences N2 - Background: Reconstruction of genome-scale metabolic networks has resulted in models capable of reproducing experimentally observed biomass yield/growth rates and predicting the effect of alterations in metabolism for biotechnological applications. The existing studies rely on modifying the metabolic network of an investigated organism by removing or inserting reactions taken either from evolutionary similar organisms or from databases of biochemical reactions (e.g., KEGG). A potential disadvantage of these knowledge-driven approaches is that the result is biased towards known reactions, as such approaches do not account for the possibility of including novel enzymes, together with the reactions they catalyze. Results: Here, we explore the alternative of increasing biomass yield in three model organisms, namely Bacillus subtilis, Escherichia coil, and Hordeum vulgare, by applying small, chemically feasible network modifications. We use the predicted and experimentally confirmed growth rates of the wild-type networks as reference values and determine the effect of inserting mass-balanced, thermodynamically feasible reactions on predictions of growth rate by using flux balance analysis. Conclusions: While many replacements of existing reactions naturally lead to a decrease or complete loss of biomass production ability, in all three investigated organisms we find feasible modifications which facilitate a significant increase in this biological function. We focus on modifications with feasible chemical properties and a significant increase in biomass yield. The results demonstrate that small modifications are sufficient to substantially alter biomass yield in the three organisms. The method can be used to predict the effect of targeted modifications on the yield of any set of metabolites (e.g., ethanol), thus providing a computational framework for synthetic metabolic engineering. KW - Metabolic networks KW - Optimization KW - Mass-balanced reactions KW - Synthetic biology Y1 - 2012 U6 - https://doi.org/10.1016/j.biosystems.2012.04.007 SN - 0303-2647 VL - 109 IS - 2 SP - 186 EP - 191 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Basler, Georg A1 - Nikoloski, Zoran T1 - JMassBalance - mass-balanced randomization and analysis of metabolic networks JF - Bioinformatics N2 - Analysis of biological networks requires assessing the statistical significance of network-based predictions by using a realistic null model. However, the existing network null model, switch randomization, is unsuitable for metabolic networks, as it does not include physical constraints and generates unrealistic reactions. We present JMassBalance, a tool for mass-balanced randomization and analysis of metabolic networks. The tool allows efficient generation of large sets of randomized networks under the physical constraint of mass balance. In addition, various structural properties of the original and randomized networks can be calculated, facilitating the identification of the salient properties of metabolic networks with a biologically meaningful null model. Y1 - 2011 U6 - https://doi.org/10.1093/bioinformatics/btr448 SN - 1367-4803 VL - 27 IS - 19 SP - 2761 EP - 2762 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Batista, A. M. M. A1 - Woodhouse, Jason Nicholas A1 - Grossart, Hans-Peter A1 - Giani, A. T1 - Methanogenic archaea associated to Microcystis sp. in field samples and in culture JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica N2 - Cyanobacterial mass developments impact the community composition of heterotrophic microorganisms with far-reaching consequences for biogeochemical and energy cycles of freshwater ecosystems including reservoirs. Here we sought to evaluate the temporal stability of methanogenic archaea in the water column and further scrutinize their associations with cyanobacteria. Monthly samples were collected from October 2009 to December 2010 in hypereutrophic Pampulha reservoir with permanently blooming cyanobacteria, and from January to December 2011 in oligotrophic Volta Grande reservoir with only sporadic cyanobacteria incidence. The presence of archaea in cyanobacterial cultures was investigated by screening numerous strains of Microcystis spp. from these reservoirs as well as from lakes in Europe, Asia, and North-America. We consistently determined the occurrence of archaea, in particular methanogenic archaea, in both reservoirs throughout the year. However, archaea were only associated with two strains (Microcystis sp. UFMG 165 and UFMG 175) recently isolated from these reservoirs. These findings do not implicate archaea in the occurrence of methane in the epilimnion of inland waters, but rather serve to highlight the potential of microhabitats associated with particles, including phytoplankton, to shelter unique microbial communities. KW - Cyanobacteria KW - Methanogenic archaea KW - Bacterial community composition KW - Microcystis sp KW - Tropical reservoir Y1 - 2018 U6 - https://doi.org/10.1007/s10750-018-3655-3 SN - 0018-8158 SN - 1573-5117 VL - 831 IS - 1 SP - 163 EP - 172 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Batista, Rita A. A1 - Figueiredo, Duarte Dionisio A1 - Santos-Gonzalez, Juan A1 - Köhler, Claudia T1 - Auxin regulates endosperm cellularization in Arabidopsis JF - Genes & Development N2 - The endosperm is an ephemeral tissue that nourishes the developing embryo, similar to the placenta in mammals. In most angiosperms, endosperm development starts as a syncytium, in which nuclear divisions are not followed by cytokinesis. The timing of endosperm cellularization largely varies between species, and the event triggering this transition remains unknown. Here we show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest. Auxin-overproducing seeds phenocopy paternal-excess triploid seeds derived from hybridizations of diploid maternal plants with tetraploid fathers. Concurrently, auxin-related genes are strongly overexpressed in triploid seeds, correlating with increased auxin activity. Reducing auxin biosynthesis and signaling reestablishes endosperm cellularization in triploid seeds and restores their viability, highlighting a causal role of increased auxin in preventing endosperm cellularization. We propose that auxin determines the time of endosperm cellularization, and thereby uncovered a central role of auxin in establishing hybridization barriers in plants. KW - auxin KW - cellularization KW - endosperm KW - hybridization barrier KW - seed development KW - triploid block Y1 - 2019 U6 - https://doi.org/10.1101/gad.316554.118 SN - 0890-9369 SN - 1549-5477 VL - 33 IS - 7-8 SP - 466 EP - 476 PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, NY ER - TY - JOUR A1 - Batista, Rita A. A1 - Moreno-Romero, Jordi A1 - Qiu, Yichun A1 - van Boven, Joram A1 - Santos-Gonzalez, Juan A1 - Figueiredo, Duarte Dionisio A1 - Köhler, Claudia T1 - The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons JF - eLife N2 - MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network. Y1 - 2019 U6 - https://doi.org/10.7554/eLife.50541 SN - 2050-084X VL - 8 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Batsios, Petros A1 - Gräf, Ralph A1 - Koonce, Michael P. A1 - Larochelle, Denis A. A1 - Meyer, Irene T1 - Nuclear envelope organization in Dictyostelium discoideum JF - The international journal of developmental biology N2 - The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export.The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun 1, as well as with the LEM/HeH-family protein Src1. Sun 1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun 1 usually forms a so-called LINC complex.Two proteins with functions reminiscent of KASH-domain proteins at the outer nuclear membrane of Dictyostelium are known; interaptin which serves as an actin connector and the kinesin Kif9 which plays a role in the microtubule-centrosome connector. However, both of these lack the conserved KASH-domain. The link of the centrosome to the nuclear envelope is essential for the insertion of the centrosome into the nuclear envelope and the appropriate spindle formation. Moreover, centrosome insertion is involved in perm eabilization of the mitotic nucleus, which ensures access of tubulin dimers and spindle assembly factors. Our recent progress in identifying key molecular players at the nuclear envelope of Dictyostelium promises further insights into the mechanisms of nuclear envelope dynamics. KW - nuclear envelop KW - Dictyostelium KW - lamin KW - NET KW - centrosome KW - centromere Y1 - 2019 U6 - https://doi.org/10.1387/ijdb.190184rg SN - 0214-6282 SN - 1696-3547 VL - 63 IS - 8-10 SP - 509 EP - 519 PB - UBC Pr CY - Bilbao ER - TY - JOUR A1 - Batsios, Petros A1 - Ishikawa-Ankerhold, Hellen Christina A1 - Roth, Heike A1 - Schleicher, Michael A1 - Wong, Catherine C. L. A1 - Müller-Taubenberger, Annette T1 - Ate1-mediated posttranslational arginylation affects substrate adhesion and cell migration in Dictyostelium discoideum JF - Molecular biology of the cell : the official publication of the American Society for Cell Biology N2 - The highly conserved enzyme arginyl-tRNA-protein transferase (Ate1) mediates arginylation, a posttranslational modification that is only incompletely understood at its molecular level. To investigate whether arginylation affects actin-dependent processes in a simple model organism, Dictyostelium discoideum, we knocked out the gene encoding Ate1 and characterized the phenotype of ate1-null cells. Visualization of actin cytoskeleton dynamics by live-cell microscopy indicated significant changes in comparison to wild-type cells. Ate1-null cells were almost completely lacking focal actin adhesion sites at the substrate-attached surface and were only weakly adhesive. In two-dimensional chemotaxis assays toward folate or cAMP, the motility of ate1-null cells was increased. However, in three-dimensional chemotaxis involving more confined conditions, the motility of ate1-null cells was significantly reduced. Live-cell imaging showed that GFP-tagged Ate1 rapidly relocates to sites of newly formed actin-rich protrusions. By mass spectrometric analysis, we identified four arginylation sites in the most abundant actin isoform of Dictyostelium, in addition to arginylation sites in other actin isoforms and several actin-binding proteins. In vitro polymerization assays with actin purified from ate1-null cells revealed a diminished polymerization capacity in comparison to wild-type actin. Our data indicate that arginylation plays a crucial role in the regulation of cytoskeletal activities. Y1 - 2019 U6 - https://doi.org/10.1091/mbc.E18-02-0132 SN - 1059-1524 SN - 1939-4586 VL - 30 IS - 4 SP - 453 EP - 466 PB - American Society for Cell Biology CY - Bethesda ER - TY - JOUR A1 - Batsios, Petros A1 - Peter, Tatjana A1 - Baumann, Otto A1 - Stick, Reimer A1 - Meyer, Irene A1 - Gräf, Ralph T1 - A lamin in lower eukaryotes? JF - Nucleus N2 - Lamins are the major components of the nuclear lamina and serve not only as a mechanical support, but are also involved in chromatin organization, epigenetic regulation, transcription and mitotic events. Despite these universal tasks, lamins have so far been found only in metazoans. Yet, recently we have identified Dictyostelium NE81 as the first lamin-like protein in a lower eukaryote. Based on the current knowledge, we draw a model for nuclear envelope organization in Dictyostelium in this Extra View and we review the experimental data that justified this classification. Furthermore we provide unpublished data underscoring the requirement of posttranslational CaaX-box processing for proper protein localization at the nuclear envelope. Sequence comparison of NE81 sequences from four Dictyostelia with bona fide lamins illustrates the evolutional relationship between these proteins. Under certain conditions these usually unicellular social amoebae congregate to form a multicellular body. We propose that the evolution of the lamin-like NE81 went along with the invention of multicellularity. KW - dictyostelium KW - lamin KW - intermediate filament KW - centrosome KW - nucleus Y1 - 2012 U6 - https://doi.org/10.4161/nucl.20149 SN - 1949-1034 VL - 3 IS - 3 SP - 237 EP - 243 PB - Landes Bioscience CY - Austin ER - TY - JOUR A1 - Batsios, Petros A1 - Ren, Xiang A1 - Baumann, Otto A1 - Larochelle, Denis A. A1 - Gräf, Ralph T1 - Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81 JF - Cells N2 - The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11–646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture. KW - Dictyostelium KW - lamin KW - nuclear lamina KW - nucleus KW - nucleolus KW - HeH-protein KW - LEM-domain protein Y1 - 2016 U6 - https://doi.org/10.3390/cells5010013 SN - 2073-4409 VL - 5 IS - 1 PB - MDPI CY - Basel ER - TY - JOUR A1 - Bauer, Barbara A1 - Jordan, Ferenc A1 - Podani, János T1 - Node centrality indices in food webs : rank orders versus distributions N2 - Network analysis examines the role of species in ecological communities. The most common approach involves measurement of centrality of species or other groups of individuals based on their topological positions in food webs, followed by establishing the