@article{EttlingerSchenkMicheeletal.2012, author = {Ettlinger, Julia and Schenk, J{\"o}rg A. and Micheel, Burkhard and Ehrentreich-F{\"o}rster, Eva and Gajovic-Eichelmann, Nenad}, title = {A direct competitive homogeneous immunoassay for progesterone - the Redox Quenching Immunoassay}, series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, volume = {24}, journal = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis}, number = {7}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1040-0397}, doi = {10.1002/elan.201200107}, pages = {1567 -- 1575}, year = {2012}, abstract = {A direct competitive amperometric immunoassay format for the detection of haptens and proteins was developed. The method is based on the quenching of electroactivity of ferrocenium, which is coupled to the antigen and used as the primary reporter, upon binding to a monoclonal anti-ferrocenium antibody, which is coupled to the detection antibody and used as a secondary reporter. A separation-free progesterone immunoassay with a lower detection limit of 1 ng?mL-1 (3.18 nmol?L-1) in 1?:?2 diluted blood serum was realised by combining two bifunctional conjugates, a ferrocenium-PEG-progesterone tracer and a bioconjugate of one anti-progesterone and one anti-ferrocenium antibody. The immune complex is formed within 30 s upon addition of progesterone, resulting in a total analysis time of 1.5 min.}, language = {en} } @article{FussmannWeithoffYoshida2007, author = {Fussmann, Gregor F. and Weithoff, Guntram and Yoshida, Takehito}, title = {A direct, experimental test of resource versus consumer dependence : reply}, issn = {0012-9658}, doi = {10.1890/06-1692}, year = {2007}, language = {en} } @article{FussmannWeithoffYoshida2005, author = {Fussmann, Gregor F. and Weithoff, Guntram and Yoshida, Takehito}, title = {A direct, experimental test of resource vs. consumer dependence}, year = {2005}, abstract = {The uptake of resources from the environment is a vital process for all organisms. Many experimental studies have revealed that the rate at which this process occurs depends critically on the resource concentration, a relationship called "functional response." However, whether the concentration of the consumer normally affects the functional response has been the subject of a long-standing, predominantly theoretical, debate in ecology. Here we present an experimental test between the alternative hypotheses that food uptake depends either only on the resource concentration or on both the resource and the consumer concentrations. In short-term laboratory experiments, we measured the uptake of radioactively labeled, unicellular green algae (Monoraphidium minutum, resource) by the rotifer Brachionus calyciflorus (a consumer) for varying combinations of resource and consumer concentrations. We found that the food uptake by Brachionus depended on the algal concentration with the relationship best described by a Holling type 3 functional response. We detected significant consumer effects on the functional response only at an extraordinarily high Brachionus density (similar to 125 rotifers/mL), which by far exceeds concentrations normally encountered in the field. We conclude that con sumer-dependent food uptake by planktonic rotifers is a phenomenon that can occur under extreme conditions, but probably plays a minor role in natural environments}, language = {en} } @article{Trindade2021, author = {Trindade, In{\^e}s}, title = {A drop of immunity}, series = {Molecular plant}, volume = {14}, journal = {Molecular plant}, number = {9}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1674-2052}, doi = {10.1016/j.molp.2021.07.022}, pages = {1437 -- 1438}, year = {2021}, language = {en} } @article{DemalHeiseReizetal.2019, author = {Demal, Till Joscha and Heise, Melina and Reiz, Benedikt and Dogra, Deepika and Braenne, Ingrid and Reichenspurner, Hermann and M{\"a}nner, J{\"o}rg and Aherrahrou, Zouhair and Schunkert, Heribert and Erdmann, Jeanette and Abdelilah-Seyfried, Salim}, title = {A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A}, series = {Scientific reports}, volume = {9}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-39648-7}, pages = {12}, year = {2019}, abstract = {The genetics of many congenital heart diseases (CHDs) can only unsatisfactorily be explained by known chromosomal or Mendelian syndromes. Here, we present sequencing data of a family with a potentially multigenic origin of CHD. Twelve of nineteen family members carry a familial mutation [NM_004329.2:c.1328 G > A (p.R443H)] which encodes a