• Fate of the UPR marker protein Kar2/Bip and autophagic processes in fed-batch cultures of secretory insulin precursor producing Pichia pastoris.

      Roth, Gustavo; Vanz, Ana Letícia; Lünsdorf, Heinrich; Nimtz, Manfred; Rinas, Ursula; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2018-08-09)
      Secretory recombinant protein production with Pichia (syn. Komagataella) pastoris is commonly associated with the induction of an unfolded protein response (UPR) usually apparent through increased intracellular levels of endoplasmic reticulum (ER) resident chaperones such as Kar2/Bip. During methanol-induced secretory production of an insulin precursor (IP) under industrially relevant fed-batch conditions the initially high level of intracellular Kar2/Bip after batch growth on glycerol unexpectedly declined in the following methanol fed-batch phase misleadingly suggesting that IP production had a low impact on UPR activation. Analysis of the protein production independent level of Kar2/Bip revealed that high Kar2/Bip levels were reached in the exponential growth phase of glycerol batch cultures followed by a strong decline of Kar2/Bip during entry into stationary phase. Ultra-structural cell morphology studies revealed autophagic processes (e.g. ER phagy) at the end of the glycerol batch phase most likely responsible for the degradation of ER resident chaperones such as Kar2/Bip. The pre-induction level of Kar2/Bip did not affect the IP secretion efficiency in the subsequent methanol-induced IP production phase. During growth on methanol intracellular Kar2/Bip levels declined in IP producing and non-producing host cells. However, extracellular accumulation of Kar2/Bip was observed in IP-producing cultures but not in non-producing controls. Most importantly, the majority of the extracellular Kar2/Bip accumulated in the culture supernatant of IP producing cells as truncated protein (approx. 35 kDa). Rapid growth leads to higher basal levels of the major UPR marker protein Kar2/Bip independent of recombinant protein production. Entry into stationary phase or slower growth on poorer substrate, e.g. methanol, leads to a lower basal Kar2/Bip level. Methanol-induced secretory IP production elicits a strong UPR activation which counteracts the reduced UPR during slow growth on methanol. The major ER chaperone Kar2/Bip is found together with recombinant IP in the culture medium where full-length Kar2/Bip accumulates in addition to large amounts of truncated Kar2/Bip. Thus, for judging UPR activating properties of the produced protein it is important to additionally analyze the medium not only for intact Kar2/Bip but also for truncated versions of this UPR reporter protein.
    • Chronic Toxoplasma infection is associated with distinct alterations in the synaptic protein composition.

      Lang, Daniel; Schott, Björn H; van Ham, Marco; Morton, Lorena; Kulikovskaja, Leonora; Herrera-Molina, Rodrigo; Pielot, Rainer; Klawonn, Frank; Montag, Dirk; Jänsch, Lothar; Gundelfinger, Eckart D; Smalla, Karl Heinz; Dunay, Ildiko Rita; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2018-08-01)
      Chronic infection with the neurotropic parasite Toxoplasma gondii has been implicated in the risk for several neuropsychiatric disorders. The mechanisms, by which the parasite may alter neural function and behavior of the host, are not yet understood completely. Here, a novel proteomic approach using mass spectrometry was employed to investigate the alterations in synaptic protein composition in a murine model of chronic toxoplasmosis. In a candidate-based strategy, immunoblot analysis and immunohistochemistry were applied to investigate the expression levels of key synaptic proteins in glutamatergic signaling. A comparison of the synaptosomal protein composition revealed distinct changes upon infection, with multiple proteins such as EAAT2, Shank3, AMPA receptor, and NMDA receptor subunits being downregulated, whereas inflammation-related proteins showed an upregulation. Treatment with the antiparasitic agent sulfadiazine strongly reduced tachyzoite levels and diminished neuroinflammatory mediators. However, in both conditions, a significant number of latent cysts persisted in the brain. Conversely, infection-related alterations of key synaptic protein levels could be partly reversed by the treatment. These results provide evidence for profound changes especially in synaptic protein composition in T. gondii-infected mice with a downregulation of pivotal components of glutamatergic neurotransmission. Our results suggest that the detected synaptic alterations are a consequence of the distinct neuroinflammatory milieu caused by the neurotropic parasite.
    • External quality assessment schemes for glucose measurements in Germany: factors for successful participation, analytical performance and medical impact.

