Publications by authors named "C Wiedemann"

71 Publications

Is Continuous Eruption Related to Periodontal Changes? A 16-Year Follow-up.

J Dent Res 2021 Mar 3:22034521999363. Epub 2021 Mar 3.

Department of Restorative Dentistry, Periodontology, Endodontology, Preventive Dentistry and Pedodontics, University Medicine Greifswald, Greifswald, Germany.

The aims of this study were to 1) determine if continuous eruption occurs in the maxillary teeth, 2) assess the magnitude of the continuous eruption, and 3) evaluate the effects of continuous eruption on the different periodontal parameters by using data from the population-based cohort of the Study of Health in Pomerania (SHIP). The jaw casts of 140 participants from the baseline (SHIP-0) and 16-y follow-up (SHIP-3) were digitized as 3-dimensional models. Robust reference points were set to match the tooth eruption stage at SHIP-0 and SHIP-3. Reference points were set on the occlusal surface of the contralateral premolar and molar teeth, the palatal fossa of an incisor, and the rugae of the hard palate. Reference points were combined to represent 3 virtual occlusal planes. Continuous eruption was measured as the mean height difference between the 3 planes and rugae fix points at SHIP-0 and SHIP-3. Probing depth, clinical attachment levels, gingiva above the cementoenamel junction (gingival height), and number of missing teeth were clinically assessed in the maxilla. Changes in periodontal variables were regressed onto changes in continuous eruption after adjustment for age, sex, number of filled teeth, and education or tooth wear. Continuous tooth eruption >1 mm over the 16 y was found in 4 of 140 adults and averaged to 0.33 mm, equaling 0.021 mm/y. In the total sample, an increase in continuous eruption was significantly associated with decreases in mean gingival height ( = -0.34; 95% CI, -0.65 to -0.03). In a subsample of participants without tooth loss, continuous eruption was negatively associated with PD. This study confirmed that continuous eruption is clearly detectable and may contribute to lower gingival heights in the maxilla.
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http://dx.doi.org/10.1177/0022034521999363DOI Listing
March 2021

Backbone and nearly complete side-chain chemical shift assignments of the human death-associated protein 1 (DAP1).

Biomol NMR Assign 2021 Apr 2;15(1):91-97. Epub 2020 Dec 2.

Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany.

Death-associated protein 1 (DAP1) is a proline-rich cytoplasmatic protein highly conserved in most eukaryotes. It has been reported to be involved in controlling cell growth and migration, autophagy and apoptosis. The presence of human DAP1 is associated to a favourable prognosis in different types of cancer. Here we describe the almost complete [Formula: see text], [Formula: see text], and [Formula: see text] chemical shift assignments of the human DAP1. The limited spectral dispersion, mainly in the [Formula: see text] region, and the lack of defined secondary structure elements, predicted based on chemical shifts, identifies human DAP1 as an intrinsically disordered protein (IDP). This work lays the foundation for further structural investigations, dynamic studies, mapping of potential interaction partners or drug screening and development.
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http://dx.doi.org/10.1007/s12104-020-09988-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7973646PMC
April 2021

Digital Transition by COVID-19 Pandemic? The German Food Online Retail.

Tijdschr Econ Soc Geogr 2020 Jun 19. Epub 2020 Jun 19.

Global South Studies Center/ Institute of Geography Albertus-Magnus-Platz 50923 Cologne Germany.

The COVID-19 pandemic has led to a sharp increase in online trade. This article examines the impact of the pandemic on online grocery retail in Germany. Here we follow and refine the multi-level perspective by Geels, and examine to what extent and why the online grocery retail expanded during the pandemic. A particular focus is on the spatial expansion into rural areas. The study shows a general upswing in the grocery trade and disproportionately high growth in online grocery trade and identifies driving and limiting factors. While COVID-19 has opened a window of opportunity, our results indicate little transition of grocery to e-grocery. This finding can be explained by the sudden and temporary constellation at the level of the socio-technical regime during the pandemic. As a result, we argue for a rethinking the temporality of windows of opportunities and the related vulnerability of the innovations which need them.
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http://dx.doi.org/10.1111/tesg.12453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7323036PMC
June 2020

CD11d is a novel antigen on chicken leukocytes.

J Proteomics 2020 08 10;225:103876. Epub 2020 Jun 10.

Research Unit Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 80939 Munich, Germany.

