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Tailoring recombinant protein quality by rational media design

David Brühlmann, Martin Jordan, Jürgen Hemberger, Markus Sauer, Matthieu Stettler, Hervé Broly
2015 Biotechnology progress (Print)  
Hemberger, J. Souquet, H. Broly and M.  ...  Hemberger, M. Sauer, M. Stettler, H. Broly, Tailoring recombinant protein quality by rational media design, Biotechnology Progress 31 (3) (2015) 615-629.  ... 
doi:10.1002/btpr.2089 pmid:25864704 fatcat:64pfqslmlnccpalywcpx3isgra

The potential of small molecules to modulate glycosylation by media design

David Brühlmann, Anaïs Muhr, Jürgen Hemberger, Markus Sauer, Henri Kornmann, Martin Jordan, Hervé Broly
2015 BMC Proceedings  
doi:10.1186/1753-6561-9-s9-p38 fatcat:nmhcogvxgnel5bogfmbeqnxd4a

PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms

Marc Bruckskotten, Mario Looso, Franz Cemic, Anne Konzer, Jurgen Hemberger, Markus Kruger, Thomas Braun
2010 BMC Bioinformatics  
Several tools have been developed to explore and search Gene Ontology (GO) databases allowing efficient GO enrichment analysis and GO tree visualization. Nevertheless, identification of highly specific GO-terms in complex data sets is relatively complicated and the display of GO term assignments and GO enrichment analysis by simple tables or pie charts is not optimal. Valuable information such as the hierarchical position of a single GO term within the GO tree (topological ordering), or
more » ... nt within a complex set of biological experiments is not displayed. Pie charts based on GO tree levels are, themselves, one-dimensional graphs, which cannot properly or efficiently represent the hierarchical specificity for the biological system being studied. Results: Here we present a new method, which we name PCA2GO, capable of GO analysis using complex multidimensional experimental settings. We employed principal component analysis (PCA) and developed a new score, which takes into account the relative frequency of certain GO terms and their specificity (hierarchical position) within the GO graph. We evaluated the correlation between our representation score R and a standard measure of enrichment, namely p-values to convey the versatility of our approach to other methods and point out differences between our method and commonly used enrichment analyses. Although p values and the R score formally measure different quantities they should be correlated, because relative frequencies of GO terms occurrences within a dataset are an indirect measure of protein numbers related to this term. Therefore they are also related to enrichment. We showed that our score enables us to identify more specific GO-terms i.e. those positioned further down the GO-graph than other common tools used for this purpose. PCA2GO allows visualization and detection of multidimensional dependencies both within the acyclic graph (GO tree) and the experimental settings. Our method is intended for the analysis of several experimental sets, not for one set, like standard enrichment tools. To demonstrate the usefulness of our approach we performed a PCA2GO analysis of a fractionated cardiomyocyte protein dataset, which was identified by enhanced liquid chromatography-mass spectrometry (GeLC-MS). The analysis enabled us to detect distinct groups of proteins, which accurately reflect properties of biochemical cell fractions. Conclusions: We conclude that PCA2GO is an alternative efficient GO analysis tool with unique features for detection and visualization of multidimensional dependencies within the dataset under study. PCA2GO reveals strongly correlated GO terms within the experimental setting (in this case different fractions) by PCA group formation and improves detection of more specific GO terms within experiment dependent GO term groups than standard p value calculations.
doi:10.1186/1471-2105-11-336 pmid:20565932 pmcid:PMC2910024 fatcat:q7nt4b2lffekbpduagnkyjbuam

