TY - THES A1 - Balk, Maria T1 - 3D structured shape-memory hydrogels with enzymatically-induced shape shifting Y1 - 2015 ER - TY - GEN A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - A balance to death T2 - Nature plants N2 - Leaf senescence plays a crucial role in nutrient recovery in late-stage plant development and requires vast transcriptional reprogramming by transcription factors such as ORESARA1 (ORE1). A proteolytic mechanism is now found to control ORE1 degradation, and thus senescence, during nitrogen starvation. Y1 - 2018 U6 - https://doi.org/10.1038/s41477-018-0279-6 SN - 2055-026X SN - 2055-0278 VL - 4 IS - 11 SP - 863 EP - 864 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Klauschies, Toni A1 - Coutinho, Renato Mendes A1 - Gaedke, Ursula T1 - A beta distribution-based moment closure enhances the reliability of trait-based aggregate models for natural populations and communities JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Ecological communities are complex adaptive systems that exhibit remarkable feedbacks between their biomass and trait dynamics. Trait-based aggregate models cope with this complexity by focusing on the temporal development of the community’s aggregate properties such as its total biomass, mean trait and trait variance. They are based on particular assumptions about the shape of the underlying trait distribution, which is commonly assumed to be normal. However, ecologically important traits are usually restricted to a finite range, and empirical trait distributions are often skewed or multimodal. As a result, normal distribution-based aggregate models may fail to adequately represent the biomass and trait dynamics of natural communities. We resolve this mismatch by developing a new moment closure approach assuming the trait values to be beta-distributed. We show that the beta distribution captures important shape properties of both observed and simulated trait distributions, which cannot be captured by a Gaussian. We further demonstrate that a beta distribution-based moment closure can strongly enhance the reliability of trait-based aggregate models. We compare the biomass, mean trait and variance dynamics of a full trait distribution (FD) model to the ones of beta (BA) and normal (NA) distribution-based aggregate models, under different selection regimes. This way, we demonstrate under which general conditions (stabilizing, fluctuating or disruptive selection) different aggregate models are reliable tools. All three models predicted very similar biomass and trait dynamics under stabilizing selection yielding unimodal trait distributions with small standing trait variation. We also obtained an almost perfect match between the results of the FD and BA models under fluctuating selection, promoting skewed trait distributions and ongoing oscillations in the biomass and trait dynamics. In contrast, the NA model showed unrealistic trait dynamics and exhibited different alternative stable states, and thus a high sensitivity to initial conditions under fluctuating selection. Under disruptive selection, both aggregate models failed to reproduce the results of the FD model with the mean trait values remaining within their ecologically feasible ranges in the BA model but not in the NA model. Overall, a beta distribution-based moment closure strongly improved the realism of trait-based aggregate models. KW - Moment closure KW - Normal and beta distribution KW - Skewed and peaked trait distributions KW - Fitness landscape and frequency-dependent selection KW - Eco-evolutionary dynamics KW - Modelling functional diversity Y1 - 2018 U6 - https://doi.org/10.1016/j.ecolmodel.2018.02.001 SN - 0304-3800 SN - 1872-7026 VL - 381 SP - 46 EP - 77 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Haueis, Lisa A1 - Stech, Marlitt A1 - Kubick, Stefan T1 - A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies JF - Frontiers in Bioengineering and Biotechnology N2 - Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, similar to 15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation. KW - cell-free protein synthesis KW - In vitro transcription KW - translation KW - nanobody KW - VHH KW - camelid KW - CHO cell lysate Y1 - 2022 U6 - https://doi.org/10.3389/fbioe.2022.896763 SN - 2296-4185 VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Krebs, Simon K. A1 - Rakotoarinoro, Nathanael A1 - Stech, Marlitt A1 - Zemella, Anne A1 - Kubick, Stefan T1 - A CHO-based cell-free dual fluorescence reporter system for the straightforward assessment of amber suppression and scFv