TY - JOUR A1 - Mao, Hailiang A1 - Nakamura, Moritaka A1 - Viotti, Corrado A1 - Grebe, Markus T1 - A Framework for Lateral Membrane Trafficking and Polar Tethering of the PEN3 ATP-Binding Cassette Transporter JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity. Y1 - 2016 U6 - https://doi.org/10.1104/pp.16.01252 SN - 0032-0889 SN - 1532-2548 VL - 172 SP - 2245 EP - 2260 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - VanDerVen, Peter F. M. A1 - Bartsch, Jörg A1 - Gautel, Mathias A1 - Jokusch, Harald A1 - Fürst, Dieter Oswald T1 - A functional knock-out of titin results in defective myofibril assembly Y1 - 2000 ER - TY - JOUR A1 - Schwarte, Sandra A1 - Tiedemann, Ralph T1 - A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana JF - Molecular biology and evolution N2 - Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated. KW - Arabidopsis thaliana KW - Arabidopsis lyrata KW - Rubisco KW - gene duplication KW - positive selection Y1 - 2011 U6 - https://doi.org/10.1093/molbev/msr008 SN - 0737-4038 VL - 28 IS - 6 SP - 1861 EP - 1876 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Sunna, Anwar A1 - Bergquist, Peter L. T1 - A gene encoding a novel extremely thermostable 1,4-beta-xylanase isolated directly from an environmental DNA sample N2 - Small-subunit (SSU) rRNA genes (rDNA) were amplified by PCR from a hot pool environmental DNA sample using Bacteria- or Archaea-specific rDNA primers. Unique rDNA types were identified by restriction fragment length polymorphism (RFLP) analysis and representative sequences were determined. Family 10 glycoside hydrolase consensus PCR primers were used to explore the occurrence and diversity of xylanase genes in the hot pool environmental DNA sample. Partial sequences for three different xylanases were obtained and genomic walking PCR (GWPCR), in combination with nested primer pairs, was used to obtained a unique 1,741-bp nucleotide sequence. Analysis of this sequence identified a putative XynA protein encoded by the xynA open reading frame. The single module novel xylanase shared sequence similarity to the family 10 glycoside hydrolases. The purified recombinant enzyme, XynA expressed in E. coli exhibited optimum activity at 100 degrees C and pH 6.0, and was extremely thermostable at 90 degrees C. The enzyme showed high specificity toward different xylans and xylooligosaccharides. Y1 - 2003 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 - Liaimer, Anton A1 - Jensen, John B. A1 - Dittmann, Elke T1 - A Genetic and Chemical Perspective on Symbiotic Recruitment of Cyanobacteria of the Genus Nostoc into the Host Plant Blasia pusilla L. JF - Frontiers in microbiology N2 - Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin. KW - Cyanobacteria KW - secondary metabolites KW - symbiosis KW - Blasia KW - Nostoc KW - allelopathy Y1 - 2016 U6 - https://doi.org/10.3389/fmicb.2016.01693 SN - 1664-302X VL - 7 SP - 449 EP - 474 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Lah, Ljerka A1 - Löber, Ulrike A1 - Hsiang, Tom A1 - Hartmann, Stefanie T1 - A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles JF - Fungal biology N2 - Ophiostomatoid fungi are vectored by their bark-beetle associates and colonize different host tree species. To survive and proliferate in the host, they have evolved mechanisms for detoxification and elimination of host defence compounds, efficient nutrient sequestration, and, in pathogenic species, virulence towards plants. Here, we assembled a draft genome of the spruce pathogen Ophiostoma bicolor. For our comparative and phylogenetic analyses, we mined the genomes of closely related species (Ophiostoma piceae, Ophiostoma ulmi, Ophiostoma novo-ulmi, and Grosmannia clavigera). Our aim was to acquire a genomic and evolutionary perspective of gene families important in host colonization. Genome comparisons showed that both the nuclear and mitochondrial genomes in our assembly were largely complete. Our O. bicolor 25.3 Mbp draft genome had 10 018 predicted genes, 6041 proteins with gene ontology (GO) annotation, 269 carbohydrate-active enzymes (CAZymes), 559 peptidases and inhibitors, and 1373 genes likely involved in pathogen-host interactions. Phylogenetic analyses of selected protein families revealed core sets of cytochrome P450 genes, ABC transporters and backbone genes involved in secondary metabolite (SM) biosynthesis (polyketide synthases (PKS) and non-ribosomal synthases), and species-specific gene losses and duplications. Phylogenetic analyses of protein families of interest provided insight into evolutionary adaptations to host biochemistry in ophiostomatoid fungi. KW - Bark beetle KW - Bluestain fungi KW - Ips typographus Y1 - 2016 U6 - https://doi.org/10.1016/j.funbio.2016.12.002 SN - 1878-6146 SN - 1878-6162 VL - 121 SP - 234 EP - 252 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Wulf, Monika A1 - Rujner, Hendrik T1 - A GIS-based method for the reconstruction of the late eighteenth century forest vegetation in the Prignitz region (NE Germany) JF - Landscape ecology N2 - Our goal was to reconstruct the late eighteenth century forest vegetation of the Prignitz region (NE Germany) at a scale of 1:50,000. We also wanted to relate the historical forest vegetation to the actual and potential natural vegetation. For these purposes, we selected 15 woody species and transferred relevant data found in historical records from various sources together with the recent localities of (very) old individuals belonging to these woody species into ArcView GIS. Following multi-step data processing including the generation of a point density layer using a moving window with kernel estimation and derivation of vegetation units applying Boolean algebra rules together with information on site conditions, we derived 17 forest communities corresponding to the potential natural vegetation. We were able to reconstruct the historical forest vegetation for 90% of the forest area ca. 1780. Only two of the 17 forest communities covered large parts of the forested area. The oak forest with Agrostis capillaris covered about 44% of the total forest area, and alder forests on fenland made up about 37%. Oak-hornbeam forests with Stellaria holostea comprised slightly less than 6% of the forest area, while all other forest communities comprised less than 1%. The historical forest vegetation is more similar to the potential forest vegetation and quite different from the actual forest vegetation because coniferous tree species currently cover approximately two-thirds of the actual forest area. The most beneficial result of this study is the map of high-resolution historical vegetation units that may serve as the basis for various further studies, e.g., modelling long-term changes in biodiversity at the landscape scale. KW - Boolean algebra KW - Historical ecology KW - Kernel estimation KW - Moving window KW - Point density KW - Potential natural vegetation KW - Schmettau map KW - Toponymy KW - Vegetation map Y1 - 2011 U6 - https://doi.org/10.1007/s10980-010-9555-1 SN - 0921-2973 VL - 26 IS - 2 SP - 153 EP - 168 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Reeg, Jette A1 - Heine, Simon A1 - Mihan, Christine A1 - McGee, Sean A1 - Preuss, Thomas G. A1 - Jeltsch, Florian T1 - A graphical user interface for the plant community model IBC-grass JF - Plos One N2 - Plants located adjacent to agricultural fields are important for maintaining biodiversity in semi-natural landscapes. To avoid undesired impacts on these plants due to herbicide application on the arable fields, regulatory risk assessments are conducted prior to registration to ensure proposed uses of plant protection products do not present an unacceptable risk. The current risk assessment approach for these non-target terrestrial plants (NTTPs) examines impacts at the individual-level as a surrogate approach for protecting the plant community due to the inherent difficulties of directly assessing population or community level impacts. However, modelling approaches are suitable higher tier tools to upscale individual-level effects to community level. IBC-grass is a sophisticated plant community model, which has already been applied in several studies. However, as it is a console application software, it was not deemed sufficiently user-friendly for risk managers and assessors to be conveniently operated without prior expertise in ecological models. Here, we present a user-friendly and open source graphical user interface (GUI) for the application of IBC-grass in regulatory herbicide risk assessment. It facilitates the use of the plant community model for predicting long-term impacts of herbicide applications on NTTP communities. The GUI offers two options to integrate herbicide impacts: (1) dose responses based on current standard experiments (acc. to testing guidelines) and (2) based on specific effect intensities. Both options represent suitable higher tier options for future risk assessments of NTTPs as well as for research on the ecological relevance of effects. Y1 - 2020 U6 - https://doi.org/10.1371/journal.pone.0230012 SN - 1932-6203 VL - 15 IS - 3 PB - Plos 1 CY - San Francisco ER - TY - JOUR A1 - Arvidsson, Samuel Janne A1 - Perez-Rodriguez, Paulino A1 - Müller-Röber, Bernd T1 - A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects JF - New phytologist : international journal of plant science N2 - To gain a deeper understanding of the mechanisms behind biomass accumulation, it is important to study plant growth behavior. Manually phenotyping large sets of plants requires important human resources and expertise and is typically not feasible for detection of weak growth phenotypes. Here, we established an automated growth phenotyping pipeline for Arabidopsis thaliana to aid researchers in comparing growth behaviors of different genotypes. The analysis pipeline includes automated image analysis of two-dimensional digital plant images and evaluation of manually annotated information of growth stages. It employs linear mixed-effects models to quantify genotype effects on total rosette area and relative leaf growth rate (RLGR) and ANOVAs to quantify effects on developmental times. Using the system, a single researcher can phenotype up to 7000 plants d(-1). Technical variance is very low (typically < 2%). We show quantitative results for the growth-impaired starch-excessmutant sex4-3 and the growth-enhancedmutant grf9. We show that recordings of environmental and developmental variables reduce noise levels in the phenotyping datasets significantly and that careful examination of predictor variables (such as d after sowing or germination) is crucial to avoid exaggerations of recorded phenotypes and thus biased conclusions. KW - development KW - growth KW - leaf area KW - modeling KW - phenotyping Y1 - 2011 U6 - https://doi.org/10.1111/j.1469-8137.2011.03756.x SN - 0028-646X VL - 191 IS - 3 SP - 895 EP - 907 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Cheng, Fuxia A1 - Hartmann, Stefanie A1 - Gupta, Mayetri A1 - Ibrahim, Joseph G. A1 - Vision, Todd J. T1 - A hierarchical model for incomplete alignments in phylogenetic inference N2 - Motivation: Full-length DNA and protein sequences that span the entire length of a gene are ideally used for multiple sequence alignments (MSAs) and the subsequent inference of their relationships. Frequently, however, MSAs contain a substantial amount of missing data. For example, expressed sequence tags (ESTs), which are partial sequences of expressed genes, are the predominant source of sequence data for many organisms. The patterns of missing data typical for EST-derived alignments greatly compromise the accuracy of estimated phylogenies. Results: We present a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data. We propose a class of hierarchical models for modeling pairwise distances between the sequences, and develop a fully Bayesian approach for estimation of the model parameters. Once the distance matrix is estimated, the phylogenetic tree may be constructed by applying neighbor-joining (or any other algorithm of choice). We also show that maximizing the marginal likelihood from the Bayesian approach yields similar results to a pro. le likelihood estimation. The proposed methods are illustrated using simulated protein families, for which the true phylogeny is known, and one real protein family. Y1 - 2009 UR - http://bioinformatics.oxfordjournals.org/ U6 - https://doi.org/10.1093/bioinformatics/btp015 SN - 1367-4803 ER - TY - JOUR A1 - Zhang, Youjun A1 - Chen, Moxian A1 - Siemiatkowska, Beata A1 - Toleco, Mitchell Rey A1 - Jing, Yue A1 - Strotmann, Vivien A1 - Zhang, Jianghua A1 - Stahl, Yvonne A1 - Fernie, Alisdair T1 - A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species JF - Plant Communications N2 - Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis. KW - transient expression KW - agro-infiltration KW - subcellular localization KW - protein-protein interaction Y1 - 2019 SN - 2590-3462 VL - 1 IS - 5 PB - Science Direct CY - New York ER - TY - JOUR A1 - Dortay, Hakan A1 - Müller-Röber, Bernd T1 - A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker N2 - Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor. Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 mu L Y1 - 2010 UR - http://www.microbialcellfactories.com/home/ U6 - https://doi.org/10.1186/1475-2859-9-29 SN - 1475-2859 ER - TY - JOUR A1 - Jantzen, Friederike A1 - Wozniak, Natalia Joanna A1 - Kappel, Christian A1 - Sicard, Adrien A1 - Lenhard, Michael T1 - A high‑throughput amplicon‑based method for estimating outcrossing rates JF - Plant Methods N2 - Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming. Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons. Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing. KW - Outcrossing KW - Mixed mating KW - Outcrossing rate KW - Capsella KW - Amplicon sequencing Y1 - 2019 U6 - https://doi.org/10.1186/s13007-019-0433-9 SN - 1746-4811 VL - 15 IS - 47 PB - BioMed Central CY - London ER - TY - JOUR A1 - Lämke, Jörn A1 - Brzezinka, Krzysztof A1 - Altmann, Simone A1 - Bäurle, Isabel T1 - A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory JF - The EMBO journal N2 - In nature, plants often encounter chronic or recurring stressful conditions. Recent results indicate that plants can remember a past exposure to stress to be better prepared for a future stress incident. However, the molecular basis of this is poorly understood. Here, we report the involvement of chromatin modifications in the maintenance of acquired thermotolerance (heat stress [HS] memory). HS memory is associated with the accumulation of histone H3 lysine 4 di- and trimethylation at memory-related loci. This accumulation outlasts their transcriptional activity and marks them as recently transcriptionally active. High accumulation of H3K4 methylation is associated with hyper-induction of gene expression upon a recurring HS. This transcriptional memory and the sustained accumulation of H3K4 methylation depend on HSFA2, a transcription factor that is required for HS memory, but not initial heat responses. Interestingly, HSFA2 associates with memory-related loci transiently during the early stages following HS. In summary, we show that transcriptional memory after HS is associated with sustained H3K4 hyper-methylation and depends on a hit-and-run transcription factor, thus providing a molecular framework for HS memory. KW - chromatin KW - H3K4 methylation KW - heat shock transcription factor KW - priming KW - transcriptional memory Y1 - 2016 U6 - https://doi.org/10.15252/embj.201592593 SN - 0261-4189 SN - 1460-2075 VL - 35 SP - 162 EP - 175 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Sellrie, Frank A1 - Beck, Michael A1 - Hildebrandt, Niko A1 - Micheel, Burkhard T1 - A homogeneous time-resolved fluoroimmunoassay (TR-FIA) using antibody mediated luminescence quenching N2 - The determination of low-molecular weight substances (haptens) is demonstrated with a homogeneous time-resolved immunoassay using antibody-induced luminescence quenching. Our novel assay technology uses the newly developed monoclonal antibody (G24-BA9) to quench the luminescence of europium trisbipyridine (EuTBP). We performed a competitive biotin immunoassay including an EuTBP-biotin conjugate, the anti-EuTBP antibody G24-BA9 and streptavidin as assay components. Steric hindrance allows only the binding of either G24-BA9 (to the EuTBP moiety) or streptavidin (to the biotin moiety) to the EuTBP-biotin conjugate. Addition of the analyte biotin resulted in the binding of streptavidin to biotin and a concomitant preferred binding of G24-BA9 to EuTBP-biotin. Since G24-BA9 quenches the luminescence of EuTBP within the conjugate, the luminescence signal could be used to indicate and quantify the presence of free biotin in the system. All experiments were carried out in solution in the presence of 5% serum demonstrating the possibility of using our novel assay for a very fast determination of low molecular weight substances in biological fluids. Y1 - 2010 UR - http://www.rsc.org/Publishing/Journals/AY/Index.asp U6 - https://doi.org/10.1039/C0ay00306a SN - 1759-9660 ER - TY - JOUR A1 - Reeve, Holly A. A1 - Nicholson, Jake A1 - Altaf, Farieha A1 - Lonsdale, Thomas H. A1 - Preissler, Janina A1 - Lauterbach, Lars A1 - Lenz, Oliver A1 - Leimkühler, Silke A1 - Hollmann, Frank A1 - Paul, Caroline E. A1 - Vincent, Kylie A. T1 - A hydrogen-driven biocatalytic approach to recycling synthetic analogues of NAD(P)H JF - Chemical communications : ChemComm N2 - We demonstrate a recycling system for synthetic nicotinamide cofactor analogues using a soluble hydrogenase with turnover number of >1000 for reduction of the cofactor analogues by H-2. Coupling this system to an ene reductase, we show quantitative conversion of N-ethylmaleimide to N-ethylsuccinimide. The biocatalyst system retained >50% activity after 7 h. Y1 - 2022 U6 - https://doi.org/10.1039/d2cc02411j SN - 1359-7345 SN - 1364-548X VL - 58 IS - 75 SP - 10540 EP - 10543 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Kabelitz, Tina A1 - Brzezinka, Krzysztof A1 - Friedrich, Thomas A1 - Gorka, Michal A1 - Graf, Alexander A1 - Kappel, Christian A1 - Bäurle, Isabel T1 - A JUMONJI Protein with E3 Ligase and Histone H3 Binding Activities Affects Transposon Silencing in Arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Transposable elements (TEs) make up a large proportion of eukaryotic genomes. As their mobilization creates genetic variation that threatens genome integrity, TEs are epigenetically silenced through several pathways, and this may spread to neighboring sequences. JUMONJI (JMJ) proteins can function as antisilencing factors and prevent silencing of genes next to TEs. Whether TE silencing is counterbalanced by the activity of antisilencing factors is still unclear. Here, we characterize JMJ24 as a regulator of TE silencing. We show that loss of JMJ24 results in increased silencing of the DNA transposon AtMu1c, while overexpression of JMJ24 reduces silencing. JMJ24 has a JumonjiC (JmjC) domain and two RING domains. JMJ24 autoubiquitinates in vitro, demonstrating E3 ligase activity of the RING domain(s). JMJ24-JmjC binds the N-terminal tail of histone H3, and full-length JMJ24 binds histone H3 in vivo. JMJ24 activity is anticorrelated with histone H3 Lys 9 dimethylation (H3K9me2) levels at AtMu1c. Double mutant analyses with epigenetic silencing mutants suggest that JMJ24 antagonizes histone H3K9me2 and requires H3K9 methyltransferases for its activity on AtMu1c. Genome-wide transcriptome analysis indicates that JMJ24 affects silencing at additional TEs. Our results suggest that the JmjC domain of JMJ24 has lost demethylase activity but has been retained as a binding domain for histone H3. This is in line with phylogenetic analyses indicating that JMJ24 (with the mutated JmjC domain) is widely conserved in angiosperms. Taken together, this study assigns a role in TE silencing to a conserved JmjC-domain protein with E3 ligase activity, but no demethylase activity. Y1 - 2016 U6 - https://doi.org/10.1104/pp.15.01688 SN - 0032-0889 SN - 1532-2548 VL - 171 SP - 344 EP - 358 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Tikhonenko, Irina A1 - Magidson, Valentin A1 - Gräf, Ralph A1 - Khodjakov, Alexey A1 - Koonce, Michael P. T1 - A kinesin-mediated mechanism that couples centrosomes to nuclei JF - Cellular and molecular life sciences N2 - The M-type kinesin isoform, Kif9, has recently been implicated in maintaining a physical connection between the centrosome and nucleus in Dictyostelium discoideum. However, the mechanism by which Kif9 functions to link these two organelles remains obscure. Here we demonstrate that the Kif9 protein is localized to the nuclear envelope and is concentrated in the region underlying the centrosome point of attachment. Nuclear anchorage appears mediated through a specialized transmembrane domain located in the carboxyl terminus. Kif9 interacts with microtubules in in vitro binding assays and effects an endwise depolymerization of the polymer. These results suggest a model whereby Kif9 is anchored to the nucleus and generates a pulling force that reels the centrosome up against the nucleus. This is a novel activity for a kinesin motor, one important for progression of cells into mitosis and to ensure centrosome-nuclear parity in a multinuclear environment. KW - Centrosome KW - Kinesin KW - Microtubule KW - Dictyostelium Y1 - 2013 U6 - https://doi.org/10.1007/s00018-012-1205-0 SN - 1420-682X VL - 70 IS - 7 SP - 1285 EP - 1296 PB - Springer CY - Basel ER - TY - JOUR A1 - Kress, H. A1 - Jarrin, A. A1 - Thuroff, E. A1 - Saunders, R. A1 - Weise, C. A1 - Schmidt am Busch, Marcel A1 - Knapp, E. W. A1 - Wedde, M. A1 - Vilcinskas, Andreas T1 - A Kunitz type protease inhibitor related protein is synthesized in Drosophila prepupal salivary glands and released into the moulting fluid during pupation N2 - From the Drosophila virilis late puff region 31C, we microcloned two neighbouring genes, Kil-1 and Kil-2, that encode putative Kunitz serine protease inhibitor like proteins. The Kil-1 gene is expressed exclusively in prepupal salivary glands. Using a size mutant of the KIL-1 protein and MALDI-TOF analysis, we demonstrate that during pupation this protein is released from the prepupal salivary glands into the pupation fluid covering the surface of the pupa. 3-D- structure predictions are consistent with the known crystal structure of the human Kunitz type protease inhibitor 2KNT. This is the first experimental proof for the extra-corporal presence of a distinct Drosophila prepupal salivary gland protein. Possible functions of KIL-1 in the context of the control of proteolytic activities in the pupation fluid are discussed. (C) 2004 Elsevier Ltd. All rights reserved Y1 - 2004 SN - 0965-1748 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 - De Frenne, P. A1 - Kolb, Annette A1 - Graae, Benete Jessen A1 - Decocq, Guillaume A1 - Baltora, S. A1 - De Schrijver, A. A1 - Brunet, J. A1 - Chabrerie, Olivier A1 - Cousins, Sara A. O. A1 - Dhondt, Rob A1 - Diekmann, Martin A1 - Gruwez, R. A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Liira, J. A1 - Saguez, R. A1 - Shevtsova, Anna A1 - Baskin, Carol C. A1 - Verheyen, Kris T1 - A latitudinal gradient in seed nutrients of the forest herb Anemone nemorosa JF - Plant biology N2 - The nutrient concentration in seeds determines many aspects of potential success of the sexual reproductive phase of plants, including the seed predation probability, efficiency of seed dispersal and seedling performance. Despite considerable research interest in latitudinal gradients of foliar nutrients, a similar gradient for seeds remains unexplored. We investigated a potential latitudinal gradient in seed nutrient concentrations within the widespread European understorey forest herb Anemone nemorosa L. We sampled seeds of A. nemorosa in 15 populations along a 1900-km long latitudinal gradient at three to seven seed collection dates post-anthesis and investigated the relative effects of growing degree-hours > 5 degrees C, soil characteristics and latitude on seed nutrient concentrations. Seed nitrogen, nitrogen:phosphorus ratio and calcium concentration decreased towards northern latitudes, while carbon:nitrogen ratios increased. When taking differences in growing degree-hours and measured soil characteristics into account and only considering the most mature seeds, the latitudinal decline remained particularly significant for seed nitrogen concentration. We argue that the decline in seed nitrogen concentration can be attributed to northward decreasing seed provisioning due to lower soil nitrogen availability or greater investment in clonal reproduction. This pattern may have large implications for the reproductive performance of this forest herb as the degree of seed provisioning ultimately co-determines seedling survival and reproductive success. KW - Collection date KW - latitude KW - nutrient stoichiometry KW - seed nitrogen KW - seed predation KW - seed provisioning KW - sexual reproduction KW - wood anemone Y1 - 2011 U6 - https://doi.org/10.1111/j.1438-8677.2010.00404.x SN - 1435-8603 VL - 13 IS - 3 SP - 493 EP - 501 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Karwinkel, Thiemo A1 - Winklhofer, Michael A1 - Janner, Lars Erik A1 - Brust, Vera A1 - Hüppop, Ommo A1 - Bairlein, Franz A1 - Schmaljohann, Heiko T1 - A magnetic pulse does not affect free-flight navigation behaviour of a medium-distance songbird migrant in spring JF - The journal of experimental biology N2 - Current evidence suggests that migratory animals extract map information from the geomagnetic field for true navigation. The sensory basis underlying this feat is elusive, but presumably involves magnetic particles. A common experimental manipulation procedure consists of pre-treating animals with a magnetic pulse, with the aim of re-magnetising particles to alter the internal representation of the external field prior to a navigation task. Although pulsing provoked deflected bearings in caged songbirds, analogous studies with free-flying songbirds yielded inconsistent results. Here, we pulsed European robins (Erithacus rubecula) at an offshore stopover site during spring migration and monitored their free-flight behaviour with a regional-scale network of radio-receiving stations. We found no pulse effect on departure probability, nocturnal departure timing departure direction or consistency of flight direction. This suggests either no use of the geomagnetic map by our birds, or that magnetic pulses do not affect the sensory system underlying geomagnetic map detection. KW - bird migration KW - magnetic map KW - magnetic-particlebased sensor KW - magnetic pulse KW - magnetoreception KW - navigation Y1 - 2022 U6 - https://doi.org/10.1242/jeb.244473 SN - 0022-0949 SN - 1477-9145 VL - 225 IS - 19 PB - Company of Biologists CY - Cambridge ER - TY - JOUR A1 - Girbig, Dorothee A1 - Selbig, Joachim A1 - Grimbs, Sergio T1 - A MATLAB toolbox for structural kinetic modeling JF - Bioinformatics N2 - Structural kinetic modeling (SKM) enables the analysis of dynamical properties of metabolic networks solely based on topological information and experimental data. Current SKM-based experiments are hampered by the time-intensive process of assigning model parameters and choosing appropriate sampling intervals for MonteCarlo experiments. We introduce a toolbox for the automatic and efficient construction and evaluation of structural kinetic models (SK models). Quantitative and qualitative analyses of network stability properties are performed in an automated manner. We illustrate the model building and analysis process in detailed example scripts that provide toolbox implementations of previously published literature models. Y1 - 2012 U6 - https://doi.org/10.1093/bioinformatics/bts473 SN - 1367-4803 VL - 28 IS - 19 SP - 2546 EP - 2547 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Wandt, Viktoria Klara Veronika A1 - Winkelbeiner, Nicola Lisa A1 - Bornhorst, Julia A1 - Witt, Barbara A1 - Raschke, Stefanie A1 - Simon, Luise A1 - Ebert, Franziska A1 - Kipp, Anna Patricia A1 - Schwerdtle, Tanja T1 - A matter of concern BT - trace element dyshomeostasis and genomic stability in neurons JF - Redox Biology N2 - Neurons are post-mitotic cells in the brain and their integrity is of central importance to avoid neurodegeneration. Yet, the inability of self-replenishment of post-mitotic cells results in the need to withstand challenges from numerous stressors during life. Neurons are exposed to oxidative stress due to high oxygen consumption during metabolic activity in the brain. Accordingly, DNA damage can occur and accumulate, resulting in genome instability. In this context, imbalances in brain trace element homeostasis are a matter of concern, especially regarding iron, copper, manganese, zinc, and selenium. Although trace elements are essential for brain physiology, excess and deficient conditions are considered to impair neuronal maintenance. Besides increasing oxidative stress, DNA damage response and repair of oxidative DNA damage are affected by trace elements. Hence, a balanced trace element homeostasis is of particular importance to safeguard neuronal genome integrity and prevent neuronal loss. This review summarises the current state of knowledge on the impact of deficient, as well as excessive iron, copper, manganese, zinc, and selenium levels on neuronal genome stability Y1 - 2021 U6 - https://doi.org/10.1016/j.redox.2021.101877 SN - 2213-2317 VL - 41 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Schmidtke, Andrea A1 - Gaedke, Ursula A1 - Weithoff, Guntram T1 - A mechanistic basis for underyielding in phytoplankton communities N2 - Species richness has been shown to increase biomass production of plant communities. Such overyielding occurs when a community performs better than its component monocultures due to the complementarity or dominance effect and is mostly detected in substrate-bound plant communities (terrestrial plants or submerged macrophytes) where resource use complementarity can be enhanced due to differences in rooting architecture and depth. Here, we investigated whether these findings arc generalizeable for free-floating phytoplankton with little potential for spatial differences in resource use. We performed aquatic microcosm experiments with eight phytoplankton species belonging to four functional groups to determine the manner in which species and community biovolume varies in relation to the number of functional groups and hypothesized that an increasing number of functional groups within a community promotes overyielding. Unexpectedly, we did not detect overyielding in any algal community. Instead. total community biovolume tended to decrease with all increasing, number of functional groups. This underyielding was mainly caused by the negative dominance effect that originated from a trade-off between growth rate and filial biovolume. In monoculture, slow-groing species built up higher biovolumes that fast-growing ones, whereas in mixture a fast-growing but low-productive species monopolized most of the nutrients and prevented competing species from developing high biovolumes expected from monocultures. Our results indicated that the Magnitude of the community biovolume was largely determined by the identify of one species. Functional diversity and resource use complementarity were of minor Importance among free-floating phytoplankton, possibly reflecting the lack of spatially heterogeneous resource distribution. As a consequence, biodiversity-ecosystem functioning relationships may not be easily generalizeable from substrate-bound plant to phytoplankton communities and vice versa. Y1 - 2010 UR - http://www.esajournals.org/doi/full/10.1890/08-2370.1 SN - 0012-9658 ER - TY - JOUR A1 - Schurr, Frank Martin A1 - Bond, William J. A1 - Midgley, Guy F. A1 - Higgins, Steven I. T1 - A mechanistic model for secondary seed dispersal by wind and its experimental validation N2 - 1 Secondary seed dispersal by wind, the wind-driven movement of seeds along the ground surface, is an important dispersal mechanism for plant species in a range of environments. 