      Bietenbeck, Andreas; Geilenkeuser, Wolf J; Klawonn, Frank; Spannagl, Michael; Nauck, Matthias; Petersmann, Astrid; Thaler, Markus A; Winter, Christof; Luppa, Peter B; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (2018-07-26)
      Determination of blood glucose concentration is one of the most important measurements in clinical chemistry worldwide. Analyzers in central laboratories (CL) and point-of-care tests (POCT) are both frequently used. In Germany, regular participation in external quality assessment (EQA) schemes is mandatory for laboratories performing glucose testing. Glucose testing data from the two German EQAs "Reference Institute for Bioanalytics" (RfB) and "INSTAND - Gesellschaft zur Förderung der Qualitätssicherung in medizinischen Laboratorien" (Instand) were analyzed from 2012 to 2016. Multivariable odds ratios (OR) for the probability to reach a "good" result were calculated. Imprecision and bias were determined and clinical risk of measurement errors estimated. The device employed was the most important variable required for a "good" performance in all EQAs. Additional participation in an EQA for CL automated analyzers improved performance in POCT EQAs. The reciprocal effect was less pronounced. New participants performed worse than experienced participants especially in CL EQAs. Imprecision was generally smaller for CL, but some POCT devices reached a comparable performance. Large lot-to-lot differences occurred in over 10% of analyzed cases. We propose the "bias budget" as a new metric to express the maximum allowable bias that still carries acceptable medical risk. Bias budgets were smallest and clinical risks of errors greatest in the low range of measurement 60-115 mg/dL (3.3-6.4 mmol/L) for most devices. EQAs help to maintain high analytical performances. They generate important data that serve as the foundation for learning and improvement in the laboratory healthcare system.
    • The interferon-stimulated gene product oligoadenylate synthetase-like protein enhances replication of Kaposi's sarcoma-associated herpesvirus (KSHV) and interacts with the KSHV ORF20 protein.

      Bussey, Kendra A; Lau, Ulrike; Schumann, Sophie; Gallo, Antonio; Osbelt, Lisa; Stempel, Markus; Arnold, Christine; Wissing, Josef; Gad, Hans Henrik; Hartmann, Rune; Brune, Wolfram; Jänsch, Lothar; Whitehouse, Adrian; Brinkmann, Melanie M; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2018-03)
      Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few oncogenic human viruses known to date. Its large genome encodes more than 85 proteins and includes both unique viral proteins as well as proteins conserved amongst herpesviruses. KSHV ORF20 is a member of the herpesviral core UL24 family, but the function of ORF20 and its role in the viral life cycle is not well understood. ORF20 encodes three largely uncharacterized isoforms, which we found were localized predominantly in the nuclei and nucleoli. Quantitative affinity purification coupled to mass spectrometry (q-AP-MS) identified numerous specific interacting partners of ORF20, including ribosomal proteins and the interferon-stimulated gene product (ISG) oligoadenylate synthetase-like protein (OASL). Both endogenous and transiently transfected OASL co-immunoprecipitated with ORF20, and this interaction was conserved among all ORF20 isoforms and multiple ORF20 homologs of the UL24 family in other herpesviruses. Characterization of OASL interacting partners by q-AP-MS identified a very similar interactome to that of ORF20. Both ORF20 and OASL copurified with 40S and 60S ribosomal subunits, and when they were co-expressed, they associated with polysomes. Although ORF20 did not have a global effect on translation, ORF20 enhanced RIG-I induced expression of endogenous OASL in an IRF3-dependent but IFNAR-independent manner. OASL has been characterized as an ISG with antiviral activity against some viruses, but its role for gammaherpesviruses was unknown. We show that OASL and ORF20 mRNA expression were induced early after reactivation of latently infected HuARLT-rKSHV.219 cells. Intriguingly, we found that OASL enhanced infection of KSHV. During infection with a KSHV ORF20stop mutant, however, OASL-dependent enhancement of infectivity was lost. Our data have characterized the interaction of ORF20 with OASL and suggest ORF20 usurps the function of OASL to benefit KSHV infection.
    • Mass-spectrometric profiling of cerebrospinal fluid reveals metabolite biomarkers for CNS involvement in varicella zoster virus reactivation.