In life sciences, antibodies are among the most commonly used tools for identifying, tracking, quantifying and isolating molecules, mainly proteins. However, it has recently become clear that antibodies often fall short with respect to specificity and selectivity and in many cases target proteins are not even known. When commercial availability of antibodies is scarce, e.g. for targeting proteins from farm animals, researchers face additional challenges: they often have to rely on cross-reactive antibodies, which are poorly characterized for their exact target, their actual cross-reactivity and the desired application. In this study, we aimed at identifying the true target of mouse monoclonal antibody 8F2, which was generated against chicken PBMC and used for decades in research, while it's actual target molecule remained unknown. We used 8F2 antibody for immunoprecipitation in chicken PBMC and subsequently identified its true target as CD11d, which was never described in chicken lymphocytes before, by quantitative LC-MSMS. The most abundant interactor of CD11d was identified as integrin beta 2. The existence of this alpha integrin was therefore clearly proven on protein level and provides a first basis to further assess the role of CD11d in chickens in future studies. Data are available via ProteomeXchange with identifier PXD017248. SIGNIFICANCE: Our studies determined CD11d as the true target of a previously uncharacterized mouse monoclonal antibody 8F2, generated against chicken peripheral blood derived mononuclear cells (PBMC). This is therefore now first member of alpha integrins in chickens, that existence was now clearly identified on protein level. The additional identification of CD11d interactors provides information on integrin-dependent regulation of signaling networks, allowing further functional studies.
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http://dx.doi.org/10.1016/j.jprot.2020.103876DOI Listing
August 2020

Cysteines and Disulfide Bonds as Structure-Forming Units: Insights From Different Domains of Life and the Potential for Characterization by NMR.

Front Chem 2020 23;8:280. Epub 2020 Apr 23.

Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany.

Disulfide bridges establish a fundamental element in the molecular architecture of proteins and peptides which are involved e.g., in basic biological processes or acting as toxins. NMR spectroscopy is one method to characterize the structure of bioactive compounds including cystine-containing molecules. Although the disulfide bridge itself is invisible in NMR, constraints obtained via the neighboring NMR-active nuclei allow to define the underlying conformation and thereby to resolve their functional background. In this mini-review we present shortly the impact of cysteine and disulfide bonds in the proteasome from different domains of life and give a condensed overview of recent NMR applications for the characterization of disulfide-bond containing biomolecules including advantages and limitations of the different approaches.
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http://dx.doi.org/10.3389/fchem.2020.00280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7191308PMC
April 2020

H, C, and N Backbone assignments of the human brain and acute leukemia cytoplasmic (BAALC) protein.

Biomol NMR Assign 2020 10 2;14(2):163-168. Epub 2020 Apr 2.

Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany.

The brain and acute leukemia cytoplasmic (BAALC; UniProt entry Q8WXS3) is a 180-residue-long human protein having six known isoforms. BAALC is expressed in either hematopoietic or neuroectodermal cells and its specific function is still to be revealed. However, as a presumably membrane-anchored protein at the cytoplasmic side it is speculated that BAALC exerts its function at the postsynaptic densities of certain neurons and might play a role in developing cytogenetically normal acute myeloid leukemia (CN-AML) when it is highly overexpressed by myeloid or lymphoid progenitor cells. In order to better understand the physiological role of BAALC and to provide the basis for a further molecular characterization of BAALC, we report here the H, C, and N resonance assignments for the backbone nuclei of its longest hematopoietic isoform (isoform 1). In addition, we present a H and N chemical shift comparison of BAALC with its shortest, neuroectodermal isoform (isoform 6) which shows only minor changes in the H and N chemical shifts.
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http://dx.doi.org/10.1007/s12104-020-09938-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462906PMC
October 2020

Body surface and body core temperatures and their associations to haemodynamics: The BOSTON-I-study: Validation of a thermodilution catheter (PiCCO) to measure body core temperature and comparison of body surface temperatures to thermodilutionderived Cardiac Index.

Math Biosci Eng 2019 11;17(2):1132-1146

Medizinische Klinik und Poliklinik II, Klinikum rechts der Isar der Technischen Universität München, Ismaninger Straße 22, D-81675 München, Germany.

