2024-03-28T22:20:53Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/84042019-08-30T11:32:37Zcom_10033_620636col_10033_620638
S/MARt DB: a database on scaffold/matrix attached regions
Liebich, Ines
Bode, Jürgen
Frisch, Matthias
Wingender, Edgar
2007-02-14
2002-01-01
2007-02-14
2002-01-01
Nucleic Acids Research 2002 30(1):372-374
0305-1048
1362-4962
11752340
http://hdl.handle.net/10033/8404
99064
en_US
http://www.nar.oupjournals.org/content/vol30/issue1/
Copyright © 2002 Oxford University Press
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/84052019-08-30T11:32:37Zcom_10033_620636col_10033_620638
TRANSCompel®: a database on composite regulatory elements in eukaryotic genes
Kel-Margoulis, Olga V.
Kel, Alexander E.
Reuter, Ingmar
Deineko, Igor V.
Wingender, Edgar
2007-02-14
2002-01-01
2007-02-14
2002-01-01
Nucleic Acids Research 2002 30(1):332-334
0305-1048
1362-4962
11752329
http://hdl.handle.net/10033/8405
99108
en_US
http://www.nar.oupjournals.org/content/vol30/issue1/
Copyright © 2002 Oxford University Press
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/84022019-08-30T11:32:38Zcom_10033_620636col_10033_620638
COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation
Kel-Margoulis, Olga V.
Romashchenko, Aida G.
Kolchanov, Nikolay A.
Wingender, Edgar
Kel, Alexander E.
2007-02-14
2000-01-01
2007-02-14
2000-01-01
Nucleic Acids Research 2000 28(1):311-315
0305-1048
1362-4962
10592258
http://hdl.handle.net/10033/8402
102399
en_US
http://www.oup.co.uk/nar/Volume_28/Issue_1/html/gkd017.htm
Copyright © 2000 Oxford University Press
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/84092019-08-30T11:32:38Zcom_10033_620636col_10033_620638
TRANSFAC: an integrated system for gene expression regulation
Wingender, E.
Chen, X.
Hehl, R.
Karas, H.
Liebich, I.
Matys, V.
Meinhardt, T.
Prüß, M.
Reuter, I.
Schacherer, F.
2007-02-14
2000-01-01
2007-02-14
2000-01-01
Nucleic Acids Research 2000 28(1):316-319
0305-1048
1362-4962
10592259
http://hdl.handle.net/10033/8409
102445
en_US
http://www.oup.co.uk/nar/Volume_28/Issue_1/html/gkd063.htm
Copyright © 2000 Oxford University Press
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/85052019-08-30T11:32:38Zcom_10033_620636col_10033_620638
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.
Heinemeyer, T
Wingender, E
Reuter, I
Hermjakob, H
Kel, A E
Kel, O V
Ignatieva, E V
Ananko, E A
Podkolodnaya, O A
Kolpakov, F A
Podkolodny, N L
Kolchanov, N A
2007-02-19
1998-01-01
2007-02-19
1998-01-01
Nucleic Acids Research 1998 26(1):362-367
0305-1048
1362-4962
9399875
http://hdl.handle.net/10033/8505
147251
en_US
oai:repository.helmholtz-hzi.de:10033/85062019-08-30T11:32:38Zcom_10033_620636col_10033_620638
Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms.
Heinemeyer, T
Chen, X
Karas, H
Kel, A E
Kel, O V
Liebich, I
Meinhardt, T
Reuter, I
Schacherer, F
Wingender, E
2007-02-19
1999-01-01
2007-02-19
1999-01-01
Nucleic Acids Research 1999 27(1):318-322
0305-1048
1362-4962
9847216
http://hdl.handle.net/10033/8506
148171
en_US
oai:repository.helmholtz-hzi.de:10033/85222019-08-30T11:32:38Zcom_10033_620636col_10033_620638
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation.