2 We formulate a mechanistic model that describes how secondary dispersal by wind is affected by seed traits, wind conditions and obstacles to seed movement. The model simulates the movement paths of individual seeds and can be fully specified using independently measured parameters. 3 We develop an explicit version of the model that uses a spatially explicit representation of obstacle patterns, and also an aggregated version that uses probability distributions to model seed retention at obstacles and seed movement between obstacles. The aggregated version is computationally efficient and therefore suited to large-scale simulations. It provides a very good approximation of the explicit version (R-2 > 0.99) if initial seed positions vary randomly relative to the obstacle pattern. 4 To validate the model, we conducted a field experiment in which we released seeds of seven South African Proteaceae species that differ in seed size and morphology into an arena in which we systematically varied obstacle patterns. When parameterized with maximum likelihood estimates obtained from independent measurements, the explicit model version explained 70-77% of the observed variation in the proportion of seeds dispersed over 25 m and 67- 69% of the observed variation in the direction of seed dispersal. 5 The model tended to underestimate dispersal rates, possibly due to the omission of turbulence from the model, although this could also be explained by imprecise estimation of one model parameter (the aerodynamic roughness length). 6 Our analysis of the aggregated model predicts a unimodal relationship between the distance of secondary dispersal by wind and seed size. The model can also be used to identify species with the potential for long-distance seed transport by secondary wind dispersal. 7 The validated model expands the domain of mechanistic dispersal models, contributes to a functional understanding of seed dispersal, and provides a tool for predicting the distances that seeds move Y1 - 2005 SN - 0022-0477 ER - TY - JOUR A1 - Schröder, Rolf A1 - VanDerVen, Peter F. M. A1 - Warlo, Irene A1 - Schumann, H. A1 - Fürst, Dieter Oswald A1 - Blümke, Ingmar A1 - Goebel, Hans H. A1 - Schmidt, M. C. A1 - Hatzfeld, Mechthild T1 - A member of the armadillo multigene family, is a constituent of sarcomeric I-bands in human skeletal muscle Y1 - 2000 ER - TY - JOUR A1 - Leimu, Roosa A1 - Koricheva, Julia T1 - A meta-analysis of genetic correlations between plant resistances to multiple enemies N2 - Genetic correlations between plant resistances to multiple natural enemies are important because they have the potential to determine the mode of selection that natural enemies impose on a host plant, the structure of herbivore and pathogen communities, and the success of plant breeding for resistance to multiple diseases and pests. We conducted a meta-analysis of 29 published studies of 16 different plant species reporting a total of 467 genetic correlations between resistances to multiple herbivores or pathogens. In general, genetic associations between resistances to multiple natural enemies tended to be positive regardless of the breeding design, type of attacker, and type of host plant. Positive genetic correlations between resistances were stronger when both attackers were pathogens or generalist herbivores and when resistance to different enemies was tested independently, suggesting that generalists may be affected by the same plant resistance traits and that interactions among natural enemies are common. Although the mean associations between resistances were positive, indicating the prevalence of diffuse selection and generalized defenses against multiple enemies, the large variation in both the strength and the direction of the associations suggests a continuum between pairwise and diffuse selection Y1 - 2006 UR - http://www.jstor.org/action/showPublication?journalCode=amernatu U6 - https://doi.org/10.1086/505766 SN - 0003-0147 ER - TY - JOUR A1 - Van Kleunen, Mark A1 - Weber, Ewald A1 - Fischer, Markus T1 - A meta-analysis of trait differences between invasive and non-invasive plant species N2 - A major aim in ecology is identifying determinants of invasiveness. We performed a meta-analysis of 117 field or experimental-garden studies that measured pair-wise trait differences of a total of 125 invasive and 196 non-invasive plant species in the invasive range of the invasive species. We tested whether invasiveness is associated with performance-related traits (physiology, leaf-area allocation, shoot allocation, growth rate, size and fitness), and whether such associations depend on type of study and on biogeographical or biological factors. Overall, invasive species had significantly higher values than non-invasive species for all six trait categories. More trait differences were significant for invasive vs. native comparisons than for invasive vs. non-invasive alien comparisons. Moreover, for comparisons between invasive species and native species that themselves are invasive elsewhere, no trait differences were significant. Differences in physiology and growth rate were larger in tropical regions than in temperate regions. Trait differences did not depend on whether the invasive alien species originates from Europe, nor did they depend on the test environment. We conclude that invasive alien species had higher values for those traits related to performance than non-invasive species. This suggests that it might become possible to predict future plant invasions from species traits. Y1 - 2010 UR - http://www3.interscience.wiley.com/journal/118545752/home SN - 1461-023X ER - TY - JOUR A1 - Schiro, Gabriele A1 - Colangeli, Pierluigi A1 - Müller, Marina E. H. T1 - A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field JF - Frontiers in microbiology KW - Fusarium KW - microclimate KW - canopy KW - fungal community KW - Alternaria KW - spatially induced variance Y1 - 2019 U6 - https://doi.org/10.3389/fmicb.2019.02095 SN - 1664-302X VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Mikhailyuk, Igor K. A1 - Lokstein, Heiko A1 - Razjivin, Andrei P. T1 - A method of spectral subband decomposition by simultaneous fitting the initial spectrum and a set of its derivatives N2 - An improved method for spectral subband decomposition based on simultaneous fitting of the initial spectrum and a set of its derivatives is introduced. Additionally, it procedure for finding an optimal smoothing filter to obtain undistorted derivatives IS Suggested. The proposed method is demonstrated with a model spectrum as well its with experimental absorption spectra of the photosynthetic antenna complexes, peridinin-chlorophyll a-protein (PCP) and the main light-harvesting complex of higher plants (LHC II). (c) 2005 Elsevier B.V. All rights reserved Y1 - 2005 ER - TY - JOUR A1 - Song, Min Ik A1 - Bier, Frank Fabian A1 - Scheller, Frieder W. T1 - A method to detect superoxide radicals using teflon membrane and superoxide dismutase Y1 - 1995 ER - TY - JOUR A1 - Garcia-Mata, Carlos A1 - Wang, Jianwen A1 - Gajdanowicz, Pawel A1 - Gonzalez, Wendy A1 - Hills, Adrian A1 - Donald, Naomi A1 - Riedelsberger, Janin A1 - Amtmann, Anna A1 - Dreyer, Ingo A1 - Blatt, Michael R. T1 - A minimal cysteine motif required to activate the SKOR K+ channel of Arabidopsis by the reactive oxygen species H2O2 N2 - Reactive oxygen species (ROS) are essential for development and stress signaling in plants. They contribute to plant defense against pathogens, regulate stomatal transpiration, and influence nutrient uptake and partitioning. Although both Ca2+ and K+ channels of plants are known to be affected, virtually nothing is known of the targets for ROS at a molecular level. Here we report that a single cysteine (Cys) residue within the Kv-like SKOR K+ channel of Arabidopsis thaliana is essential for channel sensitivity to the ROS H2O2. We show that H2O2 rapidly enhanced current amplitude and activation kinetics of heterologously expressed SKOR, and the effects were reversed by the reducing agent dithiothreitol (DTT). Both H2O2 and DTT were active at the outer face of the membrane and current enhancement was strongly dependent on membrane depolarization, consistent with a H2O2-sensitive site on the SKOR protein that is exposed to the outside when the channel is in the open conformation. Cys substitutions identified a single residue, Cys(168) located within the S3 alpha-helix of the voltage sensor complex, to be essential for sensitivity to H2O2. The same Cys residue was a primary determinant for current block by covalent Cys S-methioylation with aqueous methanethiosulfonates. These, and additional data identify Cys168 as a critical target for H2O2, and implicate ROS-mediated control of the K+ channel in regulating mineral nutrient partitioning within the plant. Y1 - 2010 UR - http://www.jbc.org/ U6 - https://doi.org/10.1074/jbc.M110.141176 SN - 0021-9258 ER - TY - JOUR A1 - Ebenhoeh, Oliver A1 - Houwaart, Torsten A1 - Lokstein, Heiko A1 - Schlede, Stephanie A1 - Tirok, Katrin T1 - A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence JF - Biosystems : journal of biological and information processing sciences N2 - Under natural conditions, plants are exposed to rapidly changing light intensities. To acclimate to such fluctuations, plants have evolved adaptive mechanisms that optimally exploit available light energy and simultaneously minimise damage of the photosynthetic apparatus through excess light. An important mechanism is the dissipation of excess excitation energy as heat which can be measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). In this paper, we present a highly simplified mathematical model that captures essential experimentally observed features of the short term adaptive quenching dynamics. We investigate the stationary and dynamic behaviour of the model and systematically analyse the dependence of characteristic system properties on key parameters such as rate constants and pool sizes. Comparing simulations with experimental data allows to derive conclusions about the validity of the simplifying assumptions and we further propose hypotheses regarding the role of the xanthophyll cycle in NPQ. We envisage that the presented theoretical description of the light reactions in conjunction with short term adaptive processes serves as a basis for the development of more detailed mechanistic models by which the molecular mechanisms of NPQ can be theoretically studied. KW - Photosynthesis KW - Light reactions KW - Nonphotochemical quenching of chlorophyll fluorescence KW - Chlorophyll fluorescence KW - Mathematical model Y1 - 2011 U6 - https://doi.org/10.1016/j.biosystems.2010.10.011 SN - 0303-2647 VL - 103 IS - 2 SP - 196 EP - 204 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Gorochowski, Thomas E. A1 - Aycilar-Kucukgoze, Irem A1 - Bovenberg, Roel A. L. A1 - Roubos, Johannes A. A1 - Ignatova, Zoya T1 - A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes JF - ACS synthetic biology N2 - Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources. KW - protein biosynthesis KW - translation KW - synthetic biology KW - systems biology Y1 - 2016 U6 - https://doi.org/10.1021/acssynbio.6b00040 SN - 2161-5063 VL - 5 SP - 710 EP - 720 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Westbury, Michael V. A1 - Baleka, Sina Isabelle A1 - Barlow, Axel A1 - Hartmann, Stefanie A1 - Paijmans, Johanna L. A. A1 - Kramarz, Alejandro A1 - Forasiepi, Analia M. A1 - Bond, Mariano A1 - Gelfo, Javier N. A1 - Reguero, Marcelo A. A1 - Lopez-Mendoza, Patricio A1 - Taglioretti, Matias A1 - Scaglia, Fernando A1 - Rinderknecht, Andres A1 - Jones, Washington A1 - Mena, Francisco A1 - Billet, Guillaume A1 - de Muizon, Christian A1 - Luis Aguilar, Jose A1 - MacPhee, Ross D. E. A1 - Hofreiter, Michael T1 - A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica JF - Nature Communications N2 - The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma (95% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives. Y1 - 2017 U6 - https://doi.org/10.1038/ncomms15951 SN - 2041-1723 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Krupinski, Pawel A1 - Bozorg, Behruz A1 - Larsson, Andre A1 - Pietra, Stefano A1 - Grebe, Markus A1 - Jönsson, Henrik T1 - A Model Analysis of Mechanisms for Radial Microtubular Patterns at Root Hair Initiation Sites JF - Frontiers in plant science N2 - Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs. KW - plant cell wall KW - finite element modeling KW - computational morphodynamics KW - root hair initiation KW - microtubules KW - cellulose fibers KW - composite material Y1 - 2016 U6 - https://doi.org/10.3389/fpls.2016.01560 SN - 1664-462X VL - 7 PB - Frontiers Research Foundation CY - Lausanne 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 - Aksu, Yilmaz A1 - Frasca, Stefano A1 - Wollenberger, Ursula A1 - Driess, Matthias A1 - Thomas, Arne T1 - A molecular precursor approach to tunable porous tin-rich indium tin oxide with durable high electrical conductivity for bioelectronic devices JF - Chemistry of materials : a publication of the American Chemical Society N2 - The preparation of porous, i.e., high surface area electrodes from transparent conducting oxides, is a valuable goal in materials chemistry as such electrodes can enable further development of optoelectronic, electrocatalytic, or bioelectronic devices. In this work the first tin-rich mesoporous indium tin oxide is prepared using the molecular heterobimetallic single-source precursor, indium tin tris-tert-butoxide, together with an appropriate structure-directing template, yielding materials with high surface areas and tailorable pore size. The resulting mesoporous tin-rich ITO films show a high and durable electrical conductivity and transparency, making them interesting materials for hosting electroactive biomolecules such as proteins. In fact, its unique performance in bioelectronic applications has been demonstrated by immobilization of high amounts of cytochrome c into the mesoporous film which undergo redox processes directly with the conductive electrode material. KW - indium tin oxide ITO KW - electrode KW - bioelectrochemistry KW - device KW - cytochrome c Y1 - 2011 U6 - https://doi.org/10.1021/cm103087p SN - 0897-4756 VL - 23 IS - 7 SP - 1798 EP - 1804 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Schittko, Conrad A1 - Bernard-Verdier, Maud A1 - Heger, Tina A1 - Buchholz, Sascha A1 - Kowarik, Ingo A1 - von der Lippe, Moritz A1 - Seitz, Birgit A1 - Joshi, Jasmin Radha A1 - Jeschke, Jonathan M. T1 - A multidimensional framework for measuring biotic novelty: How novel is a community? JF - Global Change Biology N2 - Anthropogenic changes in climate, land use, and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e., biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (a) functional differences between native and non-native introduced species with (b) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao's quadratic entropy, capturing the novel interaction component of the community's functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R code and two applications of the BNI by (a) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (b) determining the biotic novelty of plant species assemblages at a national scale. The results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help building a basis for better understanding the ecological and evolutionary consequences of global change. KW - alien species KW - biological invasions KW - coexistence KW - ecological