Assessment of peripheral perfusion and comparison of surface and body core temperature (BST; BCT) are diagnostic cornerstones of critical care. Infrared non-contact thermometers facilitate the accurate measurement of BST. Additionally, a corrected measurement of BST on the forehead provides an estimate of BCT (BCT_Forehead). In clinical routine BCT is measured by ear thermometers (BCT_Ear). The PiCCO-device (PiCCO: Pulse contour analysis) provides thermodilution-derived Cardiac Index (CI_TD) using an arterial catheter with a thermistor tip in the distal aorta. Therefore, the PiCCO-catheter might be used for BCT-measurement (BCT_PiCCO) in addition to CI-measurement. To the best of our knowledge, BCT_PiCCO has not been validated compared to standard techniques of BCT-measurement including measurement of urinary bladder temperature (BCT_Bladder). Therefore, we compared BCT_PiCCO to BCT_Ear and BCT_Bladder in 52 patients equipped with the PiCCO-device (Pulsion; Germany). Furthermore, this setting allowed to compare different BSTs and their differences to BCT with CI_TD. BCT_PiCCO, BCT_Ear (ThermoScan; Braun), BCT_Bladder (UROSID; ASID BONZ), BCT_Forehead and BSTs (Thermofocus; Tecnimed) were measured four times within 24h. BSTs were determined on the great toe, finger pad and forearm. Immediately afterwards TPTD was performed to obtain CI_TD. 32 (62%) male, 20 (38%) female patients; APACHE-II 23.8 ±8.3. Bland-Altman-analysis demonstrated low bias and percentage error (PE) values for the comparisons of BCT_PiCCO vs. BCT_Bladder (bias 0.05 ±0.27° Celsius; PE = 1.4%), BCT_PiCCO vs. BCT_Ear (bias 0.08 ±0.38° Celsius; PE = 2.0%) and BCT_Ear vs. BCT_Bladder (bias 0.04 ±0.42° Celsius; PE = 2.2). While BCT_PiCCO, BCT_Ear and BCT_Bladder can be considered interchangeable, Bland-Altman-analyses of BCT_Forehead vs. BCT_PiCCO (bias =-0.63 ±0.75° Celsius; PE = 3.9%) Celsisus, BCT_Ear (bias = -0.58 ±0.68° Celsius; PE = 3.6%) and BCT_Bladder (bias = -0.55 ±0.74° Celsius; PE = 3.9%) demonstrate a substantial underestimation of BCT by BCT_Forehead. BSTs and differences between BCT and BST (DCST) significantly correlated with CI_TD with r-values between 0.230 and 0.307 and p-values between 0.002 and p < 0.001. The strongest association with CI_TD was found for BST_forearm (r = 0.307; p < 0.001). In a multivariate analysis regarding CI_TD and including biometric data, BSTs and and their differences to core-temperatures (DCST), only higher temperatures on the forearm and the great toe, young age, low height and male gender were independently associated with CI_TD. The estimate of CI based on this model (CI_estimated) correlated with CI_TD (r = 0.594; p < 0.001). CI_estimated provided large ROC-areas under the curve (AUC) regarding the critical thresholds of CI_TD ≤ 2.5 L/min/m (AUC = 0.862) and CI_TD ≥ 5.0 L/min/m (AUC = 0.782). 1.) BCT_PiCCO, BCT_Ear and BCT_Bladder are interchangeable. 2.) BCT_Forehead significantly underestimates BCT by about 0.5° Celsius. 3.) All measured BSTs and DCSTs were significantly associated with CI_TD. 4.) CI_estimated is promising, in particular for the prediction of critical thresholds of CI.
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http://dx.doi.org/10.3934/mbe.2020059DOI Listing
November 2019

Aberrant Migratory Behavior of Immune Cells in Recurrent Autoimmune Uveitis in Horses.

Front Cell Dev Biol 2020 10;8:101. Epub 2020 Mar 10.

Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Munich, Germany.

The participating signals and structures that enable primary immune cells migrating within dense tissues are not completely revealed until now. Especially in autoimmune diseases, mostly unknown mechanisms facilitate autoreactive immune cells to migrate to endogenous tissues, infiltrating and harming organ-specific structures. In order to gain deeper insights into the migratory behavior of primary autoreactive immune cells, we examined peripheral blood-derived lymphocytes (PBLs) of horses with equine recurrent uveitis (ERU), a spontaneous animal model for autoimmune uveitis in humans. In this study, we used a three-dimensional collagen I hydrogel matrix and monitored live-cell migration of primary lymphocytes as a reaction to different chemoattractants such as fetal calf serum (FCS), cytokines interleukin-4 (IL-4), and interferon-γ (IFN-γ), and a specific uveitis autoantigen, cellular retinaldehyde binding protein (CRALBP). Through these experiments, we uncovered distinct differences between PBLs from ERU cases and PBLs from healthy animals, with significantly higher cell motility, cell speed, and straightness during migration of PBLs from ERU horses. Furthermore, we emphasized the significance of expression levels and cellular localization of septin 7, a membrane-interacting protein with decreased abundance in PBLs of autoimmune cases. To underline the importance of septin 7 expression changes and the possible contribution to migratory behavior in autoreactive immune cells, we used forchlorfenuron (FCF) as a reversible inhibitor of septin structures. FCF-treated cells showed more directed migration through dense tissue and revealed aberrant septin 7 and F-actin structures along with different protein distribution and translocalization of the latter, uncovered by immunochemistry. Hence, we propose that septin 7 and interacting molecules play a pivotal role in the organization and regulation of cell shaping and migration. With our findings, we contribute to gaining deeper insights into the migratory behavior and septin 7-dependent cytoskeletal reorganization of immune cells in organ-specific autoimmune diseases.
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http://dx.doi.org/10.3389/fcell.2020.00101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076317PMC
March 2020

NMR experiments on the transient interaction of the intrinsically disordered N-terminal peptide of cystathionine-β-synthase with heme.

J Magn Reson 2019 11 16;308:106561. Epub 2019 Jul 16.

Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany. Electronic address:

The N-terminal segment of human cystathionine-β-synthase (CBS(1-40)) constitutes an intrinsically disordered protein stretch that transiently interacts with heme. We illustrate that the HCBCACON experimental protocol provides an efficient alternative approach for probing transient interactions of intrinsically disordered proteins with heme in situations where the applicability of the conventional [H, N]-HSQC experiment may be limited. This experiment starting with the excitation of protein side chain protons delivers information about the proline residues and thereby makes it possible to use these residues in interaction mapping experiments. Employing this approach in conjunction with site-specific mutation we show that transient heme binding is mediated by the Cys-Pro motif of CBS(1-40).
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http://dx.doi.org/10.1016/j.jmr.2019.07.048DOI Listing
November 2019

H, C, and N resonance assignments of the cytokine interleukin-36β isoform-2.