predicted deleterious variant of BMPR1A. This mutation co-segregates with a linkage region on chromosome 1 that associates with the emergence of severe CHDs including Ebstein's anomaly, atrioventricular septal defect, and others. We show that the continuous overexpression of the zebrafish homologous mutation bmpr1aap.R438H within endocardium causes a reduced AV valve area, a downregulation of Wnt/ß-catenin signalling at the AV canal, and growth of additional tissue mass in adult zebrafish hearts. This finding opens the possibility of testing genetic interactions between BMPR1A and other candidate genes within linkage region 1 which may provide a first step towards unravelling more complex genetic patterns in cardiovascular disease aetiology.}, language = {en} } @article{XiaoLiuWangetal.2020, author = {Xiao, Shangbin and Liu, Liu and Wang, Wei and Lorke, Andreas and Woodhouse, Jason Nicholas and Grossart, Hans-Peter}, title = {A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water}, series = {Hydrology and earth system sciences : HESS}, volume = {24}, journal = {Hydrology and earth system sciences : HESS}, number = {7}, publisher = {European Geosciences Union (EGU) ; Copernicus}, address = {Munich}, issn = {1027-5606}, doi = {10.5194/hess-24-3871-2020}, pages = {3871 -- 3880}, year = {2020}, abstract = {Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95\%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6\% and a measurement accuracy of 0.5\% for CH4. A similar performance was observed for dissolved CO2 (t(95\%) = 10 s, equilibration ratio 67.1 \%). An equilibration ratio as high as 91.8\% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.}, language = {en} } @article{BrothersKoehlerAttermeyeretal.2014, author = {Brothers, Soren M. and Koehler, J. and Attermeyer, Katrin and Grossart, Hans-Peter and Mehner, T. and Meyer, N. and Scharnweber, Inga Kristin and Hilt, Sabine}, title = {A feedback loop links brownification and anoxia in a temperate, shallow lake}, series = {Limnology and oceanography}, volume = {59}, journal = {Limnology and oceanography}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-3590}, doi = {10.4319/lo.2014.59.4.1388}, pages = {1388 -- 1398}, year = {2014}, abstract = {This study examines a natural, rapid, fivefold increase in dissolved organic carbon (DOC) concentrations in a temperate shallow lake, describing the processes by which increased DOC resulted in anoxic conditions and altered existing carbon cycling pathways. High precipitation for two consecutive years led to rising water levels and the flooding of adjacent degraded peatlands. Leaching from the flooded soils provided an initial increase in DOC concentrations (from a 2010 mean of 12 +/- 1 mg L-1 to a maximum concentration of 53 mg L-1 by June 2012). Increasing water levels, DOC, and phytoplankton concentrations reduced light reaching the sediment surface, eliminating most benthic primary production and promoting anoxia in the hypolimnion. From January to June 2012 there was a sudden increase in total phosphorus (from 57 mg L-1 to 216 mg L-1), DOC (from 24.6 mg L-1 to 53 mg L-1), and iron (from 0.12 mg L-1 to 1.07 mg L-1) concentrations, without any further large fluxes in water levels. We suggest that anoxic conditions at the sediment surface and flooded soils produced a dramatic release of these chemicals that exacerbated brownification and eutrophication, creating anoxic conditions that persisted roughly 6 months below a water depth of 1 m and extended periodically to the water surface. This brownification-anoxia feedback loop resulted in a near-complete loss of macroinvertebrate and fish populations, and increased surface carbon dioxide (CO2) emissions by an order of magnitude relative to previous years.}, language = {en} } @article{RoethleinMiettinenIgnatova2015, author = {R{\"o}thlein, Christoph and Miettinen, Markus S. and Ignatova, Zoya}, title = {A flexible approach to assess fluorescence decay functions in complex energy transfer systems}, series = {BMC biophysics}, volume = {8}, journal = {BMC biophysics}, publisher = {BioMed Central}, address = {London}, issn = {2046-1682}, doi = {10.1186/s13628-015-0020-z}, pages = {10}, year = {2015}, abstract = {Background: Time-correlated Forster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions. Results: Here we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. This simulation solution assesses the full statistics of time-correlated photon counts and distance distributions of fluorescently labeled biomolecules. The simulations are consistent with the theoretical predictions of the dye behavior in FRET systems with defined dye distances and measurements of randomly distributed dye solutions. We validate the simulation results using a highly heterogeneous aggregation system and explore the conditions to use this tool in complex systems. Conclusion: This approach is powerful in distinguishing distance distributions in a wide variety of experimental setups, thus providing a versatile tool to accurately distinguish between different structural assemblies in highly complex systems.