novelty KW - functional diversity KW - novel ecosystems KW - novel species KW - standard metrics Y1 - 2019 VL - 26 IS - 8 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Shirzadian-Khorramabad, Reza A1 - Jing, Hai-Chun A1 - Everts, Gerja E. A1 - Schippers, Jos H. M. A1 - Hille, Jacques A1 - Dijkwel, Paul P. T1 - A mutation in the cytosolic O-acetylserine (thiol) lyase induces a genome-dependent early leaf death phenotype in Arabidopsis N2 - Background: Cysteine is a component in organic compounds including glutathione that have been implicated in the adaptation of plants to stresses. O-acetylserine (thiol) lyase (OAS-TL) catalyses the final step of cysteine biosynthesis. OAS-TL enzyme isoforms are localised in the cytoplasm, the plastids and mitochondria but the contribution of individual OAS-TL isoforms to plant sulphur metabolism has not yet been fully clarified. Results: The seedling lethal phenotype of the Arabidopsis onset of leaf death3-1 (old3-1) mutant is due to a point mutation in the OAS-A1 gene, encoding the cytosolic OAS-TL. The mutation causes a single amino acid substitution from Gly(162) to Glu(162), abolishing old3-1 OAS-TL activity in vitro. The old3-1 mutation segregates as a monogenic semidominant trait when backcrossed to its wild type accession Landsberg erecta (Ler-0) and the Di-2 accession. Consistent with its semi- dominant behaviour, wild type Ler-0 plants transformed with the mutated old3-1 gene, displayed the early leaf death phenotype. However, the old3-1 mutation segregates in an 11: 4: 1 (wild type: semi-dominant: mutant) ratio when backcrossed to the Colombia-0 and Wassilewskija accessions. Thus, the early leaf death phenotype depends on two semi- dominant loci. The second locus that determines the old3-1 early leaf death phenotype is referred to as odd-ler (for old3 determinant in the Ler accession) and is located on chromosome 3. The early leaf death phenotype is temperature dependent and is associated with increased expression of defence-response and oxidative-stress marker genes. Independent of the presence of the odd-ler gene, OAS-A1 is involved in maintaining sulphur and thiol levels and is required for resistance against cadmium stress. Conclusions: The cytosolic OAS-TL is involved in maintaining organic sulphur levels. The old3-1 mutation causes genome-dependent and independent phenotypes and uncovers a novel function for the mutated OAS- TL in cell death regulation. Y1 - 2010 UR - http://www.biomedcentral.com/1471-2229/ U6 - https://doi.org/10.1186/1471-2229-10-80 SN - 1471-2229 ER - TY - JOUR A1 - Vorgerd, M. A1 - vanderVen, Peter F. M. A1 - Bruchertseifer, V. A1 - Lowe, T. A1 - Kley, R. A. A1 - Schröder, Rolf A1 - Lochmuller, H. A1 - Himmel, Mirko A1 - Koehler, K. A1 - Fürst, Dieter Oswald A1 - Huebner, A. T1 - A mutation in the dimerization domain of filamin C causes a novel type of autosomal dominant myofibrillar myopathy N2 - Myofibrillar myopathy (MFM) is a human disease that is characterized by focal myofibrillar destruction and pathological cytoplasmic protein aggregations. In an extended German pedigree with a novel form of MFM characterized by clinical features of a limb-girdle myopathy and morphological features of MFM, we identified a cosegregating, heterozygous nonsense mutation (8130G -> A; W2710X) in the filamin c gene ( FLNC) on chromosome 7q32.1. The mutation is the first found in FLNC and is localized in the dimerization domain of filamin c. Functional studies showed that, in the truncated mutant protein, this domain has a disturbed secondary structure that leads to the inability to dimerize properly. As a consequence of this malfunction, the muscle fibers of our patients display massive cytoplasmic aggregates containing filamin c and several Z-disk-associated and sarcolemmal proteins Y1 - 2005 SN - 0002-9297 ER - TY - JOUR A1 - Thomson, M. R. A. A1 - Weber, Bernd T1 - A new and unusual fauna from the Blaiklock Glacier Group, Shackleton Range Y1 - 1995 ER - TY - JOUR A1 - Sigolaeva, L. V. A1 - Eremenko, A. V. A1 - Makower, Alexander A1 - Makhaeva, G. F. A1 - Malygin, V. V. A1 - Kurochkin, I. N. T1 - A new approach for determinitaton of neuropath target esterase activity Y1 - 1999 ER - TY - JOUR A1 - Cheng, Feng A1 - Dennis, Alice B. A1 - Osuoha, Josephine Ijeoma A1 - Canitz, Julia A1 - Kirschbaum, Frank A1 - Tiedemann, Ralph T1 - A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha JF - BMC genomics N2 - Background Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular. Results A high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862 Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A Computational Analysis of gene Family Evolution (CAFE5) comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris. Conclusions We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species. KW - Campylomormyrus KW - Pacbio sequencing KW - Gene family KW - Osteoglossomorpha KW - Kv1 Y1 - 2023 U6 - https://doi.org/10.1186/s12864-023-09196-6 SN - 1471-2164 VL - 24 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Hemp, Claudia A1 - Heller, Klaus-Gerhard A1 - Warchalowska-Sliwa, Elzbieta A1 - Hemp, Andreas T1 - A new genus and species of African Phaneropterinae (Orthoptera: Tettigoniidae), with data on its ecology, bioacoustics and chromosomes N2 - A new genus is proposed for a new East African Phaneropterinae species, Lunidia viridis, occurring on Mt. Kilimanjaro, Tanzania. Based on 33 records, notes on distribution and habitat are given, as well as acoustical data provided. Climate and vegetation parameters obtained along several transects on Mt. Kilimanjaro were evaluated describing the ecological niche of the new species. This interdisciplinary approach allows not only a profound characterisation of the ecological demands of the new genus but also predictions of the potential distribution area, which is tested for the first time for an African bush cricket species. Lunidia viridis n. gen. n. sp. occurs within humid and perhumid forests and Chagga home gardens, avoiding subhumid conditions on the mountain. It is found from 1,330 m upwards on the southern slopes, whereas the same ecological conditions are expressed from 1,930 m upwards on the drier northern slopes. Lunidia viridis has an unusually complex and variable song, which is described from field and laboratory recordings. The FISH technique for characterizing chromosomes is applied for the first time for an African species; L. viridis exhibits a karyotype typical for most Tettigoniidae. Y1 - 2010 UR - http://www.springerlink.com/content/1439-6092 U6 - https://doi.org/10.1007/s13127-010-0013-3 SN - 1439-6092 ER - TY - JOUR A1 - Hemp, Claudia A1 - Voje, Kjetil Lysne A1 - Heller, Klaus-Gerhard A1 - Warchalowska-Sliwa, Elzbieta A1 - Hemp, Andreas T1 - A new genus of African Acrometopini (Tettigoniidae: Phaneropterinae) based on morphology, chromosomes, acoustics, distribution, and molecular data, and the description of a new species N2 - A new genus, Altihoratosphaga, is erected for species formerly assigned to Horatosphaga Schaum, 1853, and a new species is described. Four species are included in Altihoratosphaga: Altihoratosphaga nomima (Karsch, 1896), Altihoratosphaga montivaga (Sjostedt, 1909), Altihoratosphaga nou (Hemp, 2007) and Altihoratosphaga hanangensis sp. nov. All four species are restricted to Tanzanian localities, and, except for A. nomima, for which no ecological data are available, are confined to montane forest habitats. Data on ecology, acoustics, chromosomes, and molecular relationships are provided, as well as a key to Altihoratosphaga species. The present-day distribution of Altihoratosphaga species suggests former migration events at times when wetter and colder climatic fluctuations favoured connections between montane forest communities, which today are isolated, enabling flightless taxa such as Altihoratosphaga and Monticolaria to spread. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0024-4082 U6 - https://doi.org/10.1111/j.1096-3642.2009.00542.x SN - 0024-4082 ER - TY - JOUR A1 - Hemp, Claudia A1 - Kehl, Siegfried A1 - Heller, Klaus-Gerhard A1 - Waegele, Johann Wolfgang A1 - Hemp, Andreas T1 - A new genus of African Karniellina (Orthoptera, Tettigoniidae, Conocephalinae, Conocephalini) : integrating morphological, molecular and bioacoustical data N2 - Melanoscirtes gen.n. is established within Karniellina. The members of this subtribe are small conocephaline bush crickets, confined to Africa. Melanoscirtes is erected on Phlesirtes kibonotensis, a species restricted to forest clearings and forest edge in the submontane and montane zones of Mt. Kilimanjaro. A subspecies, M. kibonotensis uguenoensis, is described from the North Pare mountains, a mountain range of the Eastern Arc adjacent to Mt. Kilimanjaro. Further species of Melanoscirtes occur on other mountain ranges of the northern branch of the Eastern Arc mountains of northern Tanzania and southern Kenya. The South Pare mountains harbour M. shengenae; the West Usambaras, M. usambarensis, and the Taita Hills, M. taitensis. All species and subspecies of Melanoscirtes exhibit a similar morphology and occupy analogous habitats on the respective mountains. The song patterns for all species found within this genus are very similar, and this, together with evidence from molecular data, suggests that allopatric speciation is the reason for the biogeographic pattern found in this genus. A key for the subspecies and species of Melanoscirtes is provided. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0307-6970 U6 - https://doi.org/10.1111/j.1365-3113.2010.00528.x SN - 0307-6970 ER - TY - JOUR A1 - Heiler, Katharina C. M. A1 - Nahavandi, Nahid A1 - Albrecht, Christian T1 - A new invasion into an Ancient lake : the invasion history of the dreissenid mussel Mytilopsis leucophaeata (Conrad, 1831) and its first record in the Caspian sea Y1 - 2010 UR - http://www.bioone.org/loi/mala U6 - https://doi.org/10.4002/040.053.0112 SN - 0076-2997 ER - TY - JOUR A1 - Obbard, Darren J. A1 - Shi, Mang A1 - Roberts, Katherine E. A1 - Longdon, Ben A1 - Dennis, Alice B. T1 - A new lineage of segmented RNA viruses infecting animals JF - Virus Evolution N2 - Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage. KW - metagenome KW - RNA virus KW - dark virus KW - arthropod KW - RNA interference Y1 - 2020 U6 - https://doi.org/10.1093/ve/vez061 SN - 2057-1577 VL - 6 IS - 1 SP - 1 EP - 10 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Bissinger, Vera A1 - Jander, Jörn A1 - Tittel, Jörg T1 - A new medium free of organic carbon to cultivate organisms from extremely acidic mining lakes (pH 2.7) N2 - An algal culture medium was developed which reflects the extreme chemical conditions of acidic mining lakes (pH 2.7, high concentrations of iron and sulfate) and remains stable without addition of organic carbon sources. It enables controlled experiments e.g. on the heterotrophic potential of pigmented flagellates in the laboratory. Various plankton organisms isolated from acidic lakes were successfully cultivated in this medium. The growth rates of an Chlamydomonas- isolate from acidic mining lakes were assessed by measuring cell densities under pure autotrophic and heterotrophic conditions (with glucose as organic C-source) and showed values of 0.74 and 0.40, respectively. Y1 - 2000 ER - TY - JOUR A1 - Nikoloski, Zoran A1 - May, Patrick A1 - Selbig, Joachim T1 - A new network model explains the evolution of plant-specific metabolic networks Y1 - 2009 UR - http://www.sciencedirect.com/science/journal/10956433 U6 - https://doi.org/10.1016/j.cbpa.2009.04.567 SN - 1095-6433 ER - TY - JOUR A1 - Van den Wyngaert, Silke A1 - Seto, Kensuke A1 - Rojas-Jimenez, Keilor A1 - Kagami, Maiko A1 - Grossart, Hans-Peter T1 - A New Parasitic Chytrid, Staurastromyces oculus (Rhizophydiales, Staurastromy-cetaceae fam. nov.), Infecting the Freshwater Desmid Staurastrum sp. JF - Protist N2 - Chytrids are a diverse group of ubiquitous true zoosporic fungi. The recent molecular discovery of a large diversity of undescribed chytrids has raised awareness on their important, but so far understudied ecological role in aquatic ecosystems. In the pelagic zone, of both freshwater and marine ecosystems, many chytrid species have been morphologically described as parasites on almost all major groups of phytoplankton. However, the majority of these parasitic chytrids has rarely been isolated and lack DNA sequence data, resulting in a large proportion of "dark taxa" in databases. Here, we report on the isolation and in-depth morphological, molecular and host range characterization of a chytrid infecting the common freshwater desmid Staurastrum sp. We provide first insights on the metabolic activity of the different chytrid development stages by using the vital dye FUN (R)-1 (2-chloro-4-[2,3-dihydro-3-methyl-[benzo-1,3-thiazol-2-yl]-methylidene]-1-phenylquinolinium iodide). Cross infection experiments suggest that this chytrid is an obligate parasite and specific for the genus Staurastrum sp. Phylogenetic analysis, based on ITS1-5.8S-ITS2 and 28S rDNA sequences, placed it in the order Rhizophydiales. Based on the unique zoospore ultrastructure, combined with thallus morphology, and molecular phylogenetic placement, we describe this parasitic chytrid as a new genus and species Staurastromyces oculus, within a new family Staurastromycetaceae. (C) 2017 Elsevier GmbH. All rights reserved. KW - Chytrids KW - parasite KW - phytoplankton KW - Staurastromyces oculus KW - Staurastrum sp. Y1 - 2017 U6 - https://doi.org/10.1016/j.protis.2017.05.001 SN - 1434-4610 VL - 168 SP - 392 EP - 407 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Kindermann, Liana A1 - Dobler, Magnus A1 - Niedeggen, Daniela A1 - Linstädter, Anja T1 - A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems JF - Ecological indicators : integrating monitoring, assessment and management N2 - Almost one third of global drylands are open forests and savannas, which are typically shaped by frequent natural disturbances such as wildfire and herbivory. Studies on ecosystem functions and services of woody vegetation require robust estimates of aboveground biomass (AGB). However, most methods have been developed for comparatively undisturbed forest ecosystems. As they are not tailored to accurately quantify AGB of small and irregular growth forms, their application on these growth forms may lead to unreliable or even biased AGB estimates in disturbance-prone dryland ecosystems. Moreover, these methods cannot quantify AGB losses caused by disturbance agents. Here we propose a methodology to estimate individual-and stand-level woody AGB in disturbance-prone ecosystems. It consists of flexible field sampling routines and estimation workflows for six growth classes, delineated by size and damage criteria. It also comprises a detailed damage assessment, harnessing the ecological archive of woody growth for past disturbances. Based on large inventories collected along steep gradients of elephant disturbances in African dryland ecosystems, we compared the AGB estimates generated with our proposed method against estimates from a less adapted forest inventory method. We evaluated the necessary stepwise procedures of method adaptation and analyzed each step's effect on stand-level AGB estimation. We further explored additional advantages of our proposed method with regard to disturbance impact quantification. Results indicate that a majority of growth forms and individuals in savanna vegetation could only be assessed if methods of AGB estimation were adapted to the conditions of a disturbance-prone ecosystem. Furthermore, our damage assessment demonstrated that one third to half of all woody AGB was lost to disturbances. Consequently, less adapted methods may be insufficient and are likely to render inaccurate AGB estimations. Our proposed method has the potential to accurately quantify woody AGB in