Biomol NMR Assign 2019 04 13;13(1):155-161. Epub 2019 Feb 13.

Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.

Interleukins are cytokines performing central tasks in the human immune system. Interleukin-36β (IL-36β) is a member of the interleukin-1 superfamily as are its homologues IL-36α and IL-36γ. All of them interact with a common receptor composed of IL-36R and IL-1R/acP. IL-36 cytokines can activate IL-36R to proliferation of CD4 + lymphocytes or stimulate M2 macrophages as potently as IL-1β. Within our efforts to study the structure-function relationship of the three interleukins IL-36α, IL-36β and IL-36γ by heteronuclear multidimensional NMR, we here report the H, C, and N resonance assignments for the backbone and side chain nuclei of cytokine interleukin-36β isoform-2.
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http://dx.doi.org/10.1007/s12104-018-09869-4DOI Listing
April 2019

Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity.

Sci Rep 2018 08 17;8(1):12332. Epub 2018 Aug 17.

Chair for Animal Physiology, Department of Veterinary Sciences, LMU Munich, 80539, Munich, Germany.

The GTP-binding protein septin 7 is involved in various cellular processes, including cytoskeleton organization, migration and the regulation of cell shape. Septin 7 function in lymphocytes, however, is poorly characterized. Since the intracellular signaling role of septin 7 is dependent on its interaction network, interaction proteomics was applied to attain novel knowledge about septin 7 function in hematopoietic cells. Our previous finding of decreased septin 7 expression in blood-derived lymphocytes in ERU, a spontaneous animal model for autoimmune uveitis in man, extended the role of septin 7 to a potential key player in autoimmunity. Here, we revealed novel insights into septin 7 function by identification of DOCK8 as an interaction partner in primary blood-derived lymphocytes. Since DOCK8 is associated with important immune functions, our finding of significantly decreased DOCK8 expression and altered DOCK8 interaction network in ERU might explain changes in immune response and shows the contribution of DOCK8 in pathomechanisms of spontaneous autoimmune diseases. Moreover, our analyses revealed insights in DOCK8 function, by identifying the signal transducer ILK as a DOCK8 interactor in lymphocytes. Our finding of the enhanced enrichment of ILK in ERU cases indicates a deviant influence of DOCK8 on inter- and intracellular signaling in autoimmune disease.
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http://dx.doi.org/10.1038/s41598-018-30753-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6098150PMC
August 2018

NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

Phys Chem Chem Phys 2017 Sep;19(35):24115-24125

Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle, Germany.

NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual H and C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.
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http://dx.doi.org/10.1039/c7cp03295aDOI Listing
September 2017

Characterization of the interaction between the small RNA-encoded peptide SR1P and GapA from Bacillus subtilis.

Microbiology (Reading) 2017 08 18;163(8):1248-1259. Epub 2017 Aug 18.

Struktureinheit Genetik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany.

Small regulatory RNAs (sRNAs) are the most prominent post-transcriptional regulators in all kingdoms of life. A few of them, e.g. SR1 from Bacillus subtilis, are dual-function sRNAs. SR1 acts as a base-pairing sRNA in arginine catabolism and as an mRNA encoding the small peptide SR1P in RNA degradation. Both functions of SR1 are highly conserved among 23 species of Bacillales. Here, we investigate the interaction between SR1P and GapA by a combination of in vivo and in vitro methods. De novo prediction of the structure of SR1P yielded five models, one of which was consistent with experimental circular dichroism spectroscopy data of a purified, synthetic peptide. Based on this model structure and a comparison between the 23 SR1P homologues, a series of SR1P mutants was constructed and analysed by Northern blotting and co-elution experiments. The known crystal structure of Geobacillus stearothermophilus GapA was used to model SR1P onto this structure. The hypothetical SR1P binding pocket, composed of two α-helices at both termini of GapA, was investigated by constructing and assaying a number of GapA mutants in the presence and absence of wild-type or mutated SR1P. Almost all residues of SR1P located in the two highly conserved motifs are implicated in the interaction with GapA. A critical lysine residue (K332) in the C-terminal α-helix 14 of GapA corroborated the predicted binding pocket.
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http://dx.doi.org/10.1099/mic.0.000505DOI Listing
August 2017

(1)H, (13)C, and (15)N resonance assignments for the pro-inflammatory cytokine interleukin-36α.

Biomol NMR Assign 2016 10 28;10(2):329-33. Epub 2016 Jun 28.

Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.

Interleukin-36α (IL-36α) is a recently characterised member of the interleukin-1 superfamily. It is involved in the pathogenesis of inflammatory arthritis in one third of psoriasis patients. By binding of IL-36α to its receptor IL-36R via the NF-κB pathway other cytokines involved in inflammatory and apoptotic cascade are activated. The efficacy of complex formation is controlled by N-terminal processing. To obtain a more detailed view on the structure function relationship we performed a heteronuclear multidimensional NMR investigation and here report the (1)H, (13)C, and (15)N resonance assignments for the backbone and side chain nuclei of the pro-inflammatory cytokine interleukin-36α.
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http://dx.doi.org/10.1007/s12104-016-9694-7DOI Listing
October 2016

A Set of Efficient nD NMR Protocols for Resonance Assignments of Intrinsically Disordered Proteins.