Anti-Listeria Activities of Galleria mellonella Hemolymph Proteins

Krishnendu Mukherjee, Mobarak Abu Mraheil, Silke Silva, Daniela Müller, Franz Cemic, Jürgen Hemberger, Torsten Hain, Andreas Vilcinskas, Trinad Chakraborty
2011 Applied and Environmental Microbiology  
ABSTRACTWe report the use of antimicrobial hemolymph proteins from the model hostGalleria mellonellaas an inhibitor for variousListeriastrains, providing a novel source for antilisterial therapeutics. We also have shown that specific virulence-associated genes known to mediate antimicrobial resistance ofListeriain mammalian models indicated a similar function inGalleria.
doi:10.1128/aem.02435-10 pmid:21531838 pmcid:PMC3131625 fatcat:qihss6g4drff3oziv2mivqvm34

QDPR homologues in Danio rerio regulate melanin synthesis, early gliogenesis, and glutamine homeostasis

Maximilian Breuer, Luca Guglielmi, Matthias Zielonka, Verena Hemberger, Stefan Kölker, Jürgen G. Okun, Georg F. Hoffmann, Matthias Carl, Sven W. Sauer, Thomas Opladen, Ryan Thummel
2019 PLoS ONE  
Dihydropteridine reductase (QDPR) catalyzes the recycling of tetrahydrobiopterin (BH4), a cofactor in dopamine, serotonin, and phenylalanine metabolism. QDPR-deficient patients develop neurological symptoms including hypokinesia, truncal hypotonia, intellectual disability and seizures. The underlying pathomechanisms are poorly understood. We established a zebrafish model for QDPR deficiency and analyzed the expression as well as function of all zebrafish QDPR homologues during embryonic
more » ... ent. The homologues qdpra is essential for pigmentation and phenylalanine metabolism. Qdprb1 is expressed in the proliferative zones of the optic tectum and eye. Knockdown of qdprb1 leads to up-regulation of pro-proliferative genes and increased number of phospho-histone3 positive mitotic cells. Expression of neuronal and astroglial marker genes is concomitantly decreased. Qdprb1 hypomorphic embryos develop microcephaly and reduced eye size indicating a role for qdprb1 in the transition from cell proliferation to differentiation. Glutamine accumulation biochemically accompanies the developmental changes. Our findings provide novel insights into the neuropathogenesis of QDPR deficiency.
doi:10.1371/journal.pone.0215162 pmid:30995231 pmcid:PMC6469847 fatcat:dxwqumrxevdcva5mvpk2bqjpm4

RibM from Streptomyces davawensis is a riboflavin/roseoflavin transporter and may be useful for the optimization of riboflavin production strains

Sabrina Hemberger, Danielle B Pedrolli, Jürgen Stolz, Christian Vogl, Martin Lehmann, Matthias Mack
2011 BMC Biotechnology  
The bacterium Bacillus subtilis, which is not a natural riboflavin overproducer, has been converted into an excellent production strain by classical mutagenesis and metabolic engineering. To our knowledge, the enhancement of riboflavin excretion from the cytoplasm of overproducing cells has not yet been considered as a target for (further) strain improvement. Here we evaluate the flavin transporter RibM from Streptomyces davawensis with respect to improvement of a riboflavin production strain.
more » ... esults: The gene ribM from S. davawensis, coding for a putative facilitator of riboflavin uptake, was codon optimized (ribM opt ) for expression in B. subtilis. The gene ribM opt was functionally introduced into B. subtilis using the isopropyl-β-thiogalactopyranoside (IPTG)-inducible expression plasmid pHT01: Northern-blot analysis of total RNA from IPTG treated recombinant B. subtilis cells revealed a ribM opt specific transcript. Western blot analysis showed that the his 6 -tagged heterologous gene product RibM was present in the cytoplasmic membrane. Expression of ribM in Escherichia coli increased [ 14 C]riboflavin uptake, which was not affected by the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP). Expression of ribM opt supported growth of a B. subtilis ΔribB:: Erm r ΔribU::Kan r double mutant deficient in riboflavin synthesis (ΔribB) and also deficient with respect to riboflavin uptake (ΔribU). Expression of ribM opt increased roseoflavin (a toxic riboflavin analog produced by S. davawensis) sensitivity of a B. subtilis ΔribU::Kan r strain. Riboflavin synthesis by a model riboflavin B. subtilis production strain overproducing RibM was increased significantly depending on the amount of the inducer IPTG. Conclusions: The energy independent flavin facilitator RibM could in principle catalyze riboflavin export and thus may be useful to increase the riboflavin yield in a riboflavin production process using a recombinant RibM overproducing B. subtilis strain (or any other microorganism).
doi:10.1186/1472-6750-11-119 pmid:22136195 pmcid:PMC3239331 fatcat:rkui6m7dczde5dsehs2cq7mqey