disturbance-prone ecosystems, as well as AGB losses. Our method is more time consuming than conventional allometric approaches, yet it can cover sufficient areas within reasonable timespans, and can also be easily adapted to alternative sampling schemes. KW - Damage assessment KW - Disturbance impacts KW - Tree growth classes KW - Method KW - comparison KW - Flexible sampling strategy KW - Tree allometry KW - Woody KW - aboveground biomass Y1 - 2021 U6 - https://doi.org/10.1016/j.ecolind.2021.108466 SN - 1470-160X SN - 1872-7034 VL - 135 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Sroka, Pavel A1 - Godunko, Roman J. A1 - Rutschmann, Sereina A1 - Angeli, Kamila B. A1 - Salles, Frederico F. A1 - Gattolliat, Jean-Luc T1 - A new species of Bungona in Turkey (Ephemeroptera, Baetidae) BT - an unexpected biogeographic pattern within a pantropical complex of mayflies JF - Zoosytematics and evolution N2 - By using an integrative approach, we describe a new species of mayfly, Bungona (Chopralla) pontica sp. n., from Turkey. The discovery of a representative of the tropical mayfly genus Bungona in the Middle East is rather unexpected. The new species shows all the main morphological characters of the subgenus Chopralla, which has its closest related species occurring in southeastern Asia. Barcoding clearly indicated that the new species represents an independent lineage isolated for a very long time from other members of the complex. The claw is equipped with two rows of three or four flattened denticles. This condition is a unique feature of Bungona (Chopralla) pontica sp. n. among West Palaearctic mayfly species. Within the subgenus Chopralla, the species can be identified by the presence of a simple, not bifid right prostheca (also present only in Bungona (Chopralla) liebenauae (Soldan, Braasch & Muu, 1987)), the shape of the labial palp, and the absence of protuberances on pronotum. KW - Biogeography KW - Cloeodes complex KW - Chopralla KW - integrative taxonomy KW - Middle East KW - new species Y1 - 2019 U6 - https://doi.org/10.3897/zse.95.29487 SN - 1860-0743 VL - 95 IS - 1 SP - 1 EP - 13 PB - Pensoft Publ. CY - Sofia ER - TY - JOUR A1 - Ionescu, Danny A1 - Bizic-Ionescu, Mina A1 - Khalili, Arzhang A1 - Malekmohammadi, Reza A1 - Morad, Reza Mohammad A1 - de Beer, Dirk A1 - Grossart, Hans-Peter T1 - A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect JF - Scientific reports N2 - Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods. Y1 - 2015 U6 - https://doi.org/10.1038/srep14706 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Göthel, Markus A1 - Listek, Martin A1 - Messerschmidt, Katrin A1 - Schlör, Anja A1 - Hönow, Anja A1 - Hanack, Katja T1 - A New Workflow to Generate Monoclonal Antibodies against Microorganisms JF - Applied Sciences N2 - Monoclonal antibodies are used worldwide as highly potent and efficient detection reagents for research and diagnostic applications. Nevertheless, the specific targeting of complex antigens such as whole microorganisms remains a challenge. To provide a comprehensive workflow, we combined bioinformatic analyses with novel immunization and selection tools to design monoclonal antibodies for the detection of whole microorganisms. In our initial study, we used the human pathogenic strain E. coli O157:H7 as a model target and identified 53 potential protein candidates by using reverse vaccinology methodology. Five different peptide epitopes were selected for immunization using epitope-engineered viral proteins. The identification of antibody-producing hybridomas was performed by using a novel screening technology based on transgenic fusion cell lines. Using an artificial cell surface receptor expressed by all hybridomas, the desired antigen-specific cells can be sorted fast and efficiently out of the fusion cell pool. Selected antibody candidates were characterized and showed strong binding to the target strain E. coli O157:H7 with minor or no cross-reactivity to other relevant microorganisms such as Legionella pneumophila and Bacillus ssp. This approach could be useful as a highly efficient workflow for the generation of antibodies against microorganisms. KW - monoclonal antibody KW - antibody producing cell selection KW - hybridoma KW - epitope prediction Y1 - 2021 U6 - https://doi.org/10.3390/app11209359 SN - 1454-5101 VL - 11 IS - 20 PB - MDPI CY - Basel ER - TY - JOUR A1 - Hahnewald, Rita A1 - Leimkühler, Silke A1 - Vilaseca, Antonia A1 - Acquaviva-Bourdain, Cecile A1 - Lenz, Ulrike A1 - Reiss, Jochen T1 - A novel MOCS2 mutation reveals coordinated expression of the small and large subunit of molybdopterin synthase JF - Molecular genetics and metabolism N2 - The small and large subunits of molybdopterin (MPT) synthase (MOCS2A and MOCS2B), are both encoded by the MOCS2 gene in overlapping and shifted open reading frames (ORFs), which is a highly unusual structure for eukaryotes. Theoretical analysis of genomic sequences suggested that the expression of these overlapping ORFs is facilitated by the use of alternate first exons leading to alternative transcripts. Here, we confirm the existence of these overlapping transcripts experimentally. Further, we identified a deletion in a molybdenum cofactor deficient patient, which removes the start codon for the small subunit (MOCS2A). We observed undisturbed production of both transcripts, while Western blot analysis demonstrated that MOCS2B, the large subunit, is unstable in the absence of MOCS2A. This reveals new insights into the expression of this evolutionary ancient anabolic system. KW - molybdenum cofactor deficiency KW - MOCS2 KW - overlapping reading frames Y1 - 2006 U6 - https://doi.org/10.1016/j.ymgme.2006.04.008 SN - 1096-7192 VL - 89 IS - 3 SP - 210 EP - 213 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Lütkecosmann, Steffi A1 - Warsinke, Axel A1 - Tschöpe, Winfried A1 - Eichler, Rüdiger A1 - Hanack, Katja T1 - A novel monoclonal antibody suitable for the detection of leukotriene B4 JF - Biochemical and biophysical research communications N2 - Leukotriene B4 as an inflammatory mediator is an important biomarker for different respiratory diseases like asthma, chronic obstructive pulmonary disease or cystic lung fibrosis. Therefore the detection of LTB4 is helpful in the diagnosis of these pulmonary diseases. However, until now its determination in exhaled breath condensates suffers from problems of accuracy. Reasons for that could be improper sample collection and preparation methods of condensates and the lack of consistently assay specificity and reproducibility of the used immunoassay detection system. In this study we describe the development and the characterization of a specific monoclonal antibody (S27BC6) against LTB4, its use as molecular recognition element for the development of an enzyme-linked immunoassay to detect LTB4 and discuss possible future diagnostic applications. KW - Leukotriene B4 KW - Monoclonal antibody KW - Immunosensor KW - Chronic obstructive pulmonary disease (COPD) KW - Hapten Y1 - 2017 U6 - https://doi.org/10.1016/j.bbrc.2016.11.157 SN - 0006-291X SN - 1090-2104 VL - 482 IS - 4 SP - 1054 EP - 1059 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Gajovic, Nenad A1 - Warsinke, Axel A1 - Scheller, Frieder W. T1 - A novel multienzyme electrode for the determination of citrate Y1 - 1995 ER - TY - JOUR A1 - Kagel, Heike A1 - Bier, Frank Fabian A1 - Frohme, Marcus A1 - Glökler, Jörn F. T1 - A Novel Optical Method To Reversibly Control Enzymatic Activity Based On Photoacids JF - Scientific reports N2 - Most biochemical reactions depend on the pH value of the aqueous environment and some are strongly favoured to occur in an acidic environment. A non-invasive control of pH to tightly regulate such reactions with defined start and end points is a highly desirable feature in certain applications, but has proven difficult to achieve so far. We report a novel optical approach to reversibly control a typical biochemical reaction by changing the pH and using acid phosphatase as a model enzyme. The reversible photoacid G-acid functions as a proton donor, changing the pH rapidly and reversibly by using high power UV LEDs as an illumination source in our experimental setup. The reaction can be tightly controlled by simply switching the light on and off and should be applicable to a wide range of other enzymatic reactions, thus enabling miniaturization and parallelization through non-invasive optical means. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-50867-w SN - 2045-2322 VL - 9 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Bleidorn, Christoph A1 - Lanterbecq, Deborah A1 - Eeckhaut, Igor A1 - Tiedemann, Ralph T1 - A PCR survey of Hox genes in the myzostomid Myzostoma cirriferum N2 - Using degenerate primers, we were able to identify seven Hox genes for the myzostomid Myzostoma cirriferum. The recovered fragments belong to anterior class (Mci_lab, Mci_pb), central class (Mci_Dfd, Mci_Lox5, Mci_Antp, Mci_Lox4), and posterior class (Mci_Post2) paralog groups. Orthology assignment was verified by phylogenetic analyses and presence of diagnostic regions in the homeodomain as well as flanking regions. The presence of Lox5, Lox4, and Post2 supports the inclusion of Myzostomida within Lophotrochozoa. We found signature residues within flanking regions of Lox5, which are also found in annelids, but not in Platyhelminthes. As such the available Hox genes data of myzostomids support an annelid relationship. Y1 - 2009 UR - http://www.springerlink.com/content/100526 U6 - https://doi.org/10.1007/s00427-009-0282-z SN - 0949-944X 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 - Neumann, Meina A1 - Mittelstaedt, Gerd A1 - Iobbi-Nivol, Chantal A1 - Saggu, Miguel A1 - Lendzian, Friedhelm A1 - Hildebrandt, Peter A1 - Leimkühler, Silke T1 - A periplasmic aldehyde oxidoreductase represents the first molybdopterin cytosine dinucleotide cofactor containing molybdo-flavoenzyme from Escherichia coli N2 - Three DNA regions carrying genes encoding putative homologs of xanthine dehydrogenases were identified in Escherichia coli, named xdhABC, xdhD, and yagTSRQ. Here, we describe the purification and characterization of gene products of the yagTSRQ operon, a molybdenum-containing iron-sulfur flavoprotein from E. coli, which is located in the periplasm. The 135 kDa enzyme comprised a noncovalent (alpha beta gamma) heterotrimer with a large (78.1 kDa) molybdenum cofactor (Moco)-containing YagR subunit, a medium (33.9 kDa) FAD-containing YagS subunit, and a small (21.0 kDa) 2 x [2Fe2S]-containing YagT subunit. YagQ is not a subunit of the mature enzyme, and the protein is expected to be involved in Moco modification and insertion into YagTSR. Analysis of the form of Moco present in YagTSR revealed the presence of the molybdopterin cytosine dinucleotide cofactor. Two different [2Fe2S] clusters, typical for this class of enzyme, were identified by EPR. YagTSR represents the first example of a molybdopterin cytosine dinucleotide-containing protein in E. coli. Kinetic characterization of the enzyme revealed that YagTSR converts a broad spectrum of aldehydes, with a preference for aromatic aldehydes. Ferredoxin instead of NAD(+) or molecular oxygen was used as terminal electron acceptor. Complete growth inhibition of E. coli cells devoid of genes from the yagTSRQ operon was observed by the addition of cinnamaldehyde to a low-pH medium. This finding shows that YagTSR might have a role in the detoxification of aromatic aldehydes for E. coli under certain growth conditions. Y1 - 2009 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=1742-464X U6 - https://doi.org/10.1111/j.1742-4658.2009.07000.x SN - 1742-464X ER - TY - JOUR A1 - Contin, Andrea A1 - Frasca, Stefano A1 - Vivekananthan, Jeevanthi A1 - Leimkühler, Silke A1 - Wollenberger, Ursula A1 - Plumere, Nicolas A1 - Schuhmann, Wolfgang T1 - A pH Responsive Redox Hydrogel for Electrochemical Detection of Redox Silent Biocatalytic Processes. Control of Hydrogel Solvation JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - The control of bioelectrocatalytic processes by external stimuli for the indirect detection of non-redox active species was achieved using an esterase and a redox enzyme both integrated within a redox hydrogel. The poly( vinyl) imidazole Os(bpy)(2)Cl hydrogel displays pH-responsive properties. The esterase catalysed reaction leads to a local pH decrease causing protonation of imidazole moieties thus increasing hydrogel solvation and mobility of the tethered Os-complexes. This is the key step to enable improved electron transfer between an aldehyde oxidoreductase and the polymer-bound Os-complexes. The off-on switch is further integrated in a biofuel cell system for self-powered signal generation. KW - pH responsive hydrogel KW - External stimuli KW - Biofuel cell KW - Self-powered biosensor KW - Solvation Y1 - 2015 U6 - https://doi.org/10.1002/elan.201400621 SN - 1040-0397 SN - 1521-4109 VL - 27 IS - 4 SP - 938 EP - 944 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Spikes, Montrai A1 - Rodríguez-Silva, Rodet A1 - Bennett, Kerri-Ann A1 - Bräger, Stefan A1 - Josaphat, James A1 - Torres-Pineda, Patricia A1 - Ernst, Anja A1 - Havenstein, Katja A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario JF - BMC Research Notes N2 - Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade. KW - Cytochrome b KW - Island biogeography KW - Fresh water fish KW - Phylogeny Y1 - 2021 U6 - https://doi.org/10.1186/s13104-021-05843-x SN - 1756-0500 VL - 14 SP - 1 EP - 8 PB - BMC Research Notes / Biomed Central CY - London ER - TY - JOUR A1 - Teller, C. A1 - Halamek, Jan A1 - Makower, Alexander A1 - Fournier, Didier A1 - Schulze, H. A1 - Scheller, Frieder W. T1 - A piezoelectric sensor with propidium as a recognition element for cholinesterases N2 - A piezoelectric biosensor has been developed on the basis of the reversible acetylcholinesterase (AChE) inhibitor propidium. The propidium cation was bound to a 11-mercaptoundecanoic acid monolayer on gold-coated quartz crystals. The immobilization was done via activation of carboxyl groups by 1,3-dicyclohexylcarbodiimide (DCC). Different types of cholinesterases (acetyl- and butyryl-ChE) from different origins were tested for their binding ability towards the immobilized propidium. Binding Studies were performed in a flow system, Furthermore, catalytically active and organophosphate-inhibited enzyme were compared re-aiding their binding capability. The binding constants were derived by using an one to one binding model and a refined model also including rebinding effects. It was shown that organophosphorylation of the active site hardly influences the affinity of AChE towards propidium. Furthermore the propidium-based biosensor provides equal sensitivity as compared with piezolelectric sensors with immobilized paraoxon- an active site ligand of AChE. (c) 2005 Elsevier B.V. All rights reserved Y1 - 2006 U6 - https://doi.org/10.1016/j.snb.2005.02.053 ER - TY - JOUR A1 - Liaimer, Anton A1 - Jenke-Kodama, Holger A1 - Ishida, Keishi A1 - Hinrichs, Katrin A1 - Stangeland, Janne A1 - Hertweck, Christian A1 - Dittmann-Thünemann, Elke T1 - A polyketide interferes with cellular differentiation in the symbiotic cyanobacterium Nostoc punctiforme JF - Environmental microbiology reports N2 - Nostoc punctiforme is a filamentous cyanobacterium capable of forming symbiotic associations with a wide range of plants. The strain exhibits extensive phenotypic characteristics and can differentiate three mutually exclusive cell types: nitrogen-fixing heterocysts, motile hormogonia and spore-like akinetes. Here, we provide evidence for a crucial role of an extracellular metabolite in balancing cellular differentiation. Insertional mutagenesis of a gene of the polyketide synthase gene cluster pks2 led to the accumulation of short filaments carrying mostly terminal heterocysts under diazotrophic