Chemphyschem 2016 07 9;17(13):1961-8. Epub 2016 Apr 9.

Leibniz Institute on Aging/Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.

The RF pulse scheme RN[N-CA HEHAHA]NH, which provides a convenient approach to the acquisition of different multidimensional chemical shift correlation NMR spectra leading to backbone resonance assignments, including those of the proline residues of intrinsically disordered proteins (IDPs), is experimentally demonstrated. Depending on the type of correlation data required, the method involves the generation of in-phase ((15) N)(x) magnetisation via different magnetisation transfer pathways such as H→N→CO→N, HA→CA→CO→N, H→N→CA→N and H→CA→N, the subsequent application of (15) N-(13) C(α) heteronuclear Hartmann-Hahn mixing over a period of ≈100 ms, chemical-shift labelling of relevant nuclei before and after the heteronuclear mixing step and amide proton detection in the acquisition dimension. It makes use of the favourable relaxation properties of IDPs and the presence of (1) JCαN and (2) JCαN couplings to achieve efficient correlation of the backbone resonances of each amino acid residue "i" with the backbone amide resonances of residues "i-1" and "i+1". It can be implemented in a straightforward way through simple modifications of the RF pulse schemes commonly employed in protein NMR studies. The efficacy of the approach is demonstrated using a uniformly ((15) N,(13) C) labelled sample of α-synuclein. The different possibilities for obtaining the amino-acid-type information, simultaneously with the connectivity data between the backbone resonances of sequentially neighbouring residues, have also been outlined.
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http://dx.doi.org/10.1002/cphc.201600155DOI Listing
July 2016

HN-NCA heteronuclear TOCSY-NH experiment for (1)H(N) and (15)N sequential correlations in ((13)C, (15)N) labelled intrinsically disordered proteins.

J Biomol NMR 2015 Oct 18;63(2):201-12. Epub 2015 Aug 18.

Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.

A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue 'i' with that of residues 'i-1' and 'i+1' in ((13)C, (15)N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploits the favourable relaxation properties of IDPs and the presence of (1) J CαN and (2) J CαN couplings to transfer the (15)N x magnetisation from amino acid residue 'i' to adjacent residues via the application of a band-selective (15)N-(13)C(α) heteronuclear cross-polarisation sequence of ~100 ms duration. Employing non-uniform sampling in the indirect dimensions, the efficacy of the approach has been demonstrated by the acquisition of 3D HNN chemical shift correlation spectra of α-synuclein. The experimental performance of the RF pulse sequence has been compared with that of the conventional INEPT-based HN(CA)NH pulse scheme. As the availability of data from both the HCCNH and HNN experiments will make it possible to use the information extracted from one experiment to simplify the analysis of the data of the other and lead to a robust approach for unambiguous backbone and side-chain resonance assignments, a time-saving strategy for the simultaneous collection of HCCNH and HNN data is also described.
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http://dx.doi.org/10.1007/s10858-015-9976-xDOI Listing
October 2015

Solvent Removal Induces a Reversible β-to-α Switch in Oligomeric Aβ Peptide.

J Mol Biol 2016 Jan 11;428(2 Pt A):268-273. Epub 2015 May 11.

Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research- Fritz Lipmann Institute, Beutenbergstraße 11, 07745 Jena, Germany.

Solvation and hydration are key factors for determining the stability and folding of proteins, as well as the formation of amyloid fibrils and related polypeptide aggregates. Using attenuated total reflectance Fourier-transform infrared and solid-state NMR spectroscopy, we find that the Aβ peptide experiences a remarkable conformational switch from β to α secondary structure upon solvent removal by lyophilization of oligomers. This transition is, contrary to Aβ fibrils, independent of concentration of organic co-solvents or co-solutes and is reversible upon re-addition of the solvent. Our data illuminate a previously unnoted secondary structural plasticity of the Aβ peptide in amyloid oligomers that could bear relevance for Aβ's interactions with cellular structures of low polarity.
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http://dx.doi.org/10.1016/j.jmb.2015.05.002DOI Listing
January 2016

Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex.

Nucleic Acids Res 2015 Mar 20;43(5):2958-67. Epub 2015 Feb 20.

Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany

The minichromosome maintenance complex (MCM) represents the replicative DNA helicase both in eukaryotes and archaea. Here, we describe the solution structure of the C-terminal domains of the archaeal MCMs of Sulfolobus solfataricus (Sso) and Methanothermobacter thermautotrophicus (Mth). Those domains consist of a structurally conserved truncated winged helix (WH) domain lacking the two typical 'wings' of canonical WH domains. A less conserved N-terminal extension links this WH module to the MCM AAA+ domain forming the ATPase center. In the Sso MCM this linker contains a short α-helical element. Using Sso MCM mutants, including chimeric constructs containing Mth C-terminal domain elements, we show that the ATPase and helicase activity of the Sso MCM is significantly modulated by the short α-helical linker element and by N-terminal residues of the first α-helix of the truncated WH module. Finally, based on our structural and functional data, we present a docking-derived model of the Sso MCM, which implies an allosteric control of the ATPase center by the C-terminal domain.
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http://dx.doi.org/10.1093/nar/gkv120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357721PMC
March 2015

An approach to NMR assignment of intrinsically disordered proteins.