      Kuhn, Maike; Sühs, Kurt-Wolfram; Akmatov, Manas K; Klawonn, Frank; Wang, Junxi; Skripuletz, Thomas; Kaever, Volkhard; Stangel, Martin; Pessler, Frank; TWINCORE, Zentrum für experimentelle und klinischeInfektionsforschung GmbH, Feodor-Lynen-Str. 7, 30625 Hannover, Germany. (2018-01-17)
      Varicella zoster virus (VZV) reactivation spans the spectrum from uncomplicated segmental herpes zoster to life-threatening disseminated CNS infection. Moreover, in the absence of a small animal model for this human pathogen, studies of pathogenesis at the organismal level depend on analysis of human biosamples. Changes in cerebrospinal fluid (CSF) metabolites may reflect critical aspects of host responses and end-organ damage in neuroinfection and neuroinflammation. We therefore applied a targeted metabolomics screen of CSF to three clinically distinct forms of VZV reactivation and infectious and non-infectious disease controls in order to identify biomarkers for CNS involvement in VZV reactivation.
    • Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.

      Klingen, Thorsten R; Reimering, Susanne; Loers, Jens; Mooren, Kyra; Klawonn, Frank; Krey, Thomas; Gabriel, Gülsah; McHardy, Alice Carolyn; BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56, 38106 Braunschweig, Germany. (2018-01-10)
      Monitoring changes in influenza A virus genomes is crucial to understand its rapid evolution and adaptation to changing conditions e.g. establishment within novel host species. Selective sweeps represent a rapid mode of adaptation and are typically observed in human influenza A viruses. We describe Sweep Dynamics (SD) plots, a computational method combining phylogenetic algorithms with statistical techniques to characterize the molecular adaptation of rapidly evolving viruses from longitudinal sequence data. SD plots facilitate the identification of selective sweeps, the time periods in which these occurred and associated changes providing a selective advantage to the virus. We studied the past genome-wide adaptation of the 2009 pandemic H1N1 influenza A (pH1N1) and seasonal H3N2 influenza A (sH3N2) viruses. The pH1N1 influenza virus showed simultaneous amino acid changes in various proteins, particularly in seasons of high pH1N1 activity. Partially, these changes resulted in functional alterations facilitating sustained human-to-human transmission. In the evolution of sH3N2 influenza viruses, we detected changes characterizing vaccine strains, which were occasionally revealed in selective sweeps one season prior to the WHO recommendation. Taken together, SD plots allow monitoring and characterizing the adaptive evolution of influenza A viruses by identifying selective sweeps and their associated signatures. - - all data is published on GitHub: https://github.com/hzi-bifo/SDplots/tree/v1.0.0
    • Effects of pathogen dependency in a multi-pathogen infectious disease system including population level heterogeneity - a simulation study.