conditions. The mutant has a strong tendency to form biofilms on solid surfaces as well as in liquid culture. The pks2-strain keeps forming hormogonia over the entire growth curve and shows an early onset of akinete formation. We could isolate two fractions of the wildtype supernatant that could restore the capability to form long filaments with intercalary heterocysts. Growth of the mutant cells in the neighbourhood of wild-type cells on plates led to a reciprocal influence and a partial reconstruction of wild-type and mutant phenotype respectively. We postulate that extracellular metabolites of Nostoc punctiforme act as life cycle governing factors (LCGFs) and that the ratio between distinct factors may guide the differentiation into different life stages. Y1 - 2011 U6 - https://doi.org/10.1111/j.1758-2229.2011.00258.x SN - 1758-2229 VL - 3 IS - 5 SP - 550 EP - 558 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Lorenz, Robert C. A1 - Matthias, Katja A1 - Pieper, Dawid A1 - Wegewitz, Uta Elke A1 - Morche, Johannes A1 - Nocon, Marc A1 - Rissling, Olesja A1 - Schirm, Jaqueline A1 - Jacobs, Anja T1 - A psychometric study found AMSTAR 2 to be a valid and moderately reliable appraisal tool JF - Journal of Clinical Epidemiology N2 - Objectives: The objectives of this study were to determine the interrater reliability (IRR) of assessment of multiple systematic reviews (AMSTAR) 2 for reviews of pharmacological or psychological interventions for the treatment of major depression, to compare it to that of AMSTAR and risk of bias in systematic reviews (ROBIS), and to assess the convergent validity between the appraisal tools. Results: The median kappa values as a measure of IRR indicated a moderate agreement for AMSTAR 2 (median = 0.51), a substantial agreement for AMSTAR (median = 0.62), and a fair agreement for ROBIS (median = 0.27). Validity results showed a positive association for AMSTAR and AMSTAR 2 (r = 0.91) as well as ROBIS and AMSTAR 2 (r = 0.84). For the overall rating, AMSTAR 2 showed a high concordance with ROBIS and a lower concordance with AMSTAR. Conclusion: The IRR of AMSTAR 2 was found to be slightly lower than the IRR of AMSTAR and higher than the IRR of ROBIS. Validity measurements indicate that AMSTAR 2 is closely related to both ROBIS and AMSTAR. (C) 2019 Elsevier Inc. All rights reserved. KW - AMSTAR 2 KW - AMSTAR KW - ROBIS KW - Methodological quality KW - Risk of bias KW - Systematic review Y1 - 2019 U6 - https://doi.org/10.1016/j.jclinepi.2019.05.028 SN - 0895-4356 SN - 1878-5921 VL - 114 SP - 133 EP - 140 PB - Elsevier CY - New York ER - TY - JOUR A1 - Comparot-Moss, Sylviane A1 - Koetting, Oliver A1 - Stettler, Michaela A1 - Edner, Christoph A1 - Graf, Alexander A1 - Weise, Sean E. A1 - Streb, Sebastian A1 - Lue, Wei-Ling A1 - MacLean, Daniel A1 - Mahlow, Sebastian A1 - Ritte, Gerhard A1 - Steup, Martin A1 - Chen, Jychian A1 - Zeeman, Samuel C. A1 - Smith, Alison M. T1 - A putative phosphatase, LSF1, is required for normal starch turnover in Arabidopsis leaves N2 - A putative phosphatase, LSF1 (for LIKE SEX4; previously PTPKIS2), is closely related in sequence and structure to STARCH-EXCESS4 (SEX4), an enzyme necessary for the removal of phosphate groups from starch polymers during starch degradation in Arabidopsis (Arabidopsis thaliana) leaves at night. We show that LSF1 is also required for starch degradation: lsf1 mutants, like sex4 mutants, have substantially more starch in their leaves than wild-type plants throughout the diurnal cycle. LSF1 is chloroplastic and is located on the surface of starch granules. lsf1 and sex4 mutants show similar, extensive changes relative to wild-type plants in the expression of sugar-sensitive genes. However, although LSF1 and SEX4 are probably both involved in the early stages of starch degradation, we show that LSF1 neither catalyzes the same reaction as SEX4 nor mediates a sequential step in the pathway. Evidence includes the contents and metabolism of phosphorylated glucans in the single mutants. The sex4 mutant accumulates soluble phospho- oligosaccharides undetectable in wild-type plants and is deficient in a starch granule-dephosphorylating activity present in wild-type plants. The lsf1 mutant displays neither of these phenotypes. The phenotype of the lsf1/sex4 double mutant also differs from that of both single mutants in several respects. We discuss the possible role of the LSF1 protein in starch degradation. Y1 - 2010 UR - http://www.plantphysiol.org/ U6 - https://doi.org/10.1104/pp.109.148981 SN - 0032-0889 ER - TY - JOUR A1 - Gajovic, Nenad A1 - Habermüller, K. A1 - Warsinke, Axel A1 - Schuhmann, W. A1 - Scheller, Frieder W. T1 - A pyruvate oxidase electrode based on an electrochemically deposited redox polymer Y1 - 1999 ER - TY - JOUR A1 - Blüthgen, Nico A1 - Dormann, Carsten F. A1 - Prati, Daniel A1 - Klaus, Valentin H. A1 - Kleinebecker, Till A1 - Hoelzel, Norbert A1 - Alt, Fabian A1 - Boch, Steffen A1 - Gockel, Sonja A1 - Hemp, Andreas A1 - Müller, Jörg A1 - Nieschulze, Jens A1 - Renner, Swen C. A1 - Schöning, Ingo A1 - Schumacher, Uta A1 - Socher, Stephanie A. A1 - Wells, Konstans A1 - Birkhofer, Klaus A1 - Buscot, Francois A1 - Oelmann, Yvonne A1 - Rothenwöhrer, Christoph A1 - Scherber, Christoph A1 - Tscharntke, Teja A1 - Weiner, Christiane N. A1 - Fischer, Markus A1 - Kalko, Elisabeth K. V. A1 - Linsenmair, Karl Eduard A1 - Schulze, Ernst-Detlef A1 - Weisser, Wolfgang W. T1 - A quantitative index of land-use intensity in grasslands integrating mowing, grazing and fertilization JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - Land use is increasingly recognized as a major driver of biodiversity and ecosystem functioning in many current research projects. In grasslands, land use is often classified by categorical descriptors such as pastures versus meadows or fertilized versus unfertilized sites. However, to account for the quantitative variation of multiple land-use types in heterogeneous landscapes, a quantitative, continuous index of land-use intensity (LUI) is desirable. Here we define such a compound, additive LUI index for managed grasslands including meadows and pastures. The LUI index summarizes the standardized intensity of three components of land use, namely fertilization, mowing, and livestock grazing at each site. We examined the performance of the LUI index to predict selected response variables on up to 150 grassland sites in the Biodiversity Exploratories in three regions in Germany(Alb, Hainich, Schorlheide). We tested the average Ellenberg nitrogen indicator values of the plant community, nitrogen and phosphorus concentration in the aboveground plant biomass, plant-available phosphorus concentration in the top soil, and soil C/N ratio, and the first principle component of these five response variables. The LUI index significantly predicted the principal component of all five response variables, as well as some of the individual responses. Moreover, vascular plant diversity decreased significantly with LUI in two regions (Alb and Hainich). Inter-annual changes in management practice were pronounced from 2006 to 2008, particularly due to variation in grazing intensity. This rendered the selection of the appropriate reference year(s) an important decision for analyses of land-use effects, whereas details in the standardization of the index were of minor importance. We also tested several alternative calculations of a LUI index, but all are strongly linearly correlated to the proposed index. The proposed LUI index reduces the complexity of agricultural practices to a single dimension and may serve as a baseline to test how different groups of organisms and processes respond to land use. In combination with more detailed analyses, this index may help to unravel whether and how land-use intensities, associated disturbance levels or other local or regional influences drive ecological processes. KW - Agro-ecosystems KW - Biodiversity exploratories KW - Grassland management KW - Land-use impacts KW - Livestock density KW - Meadows KW - Nitrogen KW - Pastures Y1 - 2012 U6 - https://doi.org/10.1016/j.baae.2012.04.001 SN - 1439-1791 VL - 13 IS - 3 SP - 207 EP - 220 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Abrahamczyk, Stefan A1 - Lozada Gobilard, Sissi Donna A1 - Ackermann, Markus A1 - Fischer, Eberhard A1 - Krieger, Vera A1 - Redling, Almut A1 - Weigend, Maximilian T1 - A question of data quality-Testing pollination syndromes in Balsaminaceae JF - PLoS one N2 - Pollination syndromes and their predictive power regarding actual plant-animal interactions have been controversially discussed in the past. We investigate pollination syndromes in Balsaminaceae, utilizing quantitative respectively categorical data sets of flower morphometry, signal and reward traits for 86 species to test for the effect of different types of data on the test patterns retrieved. Cluster Analyses of the floral traits are used in combination with independent pollinator observations. Based on quantitative data we retrieve seven clusters, six of them corresponding to plausible pollination syndromes and one additional, well-supported cluster comprising highly divergent floral architectures. This latter cluster represents a non-syndrome of flowers not segregated by the specific data set here used. Conversely, using categorical data we obtained only a rudimentary resolution of pollination syndromes, in line with several earlier studies. The results underscore that the use of functional, exactly quanitified trait data has the power to retrieve pollination syndromes circumscribed by the specific data used. Data quality can, however, not be replaced by sheer data volume. With this caveat, it is possible to identify pollination syndromes from large datasets and to reliably extrapolate them for taxa for which direct observations are unavailable. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0186125 SN - 1932-6203 VL - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Fiorentino, V. A1 - Manganelli, Giuseppe A1 - Giusti, Folco A1 - Tiedemann, Ralph A1 - Ketmaier, Valerino T1 - A question of time the land snail Murella muralis (Gastropoda: Pulmonata) reveals constraints on past ecological speciation JF - Molecular ecology N2 - The lively debate about speciation currently focuses on the relative importance of factors driving population differentiation. While many studies are increasingly producing results on the importance of selection, little is known about the interaction between drift and selection. Moreover, there is still little knowledge on the spatial-temporal scales at which speciation occurs, that is, arrangement of habitat patches, abruptness of habitat transitions, climate and habitat changes interacting with selective forces. To investigate these questions, we quantified variation on a fine geographical scale analysing morphological (shell) and genetic data sets coupled with environmental data in the land snail Murella muralis, endemic to the Mediterranean island of Sicily. Analysis of a fragment of the mitochondrial DNA cytochrome oxidase I gene (COI) and eight nuclear microsatellite loci showed that genetic variation is highly structured at a very fine spatial scale by local palaeogeographical events and historical population dynamics. Molecular clock estimates, calibrated here specifically for Tyrrhenian land snails, provided a framework of palaeogeographical events responsible for the observed geographical variations and migration routes. Finally, we showed for the first time well-documented lines of evidence of selection in the past, which explains divergence of land snail shell shapes. We suggest that time and palaeogeographical history acted as constraints in the progress along the ecological speciation continuum. Our study shows that testing for correlation among palaeogeography, morphology and genetic data on a fine geographical scale provides information fundamental for a detailed understanding of ecological speciation processes. KW - allopatry KW - cytochrome oxidase I gene KW - ecological speciation KW - land snails KW - microsatellites KW - Murella Y1 - 2013 U6 - https://doi.org/10.1111/mec.12107 SN - 0962-1083 SN - 1365-294X VL - 22 IS - 1 SP - 170 EP - 186 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Petrović, Saša A1 - Wendler, Petra T1 - A RADD approach to probing AAA plus protein function JF - Nature structural & molecular biology N2 - AAA+ proteins (ATPases associated with various cellular activities) catalyze the energy-dependent movement or rearrangement of macromolecules. A new study addresses the important question of how to design a selective chemical inhibitor for specific proteins in this diverse superfamily. The powerful chemical genetics approach adds to a growing toolbox of applications that allow dissection of the functions of distinct AAA+ proteins in vivo, facilitating the first steps toward effective drug development. Y1 - 2021 U6 - https://doi.org/10.1038/s41594-021-00579-5 SN - 1545-9993 SN - 1545-9985 VL - 28 IS - 4 SP - 329 EP - 330 PB - Nature Publishing Group CY - Berlin ER - TY - JOUR A1 - Fiorini, Vanina D. A1 - Domínguez, Marisol A1 - Reboreda, Juan C. A1 - Swaddle, John P. T1 - A recent invasive population of the European starling sturnus vulgaris has lower genetic diversity and higher fluctuating asymmetry than primary invasive and native populations JF - Biological invasions : unique international journal uniting scientists in the broad field of biological invasions N2 - Fluctuating asymmetries (FA) are small stress-induced random deviations from perfect symmetry that arise during the development of bilaterally symmetrical traits. One of the factors that can reduce developmental stability of the individuals and cause FA at a population level is the loss of genetic variation. Populations of founding colonists frequently have lower genetic variation than their ancestral populations that could be reflected in a higher level of FA. The European starling (Sturnus vulgaris) is native to Eurasia and was introduced successfully in the USA in 1890 and Argentina in 1983. In this study, we documented the genetic diversity and FA of starlings from England (ancestral population), USA (primary introduction) and Argentina (secondary introduction). We predicted the Argentinean starlings would have the highest level of FA and lowest genetic diversity of the three populations. We captured wild adult European starlings in England, USA, and Argentina, measured their mtDNA diversity and allowed them to molt under standardized conditions to evaluate their FA of primary feathers. For genetic analyses, we extracted DNA from blood samples of individuals from Argentina and USA and from feather samples from individuals from England and sequenced the mitochondrial control region. Starlings in Argentina showed the highest composite FA and exhibited the lowest haplotype and nucleotide diversity. The USA population showed a level of FA and genetic diversity similar to the native population. Therefore, the level of asymmetry and genetic diversity found among these populations was consistent with our predictions based on their invasion history. KW - Exotic bird species KW - Fluctuating asymmetry KW - Genetic variability KW - Sturnus KW - vulgaris Y1 - 2022 U6 - https://doi.org/10.1007/s10530-021-02653-x SN - 1387-3547 SN - 1573-1464 VL - 24 IS - 2 SP - 437 EP - 448 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Kersting, Sebastian A1 - Rausch, Valentina A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - A recombinase polymerase amplification assay for the diagnosis of atypical pneumonia JF - Analytical biochemistry : methods in the biological sciences N2 - Pneumonia is one of the most common and potentially lethal infectious conditions worldwide. Streptococcus pneumoniae is the pathogen most frequently associated with bacterial community-acquired pneumonia, while Legionella pneumophila