rank order of importance of these groups. However, ranking may differ considerably with indices of centrality and therefore comparison of rank orders is essential to obtain more meaningful results on species performance. Since ranking ignores absolute differences between centrality values, species orders may neglect important structural information in food webs. Consequently, simultaneous examination of the distribution of index values is inevitable. Hierarchical clustering and consensus generation revealed that rank orders of centrality exhibit a similar pattern over six example food webs, while distributions differ not only with indices because their relationships are largely inconsistent with food webs as well. Therefore, optimal analysis of networks and the selection of keystone species in any ecological study should rely upon both of these procedures. Similar conclusions are drawn from the detailed evaluation of a sample food web from the Florida Bay. Y1 - 2010 UR - http://www.sciencedirect.com/science/journal/1476945X U6 - https://doi.org/10.1016/j.ecocom.2009.11.006 SN - 1476-945X ER - TY - JOUR A1 - Bauer, Barbara A1 - Sommer, Ulrich A1 - Gaedke, Ursula T1 - High predictability of spring phytoplankton biomass in mesocosms at the species, functional group and community level JF - Freshwater biology N2 - 1. Models aim to predict phytoplankton dynamics based on observed initial conditions and a set of equations and parameters. However, our knowledge about initial conditions in nature is never perfect. Thus, if phytoplankton dynamics are sensitive to small variations in initial conditions, they are difficult to predict. 2. We used time-series data from indoor mesocosm experiments with natural phyto- and zooplankton communities to quantify the extent to which small initial differences in the species, functional group and community biomass in parallel treatments were amplified or buffered over time. We compared the differences in dynamics between replicates and among all mesocosms of 1year. 3. Temperature-sensitive grazing during the exponential growth phase of phytoplankton caused divergence. In contrast, negative density dependence caused convergence. 4. Mean differences in biomass between replicates were similar for all hierarchical levels. This indicates that differences in their initial conditions were amplified to the same extent. Even though large differences in biomass occasionally occurred between replicates for a short time, dynamics returned to the same path at all hierarchical levels. This suggests that internal feedback mechanisms make the spring development of phytoplankton highly predictable. KW - divergence KW - hierarchical level KW - mesocosms KW - predictability KW - replicates Y1 - 2013 U6 - https://doi.org/10.1111/j.1365-2427.2012.02780.x SN - 0046-5070 VL - 58 IS - 3 SP - 588 EP - 596 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Bauer, Barbara A1 - Vos, Matthijs A1 - Klauschies, Toni A1 - Gaedke, Ursula T1 - Diversity, functional similarity, and top-down control drive synchronization and the reliability of ecosystem function JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - The concept that diversity promotes reliability of ecosystem function depends on the pattern that community-level biomass shows lower temporal variability than species-level biomasses. However, this pattern is not universal, as it relies on compensatory or independent species dynamics. When in contrast within--trophic level synchronization occurs, variability of community biomass will approach population-level variability. Current knowledge fails to integrate how species richness, functional distance between species, and the relative importance of predation and competition combine to drive synchronization at different trophic levels. Here we clarify these mechanisms. Intense competition promotes compensatory dynamics in prey, but predators may at the same time increasingly synchronize, under increasing species richness and functional similarity. In contrast, predators and prey both show perfect synchronization under strong top-down control, which is promoted by a combination of low functional distance and high net growth potential of predators. Under such conditions, community-level biomass variability peaks, with major negative consequences for reliability of ecosystem function. KW - biodiversity KW - ecosystem services KW - population dynamics KW - predator-prey system KW - species richness KW - synchrony Y1 - 2014 U6 - https://doi.org/10.1086/674906 SN - 0003-0147 SN - 1537-5323 VL - 183 IS - 3 SP - 394 EP - 409 PB - Univ. of Chicago Press CY - Chicago ER - TY - JOUR A1 - Bauer, Christian G. A1 - Eremenko, A. V. A1 - Ehrentreich-Förster, Eva A1 - Bier, Frank Fabian A1 - Makower, Alexander A1 - Halsall, H. B. A1 - Heineman, W. R. A1 - Scheller, Frieder W. T1 - Zeptomole-detecting biosensor for alkaline phosphatase in an electroche mical immunoassay for 2,4- dichlorophenoacetic acid Y1 - 1996 ER - TY - JOUR A1 - Bauer, Christian G. A1 - Eremenko, A. V. A1 - Kühn, A. A1 - Kürzinger, K. A1 - Markower, Alexander A1 - Scheller, Frieder W. T1 - Automated amplifield flow immunoassay for cocaine Y1 - 1998 ER - TY - JOUR A1 - Bauer, Christian G. A1 - Kühn, A. A1 - Gajovic, Nenad A1 - Skorobogatko, O. V. A1 - Holt, P. J. A1 - Bruce, N. C. A1 - Makower, Alexander A1 - Lowe, Ch. R. A1 - Scheller, Frieder W. T1 - New enzymen sensors for morphine and codeine based on morphine dehydrogenase and laccase Y1 - 1999 ER - TY - JOUR A1 - Bauer, Daniel A1 - Werth, Felix A1 - Ha An Nguyen, A1 - Kiecker, Felix A1 - Eberle, Jürgen T1 - Critical role of reactive oxygen species (ROS) for synergistic enhancement of apoptosis by vemurafenib and the potassium channel inhibitor TRAM-34 in melanoma cells JF - Cell death & disease N2 - Inhibition of MAP kinase pathways by selective BRAF inhibitors, such as vemurafenib and dabrafenib, have evolved as key therapies of BRAF-mutated melanoma. However, tumor relapse and therapy resistance have remained as major problems, which may be addressed by combination with other pathway inhibitors. Here we identified the potassium channel inhibitor TRAM-34 as highly effective in combination with vemurafenib. Thus apoptosis was significantly enhanced and cell viability was decreased. The combination vemurafenib/TRAM-34 was also effective in vemurafenib-resistant cells, suggesting that acquired resistance may be overcome. Vemurafenib decreased ERK phosphorylation, suppressed antiapoptotic Mcl-1 and enhanced proapoptotic Puma and Bim. The combination resulted in enhancement of proapoptotic