A Protein from the Salivary Glands of the Giant Amazon Leech with High Sequence Homology to a Nicotinic Acetylcholine Receptor Subunit

Sancha Salgueiro, Susan Potts, E. Ann Mcllgorm, Keith H. Ansell, Jürgen Hemberger, Detlef Güssow
1999 Zeitschrift für Naturforschung C - A Journal of Biosciences  
A gene coding for a soluble protein with homology to the β subunit of the nicotinic acetyl­choline receptor from goldfish was isolated from a cDNA library of Haementeria ghilianii salivary glands. Comparison of the leech protein sequence with the database showed that the N terminus has high homology with the extracellular portion of acetylcholine receptor β subunits, whilst the C terminus, highly charged, has homology to proteins which may be involved in chelating divalent cations. The leech
more » ... tein was expressed in mammalian cells and the product compared to the native protein. Both proteins are glycosylated and form polymers which are disrupted by heat but not by reducing agents. A role for this protein in salivary gland secretion is suggested.
doi:10.1515/znc-1999-1118 fatcat:bnyhwvfe25cwhleoggw5uez32y

Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application

Mobarak A. Mraheil, André Billion, Carsten Kuenne, Jordan Pischimarov, Bernd Kreikemeyer, Susanne Engelmann, Axel Hartke, Jean-Christophe Giard, Maja Rupnik, Sonja Vorwerk, Markus Beier, Julia Retey (+6 others)
2010 Microbial Biotechnology  
In the recent years, the number of drug-and multidrug-resistant microbial strains has increased rapidly. Therefore, the need to identify innovative approaches for development of novel anti-infectives and new therapeutic targets is of high priority in global health care. The detection of small RNAs (sRNAs) in bacteria has attracted considerable attention as an emerging class of new gene expression regulators. Several experimental technologies to predict sRNA have been established for the
more » ... tive model organism Escherichia coli. In many respects, sRNA screens in this model system have set a blueprint for the global and functional identification of sRNAs for Gram-positive microbes, but the functional role of sRNAs in colonization and pathogenicity for Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis and Clostridium difficile is almost completely unknown. Here, we report the current knowledge about the sRNAs of these socioeconomically relevant Gram-positive pathogens, overview the state-of-theart high-throughput sRNA screening methods and summarize bioinformatics approaches for genomewide sRNA identification and target prediction. Finally, we discuss the use of modified peptide nucleic acids (PNAs) as a novel tool to inactivate potential sRNA and their applications in rapid and specific detection of pathogenic bacteria.
doi:10.1111/j.1751-7915.2010.00171.x pmid:21255362 pmcid:PMC3815340 fatcat:oslpivyxu5fa5pnowervlwmpga

Page 553 of American Ceramic Society Bulletin Vol. 38, Issue 10 [page]

1959 American Ceramic Society Bulletin  
., Box 835 Alliance, Ohio HARTWIG, Jurgen (R) Box 521, Fostoria, Ohio (National Carbon Co.) HARTY, R. Philip (R) Exolon Co. 1000 E. Niagara St., Tonawanda, N. Y. HARVEY, A. M., Jr.  ...  Geological Survey) HEMBERG, Per Surte Glasswork, Surte, Sweden HEMSTEGER, Samuel E. (EI) 4155 Audubon Rd., Detroit 24, Mich. (Consulting Engineer) HENDERSON CLAY PRODUCTS (Homer L.  ... 