      Bakuli, Abhishek; Klawonn, Frank; Karch, André; Mikolajczyk, Rafael T; Helmholtz-Zentrum für Infektionsforschung, GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-12-13)
      Increased computational resources have made individual based models popular for modelling epidemics. They have the advantage of incorporating heterogeneous features, including realistic population structures (like e.g. households). Existing stochastic simulation studies of epidemics, however, have been developed mainly for incorporating single pathogen scenarios although the effect of different pathogens might directly or indirectly (e.g. via contact reductions) effect the spread of each pathogen. The goal of this work was to simulate a stochastic agent based system incorporating the effect of multiple pathogens, accounting for the household based transmission process and the dependency among pathogens.
    • TCR signalling network organization at the immunological synapses of murine regulatory T cells.

      van Ham, Marco; Teich, René; Philipsen, Lars; Niemz, Jana; Amsberg, Nicole; Wissing, Josef; Nimtz, Manfred; Gröbe, Lothar; Kliche, Stefanie; Thiel, Nadine; Klawonn, Frank; Hubo, Mario; Jonuleit, Helmut; Reichardt, Peter; Müller, Andreas J; Huehn, Jochen; Jänsch, Lothar; Helmholtz-Zetrum für Infektionsforschung GmbH, Inhoffenstr.7, 38124 Braunschweig, Germany. (2017-08-17)
      Regulatory T (Treg) cells require T-cell receptor (TCR) signalling to exert their immunosuppressive activity, but the precise organization of the TCR signalling network compared to conventional T (Tconv) cells remains elusive. By using accurate mass spectrometry and multi-epitope ligand cartography (MELC) we characterized TCR signalling and recruitment of TCR signalling components to the immunological synapse (IS) in Treg cells and Tconv cells. With the exception of Themis which we detected in lower amounts in Treg cells, other major TCR signalling components were found equally abundant, however, their phosphorylation-status notably discriminates Treg cells from Tconv cells. Overall, this study identified 121 Treg cell-specific phosphorylations. Short-term triggering of T cell subsets via CD3 and CD28 widely harmonized these variations with the exception of eleven TCR signalling components that mainly regulate cytoskeleton dynamics and molecular transport. Accordingly, conjugation with B cells indeed caused variant cellular morphology and revealed a Treg cell-specific recruitment of TCR signalling components such as PKCθ, PLCγ1 and ZAP70 as well as B cell-derived CD86 into the IS. Together, results from this study support the existence of a Treg cell-specific IS and suggest Treg cell-specific cytoskeleton dynamics as a novel determinant for the unique functional properties of Treg cells.
    • Chronic lung inflammation primes humoral immunity and augments antipneumococcal resistance.

      Boehme, Julia D; Stegemann-Koniszewski, Sabine; Autengruber, Andrea; Peters, Nicole; Wissing, Josef; Jänsch, Lothar; Jeron, Andreas; Bruder, Dunja; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-07-10)
      Airway epithelial cells (AECs) display remarkable plasticity in response to infectious stimuli and their functional adaptations are critical for antimicrobial immunity. However, the roles of AECs and humoral mediators to host defense in non-communicable lung inflammation remain elusive. We dissected pulmonary defense against Streptococcus pneumoniae in hosts with pre-existing inflammatory conditions (SPC-HAxTCR-HA mice). Lung tissue transcriptomics and bronchoalveolar lavage fluid (BALF) proteomics revealed an induction of humoral defense mechanisms in inflamed lungs. Accordingly, besides antibacterial proteins and complement components being overrepresented in inflamed lungs, elevated polymeric immunoglobulin receptor (pIgR)-expression in AECs correlated with increased secretory immunoglobulin (SIg) transport. Consequently, opsonization assays revealed augmented pneumococcal coverage by SIgs present in the BALF of SPC-HAxTCR-HA mice, which was associated with enhanced antipneumococcal resistance. These findings emphasize the immunologic potential of AECs as well as their central role in providing antibacterial protection and put forward pIgR as potential target for therapeutic manipulation in infection-prone individuals.
    • Global proteome response of Escherichia coli BL21 to production of human basic fibroblast growth factor in complex and defined medium

      Li, Zhaopeng; Nimtz, Manfred; Rinas, Ursula; Helmholtz Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.; Technical Chemistry - Life Science; Leibniz University of Hannover; Hannover Germany; Helmholtz Centre for Infection Research; Braunschweig Germany; Technical Chemistry - Life Science; Leibniz University of Hannover; Hannover Germany (2017-06-20)
    • Degradable magnesium implant-associated infections by bacterial biofilms induce robust localized and systemic inflammatory reactions in a mouse model.