functionality JF - Frontiers in Bioengineering and Biotechnology N2 - Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein's coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyr(CUA) were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs). KW - expanded genetic code KW - orthogonal system KW - noncanonical amino acid KW - unnatural amino acid KW - antibody KW - cell-free protein synthesis KW - mRFP1 KW - sfGFP Y1 - 2022 U6 - https://doi.org/10.3389/fbioe.2022.873906 SN - 2296-4185 VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Çabuk, Uğur A1 - Ünlü, Ercan Selçuk T1 - A combined de novo assembly approach increases the quality of prokaryotic draft genomes JF - Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology N2 - Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes. KW - De novo assembly KW - Prokaryotes KW - Bacteria KW - NGS KW - Short reads KW - Draft genome Y1 - 2022 U6 - https://doi.org/10.1007/s12223-022-00980-7 SN - 0015-5632 SN - 1874-9356 VL - 67 SP - 801 EP - 810 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Mbebi, Alain J. A1 - Breitler, Jean-Christophe A1 - Bordeaux, M'elanie A1 - Sulpice, Ronan A1 - McHale, Marcus A1 - Tong, Hao A1 - Toniutti, Lucile A1 - Castillo, Jonny Alonso A1 - Bertrand, Benoit A1 - Nikoloski, Zoran T1 - A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids JF - G3: Genes, genomes, genetics N2 - Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops. KW - genomic prediction KW - phenomic prediction KW - 3-way coffee hybrids KW - chlorophyll a fluorescence KW - GenPred KW - Shared Data Resource Y1 - 2022 U6 - https://doi.org/10.1093/g3journal/jkac170 SN - 2160-1836 VL - 12 IS - 9 PB - Genetics Soc. of America CY - Pittsburgh, PA ER - TY - JOUR A1 - Zoccarato, Luca A1 - Sher, Daniel A1 - Miki, Takeshi A1 - Segre, Daniel A1 - Grossart, Hans-Peter T1 - A comparative whole-genome approach identifies bacterial traits for marine microbial interactions JF - Communications biology N2 - Luca Zoccarato, Daniel Sher et al. leverage publicly available bacterial genomes from marine and other environments to examine traits underlying microbial interactions. Their results provide a valuable resource to investigate clusters of functional and linked traits to better understand marine bacteria community assembly and dynamics. Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics. Y1 - 2022 U6 - https://doi.org/10.1038/s42003-022-03184-4 SN - 2399-3642 VL - 5 IS - 1 PB - Springer Nature CY - Berlin ER - TY - JOUR A1 - Noonan, Michael J. A1 - Tucker, Marlee A. A1 - Fleming, Christen H. A1 - Akre, Thomas S. A1 - Alberts, Susan C. A1 - Ali, Abdullahi H. A1 - Altmann, Jeanne A1 - Antunes, Pamela Castro A1 - Belant, Jerrold L. A1 - Beyer, Dean A1 - Blaum, Niels A1 - Boehning-Gaese, Katrin A1 - Cullen Jr, Laury A1 - de Paula, Rogerio Cunha A1 - Dekker, Jasja A1 - Drescher-Lehman, Jonathan A1 - Farwig, Nina A1 - Fichtel, Claudia A1 - Fischer, Christina A1 - Ford, Adam T. A1 - Goheen, Jacob R. A1 - Janssen, Rene A1 - Jeltsch, Florian A1 - Kauffman, Matthew A1 - Kappeler, Peter M. A1 - Koch, Flavia A1 - LaPoint, Scott A1 - Markham, A. Catherine A1 - Medici, Emilia Patricia A1 - Morato, Ronaldo G. A1 - Nathan, Ran A1 - Oliveira-Santos, Luiz Gustavo R. A1 - Olson, Kirk A. A1 - Patterson, Bruce D. A1 - Paviolo, Agustin A1 - Ramalho, Emiliano Estero A1 - Rosner, Sascha A1 - Schabo, Dana G. A1 - Selva, Nuria A1 - Sergiel, Agnieszka A1 - da Silva, Marina Xavier A1 - Spiegel, Orr A1 - Thompson, Peter A1 - Ullmann, Wiebke A1 - Zieba, Filip A1 - Zwijacz-Kozica, Tomasz A1 - Fagan, William F. A1 - Mueller, Thomas A1 - Calabrese, Justin M. T1 - A comprehensive analysis of autocorrelation and bias in home range estimation JF - Ecological monographs : a publication of the Ecological Society of America. N2 - Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of the effects of autocorrelation on home range estimation. We base our study on an extensive data set of GPS locations from 369 individuals representing 27 species distributed across five continents. We first assemble a broad array of home range estimators, including Kernel Density Estimation (KDE) with four bandwidth optimizers (Gaussian reference function, autocorrelated‐Gaussian reference function [AKDE], Silverman's rule of thumb, and least squares cross‐validation), Minimum Convex Polygon, and Local Convex Hull methods. Notably, all of these estimators except AKDE assume independent and identically distributed (IID) data. We then employ half‐sample cross‐validation to objectively quantify estimator performance, and the