pathways as caspase-3 and loss of mitochondrial membrane potential. Indicating a special mechanism of vemurafenib-induced apoptosis, we found strong enhancement of intracellular ROS levels already at 1 h of treatment. The critical role of ROS was demonstrated by the antioxidant vitamin E (alpha-tocopherol), which decreased intracellular ROS as well as apoptosis. Also caspase activation and loss of mitochondrial membrane potential were suppressed, proving ROS as an upstream effect. Thus ROS represents an initial and independent apoptosis pathway in melanoma cells that is of particular importance for vemurafenib and its combination with TRAM-34. Y1 - 2017 U6 - https://doi.org/10.1038/cddis.2017.6 SN - 2041-4889 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Baumann, Ingrid A1 - Eckermann, Nora T1 - Ploidy level and chlorophyll content of single plastids and cells from callus cultures during conversion to autotrophic growth Y1 - 1994 ER - TY - JOUR A1 - Baumann, Ingrid A1 - Eckermann, Nora A1 - Krause, Udo A1 - Baumann, Guido T1 - Effects of sucrose in the culture medium on cytological characteristics, pigments and photosynthetic activity of green callus cultures of sugar beet Y1 - 1994 ER - TY - JOUR A1 - Baumann, Otto T1 - Spatial pattern of nonmuscle myosin-II distribution during the development of the Drosophila compound eye and implications for retinal morphogenesis N2 - Nonmuscle myosin-II is a motor protein that drives cell movement and changes in cell shape during tissue and organ development. This study has determined he dynamic changes in myosin-II distribution during Drosophila compound eye morphogenesis. In photoreceptor neurons, myosin-II is undetectable at the apical domain throughout the first half of pupal life, at which time this membrane domain is involuted into the epithelium and progresses toward the retinal floor. Myosin-II is deployed at the apical surface at about 60% of pupal development, once the developing rhabdomeres reach the retinal floor. Subsequently, myosin-II becomes restricted to two stripes at the sides of the developing rhabdomere, adopting its final position within the visual cells R1-6; here, myosin-II is associated with a set of actin filaments that extend alongside the rhabdomeres. At the midpupal stage, myosin-II is also incorporated into stress-fiber-like arrays within the basal endfeet of the pigment cells that then change their shape. This spatiotemporal pattern of myosin- II localization and the morphological defects observed in the eyes of a myosin-II mutant suggest that the myosin-II/F- actin system is involved in the alignment of the rhabdomeres within the retina and in the flattening of the retinal floor. The observation that the myosin-II/F-actin arrays are incomplete or disorganized in R7/R8 and in rhodopsin-1-null R1-6 suggests further that the establishment and stability of this cytoskeletal system depend on rhodopsin-1 expression. (C) 2004 Elsevier Inc. All rights reserved Y1 - 2004 ER - TY - JOUR A1 - Baumann, Otto T1 - The Golgi apparatus in honeybee photoreceptor cells: Structural organization and spatial relationship to microtubules and actin filaments Y1 - 1998 ER - TY - JOUR A1 - Baumann, Otto T1 - Association of spectrin with a subcompartment of the endoplasmic reticulum in honeybee photoreceptor cells. Y1 - 1998 ER - TY - JOUR A1 - Baumann, Otto T1 - Biogenesis of surface domains in fly photoreceptor cells: Fine-structural analysis of the plasma membrane and immunolocalization of Na+, K+-ATPase und alpha-spectrin during cell differentiation. Y1 - 1997 ER - TY - JOUR A1 - Baumann, Otto T1 - Distribution of Na+, K+-ATPase in photoreceptor cells of insects. Y1 - 1997 ER - TY - JOUR A1 - Baumann, Otto T1 - Disruption of actin filaments causes redistribution of ryanodine receptor Ca2+ channels in honeybee photoreceptor cells Y1 - 2001 ER - TY - JOUR A1 - Baumann, Otto T1 - Distribution of nonmuscle myosin-II in honeybee photoreceptor cells and its possible role in maintaining compound eye architecture Y1 - 2001 ER - TY - JOUR A1 - Baumann, Otto T1 - Posterior midgut epithelial cells differ in their organization of the membrane skeleton from other Drosophila epithelia Y1 - 2001 ER - TY - JOUR A1 - Baumann, Otto T1 - Distribution of ryanodine receptor Ca2+ channels in insect photoreceptor cells Y1 - 2000 ER - TY - JOUR A1 - Baumann, Otto A1 - Arlt, Kathleen A1 - Römmling, Katja A1 - Goller, Helmut A1 - Walz, Bernd T1 - Characterization of an extremely motile cellular network in the rotifer Asplanchna spp. : structure, kinetics, and cytoskeleton Y1 - 2000 ER - TY - JOUR A1 - Baumann, Otto A1 - Arlt, Kathleen A1 - Römmling, Katja A1 - Goller, Helmut A1 - Walz, Bernd T1 - Characterization of an extremely motile cellular network in the rotifer Asplanchna : Structure, kinetics and the cytoskeleton Y1 - 2000 ER - TY - JOUR A1 - Baumann, Otto A1 - Bauer, Alexandra T1 - Development of apical membrane organization and V-ATPase regulation in blowfly salivary glands JF - The journal of experimental biology N2 - Secretory cells in blowfly salivary gland are specialized via morphological and physiological attributes in order to serve their main function, i.e. the transport of solutes at a high rate in response to a hormonal stimulus, namely serotonin (5-HT). This study examines the way that 5-HT-insensitive precursor cells differentiate into morphologically complex 5-HT-responsive secretory cells. By means of immunofluorescence microscopy, immunoblotting and measurements of the transepithelial potential changes, we show the following. (1) The apical membrane of the secretory cells becomes organized into an elaborate system of canaliculi and is folded into pleats during the last pupal day and the first day of adulthood. (2) The structural reorganization of the apical membrane is accompanied by an enrichment of actin filaments and phosphorylated ERM protein (phospho-moesin) at this membrane domain and by the deployment of the membrane-integral part of vacuolar-type H+-ATPase (V-ATPase). These findings suggest a role for phospho-moesin, a linker between actin filaments and membrane components, in apical membrane morphogenesis. (3) The assembly and activation of V-ATPase can be induced immediately after eclosion by way of 8-CPT-cAMP, a membrane-permeant cAMP analogue. (4) 5-HT, however, produces the assembly and activation of V-ATPase only in flies aged for at least 2 h after eclosion, indicating that, at eclosion, the 5-HT receptor/adenylyl cyclase/cAMP signalling pathway is inoperative upstream of cAMP. (5) 5-HT activates both the Ca2+ signalling pathway and