Wingender, E
Kel, A E
Kel, O V
Karas, H
Heinemeyer, T
Dietze, P
Knüppel, R
Romaschenko, A G
Kolchanov, N A
2007-02-19
1997-01-01
2007-02-19
1997-01-01
Nucleic Acids Research 1997 25(1):265-268
0305-1048
1362-4962
9016550
http://hdl.handle.net/10033/8522
146363
en_US
oai:repository.helmholtz-hzi.de:10033/86122019-08-30T11:32:39Zcom_10033_620636col_10033_620638
In Silico Prediction of Scaffold/Matrix Attachment Regions in Large Genomic Sequences
Frisch, Matthias
Frech, Kornelie
Klingenhoff, Andreas
Cartharius, Kerstin
Liebich, Ines
Werner, Thomas
2007-02-20
2002-02
2007-02-20
2002-02
Genome Research 2002 12(2):349-354
1088-9051
11827955
10.1101/gr.206602
http://hdl.handle.net/10033/8612
155272
en_US
Copyright © 2002, Cold Spring Harbor Laboratory Press
Cold Spring Harbor Laboratory Press
oai:repository.helmholtz-hzi.de:10033/85372019-08-30T11:32:15Zcom_10033_620636col_10033_620638
PRODORIC: prokaryotic database of gene regulation
Münch, Richard
Hiller, Karsten
Barg, Heiko
Heldt, Dana
Linz, Simone
Wingender, Edgar
Jahn, Dieter
2007-02-19
2003-01-01
2007-02-19
2003-01-01
Nucleic Acids Research 2003 31(1):266-269
0305-1048
1362-4962
12519998
http://hdl.handle.net/10033/8537
165484
en_US
http://www.nar.oupjournals.org/content/vol31/issue1//
Copyright © 2003 Oxford University Press
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/85382019-08-30T11:31:48Zcom_10033_620636col_10033_620638
TRANSPATH®: an integrated database on signal transduction and a tool for array analysis
Krull, Mathias
Voss, Nico
Choi, Claudia
Pistor, Susanne
Potapov, Anatolij
Wingender, Edgar
2007-02-19
2003-01-01
2007-02-19
2003-01-01
Nucleic Acids Research 2003 31(1):97-100
0305-1048
1362-4962
12519957
http://hdl.handle.net/10033/8538
165536
en_US
http://www.nar.oupjournals.org/content/vol31/issue1//
Copyright © 2003 Oxford University Press
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/85432019-08-30T11:31:48Zcom_10033_620636col_10033_620638
TRANSFAC®: transcriptional regulation, from patterns to profiles
Matys, V.
Fricke, E.
Geffers, Robert
Gößling, E.
Haubrock, M.
Hehl, R.
Hornischer, K.
Karas, D.
Kel, A. E.
Kel-Margoulis, O. V.
Kloos, D.-U.
Land, S.
Lewicki-Potapov, B.
Michael, H.
Münch, R.
Reuter, I.
Rotert, S.
Saxel, H.
Scheer, M.
Thiele, S.
Wingender, E.
2007-02-19
2003-01-01
2007-02-19
2003-01-01
Nucleic Acids Research 2003 31(1):374-378
0305-1048
1362-4962
12520026
http://hdl.handle.net/10033/8543
165555
en_US
http://www.nar.oupjournals.org/content/vol31/issue1//
Copyright © 2003 Oxford University Press
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/86752019-08-30T11:31:49Zcom_10033_620636col_10033_620638
Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways
Sun, Jibin
Daniel, Rolf
Wagner-Döbler, Irene
Zeng, An-Ping
Background Quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. Recently, it has been proposed that autoinducer-2 (AI-2), a furanosyl borate diester derived from the recycling of S-adenosyl-homocysteine (SAH) to homocysteine, serves as a universal signal for interspecies communication. Results In this study, 138 completed genomes were examined for the genes involved in the synthesis and detection of AI-2. Except for some symbionts and parasites, all organisms have a pathway to recycle SAH, either using a two-step enzymatic conversion by the Pfs and LuxS enzymes or a one-step conversion using SAH-hydrolase (SahH). 51 organisms including most Gamma-, Beta-, and Epsilonproteobacteria, and Firmicutes possess the Pfs-LuxS pathway, while Archaea, Eukarya, Alphaproteobacteria, Actinobacteria and Cyanobacteria prefer the SahH pathway. In all 138 organisms, only the three Vibrio strains had strong, bidirectional matches to the periplasmic AI-2 binding protein LuxP and the central signal relay protein LuxU. The initial two-component sensor kinase protein LuxQ, and the terminal response regulator luxO are found in most Proteobacteria, as well as in some Firmicutes, often in several copies. Conclusions The genomic analysis indicates that the LuxS enzyme required for AI-2 synthesis is widespread in bacteria, while the periplasmic binding protein LuxP is only present in Vibrio strains. Thus, other organisms may either use components different from the AI-2 signal transduction system of Vibrio strains to sense the signal of AI-2, or they do not have such a quorum sensing system at all.