recently introduced effective sample size for home range area estimation ( N̂ area ) to quantify the information content of each data set. We found that AKDE 95% area estimates were larger than conventional IID‐based estimates by a mean factor of 2. The median number of cross‐validated locations included in the hold‐out sets by AKDE 95% (or 50%) estimates was 95.3% (or 50.1%), confirming the larger AKDE ranges were appropriately selective at the specified quantile. Conversely, conventional estimates exhibited negative bias that increased with decreasing N̂ area. To contextualize our empirical results, we performed a detailed simulation study to tease apart how sampling frequency, sampling duration, and the focal animal's movement conspire to affect range estimates. Paralleling our empirical results, the simulation study demonstrated that AKDE was generally more accurate than conventional methods, particularly for small N̂ area. While 72% of the 369 empirical data sets had >1,000 total observations, only 4% had an N̂ area >1,000, where 30% had an N̂ area <30. In this frequently encountered scenario of small N̂ area, AKDE was the only estimator capable of producing an accurate home range estimate on autocorrelated data. KW - animal movement KW - kernel density estimation KW - local convex hull KW - minimum convex polygon KW - range distribution KW - space use KW - telemetry KW - tracking data Y1 - 2018 U6 - https://doi.org/10.1002/ecm.1344 SN - 0012-9615 SN - 1557-7015 VL - 89 IS - 2 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Palkopoulou, Eleftheria A1 - Lipson, Mark A1 - Mallick, Swapan A1 - Nielsen, Svend A1 - Rohland, Nadin A1 - Baleka, Sina Isabelle A1 - Karpinski, Emil A1 - Ivancevici, Atma M. A1 - Thu-Hien To, A1 - Kortschak, Daniel A1 - Raison, Joy M. A1 - Qu, Zhipeng A1 - Chin, Tat-Jun A1 - Alt, Kurt W. A1 - Claesson, Stefan A1 - Dalen, Love A1 - MacPhee, Ross D. E. A1 - Meller, Harald A1 - Rocar, Alfred L. A1 - Ryder, Oliver A. A1 - Heiman, David A1 - Young, Sarah A1 - Breen, Matthew A1 - Williams, Christina A1 - Aken, Bronwen L. A1 - Ruffier, Magali A1 - Karlsson, Elinor A1 - Johnson, Jeremy A1 - Di Palma, Federica A1 - Alfoldi, Jessica A1 - Adelsoni, David L. A1 - Mailund, Thomas A1 - Munch, Kasper A1 - Lindblad-Toh, Kerstin A1 - Hofreiter, Michael A1 - Poinar, Hendrik A1 - Reich, David T1 - A comprehensive genomic history of extinct and living elephants JF - Proceedings of the National Academy of Sciences of the United States of America KW - paleogenomics KW - elephantid evolution KW - mammoth KW - admixture KW - species divergence Y1 - 2018 U6 - https://doi.org/10.1073/pnas.1720554115 SN - 0027-8424 VL - 115 IS - 11 SP - E2566 EP - E2574 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Chapman, Eric M. A1 - Lant, Benjamin A1 - Ohashi, Yota A1 - Yu, Bin A1 - Schertzberg, Michael A1 - Go, Christopher A1 - Dogra, Deepika A1 - Koskimaki, Janne A1 - Girard, Romuald A1 - Li, Yan A1 - Fraser, Andrew G. A1 - Awad, Issam A. A1 - Abdelilah-Seyfried, Salim A1 - Gingras, Anne-Claude A1 - Derry, William Brent T1 - A conserved CCM complex promotes apoptosis non-autonomously by regulating zinc homeostasis JF - Nature Communications N2 - Apoptotic death of cells damaged by genotoxic stress requires regulatory input from surrounding tissues. The C. elegans scaffold protein KRI-1, ortholog of mammalian KRIT1/CCM1, permits DNA damage-induced apoptosis of cells in the germline by an unknown cell non-autonomous mechanism. We reveal that KRI-1 exists in a complex with CCM-2 in the intestine to negatively regulate the ERK-5/MAPK pathway. This allows the KLF-3 transcription factor to facilitate expression of the SLC39 zinc transporter gene zipt-2.3, which functions to sequester zinc in the intestine. Ablation of KRI-1 results in reduced zinc sequestration in the intestine, inhibition of IR-induced MPK-1/ERK1 activation, and apoptosis in the germline. Zinc localization is also perturbed in the vasculature of krit1(-/-) zebrafish, and SLC39 zinc transporters are mis-expressed in Cerebral Cavernous Malformations (CCM) patient tissues. This study provides new insights into the regulation of apoptosis by cross-tissue communication, and suggests a link between zinc localization and CCM disease. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-09829-z SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Wolff, Martin A1 - Gast, Klaus A1 - Evers, Andreas A1 - Kurz, Michael A1 - Pfeiffer-Marek, Stefania A1 - Schüler, Anja A1 - Seckler, Robert A1 - Thalhammer, Anja T1 - A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4 JF - Biomolecules N2 - Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers. KW - biophysics KW - diabetes KW - peptides KW - oligomerization KW - conformational change KW - molecular modeling KW - static and dynamic light scattering KW - spectroscopy Y1 - 2021 U6 - https://doi.org/10.3390/biom11091305 SN - 2218-273X VL - 11 IS - 9 PB - MDPI CY - Basel ER - TY - GEN A1 - Wolff, Martin A1 - Gast, Klaus A1 - Evers, Andreas A1 - Kurz, Michael A1 - Pfeiffer-Marek, Stefania A1 - Schüler, Anja A1 - Seckler, Robert A1 - Thalhammer, Anja T1 - A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4 T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1161 KW - biophysics KW - diabetes KW - peptides KW - oligomerization KW - conformational change KW - molecular modeling KW - static and dynamic light scattering KW - spectroscopy Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-522081 SN - 1866-8372 IS - 9 ER - TY - JOUR A1 - Luetkecosmann, Steffi A1 - Faupel, Thomas A1 - Porstmann, Silvia A1 - Porstmann, Tomas A1 - Micheel, Burkhard A1 - Hanack, Katja T1 - A cross-reactive monoclonal antibody as universal detection antibody in autoantibody diagnostic assays JF - Clinica chimica acta N2 - Diagnostics of Autoimmune Diseases involve screening of patient samples for containing autoantibodies against various antigens. To ensure quality of diagnostic assays a calibrator is needed in each assay system. Different calibrators as recombinant human monoclonal antibodies as well as chimeric antibodies against the autoantigens of interest are described. A less cost-intensive and also more representative possibility covering different targets on the antigens is the utilization of polyclonal sera from other species. Nevertheless, the detection of human autoantibodies as well as the calibration reagent containing antibodies from other species in one assay constitutes a challenge in terms of assay calibration. We therefore developed a cross-reactive monoclonal antibody which binds human as well as rabbit sera with similar affinities in the nanomolar range. We tested our monoclonal antibody S38CD11B12 successfully in the commercial Serazym (R) Anti-Cardiolipin-beta 2-GPI IgG/IgM assay and could thereby prove the eligibility of S38CD11B12 as detection antibody in autoimmune diagnostic assays using rabbit derived sera as reference material. KW - Monoclonal antibody KW - Detection KW - Autoimmune diagnostics KW - Cross reactivity KW - Assay calibration Y1 - 2019 U6 - https://doi.org/10.1016/j.cca.2019.09.003 SN - 0009-8981 SN - 1873-3492 VL - 499 SP - 87 EP - 92 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Demal, Till Joscha A1 - Heise, Melina A1 - Reiz, Benedikt A1 - Dogra, Deepika A1 - Braenne, Ingrid A1 - Reichenspurner, Hermann A1 - Männer, Jörg A1 - Aherrahrou, Zouhair A1 - Schunkert, Heribert A1 - Erdmann, Jeanette A1 - Abdelilah-Seyfried, Salim T1 - A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A JF - Scientific reports N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-39648-7 SN - 2045-2322 VL - 9 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Xiao, Shangbin A1 - Liu, Liu A1 - Wang, Wei A1 - Lorke, Andreas A1 - Woodhouse, Jason Nicholas A1 - Grossart, Hans-Peter T1 - A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water JF - Hydrology and earth system sciences : HESS N2 - 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. Y1 - 2020 U6 - https://doi.org/10.5194/hess-24-3871-2020 SN - 1027-5606 SN - 1607-7938 VL - 24 IS - 7 SP - 3871 EP - 3880 PB - European Geosciences Union (EGU) ; Copernicus CY - Munich ER - TY - JOUR A1 - Sharma, Neha A1 - Ruelens, Philip A1 - Maggen, Thomas A1 - Dochy, Niklas A1 - Torfs, Sanne A1 - Kaufmann, Kerstin A1 - Rohde, Antje A1 - Geuten, Koen T1 - A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - 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. Y1 - 2016 U6 - https://doi.org/10.1104/pp.16.01161 SN - 0032-0889 SN - 1532-2548 VL - 173 IS - 2 SP - 1301 EP - 1315 PB - American Society of Plant Physiologists CY - Rockville ER - TY - GEN A1 - Liaimer, Anton A1 - Jensen, John B. A1 - Dittmann-Thünemann, Elke T1 - A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L. T2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 434 KW - cyanobacteria KW - secondary metabolites KW - symbiosis KW - Blasia KW - Nostoc KW - allelopathy Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407179 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 - 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 R. 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 -