Chemphyschem 2015 Mar 30;16(4):739-46. Epub 2015 Jan 30.

Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Beutenbergstr. 11, 07745 Jena (Germany).

An efficient approach to NMR assignments in intrinsically disordered proteins is presented, making use of the good dispersion of cross peaks observed in [(15) N,(13) C']- and [(13) C',(1) H(N) ]-correlation spectra. The method involves the simultaneous collection of {3D (H)NCO(CAN)H and 3D (HACA)CON(CA)HA} spectra for backbone assignments via sequential H(N) and H(α) correlations and {3D (H)NCO(CACS)HS and 3D (HS)CS(CA)CO(N)H} spectra for side-chain (1) H and (13) C assignments, employing sequential (1) H data acquisitions with direct detection of both the amide and aliphatic protons. The efficacy of the approach for obtaining resonance assignments with complete backbone and side-chain chemical shifts is demonstrated experimentally for the 61-residue [(13) C,(15) N]-labelled peptide of a voltage-gated potassium channel protein of the Kv1.4 channel subunit. The general applicability of the approach for the characterisation of moderately sized globular proteins is also demonstrated.
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http://dx.doi.org/10.1002/cphc.201402872DOI Listing
March 2015

An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.

J Biomol NMR 2014 Aug 19;59(4):211-7. Epub 2014 Jun 19.

Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 , Jena, Germany.

A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential [Formula: see text] data acquisition for moderately sized proteins is presented. The suitability of the approach for obtaining sequential resonance assignments, including complete [Formula: see text] and [Formula: see text] chemical shift information, is demonstrated experimentally for a [Formula: see text] and [Formula: see text] labelled sample of the C-terminal winged helix (WH) domain of the minichromosome maintenance (MCM) complex of Sulfolobus solfataricus. The chemical shift information obtained was used to calculate the global fold of this winged helix domain via CS-Rosetta. This demonstrates that our procedure provides a reliable and straight-forward protocol for a quick global fold determination of moderately-sized proteins.
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http://dx.doi.org/10.1007/s10858-014-9842-2DOI Listing
August 2014

Sequential acquisition of multi-dimensional heteronuclear chemical shift correlation spectra with ¹H detection.

Sci Rep 2014 Mar 27;4:4490. Epub 2014 Mar 27.

Leibniz Institute for Age Research - Fritz Lipmann Institute, Department Biomolecular NMR Spectroscopy, Beutenbergstraße 11, 07745 Jena, Germany.

RF pulse schemes for the simultaneous acquisition of heteronuclear multi-dimensional chemical shift correlation spectra, such as {HA(CA)NH & HA(CACO)NH}, {HA(CA)NH & H(N)CAHA} and {H(N)CAHA & H(CC)NH}, that are commonly employed in the study of moderately-sized protein molecules, have been implemented using dual sequential (1)H acquisitions in the direct dimension. Such an approach is not only beneficial in terms of the reduction of experimental time as compared to data collection via two separate experiments but also facilitates the unambiguous sequential linking of the backbone amino acid residues. The potential of sequential (1)H data acquisition procedure in the study of RNA is also demonstrated here.
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http://dx.doi.org/10.1038/srep04490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967198PMC
March 2014

Sequential protein NMR assignments in the liquid state via sequential data acquisition.

J Magn Reson 2014 Feb 14;239:23-8. Epub 2013 Dec 14.

Research Group Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany. Electronic address:

Two different NMR pulse schemes involving sequential (1)H data acquisition are presented for achieving protein backbone sequential resonance assignments: (i) acquisition of 3D {HCCNH and HNCACONH} and (ii) collection of 3D {HNCOCANH and HNCACONH} chemical shift correlation spectra using uniformly (13)C,(15)N labelled proteins. The sequential acquisition of these spectra reduces the overall experimental time by a factor of ≈2 as compared to individual acquisitions. The suitability of this approach is experimentally demonstrated for the C-terminal winged helix (WH) domain of the minichromosome maintenance (MCM) complex of Sulfolobus solfataricus.
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http://dx.doi.org/10.1016/j.jmr.2013.12.002DOI Listing
February 2014

Steroid exposure during larval development of Xenopus laevis affects mRNA expression of the reproductive pituitary-gonadal axis in a sex- and stage-dependent manner.

Comp Biochem Physiol C Toxicol Pharmacol 2014 Mar 13;160:1-8. Epub 2013 Nov 13.

Department of Ecophysiology and Aquaculture, Leibniz-Institute for Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany; Department of Endocrinology, Institute of Biology, Humboldt-University, Berlin, Germany.