}, language = {en} } @article{SharmaRuelensMaggenetal.2017, author = {Sharma, Neha and Ruelens, Philip and Maggen, Thomas and Dochy, Niklas and Torfs, Sanne and Kaufmann, Kerstin and Rohde, Antje and Geuten, Koen}, title = {A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {173}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.16.01161}, pages = {1301 -- 1315}, year = {2017}, abstract = {Winter cereals require prolonged cold to transition from vegetative to reproductive development. This process, referred to as vernalization, has been extensively studied in Arabidopsis (Arabidopsis thaliana). In Arabidopsis, a key flowering repressor called FLOWERING LOCUS C (FLC) quantitatively controls the vernalization requirement. By contrast, in cereals, the vernalization response is mainly regulated by the VERNALIZATION genes, VRN1 and VRN2. Here, we characterize ODDSOC2, a recently identified FLC ortholog in monocots, knowing that it belongs to the FLC lineage. By studying its expression in a diverse set of Brachypodium accessions, we find that it is a good predictor of the vernalization requirement. Analyses of transgenics demonstrated that BdODDSOC2 functions as a vernalization-regulated flowering repressor. In most Brachypodium accessions BdODDSOC2 is down-regulated by cold, and in one of the winter accessions in which this down-regulation was evident, BdODDSOC2 responded to cold before BdVRN1. When stably down-regulated, the mechanism is associated with spreading H3K27me3 modifications at the BdODDSOC2 chromatin. Finally, homoeolog-specific gene expression analyses identify TaAGL33 and its splice variant TaAGL22 as the FLC orthologs in wheat (Triticum aestivum) behaving most similar to Brachypodium ODDSOC2. Overall, our study suggests that ODDSOC2 is not only phylogenetically related to FLC in eudicots but also functions as a flowering repressor in the vernalization pathway of Brachypodium and likely other temperate grasses. These insights could prove useful in breeding efforts to refine the vernalization requirement of temperate cereals and adapt varieties to changing climates.}, language = {en} } @article{SchlaegelLewis2016, author = {Schl{\"a}gel, Ulrike E. and Lewis, Mark A.}, title = {A framework for analyzing the robustness of movement models to variable step discretization}, series = {Journal of mathematical biology}, volume = {73}, journal = {Journal of mathematical biology}, publisher = {Springer}, address = {Heidelberg}, issn = {0303-6812}, doi = {10.1007/s00285-016-0969-5}, pages = {815 -- 845}, year = {2016}, abstract = {When sampling animal movement paths, the frequency at which location measurements are attempted is a critical feature for data analysis. Important quantities derived from raw data, e.g. travel distance or sinuosity, can differ largely based on the temporal resolution of the data. Likewise, when movement models are fitted to data, parameter estimates have been demonstrated to vary with sampling rate. Thus, biological statements derived from such analyses can only be made with respect to the resolution of the underlying data, limiting extrapolation of results and comparison between studies. To address this problem, we investigate whether there are models that are robust against changes in temporal resolution. First, we propose a mathematically rigorous framework, in which we formally define robustness as a model property. We then use the framework for a thorough assessment of a range of basic random walk models, in which we also show how robustness relates to other probabilistic concepts. While we found robustness to be a strong condition met by few models only, we suggest a new method to extend models so as to make them robust. Our framework provides a new systematic, mathematically founded approach to the question if, and how, sampling rate of movement paths affects statistical inference.