the cAMP signalling cascade in fully differentiated secretory cells. However, the functionality of these signalling cascades does not seem to be established in a tightly coordinated manner during cell differentation. KW - secretory cell KW - moesin KW - morphogenesis KW - serotonin KW - vacuolar ATPase KW - cAMP Y1 - 2013 U6 - https://doi.org/10.1242/jeb.077420 SN - 0022-0949 VL - 216 IS - 7 SP - 1225 EP - 1234 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Baumann, Otto A1 - Dames, Petra A1 - Kühnel, Dana A1 - Walz, Bernd T1 - Distribution of serotonergic and dopaminergic nerve fibers in the salivary gland complex of the cockroach Periplaneta americana Y1 - 2002 UR - http://www.biomedcentral.com/1472-6793/2/9 ER - TY - JOUR A1 - Baumann, Otto A1 - Kühnel, Dana A1 - Dames, Petra A1 - Walz, Bernd T1 - Dopaminergic and serotonergic innervation of cockroach salivary glands : distribution and morphology of synapses and release sites N2 - The paired salivary glands in the cockroach are composed of acini with ion-transporting peripheral P-cells and protein-secreting central C-cells, and a duct system for the modification of the primary saliva. Secretory activity is controlled by serotonergic and dopaminergic neurons, whose axons form a dense plexus on the glands. The spatial relationship of release sites for serotonin and dopamine to the various cell types was determined by anti-synapsin immunofluorescence confocal microscopy and electron microscopy. Every C-cell apparently has only serotonergic synapses on its surface. Serotonergic and dopaminergic fibres on the acini have their release zones at a distance of similar to0.5 mum from the P-cells. Nerves between acinar lobules may serve as neurohaemal organs and contain abundant dopaminergic and few serotonergic release sites. Some dopaminergic and serotonergic release sites reside in the duct epithelium, the former throughout the duct system, the latter only in segments next to acini. These findings are consistent with the view that C-cells respond exclusively to serotonin, P-cells to serotonin and dopamine, and most duct cells only to dopamine. Moreover, the data suggest that C-cells are stimulated by serotonin released close to their surface, whereas P-cells and most duct cells are exposed to serotonin/dopamine liberated at some distance Y1 - 2004 ER - TY - JOUR A1 - Baumann, Otto A1 - Lutz, Kathleen T1 - Photoreceptor morphogenesis in the Drosophila compound eye : R1-R6 rhabdomeres become twisted just before eclosion N2 - The photosensitive microvilli of Drosophila photoreceptors R1-R6 are not aligned in parallel over the entire length of the visual cells. In the distal half of each cell, the microvilli are slightly tilted toward one side and, in the proximal half, extremely toward the opposite side. This phenomenon, termed rhabdomere twisting, has been known for several decades, but the developmental and cell biological basis of rhabdomere twisting has not been studied so far. We show that rhabdomere twisting is also manifested as molecular polarization of the visual cell, because phosphotyrosine- containing proteins are selectively partitioned to different sides of the rhabdomere stalk in the distal. and proximal sections of each R1-R6 photoreceptor. Both the asymmetrical segregation of phosphotyrosine proteins and the tilting of the microvilli occur shortly before eclosion of the flies, when eye development in all other aspects is considered to be essentially complete. Establishment of rhabdomere twisting occurs in a light-independent manner, because phosphotyrosine staining is unchanged in dark-reared wild-type flies and in mutants with defects in the phototransduction cascade, ninaE(17) and norpA(P24). We conclude that antiphosphotyrosine immunofluorescence can be used as a light microscopic probe for the analysis of rhabdomere twisting and that microvilli tilting represents a type of planar cell polarity that is established by an active process in the last phase of photoreceptor morphogenesis, just prior to eclosion of the flies. Y1 - 2006 UR - http://www3.interscience.wiley.com/cgi-bin/jhome/31248 U6 - https://doi.org/10.1002/Cne.21030 SN - 0021-9967 ER - TY - JOUR A1 - Baumann, Otto A1 - Murphy, Douglas B. T1 - Microtubule-associated movement of mitochondria and small particles in Acanthamoeba castellanii. Y1 - 1995 ER - TY - JOUR A1 - Baumann, Otto A1 - Salvaterra, Paul M. A1 - Takeyasu, Kunio T1 - Developmental changes in beta-subunit composition of Na,K-ATPase in the Drosophila eye N2 - The Drosophila genome contains at least three loci for the Na,K-ATPase beta-subunit; however, only the protein products of nrv1 and nrv2 have been characterized hitherto. Here, we provide evidence that nrv3 also encodes for a functional Na,K-ATPase beta-subunit, as its protein product co-precipitates with the Na,K-ATPase alpha-subunit. Nrv3 expression in adult flies is restricted to the nervous system in which Nrv3 is enriched in selective types of sensory cells. Because Nrv3 expression is especially prominent in the compound eye, we have analyzed the subcellular and developmental distribution of Nrv3 within the visual cells and related this distribution to those of the alpha-subunit and of the beta-subunits Nrv1 and Nrv2. Prospective visual cells express Nrv2 in the third larval instar stage and during the first half of pupal development. During the last third of pupal life, Nrv3 gradually replaces Nrv2 as the Na,K-ATPase beta-subunit in the photoreceptor cells. Adult photoreceptors express Nrv3 as their major beta-subunit; the visual cells R1-R6 co-express Nrv2 at a low level, whereas R7 and R8 co-express Nrv1. Notably, beta-subunits do not co- distribute exactly with the alpha-subunit at some developmental stages, supporting the concept that the alpha-subunit and beta-subunit can exist in the plasma membrane without being engaged in alpha/beta heterodimers. The non-visual cells within the compound eye express almost exclusively Nrv2, which segregates together with the alpha-subunit to septate junctions throughout development. Y1 - 2010 UR - http://www.springerlink.com/content/100524 U6 - https://doi.org/10.1007/s00441-010-0948-x SN - 0302-766X ER - TY - JOUR A1 - Baumann, Otto A1 - Walz, Bernd T1 - The endoplasmic reticulum of animal cells and its organization into structural and functional domains Y1 - 2001 ER - TY - JOUR A1 - Baumann, Tobias A1 - Arndt, Katja Maren A1 - Müller, Kristian M. T1 - Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V JF - BMC biotechnology N2 - Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed. KW - Cohesive ends