      Rahim, Muhammad Imran; Babbar, Anshu; Lienenklaus, Stefan; Pils, Marina; Rohde, M; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-06-01)
      Biomaterial-associated Pseudomonas aeruginosa biofilm infections constitute cascade of host immune reactions ultimately leading towards implant failure. Due to lack of relevant in vivo biofilm models, majority of the studies report host immune responses against free living or planktonic bacteria while bacteria in clinical situations live more frequently as biofilm communities than as single cells. Present study investigated host immune responses against biomaterial-associated P. aeruginosa biofilms in a clinically relevant mouse model. Previously, we reported metallic magnesium, a prospective biodegradable implant, to be permissive for bacterial biofilms in vivo even though it exhibits antibacterial properties in vitro. Therefore, magnesium was employed as biomaterial to investigate in vivo biofilm formation and associated host immune responses by using two P. aeruginosa strains and two mouse strains. P. aeruginosa formed biofilms on subcutaneously implanted magnesium discs. Non-invasive in vivo imaging indicated transient inflammatory responses at control sites whereas robust prolonged interferon-β (IFN-β) expression was observed from biofilms in a transgenic animal reporter. Further, immunohistology and electron microscopic results showed that bacterial biofilms were located in two dimensions immediately on the implant surface and at a short distance in the adjacent tissue. These biofilms were surrounded by inflammatory cells (mainly polymorphonuclear cells) as compared to controls. Interestingly, even though the number of live bacteria in various organs remained below detectable levels, splenomegaly indicated systemic inflammatory processes. Overall, these findings confirmed the resistance of biofilm infections in vivo to potentially antibacterial properties of magnesium degradation products. In vivo imaging and histology indicated the induction of both, local and systemic host inflammatory responses against P. aeruginosa biofilms. Even though the innate host immune defenses could not eliminate the local infection for up to two weeks, there was no apparent systemic bacteremia and all animals investigated survived the infection.
    • Iron affinity gel and gallium immobilized metal affinity chromatographic technique for phosphopeptide enrichment: a comparative study

      Biswas, Sagarika; Sarkar, Ashish; Misra, Richa; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr.7, 38124 Braunschweig, Germany.; Department of Genomics and Molecular Medicine, CSIR – Institute of Genomics and Integrative Biology, Delhi, India; Department of Genomics and Molecular Medicine, CSIR – Institute of Genomics and Integrative Biology, Delhi, India; Department of Genomics and Molecular Medicine, CSIR – Institute of Genomics and Integrative Biology, Delhi, India (2017-02-28)
    • The zlog value as a basis for the standardization of laboratory results

      Hoffmann, Georg; Klawonn, Frank; Lichtinghagen, Ralf; Orth, Matthias; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-01-26)
      Abstract Background: With regard to the German E-Health Law of 2016, the German Society for Clinical Chemistry and Laboratory Medicine (DGKL) has been invited to develop a standard procedure for the storage and transmission of laboratory results. We suggest the commonly used z-transformation. Methods: This method evaluates by how many standard deviations (SDs) a given result deviates from the mean of the respective reference population. We confirm with real data that laboratory results of healthy individuals can be adjusted to a normal distribution by logarithmic transformation. Results: Thus, knowing the lower and upper reference limits LL and UL, one can transform any result x into a zlog value using the following equation: $\eqalign{ {\rm{zlog}} = & {\rm{(log(x)}}-{\rm{(log(LL)}} + {\rm{log(UL))/2)\cdot3}}{\rm{.92/(log(UL)}} \cr -{\bf{ }}{\rm{log(LL))}} \cr} $ The result can easily be interpreted, as its reference interval (RI) is –1.96 to +1.96 by default, and very low or high results yield zlog values around –5 and +5, respectively. For intuitive data presentation, the zlog values may be transformed into a continuous color scale, e.g. from blue via white to orange. Using the inverse function, any zlog value can then be translated into the theoretical result of an analytical method with another RI: (1) $${\rm{x}} = {\rm{L}}{{\rm{L}}^{0.5 - {\rm{zlog}}/3.92}} \cdot {\rm{U}}{{\rm{L}}^{0.5 + {\rm{zlog}}/3.92}}$$ Conclusions: Our standardization proposal can easily be put into practice and may effectively contribute to data quality and patient safety in the frame of the German E-health law. We suggest for the future that laboratories should provide the zlog value in addition to the original result, and that the data transmission protocols (e.g. HL7, LDT) should contain a special field for this additional value.
    • Der zlog-Wert als Basis für die Standardisierung von Laborwerten