is the major cause for local outbreaks of legionellosis. Both pathogens can be difficult to diagnose since signs and symptoms are nonspecific and do not differ from other causes of pneumonia. Therefore, a rapid diagnosis within a clinically relevant time is essential for a fast onset of the proper treatment. Although methods based on polymerase chain reaction significantly improved the identification of pathogens, they are difficult to conduct and need specialized equipment. We describe a rapid and sensitive test using isothermal recombinase polymerase amplification and detection on a disposable test strip. This method does not require any special instrumentation and can be performed in less than 20 min. The analytical sensitivity in the multiplex assay amplifying specific regions of S. pneumoniae and L. pneumophila simultaneously was 10 CFUs of genomic DNA per reaction. In cross detection studies with closely related strains and other bacterial agents the specificity of the RPA was confirmed. The presented method is applicable for near patient and field testing with a rather simple routine and the possibility for a read out with the naked eye. Y1 - 2018 U6 - https://doi.org/10.1016/j.ab.2018.04.014 SN - 0003-2697 SN - 1096-0309 VL - 550 SP - 54 EP - 60 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Bier, Frank Fabian A1 - Ehrentreich-Förster, Eva A1 - Dölling, R. A1 - Eremenko, A. V. A1 - Scheller, Frieder W. T1 - A redox-label immunosensor on basis of a bi-enzyme electrode Y1 - 1997 ER - TY - JOUR A1 - Brothers, Soren M. A1 - Hilt, Sabine A1 - Attermeyer, Katrin A1 - Grossart, Hans-Peter A1 - Kosten, Sarian A1 - Lischke, Betty A1 - Mehner, Thomas A1 - Meyer, Nils A1 - Scharnweber, Inga Kristin A1 - Köhler, Jan T1 - A regime shift from macrophyte to phytoplankton dominance enhances carbon burial in a shallow, eutrophic lake JF - Ecosphere : the magazine of the International Ecology University N2 - Ecological regime shifts and carbon cycling in aquatic systems have both been subject to increasing attention in recent years, yet the direct connection between these topics has remained poorly understood. A four-fold increase in sedimentation rates was observed within the past 50 years in a shallow eutrophic lake with no surface in-or outflows. This change coincided with an ecological regime shift involving the complete loss of submerged macrophytes, leading to a more turbid, phytoplankton-dominated state. To determine whether the increase in carbon (C) burial resulted from a comprehensive transformation of C cycling pathways in parallel to this regime shift, we compared the annual C balances (mass balance and ecosystem budget) of this turbid lake to a similar nearby lake with submerged macrophytes, a higher transparency, and similar nutrient concentrations. C balances indicated that roughly 80% of the C input was permanently buried in the turbid lake sediments, compared to 40% in the clearer macrophyte-dominated lake. This was due to a higher measured C burial efficiency in the turbid lake, which could be explained by lower benthic C mineralization rates. These lower mineralization rates were associated with a decrease in benthic oxygen availability coinciding with the loss of submerged macrophytes. In contrast to previous assumptions that a regime shift to phytoplankton dominance decreases lake heterotrophy by boosting whole-lake primary production, our results suggest that an equivalent net metabolic shift may also result from lower C mineralization rates in a shallow, turbid lake. The widespread occurrence of such shifts may thus fundamentally alter the role of shallow lakes in the global C cycle, away from channeling terrestrial C to the atmosphere and towards burying an increasing amount of C. KW - calcite precipitation KW - CO2 emissions KW - global carbon cycle KW - metabolism KW - regime shift KW - sedimentation KW - submerged macrophytes KW - temperate zone KW - trophic status Y1 - 2013 U6 - https://doi.org/10.1890/ES13-00247.1 SN - 2150-8925 VL - 4 IS - 11 PB - Wiley CY - Washington ER - TY - JOUR A1 - Sedaghatmehr, Mastoureh A1 - Thirumalaikumar, Venkatesh P. A1 - Kamranfar, Iman A1 - Marmagne, Anne A1 - Masclaux-Daubresse, Celine A1 - Balazadeh, Salma T1 - A regulatory role of autophagy for resetting the memory of heat stress in plants JF - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology N2 - As sessile life forms, plants are repeatedly confronted with adverse environmental conditions, which can impair development, growth, and reproduction. During evolution, plants have established mechanisms to orchestrate the delicate balance between growth and stress tolerance, to reset cellular biochemistry once stress vanishes, or to keep a molecular memory, which enables survival of a harsher stress that may arise later. Although there are several examples of memory in diverse plants species, the molecular machinery underlying the formation, duration, and resetting of stress memories is largely unknown so far. We report here that autophagy, a central self-degradative process, assists in resetting cellular memory of heat stress (HS) in Arabidopsis thaliana. Autophagy is induced by thermopriming (moderate HS) and, intriguingly, remains high long after stress termination. We demonstrate that autophagy mediates the specific degradation of heat shock proteins at later stages of the thermorecovery phase leading to the accumulation of protein aggregates after the second HS and a compromised heat tolerance. Autophagy mutants retain heat shock proteins longer than wild type and concomitantly display improved thermomemory. Our findings reveal a novel regulatory mechanism for HS memory in plants. KW - Arabidopsis KW - heat shock proteins KW - priming KW - resetting Y1 - 2019 U6 - https://doi.org/10.1111/pce.13426 SN - 0140-7791 SN - 1365-3040 VL - 42 IS - 3 SP - 1054 EP - 1064 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Albers, Philip A1 - Üstün, Suayib A1 - Witzel, Katja A1 - Kraner, Max Erdmund A1 - Börnke, Frederik T1 - A Remorin from Nicotiana benthamiana Interacts with the Pseudomonas Type-III Effector Protein HopZ1a and is Phosphorylated by the Immune-Related Kinase PBS1 JF - Molecular Plant-Microbe Interactions N2 - The plasma membrane (PM) is at the interface of plant-pathogen interactions and, thus, many bacterial type-III effector (T3E) proteins target membrane-associated processes to interfere with immunity. The Pseudomonas syringae T3E HopZ1a is a host cell PM-localized effector protein that has several immunity-associated host targets but also activates effector-triggered immunity in resistant backgrounds. Although HopZ1a has been shown to interfere with early defense signaling at the PM, no dedicated PM-associated HopZ1a target protein has been identified until now. Here, we show that HopZ1a interacts with the PM-associated remorin protein NbREM4 from Nicotiana benthamiana in several independent assays. NbREM4 relocalizes to membrane nanodomains after treatment with the bacterial elicitor flg22 and transient overexpression of NbREM4 in N. benthamiana induces the expression of a subset of defense-related genes. We can further show that NbREM4 interacts with the immune-related receptor-like cytoplasmic kinase avrPphB-susceptible 1 (PBS1) and is phosphorylated by PBS1 on several residues in vitro. Thus, we conclude that NbREM4 is associated with early defense signaling at the PM. The possible relevance of the HopZ1a-NbREM4 interaction for HopZ1a virulence and avirulence functions is discussed. KW - bacterial pathogenesis KW - defense signaling pathways KW - effectors KW - elicitors KW - HopZ1a KW - MAMPs KW - PAMPs KW - PBS1 KW - Pseudomonas syringae KW - remorin KW - type-3 secretion Y1 - 2019 U6 - https://doi.org/10.1094/MPMI-04-19-0105-R SN - 0894-0282 SN - 1943-7706 VL - 32 IS - 9 SP - 1229 EP - 1242 PB - Amer phytopathological SOC CY - ST Paul ER - TY - JOUR A1 - Miller, Stefan A1 - Schuler, Benjamin A1 - Seckler, Robert T1 - A reversibly unfolding fragment of P22 tailspike protein with native structure : the isolated beta-helix domain Y1 - 1998 ER - TY - JOUR A1 - Hauser, Frank A1 - Cazzamali, Giuseppe A1 - Williamson, Michael A1 - Blenau, Wolfgang A1 - Grimmelikhuijzen, CJ. T1 - A review of neurohormone GPCRs present in the fruitfly "Drosophila melanogaster" and the honey bee "Apis mellifera" N2 - G protein-coupled receptor (GPCR) genes are large gene families in every animal, sometimes making up to 1-2% of the animal's genome. Of all insect GPCRs, the neurohormone (neuropeptide, protein hormone, biogenic amine) GPCRs are especially important, because they, together with their ligands, occupy a high hierarchic position in the physiology of insects and steer crucial processes such as development, reproduction, and behavior. In this paper, we give a review of our current knowledge on Drosophila melanogaster GPCRs and use this information to annotate the neurohormone GPCR genes present in the recently sequenced genome from the honey bee Apis mellifera. We found 35 neuropeptide receptor genes in the honey bee (44 in Drosophila) and two genes, coding for leucine-rich repeats-containing protein hormone GPCRs (4 in Drosophila). In addition, the honey bee has 19 biogenic amine receptor genes (21 in Drosophila). The larger numbers of neurohormone receptors in Drosophila are probably due to gene duplications that occurred during recent evolution of the fly. Our analyses also yielded the likely ligands for 40 of the 56 honey bee neurohormone GPCRs identified in this study. In addition, we made some interesting observations on neurohormone GPCR evolution and the evolution and co-evolution of their ligands. For neuropeptide and protein hormone GPCRs, there appears to be a general co-evolution between receptors and their ligands. This is in contrast to biogenic amine GPCRs, where evolutionarily unrelated GPCRs often bind to the same biogenic amine, suggesting frequent ligand exchanges ("ligand hops") during GPCR evolution. Y1 - 2006 UR - http://www.sciencedirect.com/science/journal/03010082 U6 - https://doi.org/10.1016/j.pneurobio.2006.07.005 SN - 0301-0082 ER - TY - JOUR A1 - Bianco, Pier Giorgio A1 - Ketmaier, Valerio T1 - A revision of the Rutilus complex from Mediterranean Europe with description of a new genus, Sarmarutilus, and a new species, Rutilus stoumboudae (Teleostei: Cyprinidae) JF - Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists N2 - By combining morphology, ecology, biology, and biogeography with the available molecular (sequence variation of the entire mitochondrial cytochrome b gene; cyt-b) and karyology data, the taxonomy of several species of the Rutilus complex inhabiting southern Europe is revised. Rutilus stoumboudae, new species, is described from Lake Volvi, Greece. It differs from Rutilus rutilus in possessing more total GR and less branched rays in both dorsal and anal fins and in its placement in the cyt-b based phylogeny of the genus. The resurrected genus Leucos Heckel, 1843 (type species Leucos aula, Bonaparte, 1841), which according to molecular data diverged from Rutilus more than 5 million years ago, during the Messinian salinity crisis, includes five species of small size, without spinous tubercles on scales and head in reproductive males, pharyngeal teeth formula 5-5, and all show a preference for still waters. Leucos aula is the Italian species endemic in the Padany-Venetian district: L. basak is widespread in Croatia, Albania, Montenegro and former Yugoslav Republic of Macedonia (FYROM); L. albus, recently described from Lake Skadar, Montenegro, is also found in rivers Moraca and Zeta (Montenegro). L. albus differs from L. basak, its closest relative, in having more scales on the LL and less anal-fin rays; L. panosi is endemic to the western-Greece district, and L. ylikiensis is endemic to lakes Yliki and Paralimni in eastern Greece (introduced in Lake Volvi). Among the nominal species examined, Rutilus karamani, R. ohridanus, R. prespensis and R. prespensis vukovici are all junior synonyms of Leucos basak. Rutilus vegariticus is definitively regarded as junior synonym for R. rutilus. Sarmarutilus n.gen. is a monotypic genus, with Sarmarutilus rubilio as the type species. According to phylogenetic data, Sarmarutilus rubilio is basal to a cluster of species that includes Leucos basak, L. albus, L. aula, L. panosi and L. ylikiensis. Sarmarutilus possibly evolved in pre-Messinian time, in the Lago Mare, entered the Mediterranean area during the Messinian Lago Mare phase of the Mediterranean Sea and survived only in the Tuscany-Latium district. This genus differs from Leucos in having large pearl organs on the central part of head and body scales in mature males and for the habitat preference, being a riverine-adapted species. It differs from Rutilus in pharyngeal teeth formula (5-5 in Sarmarutilus and 6-5 in Rutilus), size (small in Sarmarutilus and large in Rutilus) and for the preferential habitat (riverine vs. still water). Finally, lectotypes for Leucos basak, Leucos aula, and Sarmarutilus rubilio are designated. KW - Freshwater fish KW - Mediterranean Europe KW - Cyprinidae KW - genera Rutilus KW - Leucos KW - Sarmarutilus new genus KW - new species Y1 - 2014 SN - 1175-5326 SN - 1175-5334 VL - 3841 IS - 3 SP - 379 EP - 402 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Gisin, Jonathan A1 - Mueller, Alexandra A1 - Pfaender, Yvonne A1 - Leimkühler, Silke A1 - Narberhaus, Franz A1 - Masepohl, Bernd T1 - A Rhodobacter capsulatus member of a universal permease family imports molybdate and other oxyanions N2 - Molybdenum (Mo) is an important trace element that is toxic at high concentrations. To resolve the mechanisms underlying Mo toxicity, Rhodobacter capsulatus mutants tolerant to high Mo concentrations were isolated by random transposon Tn5 mutagenesis. The insertion sites of six independent isolates mapped within the same gene predicted to code for a permease of unknown function located in the cytoplasmic membrane. During growth under Mo-replete conditions, the wild-type strain accumulated considerably more Mo than the permease mutant. For mutants defective for the permease, the high-affinity molybdate importer ModABC, or both transporters, in vivo Mo-dependent nitrogenase (Mo-nitrogenase) activities at different Mo concentrations suggested that ModABC and the permease import molybdate in nanomolar and micromolar ranges, respectively. Like the permease mutants, a mutant defective for ATP sulfurylase tolerated high Mo concentrations, suggesting that ATP sulfurylase is the main target of Mo inhibition in R. capsulatus. Sulfate-dependent growth of a double mutant defective for the permease and the high-affinity sulfate importer CysTWA was reduced compared to those of the single mutants, implying that the permease plays an important role in sulfate uptake. In addition, permease mutants tolerated higher tungstate and vanadate concentrations than the wild type, suggesting that the permease acts as a general oxyanion importer. We propose to call this permease PerO (for oxyanion permease). It is the first reported bacterial molybdate transporter outside the ABC transporter family. Y1 - 2010 UR - http://jb.asm.org/ U6 - https://doi.org/10.1128/Jb.00742-10 SN - 0021-9193 ER - TY - JOUR A1 - Xu, J. A1 - Brearley, C. A. A1 - Lin, W. H. A1 - Wang, Y. A1 - Ye, R. A1 - Müller-Röber, Bernd A1 - Xu, Z. H. A1 - Xue, H. W. T1 - A role of Arabidopsis inositol polyphosphate kinase, AtIPK2 alpha, in pollen germination and root growth N2 - Inositol polyphosphates, such as inositol trisphosphate, are pivotal intracellular signaling molecules in eukaryotic cells. In higher plants the mechanism for the regulation of the type and the level of these signaling molecules is poorly understood. In this study we investigate the physiological function of an Arabidopsis (Arabidopsis thaliana) gene encoding inositol polyphosphate kinase (AtIPK2alpha), which