KW - DNA cleavage KW - Genetic vectors KW - Modified primers KW - Molecular methods KW - Polymerase chain reaction KW - Recombinant Escherichia coli KW - Restriction enzymes Y1 - 2013 U6 - https://doi.org/10.1186/1472-6750-13-81 SN - 1472-6750 VL - 13 IS - 10 PB - BioMed Central CY - London ER - TY - JOUR A1 - Baunach, Martin A1 - Chowdhury, Somak A1 - Stallforth, Pierre A1 - Dittmann-Thünemann, Elke T1 - The landscape of recombination events that create nonribosomal peptide diversity JF - Molecular biology and evolution : MBE N2 - Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing andmatching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the A(core) domains, yet domain interfaces and the flexible A(sub) domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches. KW - evolution KW - recombination KW - structural diversity KW - natural products KW - nonribosomal peptide synthetases KW - microbial ecology Y1 - 2021 U6 - https://doi.org/10.1093/molbev/msab015 SN - 0737-4038 SN - 1537-1719 VL - 38 IS - 5 SP - 2116 EP - 2130 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Baxa, Ulrich A1 - Cooper, Alan A1 - Weintraub, N. A1 - Pfeil, Wolfgang A1 - Seckler, Robert T1 - Enthalpic barriers to the hydrophobic binding of oligosaccharides to phage P22 tailspike protein Y1 - 2001 ER - TY - JOUR A1 - Baxa, Ulrich A1 - Steinbacher, Stefan A1 - Weintraub, Andrej A1 - Huber, Robert A1 - Seckler, Robert T1 - Mutations improving the folding of phage P22 tailspike protein affect its receptor binfing activity Y1 - 1999 ER - TY - JOUR A1 - Baxa, Ulrich A1 - Weintraub, Andrej A1 - Seckler, Robert T1 - Self-competitive inhibition of the bacteriophage P22 Tailspike endorhamnosidase by O-antigen oligosaccharides JF - Biochemistry N2 - The P22 tailspike endorhamnosidase confers the high specificity of bacteriophage P22 for some serogroups of Salmonella differing only slightly in their O-antigen polysaccharide. We used several biophysical methods to study the binding and hydrolysis of O-antigen fragments of different lengths by P22 tailspike protein. O-Antigen saccharides of defined length labeled with fluorophors could be purified with higher resolution than previously possible. Small amounts of naturally occurring variations of 0antigen fragments missing the nonreducing terminal galactose could be used to determine the contribution of this part to the free energy of binding to be similar to 7 kJ/mol. We were able to show via several independent lines of evidence that an unproductive binding mode is highly favored in binding over all other possible binding modes leading to hydrolysis. This is true even under circumstances under which the O-antigen fragment is long enough to be cleaved efficiently by the enzyme. The high-affinity unproductive binding mode results in a strong self-competitive inhibition in addition to product inhibition observed for this system. Self-competitive inhibition is observed for all substrates that have a free reducing end rhamnose. Naturally occurring O-antigen, while still attached to the bacterial outer membrane, does not have a free reducing end and therefore does not perform self-competitive inhibition. Y1 - 2020 U6 - https://doi.org/10.1021/acs.biochem.0c00872 SN - 0006-2960 VL - 59 IS - 51 SP - 4845 EP - 4855 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Bayerl, Helmut A1 - Kraus, Robert H. S. A1 - Nowak, Carsten A1 - Foerster, Daniel W. A1 - Fickel, Jörns A1 - Kühn, Ralph T1 - Fast and cost-effective single nucleotide polymorphism (SNP) detection in the absence of a reference genome using semideep next-generation Random Amplicon Sequencing (RAMseq) JF - Molecular ecology resources N2 - Biodiversity has suffered a dramatic global decline during the past decades, and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and on a genetic level. However, in wild species, the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article, we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in nonmodel species by semideep sequencing of random amplicons. By applying RAMseq to the Eurasian otter (Lutra lutra), we identified 238 putative SNPs after quality filtering of all candidate loci and were able to validate 32 of 77 loci tested. In a second step, we evaluated the genotyping performance of these SNP loci in noninvasive samples, one of the most challenging genotyping applications, by comparing it with genotyping results of the same faecal samples at microsatellite markers. We compared (i) polymerase chain reaction (PCR) success rate, (ii) genotyping errors and (iii) Mendelian inheritance (population parameters). SNPs produced a significantly higher PCR success rate (75.5% vs. 65.1%) and lower mean allelic error rate (8.8% vs. 13.3%) than microsatellites, but showed a higher allelic dropout rate (29.7% vs. 19.8%). Genotyping results showed no deviations from Mendelian inheritance in any of the SNP loci. Hence, RAMseq appears to be a valuable tool for the detection of genetic markers in nonmodel species, which is a common challenge in conservation genetic studies. KW - high-throughput sequencing KW - Lutra lutra KW - nonmodel species KW - RAMseq KW - RAPD KW - variant detection Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12717 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 1 SP - 107 EP - 117 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Baylis, Alastair M. M. A1 - Kowalski, Gabriele Joanna A1 - Voigt, Christian C. A1 - Orben, Rachael A. A1 - Trillmich, Fritz A1 - Staniland, Iain J. A1 - Hoffman, Joseph I. T1 - Pup Vibrissae Stable Isotopes Reveal Geographic Differences in Adult Female Southern Sea Lion Habitat Use during Gestation JF - PLoS one N2 - Individuals within populations often differ substantially in habitat use, the ecological consequences of which can be far reaching. Stable isotope analysis provides a convenient and often cost effective means of indirectly assessing the habitat use of individuals that can yield valuable insights into the spatiotemporal distribution of foraging specialisations within a population. Here we use the stable isotope ratios of southern sea lion (Otaria flavescens) pup vibrissae at the Falkland Islands, in the South Atlantic, as a proxy for adult female habitat use during gestation. A previous study found that adult females from one breeding colony (Big Shag Island) foraged in two discrete habitats, inshore (coastal) or offshore (outer Patagonian Shelf). However, as this species breeds at over 70 sites around the Falkland Islands, it is unclear if this pattern is representative of the Falkland Islands as a whole. In order to characterize habitat use, we therefore assayed carbon (delta C-13) and nitrogen (delta N-15) ratios from 65 southern sea lion pup vibrissae, sampled across 19 breeding colonies at the Falkland Islands. Model-based clustering of pup isotope ratios identified three distinct clusters, representing adult females that foraged inshore, offshore, and a cluster best described as intermediate. A significant difference was found in the use of inshore and offshore habitats between West and East Falkland and between the two colonies with the largest sample sizes, both of which are located in East Falkland. However, habitat use was unrelated to the proximity of breeding colonies to the Patagonian Shelf, a region associated with enhanced biological productivity. Our study thus points towards other factors, such as local oceanography and its influence on resource distribution, playing a prominent role in inshore and offshore habitat use. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0157394 SN - 1932-6203 VL - 11 SP - 1824 EP - 1835 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Beatham, Jane L. A1 - Middleton, A. A1 - Romero, Rosario A1 - VanderVen, Peter F. M. A1 - Blanco, Gonzalo T1 - Functional characterisation of the Ky protein Y1 - 2004 SN - 0960-8966 ER - TY - JOUR A1 - Beatham, Jane L. A1 - Romero, Rosario A1 - Townsend, Stuart K.M. A1 - Hacker, Terry A1 - VanderVen, Peter F. M. A1 - Blanco, Gonzalo T1 - Filamin C interacts with the muscular dystrophy KY protein and is abnormally distributed in mouse KY deficient muscle fibres N2 - The KY protein has been implicated in a neuromuscular dystrophy in the mouse, but its role in muscle function remains unclear. Here, we show that KY interacts with several sarcomeric cytoskeletal proteins including, amongst others, filamin C and the slow isoform of the myosin-binding protein C. These interactions were confirmed in vitro and because of its central role in skeletal muscle disease, characterized in more detail for filamin C. A role for KY in regulating filamin C function in vivo is supported by the expression analysis of filamin C in the null ky mouse mutant, where distinct irregular subcellular localization of filamin C was found in subsets of muscle fibres, which appears to be a specific outcome of KY deficiency. Furthermore, KY shows protease activity in in vitro assays, and specific degradation of filamin C by KY is shown in transfected cells. Given the enzymatic nature of the KY protein, it is likely that some of the identified partners are catalytic substrates. These results suggest that KY is an intrinsic part of the protein networks underlying the molecular mechanism of several limb-girdle muscular dystrophies, particularly those where interactions between filamin C and disease causing proteins have been shown Y1 - 2004 SN - 0964-6906 ER - TY - JOUR A1 - Beaumont, Robin N. A1 - Warrington, Nicole M. A1 - Cavadino, Alana A1 - Tyrrell, Jessica A1 - Nodzenski, Michael A1 - Horikoshi, Momoko A1 - Geller, Frank A1 - Myhre, Ronny A1 - Richmond, Rebecca C. A1 - Paternoster, Lavinia A1 - Bradfield, Jonathan P. A1 - Kreiner-Moller, Eskil A1 - Huikari, Ville A1 - Metrustry, Sarah A1 - Lunetta, Kathryn L. A1 - Painter, Jodie N. A1 - Hottenga, Jouke-Jan A1 - Allard, Catherine A1 - Barton, Sheila J. A1 - Espinosa, Ana A1 - Marsh, Julie A. A1 - Potter, Catherine A1 - Zhang, Ge A1 - Ang, Wei A1 - Berry, Diane J. A1 - Bouchard, Luigi A1 - Das, Shikta A1 - Hakonarson, Hakon A1 - Heikkinen, Jani A1 - Helgeland, Oyvind A1 - Hocher, Berthold A1 - Hofman, Albert A1 - Inskip, Hazel M. A1 - Jones, Samuel E. A1 - Kogevinas, Manolis A1 - Lind, Penelope A. A1 - Marullo, Letizia A1 - Medland, Sarah E. A1 - Murray, Anna A1 - Murray, Jeffrey C. A1 - Njolstad, Pal R. A1 - Nohr, Ellen A. A1 - Reichetzeder, Christoph A1 - Ring, Susan M. A1 - Ruth, Katherine S. A1 - Santa-Marina, Loreto A1 - Scholtens, Denise M. A1 - Sebert, Sylvain A1 - Sengpiel, Verena A1 - Tuke, Marcus A. A1 - Vaudel, Marc A1 - Weedon, Michael N. A1 - Willemsen, Gonneke A1 - Wood, Andrew R. A1 - Yaghootkar, Hanieh A1 - Muglia, Louis J. A1 - Bartels, Meike A1 - Relton, Caroline L. A1 - Pennell, Craig E. A1 - Chatzi, Leda A1 - Estivill, Xavier A1 - Holloway, John W. A1 - Boomsma, Dorret I. A1 - Montgomery, Grant W. A1 - Murabito, Joanne M. A1 - Spector, Tim D. A1 - Power, Christine A1 - Jarvelin, Marjo-Ritta A1 - Bisgaard, Hans A1 - Grant, Struan F. A. A1 - Sorensen, Thorkild I. A. A1 - Jaddoe, Vincent W. A1 - Jacobsson, Bo A1 - Melbye, Mads A1 - McCarthy, Mark I. A1 - Hattersley, Andrew T. A1 - Hayes, M. Geoffrey A1 - Frayling, Timothy M. A1 - Hivert, Marie-France A1 - Felix, Janine F. A1 - Hypponen, Elina A1 - Lowe, William L. A1 - Evans, David M. A1 - Lawlor, Debbie A. A1 - Feenstra, Bjarke A1 - Freathy, Rachel M. T1 - Genome-wide association study of offspring birth weight in 86 577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics JF - Human molecular genetics N2 - Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86 577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother-child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B, HMGA2, SH2B3, KCNAB1, L3MBTL3, GCK, EBF1, TCF7L2, ACTL9, CYP3A7) were associated with offspring birth weight at P< 5 x 10(-8). In SEM analyses, at least 7 of the 10 associations were consistent with effects of the maternal genotype acting via the intrauterine environment, rather than via effects of shared alleles with the fetus. Variants, or correlated proxies, at many of the loci had been previously associated with adult traits, including fasting glucose (MTNR1B, GCK and TCF7L2) and sex hormone levels (CYP3A7), and one (EBF1) with gestational duration. The identified associations indicate that genetic effects on maternal glucose, cytochrome P450 activity and gestational duration, and potentially on maternal blood pressure and immune function, are relevant for fetal growth. Further characterization of these associations in mechanistic and causal analyses will enhance understanding of the potentially modifiable maternal determinants of fetal growth, with the goal of reducing the morbidity and mortality associated with low and high birth weights. Y1 - 2018 U6 - https://doi.org/10.1093/hmg/ddx429 SN - 0964-6906 SN - 1460-2083 VL - 27 IS - 4 SP - 742 EP - 756 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Becher, Matthias A. A1 - Grimm, Volker A1 - Thorbek, Pernille A1 - Horn, Juliane A1 - Kennedy, Peter J. A1 - Osborne, Juliet L. T1 - BEEHAVE: a systems model of honeybee colony dynamics and foraging to explore multifactorial causes of colony failure JF - Journal of applied ecology : an official journal of the British Ecological Society N2 - BEEHAVE offers a valuable tool for researchers to design and focus field experiments, for regulators to explore the relative importance of stressors to devise management and policy advice and for beekeepers to understand and predict varroa dynamics and effects of management interventions. We expect that scientists and stakeholders will find a variety of applications for BEEHAVE, stimulating further model development and the possible inclusion of other stressors of potential importance to honeybee colony dynamics. KW - Apis mellifera KW - colony decline KW - cross-level interactions KW - feedbacks KW - foraging KW - modelling KW - multiple stressors KW - multi-agent simulation KW - predictive systems ecology KW - Varroa destructor Y1 - 2014 U6 - https://doi.org/10.1111/1365-2664.12222 SN - 0021-8901 SN - 1365-2664 VL - 51 IS - 2 SP - 470 EP - 482 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Bechi, Beatrice A1 - Herter, Susanne A1 - McKenna, Shane A1 - Riley, Christopher A1 - Leimkühler, Silke A1 - Turner, Nicholas J. A1 - Carnell, Andrew J. T1 - Catalytic bio-chemo and bio-bio tandem oxidation reactions for amide and carboxylic acid synthesis JF - Green chemistry : an international journal and green chemistry resource N2 - A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or Cul(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields. Y1 - 2014 U6 - https://doi.org/10.1039/c4gc01321b SN - 1463-9262 SN - 1463-9270 VL - 16 IS - 10 SP - 4524 EP - 4529 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Beck, Samantha V. A1 - Carvalho, Gary R. A1 - Barlow, Axel A1 - Ruber, Lukas A1 - Tan, Heok Hui A1 - Nugroho, Estu A1 - Wowor, Daisy A1 - Nor, Siti Azizah Mohd A1 - Herder, Fabian A1 - Muchlisin, Zainal A. A1 - de Bruyn, Mark T1 - Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax JF - PLoS one Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0179557 SN - 1932-6203 VL - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Becker, Dirk A1 - Geiger, D. A1 - Dunkel, M. A1 - Roller, A. A1 - Bertl, Adam A1 - Latz, A. A1 - Carpaneto, Armando A1 - Dietrich, Peter A1 - Roelfsema, M. R. G. A1 - Voelker, C. A1 - Schmidt, D. A1 - Müller-Röber, Bernd A1 - Czempinski, Katrin A1 - Hedrich, R. T1 - AtTPK4, an Arabidopsis tandem-pore K+ channel, poised to control the pollen membrane voltage in a pH- and Ca2+- dependent manner N2 - The Arabidopsis tandem-pore K+ (TPK) channels displaying four transmembrane domains and two pore regions share structural homologies with their animal counterparts of the KCNK family. In contrast to the Shaker-like Arabidopsis channels (six transmembrane domains/one pore region), the functional properties and the biological role of plant TPK channels have not been elucidated yet. Here, we show that AtTPK4 (KCO4) localizes to the plasma membrane and is predominantly expressed in pollen. AtTPK4 (KCO4) resembles the electrical properties of a voltage-independent K+ channel after expression in Xenopus oocytes and yeast. Hyperpolarizing as well as depolarizing membrane voltages elicited instantaneous K+ currents, which were blocked by extracellular calcium and cytoplasmic protons. Functional complementation assays using a K+ transport-deficient yeast confirmed the biophysical and pharmacological properties of the AtTPK4 channel. The features of AtTPK4 point toward a role in potassium homeostasis and membrane voltage control of the growing pollen tube. Thus, AtTPK4 represents a member of plant tandem-pore-K+ channels, resembling the characteristics of its animal counterparts as well as plant-specific features with respect to modulation of channel activity by acidosis and calcium Y1 - 2004 SN - 0027-8424 ER - TY - JOUR A1 - Becker, Thorsten A1 - Getzin, Stephan T1 - The fairy circles of Kaokoland (North-West-Namibia) : origin, distribution, and characteristics Y1 - 2000 ER - TY - JOUR A1 - Beckmann, Nadine A1 - Becker, Katrin Anne A1 - Kadow, Stephanie A1 - Schumacher, Fabian A1 - Kramer, Melanie A1 - Kuehn, Claudine A1 - Schulz-Schaeffer, Walter J. A1 - Edwards, Michael J. A1 - Kleuser, Burkhard A1 - Gulbins, Erich A1 - Carpinteiro, Alexander T1 - Acid Sphingomyelinase Deficiency Ameliorates Farber Disease JF - International journal of molecular sciences N2 - Farber disease is a rare lysosomal storage disorder resulting from acid ceramidase deficiency and subsequent ceramide accumulation. No treatments for Farber disease are clinically available, and affected patients have a severely shortened lifespan. We have recently reported a novel acid ceramidase deficiency model that mirrors the human disease closely. Acid sphingomyelinase is the enzyme that generates ceramide upstream of acid ceramidase in the lysosomes. Using our acid ceramidase deficiency model, we tested if acid sphingomyelinase could be a potential novel therapeutic target for the treatment of Farber disease. A number of functional acid sphingomyelinase inhibitors are clinically available and have been used for decades to treat major depression. Using these as a therapeutic for Farber disease, thus, has the potential to improve central nervous symptoms of the disease as well, something all other treatment options for Farber disease can’t achieve so far. As a proof-of-concept study, we first cross-bred acid ceramidase deficient mice with acid sphingomyelinase deficient mice in order to prevent ceramide accumulation. Double-deficient mice had reduced ceramide accumulation, fewer disease manifestations, and prolonged survival. We next targeted acid sphingomyelinase pharmacologically, to test if these findings would translate to a setting with clinical applicability. Surprisingly, the treatment of acid ceramidase deficient mice with the acid sphingomyelinase inhibitor amitriptyline was toxic to acid ceramidase deficient mice and killed them within a few days of treatment. In conclusion, our study provides the first proof-of-concept that acid sphingomyelinase could be a potential new therapeutic target for Farber disease to reduce disease manifestations and prolong survival. However, we also identified previously unknown toxicity of the functional acid sphingomyelinase inhibitor amitriptyline in the context of Farber disease, strongly cautioning against the use of this substance class for Farber disease patients. KW - Farber disease KW - lysosomal storage disorders KW - acid ceramidase KW - acid sphingomyelinase KW - amitriptyline Y1 - 2019 U6 - https://doi.org/10.3390/ijms20246253 SN - 1422-0067 VL - 20 IS - 24 PB - MDPI CY - Basel ER -