      Hoffmann, Georg; Klawonn, Frank; Lichtinghagen, Ralf; Orth, Matthias; Helmholtz-Zentrum für Infektionsforshung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-01-01)
      Zusammenfassung Hintergrund Im Zuge des deutschen E-Health-Gesetzes von 2016 wurde die DGKL aufgefordert, Vorschläge für die standardisierte Speicherung und Übermittlung von Labordaten zu erarbeiten. Wir schlagen dafür die in der Statistik weit verbreitete z-Transformation vor. Methoden Man erhält mit diesem Verfahren einen Relativwert, der angibt, um wie viele Standardabweichungen ein Messwert vom Mittelwert des Referenzkollektivs abweicht. Anhand realer Daten belegen wir die Annahme, dass die Werte gesunder Referenzpersonen durch logarithmische Transformation einer Normalverteilung angenähert werden können. Ergebnisse Kennt man somit die Unter- und Obergrenze UG und OG des Referenzintervalls, so kann man jedes Laborergebnis mit folgender Gleichung transformieren: Der zlog-Wert ist leicht interpretierbar: Sein Referenzintervall liegt methodenunabhängig stets zwischen –1,96 und +1,96; stark erniedrigte oder erhöhte Laborergebnisse führen zu zlog-Werten um –5 bzw. +5. Für eine intuitive Befunddarstellung kann man zlog-Werte auch in eine kontinuierliche Farbskala, z. B. von Blau über Weiß bis Orange umrechnen. Mithilfe der Umkehrfunktion lässt sich aus dem zlog-Wert auch das theoretische Resultat einer Messmethode mit einem anderen Referenzintervall berechnen: Schlussfolgerung Unser Standardisierungsvorschlag ist ein leicht realisierbarer und effektiver Beitrag zur Verbesserung der Datenqualität und Patientensicherheit im Rahmen des E-Health-Gesetzes. Es wird gefordert, dass alle Labore künftig zusätzlich zum Originalwert den zlog-Wert zur Verfügung stellen und dass in die Protokolle für die elektronische Labordatenübertragung (HL7, LDT) ein eigenes Feld für diesen zusätzlichen Wert eingefügt wird.
    • Diagnostic needs for rare diseases and shared prediagnostic phenomena: Results of a German-wide expert Delphi survey.

      Blöß, Susanne; Klemann, Christian; Rother, Ann-Katrin; Mehmecke, Sandra; Schumacher, Ulrike; Mücke, Urs; Mücke, Martin; Stieber, Christiane; Klawonn, Frank; Kortum, Xiaowei; Lechner, Werner; Grigull, Lorenz; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017)
      Worldwide approximately 7,000 rare diseases have been identified. Accordingly, 4 million individuals live with a rare disease in Germany. The mean time to diagnosis is about 6 years and patients receive several incorrect diagnoses during this time. A multiplicity of factors renders diagnosing a rare disease extremely difficult. Detection of shared phenomena among individuals with different rare diseases could assist the diagnostic process. In order to explore the demand for diagnostic support and to obtain the commonalities among patients, a nationwide Delphi survey of centers for rare diseases and patient groups was conducted.
    • Patient's Experience in Pediatric Primary Immunodeficiency Disorders: Computerized Classification of Questionnaires.