phosphorylates inositol 1,4,5-trisphosphate successively at the D-6 and D-3 positions, and inositol 1,3,4,5-tetrakisphosphate at D-6, resulting in the generation of inositol 1,3,4,5,6-pentakisphosphate. Semiquantitative reverse transcription-PCR and promoter-beta-glucuronidase reporter gene analyses showed that AtIPK2alpha is expressed in various tissues, including roots and root hairs, stem, leaf, pollen grains, pollen tubes, the flower stigma, and siliques. Transgenic Arabidopsis plants expressing the AtIPK2alpha antisense gene under its own promoter were generated. Analysis of several independent transformants exhibiting strong reduction in AtIPK2alpha transcript levels showed that both pollen germination and pollen tube growth were enhanced in the antisense lines compared to wild-type plants, especially in the presence of nonoptimal low Ca2+ concentrations in the culture medium. Furthermore, root growth and root hair development were also stimulated in the antisense lines, in the presence of elevated external Ca2+ concentration or upon the addition of EGTA. In addition, seed germination and early seedling growth was stimulated in the antisense lines. These observations suggest a general and important role of AtIPK2alpha, and hence inositol polyphosphate metabolism, in the regulation of plant growth most likely through the regulation of calcium signaling, consistent with the well-known function of inositol trisphosphate in the mobilization of intracellular calcium stores Y1 - 2005 SN - 0032-0889 ER - TY - JOUR A1 - Rojas-Jimenez, Keilor A1 - Rieck, Angelika A1 - Wurzbacher, Christian A1 - Jürgens, Klaus A1 - Labrenz, Matthias A1 - Grossart, Hans-Peter T1 - A Salinity Threshold Separating Fungal Communities in the Baltic Sea JF - Frontiers in Microbiology N2 - Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world’s largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales, and Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm. KW - fungal diversity KW - baltic sea KW - salinity gradient KW - brackish waters KW - chytridiomycota KW - cryptomycota Y1 - 2019 U6 - https://doi.org/10.3389/fmicb.2019.00680 SN - 1664-302X VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Vasseur, David A1 - Gaedke, Ursula A1 - McCann, Kevin S. T1 - A seasonal alternation of coherent and compensatory dynamics occurs in phytoplankton N2 - Functional groups with diverse responses to environmental factors sum to produce communities with less temporal variability in their biomass than those lacking this diversity. The detection of these compensatory dynamics can be complicated by a spatio-temporal alternation in the environmental factors limiting growth (both abiotic and biotic), which restricts the occurrence of compensatory dynamics to certain periods or locations. Hence, resolving the spatio- temporal scale may uncover important spatial and/or temporal components in community variability. Using long-term data from Lake Constance (Bodensee), we find that a reduction in grazing pressure and relaxed competition for nutrients during winter and spring generates coherent dynamics among edible and less edible phytoplankton. During summer and fall, when both grazing pressure and nutrient limitation are present, edible and less edible phytoplankton exhibit compensatory dynamics. This study supports recent work suggesting that both abiotic and biotic interactions promote compensatory dynamics and to our knowledge, this is the first example of a system where compensatory and coherent dynamics seasonally alternate. Y1 - 2005 ER - TY - JOUR A1 - Sonnewald, Uwe A1 - Basner, Astrid A1 - Greve, Burkhard A1 - Steup, Martin T1 - A second L-type isozyme of potato glucan phosphorylase : cloning, antisense inhibition and expression analysis Y1 - 1995 ER - TY - JOUR A1 - Trindade, Ines T1 - A shelter for the future BT - how WUSCHEL protects the shoot apical meristem from viral infection JF - Molecular plant N2 - Plant development in its majority occurs post-embryonically through the activity of local meristems that provide daughter cells for the development of new organs. It has long been acknowledged that the shoot apical meristem (SAM), which holds the stem cells that will form above-ground organs, is recalcitrant to infection by multiple pathogens, a crucial strategy to safeguard normal devel- opment and subsequent generations. However, the molecular mechanisms underlying SAM immunity remain largely unknown. Y1 - 2020 U6 - https://doi.org/10.1016/j.molp.2020.11.009 SN - 1674-2052 SN - 1752-9867 VL - 13 IS - 12 SP - 1675 EP - 1675 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Mumm, Rebekka A1 - Hermanussen, Michael T1 - A short note on the BMI and on secular changes in BMI JF - Human biology and public health N2 - Human size changes over time with worldwide secular trends in height, weight, and body mass index (BMI). There is general agreement to relate the state of nutrition to height and weight, and to ratios of weight-to-height. The BMI is a ratio. It is commonly used to classify underweight, overweight and obesity in adults. Yet, the BMI is inappropriate to provide any immediate information on body composition. It is accepted that the BMI is “a simple index to classify underweight, overweight and obesity in adults”. It is stated that “policies, programmes and investments need to be “nutrition-sensitive”, which means they must have positive impacts on nutrition”. It is also stated that “a need for policies that address all forms of malnutrition by making healthy foods accessible and affordable, while restricting unhealthy foods through fiscal and regulatory restrictions“. But these statements are neither warranted by arithmetic considerations, nor by historic evidence. Measuring the BMI is an appropriate screening tool for detecting an unusual weight-to-height ratio, but the BMI is an inappropriate tool for estimating body composition, or suggesting medical and health policy decisions. KW - body mass index KW - secular trend KW - weight-to-height ratio KW - malnutrition KW - obesity Y1 - 2021 U6 - https://doi.org/10.52905/hbph.v2.17 SN - 2748-9957 IS - 2 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Küken, Anika A1 - Treves, Haim A1 - Nikoloski, Zoran T1 - A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae JF - Frontiers in plant science : FPLS N2 - Introduction Flux phenotypes from different organisms and growth conditions allow better understanding of differential metabolic networks functions. Fluxes of metabolic reactions represent the integrated outcome of transcription, translation, and post-translational modifications, and directly affect growth and fitness. However, fluxes of intracellular metabolic reactions cannot be directly measured, but are estimated via metabolic flux analysis (MFA) that integrates data on isotope labeling patterns of metabolites with metabolic models. While the application of metabolomics technologies in photosynthetic organisms have resulted in unprecedented data from 13CO2-labeling experiments, the bottleneck in flux estimation remains the application of isotopically nonstationary MFA (INST-MFA). INST-MFA entails fitting a (large) system of coupled ordinary differential equations, with metabolite pools and reaction fluxes as parameters. Here, we focus on the Calvin-Benson cycle (CBC) as a key pathway for carbon fixation in photosynthesizing organisms and ask if approaches other than classical INST-MFA can provide reliable estimation of fluxes for reactions comprising this pathway. Methods First, we show that flux estimation with the labeling patterns of all CBC intermediates can be formulated as a single constrained regression problem, avoiding the need for repeated simulation of time-resolved labeling patterns. Results We then compare the flux estimates of the simulation-free constrained regression approach with those obtained from the classical INST-MFA based on labeling patterns of metabolites from the microalgae Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii under different growth conditions. Discussion Our findings indicate that, in data-rich scenarios, simulation-free regression-based approaches provide a suitable alternative for flux estimation from classical INST-MFA since we observe a high qualitative agreement (rs=0.89) to predictions obtained from INCA, a state-of-the-art tool for INST-MFA. KW - metabolic flux analysis KW - INST-MFA KW - regression KW - 13C labeling KW - algae Y1 - 2023 U6 - https://doi.org/10.3389/fpls.2023.1140829 SN - 1664-462X VL - 14 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Foti, Alessandro A1 - Dorendorf, Frank A1 - Leimkühler, Silke T1 - A single nucleotide polymorphism causes enhanced radical oxygen species production by human aldehyde oxidase JF - PLoS one N2 - Aldehyde oxidases (AOXs) are molybdo-flavoenzymes characterized by broad substrate specificity, oxidizing aromatic/aliphatic aldehydes into the corresponding carboxylic acids and hydroxylating various heteroaromatic rings. The enzymes use oxygen as the terminal electron acceptor and produce reduced oxygen species during turnover. The physiological function of mammalian AOX isoenzymes is still unclear, however, human AOX (hAOX1) is an emerging enzyme in phase-I drug metabolism. Indeed, the number of xenobiotics acting as hAOX1 substrates is increasing. Further, numerous single-nucleotide polymorphisms (SNPs) have been identified within the hAOX1 gene. SNPs are a major source of inter-individual variability in the human population, and SNP-based amino acid exchanges in hAOX1 reportedly modulate the catalytic function of the enzyme in either a positive or negative fashion. In this report we selected ten novel SNPs resulting in amino acid exchanges in proximity to the FAD site of hAOX1 and characterized the purified enzymes after heterologous expression in Escherichia coli. The hAOX1 variants were characterized carefully by quantitative differences in their ability to produce superoxide radical. ROS represent prominent key molecules in physiological and pathological conditions in the cell. Our data reveal significant alterations in superoxide anion production among the variants. In particular the SNP-based amino acid exchange L438V in proximity to the isoalloxanzine ring of the FAD cofactor resulted in increased rate of superoxide radical production of 75%. Considering the high toxicity of the superoxide in the cell, the hAOX1-L438V SNP variant is an eventual candidate for critical or pathological roles of this natural variant within the human population. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0182061 SN - 1932-6203 VL - 12 SP - 18338 EP - 18347 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Paeschke, Manfred A1 - Wollenberger, Ursula A1 - Uhlig, A. A1 - Schnakenberg, Uwe A1 - Wagner, B. A1 - Hintsche, R. T1 - A stacked multichannel amperometric detection system Y1 - 1995 ER - TY - JOUR A1 - Grimm, Volker A1 - Berger, Uta A1 - Bastiansen, Finn A1 - Eliassen, Sigrunn A1 - Ginot, Vincent A1 - Giske, Jarl A1 - Goss-Custard, John A1 - Grand, Tamara A1 - Heinz, Simone K. A1 - Huse, Geir A1 - Huth, Andreas A1 - Jepsen, Jane U. A1 - Jorgensen, Christian A1 - Mooij, Wolf M. A1 - Mueller, Birgit A1 - Piou, Cyril A1 - Railsback, Steven Floyd A1 - Robbins, Andrew M. A1 - Robbins, Martha M. A1 - Rossmanith, Eva A1 - Rueger, Nadja A1 - Strand, Espen A1 - Souissi, Sami A1 - Stillman, Richard A. A1 - Vabo, Rune A1 - Visser, Ute A1 - DeAngelis, Donald L. T1 - A standard protocol for describing individual-based and agent-based models JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers. (c) 2006 Elsevier B.V. All rights reserved. KW - individual-based model KW - agent-based model KW - model description KW - scientific communication KW - standardization Y1 - 2006 U6 - https://doi.org/10.1016/j.ecolmodel.2006.04.023 SN - 0304-3800 VL - 198 SP - 115 EP - 126 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Scheffler, Christiane T1 - A stature of one meter : how is the variability? Y1 - 2002 ER - TY - JOUR A1 - Omidbakhshfard, Mohammad Amin A1 - Winck, Flavia Vischi A1 - Arvidsson, Samuel Janne A1 - Riano-Pachon, Diego M. A1 - Müller-Röber, Bernd T1 - A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana JF - Journal of integrative plant biology N2 - The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species. KW - Arabidopsis thaliana KW - chromatin KW - cis-regulatory elements KW - epigenomics KW - FAIRE-qPCR KW - FAIRE-seq KW - gene expression KW - gene regulatory network KW - transcription factor Y1 - 2014 U6 - https://doi.org/10.1111/jipb.12151 SN - 1672-9072 SN - 1744-7909 VL - 56 IS - 6 SP - 527 EP - 538 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Küken, Anika A1 - Wendering, Philipp A1 - Langary, Damoun A1 - Nikoloski, Zoran T1 - A structural property for reduction of biochemical networks JF - Scientific reports N2 - Large-scale biochemical models are of increasing sizes due to the consideration of interacting organisms and tissues. Model reduction approaches that preserve the flux phenotypes can simplify the analysis and predictions of steady-state metabolic phenotypes. However, existing approaches either restrict functionality of reduced models or do not lead to significant decreases in the number of modelled metabolites. Here, we introduce an approach for model reduction based on the structural property of balancing of complexes that preserves the steady-state fluxes supported by the network and can be efficiently determined at genome scale. Using two large-scale mass-action kinetic models of Escherichia coli, we show that our approach results in a substantial reduction of 99% of metabolites. Applications to genome-scale metabolic models across kingdoms of life result in up to 55% and 85% reduction in the number of metabolites when arbitrary and mass-action kinetics is assumed, respectively. We also show that predictions of the specific growth rate from the reduced models match those based on the original models. Since steady-state flux phenotypes from the original model are preserved in the reduced, the approach paves the way for analysing other metabolic phenotypes in large-scale biochemical networks. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-96835-1 SN - 2045-2322 VL - 11 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER - TY - JOUR A1 - Beissenhirtz, Moritz Karl A1 - Scheller, Frieder W. A1 - Lisdat, Fred T1 - A superoxide sensor based on a multilayer cytochrome c electrode N2 - A novel multilayer cytochrome c electrode for the quantification of superoxide radical concentrations is introduced. The electrode consists of alternating layers of cytochrome c and poly(aniline(sulfonic acid)) on a gold wire electrode. The formation of multilayer structures was proven by SPR experiments. Assemblies with 2-15 protein layers showed electrochemical communication with the gold electrode. For every additional layer, a substantial increase in electrochemically active cytochrome c (cyt. c) was found. For electrodes of more than 10 layers, the increase was more than 1 order of magnitude as compared to monolayer electrode systems. Thermodynamic and kinetic parameters of the electrodes were characterized. The mechanism of electron transfer within the multilayer assembly was studied, with results suggesting a protein-protein electron-transfer model. Electrodes of 2-15 layers were applied to the in vitro quantification of enzymatically generated superoxide, showing superior sensitivity as compared to a monolayer-based sensor. An electrode with 6 cyt. c/PASA layers showed the highest sensitivity of the systems studied, giving an increase in sensitivity of half an order of magnitude versus the that of the monolayer electrode. The stability of the system was optimized using thermal treatment, resulting in no loss in sensor signal or protein loading after 10 successive measurements or 2 days of storage Y1 - 2004 SN - 0003-2700 ER -