Steroids are known to influence the reproductive pituitary-gonadal axis in adult amphibians. Here, we studied the effects of hormones on pituitary and gonadal mRNA expression during the development of Xenopus laevis. Tadpoles at NF 58 (prometamorphosis) and at NF 66 (freshly metamorphosed) were exposed for three days to 17β-estradiol (E2), tamoxifen (TAM), testosterone (T), dihydrotestosterone (DHT) at 10(-7)M, and flutamide (FLU) at 10(-6)M. In both genders at NF 58 and 66, T and DHT decreased luteinizing hormone beta (lhβ), but increased follicle stimulating hormone beta (fshβ), while FLU induced lhβ specifically in males. In the testis steroidogenic genes (p450 side chain cleavage enzyme, p450scc; steroid acute regulatory protein, star) at NF 58 showed a similar pattern as for lhβ, while the response at NF 66 was only partially present. In females, TAM induced lhβ at NF 58, while E2 decreased lhβ and increased fshβ at NF 66. In the ovaries, no alterations were observed for the steroidogenic genes. Summarizing, gonadotropic and steroidogenic mRNA expression may indicate control of androgen level during testis differentiation in male tadpoles at NF 58. In females the non-responsiveness of steroidogenic genes could be a sign of gonadal quiescence during pre-pubertal stages.
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http://dx.doi.org/10.1016/j.cbpc.2013.11.003DOI Listing
March 2014

¹H, ¹⁵N, and ¹³C chemical shift assignments for the winged helix domains of two archeal MCM C-termini.

Biomol NMR Assign 2014 Oct 10;8(2):357-60. Epub 2013 Aug 10.

Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipman Institute, Beutenbergstr. 11, 07745, Jena, Germany,

High-fidelity replication guarantees the stable inheritance of genetic information stored in the DNA of living organisms. The minichromosome maintenance (MCM) complex functions as replicative DNA-unwinding helicase and has been identified as one key player in the replication process of archea and eukarya. Despite the availability of considerable structural information on archeal MCMs, such information was missing for their C-terminal domain. In order to obtain more detailed structural information, we assigned the NMR chemical shifts for backbone and side chain nuclei for the MCM C-terminal winged helix domains of the archeal species Methanothermobacter thermautrophicus and Sulfolobus solfataricus.
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http://dx.doi.org/10.1007/s12104-013-9516-0DOI Listing
October 2014

CAPITO--a web server-based analysis and plotting tool for circular dichroism data.

Bioinformatics 2013 Jul 15;29(14):1750-7. Epub 2013 May 15.

Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany.

Motivation: Circular dichroism (CD) spectroscopy is one of the most versatile tools to study protein folding and to validate the proper fold of purified proteins. Here, we aim to provide a readily accessible, user-friendly and platform-independent tool capable of analysing multiple CD datasets of virtually any format and returning results as high-quality graphical output to the user.

Results: CAPITO (CD Anaylsis and Plotting Tool) is a novel web server-based tool for analysing and plotting CD data. It allows reliable estimation of secondary structure content utilizing different approaches. CAPITO accepts multiple CD datasets and, hence, is well suited for a wide application range such as the analysis of temperature or pH-dependent (un)folding and the comparison of mutants.

Availability: http://capito.nmr.fli-leibniz.de.

Contact: cwiede@fli-leibniz.de or mago@fli-leibniz.de

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btt278DOI Listing
July 2013

Short-term culture of ovarian cortex pieces to assess the cryopreservation outcome in wild felids for genome conservation.

BMC Vet Res 2013 Feb 22;9:37. Epub 2013 Feb 22.

Leibniz Institute for Zoo and Wildlife Research (IZW), PF 700430, Berlin 10324, Germany.

Background: Cryopreservation of ovarian tissue has the potential to preserve female germ cells of endangered mammals. In the present study, a freezing protocol successfully used for human tissue, was adapted for preserving ovarian tissue of domestic and non-domestic felids. Ovaries from non-domestic felid species were obtained from seven freshly euthanized and two recently deceased wild felids kept in different European Zoos. In addition, ovaries from domestic cats were obtained after ovariectomy from local veterinary clinics for methological adaptations.Ovarian cortex was dissected and uniform sized pieces of 2 mm diameter were obtained. Using a slow freezing protocol (-0.3°C per min) in 1.5 mol/L ethylene glycol, 0.1 mol/L sucrose, the pieces were cultured for up to 14 days both before and after cryopreservation. The integrity of primordial follicles was assessed by histology, and the impact of different protein sources (FCS or BSA) and Vitamin C was determined during two weeks of culture.

Results And Conclusion: During culture the number of primordial follicles decreased within the ovarian pieces (p < 0.05). This effect was less pronounced when FCS was used as the protein source instead of BSA. Supplementation with Vitamin C had a detrimental effect on follicle survival. Since the procedure of cryopreservation had no effect on the follicle survival after one week of culture we conclude that the freezing protocol was suitable for felids. This is the first report of preserving a huge amount of follicles within ovarian tissue by slow freezing performed in several wild feline species.
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http://dx.doi.org/10.1186/1746-6148-9-37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614466PMC
February 2013

Preservation of primordial follicles from lions by slow freezing and xenotransplantation of ovarian cortex into an immunodeficient mouse.