»Das Reichsbanner Schwarz-Rot-Gold – Forschungsstand und Perspektiven«

Dennis Werberg
2019 Militärgeschichtliche Zeitschrift  
Jürgen Weber ( Zwei weitere Vorträge setzten sich mit den Presseorganen des Reichsbanners auseinander.  ...  Valentin Hemberger (Gießen) legte eine Quellenanalyse zur »Illustrierten Reichsbanner-Zeitung«, die ab 1929 in »Illustrierte Republikanische Zeitung« (IRZ) umbenannt wurde, vor.  ... 
doi:10.1515/mgzs-2019-0005 fatcat:uwrt2zpjyngo7bmyt7czssqbeq

Self-Renewing Trophoblast Organoids Recapitulate the Developmental Program of the Early Human Placenta

Sandra Haider, Gudrun Meinhardt, Leila Saleh, Viktoria Kunihs, Magdalena Gamperl, Ulrich Kaindl, Adolf Ellinger, Thomas R. Burkard, Christian Fiala, Jürgen Pollheimer, Sasha Mendjan, Paulina A. Latos (+1 others)
2018 Stem Cell Reports  
Expression of the ELF5 gene and demethylation of its promoter region were shown to be indicative for human CTB origin (Hemberger et al., 2010; Lee et al., 2016) .  ...  The ELF5 gene promoter was found to be hypomethylated in CTB-ORGs, another indication for their trophoblast origin (Hemberger et al., 2010; Lee et al., 2016) .  ... 
doi:10.1016/j.stemcr.2018.07.004 pmid:30078556 pmcid:PMC6092984 fatcat:ijsec47sxbc2der3rzyhds4kqa

Page 126 of Die Unterrichtspraxis Vol. 29, Issue 1 [page]

Die Unterrichtspraxis  
Liontas Berka, Sigrid, and Stefan Fink Bolten, Jürgen Brown, H. Douglas Briiggemann, Wilhelm, and Karl Hemberger Bullivant, Keith, and Mechthild Borries, eds.  ... 

Page 154 of Die Unterrichtspraxis Vol. 27, Issue 1 [page]

Die Unterrichtspraxis  
Bolten, Jürgen. Marktchance Wirtschaftsdeutsch. München: Klett Edition Deutsch, 1993. Brüggemann, Wilhelm, and Karl Hemberger. Testfragen Wirtschaftsdeutsch. Miinchen: Klett Edition Deutsch, 1993.  ... 

Page 230 of Florida Bar Journal Vol. 65, Issue 8 [page]

1991 Florida Bar Journal  
Frederick M . (407)336-7711 72m WPaknelto Park Rd PO Bn 810516 Boca Raton 33481 HEMBERG. Paul Edward . (407)332-90m Tmow'^alniM^ Rd Boca Raton 33433 HEW6URG. Col Charles 6 .  ...  Courthouse Annex Tampa 33602 HEBE, Beth R . (613)3324006 do Magistrale George Schwarz PO Bn X10R Myers 33902 HEBE, Caihryn Mitchel . (305)3556151 im Chopin Plaza XI S Biscayne BM >4m Miami X131 HEBE, Mark Jurgen  ... 

Unique trophoblast chromatin environment mediated by the PcG protein SFMBT2

Priscilla Tang, Kamelia Miri, Susannah Varmuza
2019 Biology Open  
Pioneering genetic studies in fruit flies have revealed that gene silencing is rooted in complexes of chromatin proteins (Lewis, 1978; Struhl, 1981; Jürgens, 1985) .  ...  In mice, these three types of cell can be induced to form specialized stem or progenitor cells in vitrotrophoblast stem cells (TSC), embryonic stem cells (ESC) and extraembryonic stem cells (XEN) (Hemberger  ... 
doi:10.1242/bio.043638 fatcat:ozjy4bxvwvcwrdi3g3rqhv6w3e
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