}, language = {en} } @article{MaoNakamuraViottietal.2016, author = {Mao, Hailiang and Nakamura, Moritaka and Viotti, Corrado and Grebe, Markus}, title = {A Framework for Lateral Membrane Trafficking and Polar Tethering of the PEN3 ATP-Binding Cassette Transporter}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {172}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.16.01252}, pages = {2245 -- 2260}, year = {2016}, abstract = {The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity.}, language = {en} } @article{VanDerVenBartschGauteletal.2000, author = {VanDerVen, Peter F. M. and Bartsch, J{\"o}rg and Gautel, Mathias and Jokusch, Harald and F{\"u}rst, Dieter Oswald}, title = {A functional knock-out of titin results in defective myofibril assembly}, year = {2000}, language = {en} } @article{SchwarteTiedemann2011, author = {Schwarte, Sandra and Tiedemann, Ralph}, title = {A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana}, series = {Molecular biology and evolution}, volume = {28}, journal = {Molecular biology and evolution}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msr008}, pages = {1861 -- 1876}, year = {2011}, abstract = {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.}, language = {en} } @article{SunnaBergquist2003, author = {Sunna, Anwar and Bergquist, Peter L.}, title = {A gene encoding a novel extremely thermostable 1,4-beta-xylanase isolated directly from an environmental DNA sample}, year = {2003}, abstract = {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.}, language = {en} } @article{BalazadehSiddiquiAlluetal.2010, author = {Balazadeh, Salma and Siddiqui, Hamad and Allu, Annapurna Devi and Matallana-Ramirez, Lilian Paola and Caldana, Camila and Mehrnia, Mohammad and Zanor, Maria-In{\´e}s and Koehler, Barbara and M{\"u}ller-R{\"o}ber, Bernd}, title = {A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence}, issn = {0960-7412}, doi = {10.1111/j.1365-313X.2010.04151.x}, year = {2010}, abstract = {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.}, language = {en} } @article{LiaimerJensenDittmann2016, author = {Liaimer, Anton and Jensen, John B. and Dittmann, Elke}, title = {A Genetic and Chemical Perspective on Symbiotic Recruitment of Cyanobacteria of the Genus Nostoc into the Host Plant Blasia pusilla L.}, series = {Frontiers in microbiology}, volume = {7}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2016.01693}, pages = {449 -- 474}, year = {2016}, abstract = {Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.}, language = {en} } @article{LahLoeberHsiangetal.2017, author = {Lah, Ljerka and L{\"o}ber, Ulrike and Hsiang, Tom and Hartmann, Stefanie}, title = {A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles}, series = {Fungal biology}, volume = {121}, journal = {Fungal biology}, publisher = {Elsevier}, address = {Oxford}, issn = {1878-6146}, doi = {10.1016/j.funbio.2016.12.002}, pages = {234 -- 252}, year = {2017}, abstract = {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.}, language = {en} } @article{WulfRujner2011, author = {Wulf, Monika and Rujner, Hendrik}, title = {A GIS-based method for the reconstruction of the late eighteenth century forest vegetation in the Prignitz region (NE Germany)}, series = {Landscape ecology}, volume = {26}, journal = {Landscape ecology}, number = {2}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2973}, doi = {10.1007/s10980-010-9555-1}, pages = {153 -- 168}, year = {2011}, abstract = {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.}, language = {en} } @article{ReegHeineMihanetal.2020, author = {Reeg, Jette and Heine, Simon and Mihan, Christine and McGee, Sean and Preuss, Thomas G. and Jeltsch, Florian}, title = {A graphical user interface for the plant community model IBC-grass}, series = {Plos One}, volume = {15}, journal = {Plos One}, number = {3}, publisher = {Plos 1}, address = {San Francisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0230012}, pages = {18}, year = {2020}, abstract = {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.}, language = {en} } @article{ArvidssonPerezRodriguezMuellerRoeber2011, author = {Arvidsson, Samuel Janne and Perez-Rodriguez, Paulino and M{\"u}ller-R{\"o}ber, Bernd}, title = {A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects}, series = {New phytologist : international journal of plant science}, volume = {191}, journal = {New phytologist : international journal of plant science}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0028-646X}, doi = {10.1111/j.1469-8137.2011.03756.x}, pages = {895 -- 907}, year = {2011}, abstract = {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.}, language = {en} }