Reprod Domest Anim 2012 Dec;47 Suppl 6:300-4

Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.

Assisted reproductive technology (ART) is considered an important tool in the conservation of endangered species, but often the most limiting factor of ART is the availability of mature oocytes. The aim of the present study was to investigate the feasibility of preserving female germ cells from ovaries of female lions (Panthera leo). Good quality cumulus-oocyte complexes (COCs) were isolated and subjected to in vitro maturation (IVM). In addition, ovarian cortex was obtained and cut into pieces for culture and cryopreservation by slow freezing. The survival of ovarian follicles was assessed by histology. Frozen-thawed samples of ovarian cortex samples were xenotransplanted under the skin of ovariectomized immunodeficient mouse for 28 days. Overall, 178 intact COCs were obtained from 13 lions, but only 28.1% were matured in vitro indicating insufficient IVM conditions. In contrast, almost all follicles within the ovarian cortex survived culture when the original sample was from a young healthy lion collected immediately after euthanasia. Within the xenotransplants, the number of primordial follicles decreased after 28 days by 20%, but the relation between primordial and growing follicles changed in favour of follicular growth. Female gamete rescue from valuable felids may be performed by slow freeze cryopreservation of ovarian cortex. Although the IVM protocol for lions is not yet optimized, mature oocytes may be obtained after long-term xenotransplantation and IVM and could potentially represent one way of salvage of endangered felid species in the future.
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http://dx.doi.org/10.1111/rda.12081DOI Listing
December 2012

BsrG/SR4 from Bacillus subtilis--the first temperature-dependent type I toxin-antitoxin system.

Mol Microbiol 2012 Feb 9;83(3):579-98. Epub 2012 Jan 9.

Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät, AG Bakteriengenetik, Philosophenweg 12, Jena, Germany.

Here, we describe bsrG/SR4, a novel type I toxin-antitoxin system from the SPβ prophage region of the Bacillus subtilis chromosome. The 294-nucleotide bsrG RNA encodes a 38-amino-acid toxin, whereas SR4 is a 180-nucleotide antisense RNA that acts as the antitoxin. Both genes overlap by 123 nucleotides. BsrG expression increases at the onset of stationary phase. The sr4 promoter is 6- to 10-fold stronger than the bsrG promoter. Deletion of sr4 stabilizes bsrG mRNA and causes cell lysis on agar plates, which is due to the BsrG peptide and not the bsrG mRNA. SR4 overexpression could compensate cell lysis caused by overexpression of bsrG. SR4 interacts with the 3' UTR of bsrG RNA, thereby promoting its degradation. RNase III cleaves the bsrG RNA/SR4 duplex at position 185 of bsrG RNA, but is not essential for the function of the toxin-antitoxin system. Endoribonuclease Y and 3'-5' exoribonuclease R participate in the degradation of both bsrG RNA and SR4, whereas PnpA processes three SR4 precursors to the mature RNA. A heat shock at 48°C results in faster degradation and, therefore, significantly decreased amounts of bsrG RNA.
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http://dx.doi.org/10.1111/j.1365-2958.2011.07952.xDOI Listing
February 2012

Combining scale-space and similarity-based aspect graphs for fast 3D object recognition.

IEEE Trans Pattern Anal Mach Intell 2012 Oct;34(10):1902-14

MVTec Software GmbH, Neherstr. 1, 81675 München, Germany.

This paper describes an approach for recognizing instances of a 3D object in a single camera image and for determining their 3D poses. A hierarchical model is generated solely based on the geometry information of a 3D CAD model of the object. The approach does not rely on texture or reflectance information of the object's surface, making it useful for a wide range of industrial and robotic applications, e.g., bin-picking. A hierarchical view-based approach that addresses typical problems of previous methods is applied: It handles true perspective, is robust to noise, occlusions, and clutter to an extent that is sufficient for many practical applications, and is invariant to contrast changes. For the generation of this hierarchical model, a new model image generation technique by which scale-space effects can be taken into account is presented. The necessary object views are derived using a similarity-based aspect graph. The high robustness of an exhaustive search is combined with an efficient hierarchical search. The 3D pose is refined by using a least-squares adjustment that minimizes geometric distances in the image, yielding a position accuracy of up to 0.12 percent with respect to the object distance, and an orientation accuracy of up to 0.35 degree in our tests. The recognition time is largely independent of the complexity of the object, but depends mainly on the range of poses within which the object may appear in front of the camera. For efficiency reasons, the approach allows the restriction of the pose range depending on the application. Typical runtimes are in the range of a few hundred ms.
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http://dx.doi.org/10.1109/TPAMI.2011.266DOI Listing
October 2012

Development: Schwann cells roll the dice.

Nat Rev Neurosci 2010 Jul 16;11(7):456-7. Epub 2010 Jun 16.

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http://dx.doi.org/10.1038/nrn2873DOI Listing
July 2010