      Mücke, Urs; Klemann, Christian; Baumann, Ulrich; Meyer-Bahlburg, Almut; Kortum, Xiaowei; Klawonn, Frank; Lechner, Werner M; Grigull, Lorenz; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017)
      Primary immunodeficiency disorders (PIDs) are a heterogeneous group of more than 200 rare diseases. Timely diagnosis is of uttermost importance. Therefore, we aimed to develop a diagnostic questionnaire with computerized pattern-recognition in order to support physicians to identify suspicious patient histories.
    • Effects of drift and noise on the optimal sliding window size for data stream regression models

      Tschumitschew, Katharina; Klawonn, Frank; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124Braunschweig, Germany. (2016-05-27)
    • Relative ion intensities of maltooligosaccharide ethers in electrospray ionization ion trap mass spectrometry: A quantitative evaluation

      Gangula, Sheetal; Nimtz, Manfred; Mischnick, Petra; Technische Universität Braunschweig, Institute of Food Chemistry, Schleinitzstr. 20, Braunschweig, Germany. (2016-05)
    • The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C-H Bond Cleavage and Oxygen Atom Transfer Reactions.

      Hartmann, Tobias; Schrapers, Peer; Utesch, Tillmann; Nimtz, Manfred; Rippers, Yvonne; Dau, Holger; Mroginski, Maria Andrea; Haumann, Michael; Leimkühler, Silke; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2016-04-26)
      Formate dehydrogenases (FDHs) are capable of performing the reversible oxidation of formate and are enzymes of great interest for fuel cell applications and for the production of reduced carbon compounds as energy sources from CO2. Metal-containing FDHs in general contain a highly conserved active site, comprising a molybdenum (or tungsten) center coordinated by two molybdopterin guanine dinucleotide molecules, a sulfido and a (seleno-)cysteine ligand, in addition to a histidine and arginine residue in the second coordination sphere. So far, the role of these amino acids in catalysis has not been studied in detail, because of the lack of suitable expression systems and the lability or oxygen sensitivity of the enzymes. Here, the roles of these active site residues is revealed using the Mo-containing FDH from Rhodobacter capsulatus. Our results show that the cysteine ligand at the Mo ion is displaced by the formate substrate during the reaction, the arginine has a direct role in substrate binding and stabilization, and the histidine elevates the pKa of the active site cysteine. We further found that in addition to reversible formate oxidation, the enzyme is further capable of reducing nitrate to nitrite. We propose a mechanistic scheme that combines both functionalities and provides important insights into the distinct mechanisms of C-H bond cleavage and oxygen atom transfer catalyzed by formate dehydrogenase.
    • Analysis of Practical Identifiability of a Viral Infection Model.

      Nguyen, Van Kinh; Klawonn, Frank; Mikolajczyk, Rafael; Hernandez-Vargas, Esteban A.; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2016)
      Mathematical modelling approaches have granted a significant contribution to life sciences and beyond to understand experimental results. However, incomplete and inadequate assessments in parameter estimation practices hamper the parameter reliability, and consequently the insights that ultimately could arise from a mathematical model. To keep the diligent works in modelling biological systems from being mistrusted, potential sources of error must be acknowledged. Employing a popular mathematical model in viral infection research, existing means and practices in parameter estimation are exemplified. Numerical results show that poor experimental data is a main source that can lead to erroneous parameter estimates despite the use of innovative parameter estimation algorithms. Arbitrary choices of initial conditions as well as data asynchrony distort the parameter estimates but are often overlooked in modelling studies. This work stresses the existence of several sources of error buried in reports of modelling biological systems, voicing the need for assessing the sources of error, consolidating efforts in solving the immediate difficulties, and possibly reconsidering the use of mathematical modelling to quantify experimental data.