2007-02-20
2004-09-29
2007-02-20
2004-09-29
BMC Evolutionary Biology 2004 4:36
1471-2148
15456522
10.1186/1471-2148-4-36
http://hdl.handle.net/10033/8675
524169
en_US
http://www.biomedcentral.com/1471-2148/4/36
http://creativecommons.org/licenses/by/2.0
Copyright © 2004 Sun et al; licensee BioMed Central Ltd.
BioMed Central
oai:repository.helmholtz-hzi.de:10033/86792019-08-30T11:32:12Zcom_10033_620636col_10033_620638
Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs
Wiemann, Stefan
Weil, Bernd
Wellenreuther, Ruth
Gassenhuber, Johannes
Glassl, Sabine
Ansorge, Wilhelm
Böcher, Michael
Blöcker, Helmut
Bauersachs, Stefan
Blum, Helmut
Lauber, Jürgen
Düsterhöft, Andreas
Beyer, Andreas
Köhrer, Karl
Strack, Normann
Mewes, Hans-Werner
Ottenwälder, Birgit
Obermaier, Brigitte
Tampe, Jens
Heubner, Dagmar
Wambutt, Rolf
Korn, Bernhard
Klein, Michaela
Poustka, Annemarie
2007-02-21
2001-03
2007-02-21
2001-03
Genome Research 2001 11(3):422-435
1088-9051
11230166
10.1101/gr.154701
http://hdl.handle.net/10033/8679
311072
en_US
Copyright © 2001, Cold Spring Harbor Laboratory Press
Cold Spring Harbor Laboratory Press
oai:repository.helmholtz-hzi.de:10033/86852019-08-30T11:24:26Zcom_10033_620636col_10033_620638
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
Ma, Hong-Wu
Kumar, Bharani
Ditges, Uta
Gunzer, Florian
Buer, Jan
Zeng, An-Ping
2007-02-21
2004
2007-02-21
2004
Nucleic Acids Research 2004 32(22):6643-6649
0305-1048
1362-4962
15604458
10.1093/nar/gkh1009
http://hdl.handle.net/10033/8685
545451
en_US
http://www.nar.oupjournals.org/content/vol32/issue22//
Copyright © 2004 Oxford University Press
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/86992019-08-30T11:31:49Zcom_10033_620636col_10033_620638
Gin-mediated site-specific recombination in bacteriophage Mu DNA: overproduction of the protein and inversion in vitro
Mertens, Gabriele
Hoffmann, Andrea
Blöcker, Helmut
Frank, Ronald
Kahmann, Regine
Images
2007-02-21
1984-10
2007-02-21
1984-10
The EMBO Journal 1984 3(10):2415-2421
0261-4189
1460-2075
16453561
http://hdl.handle.net/10033/8699
557702
en_US
© IRL Press Limited, Oxford, England.
oai:repository.helmholtz-hzi.de:10033/87062019-08-30T11:24:27Zcom_10033_620636col_10033_620638
S434F in NrdE Generates the Thermosensitive Phenotype of Corynebacterium ammoniagenes CH31 and Enhances Thermolability by Increasing the Surface Hydrophobicity of the NrdE(Ts) Protein
Elhariry, Hesham M.
Meens, Jochen
Stehr, Matthias
Auling, Georg
2007-02-21
2005-09
2007-02-21
2005-09
Applied and Environmental Microbiology 2005 71(9):5582-5586
0099-2240
1098-5336
10.1128/AEM.71.9.5582-5586.2005
http://hdl.handle.net/10033/8706
1214679
en_US
Copyright © 2005, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/87682019-08-30T11:34:20Zcom_10033_620636col_10033_620665
Effects of Type I Interferons on Friend Retrovirus Infection
Gerlach, Nicole
Schimmer, Simone
Weiss, Siegfried
Kalinke, Ulrich
Dittmer, Ulf
2007-02-22
2006-04
2007-02-22
2006-04
Journal of Virology 2006 80(7):3438-3444
0022-538X
1098-5514
16537611
10.1128/JVI.80.7.3438-3444.2006
http://hdl.handle.net/10033/8768
1440373
en_US
Copyright © 2006, American Society for Microbiology
American Society for Microbiology
oai:repository.helmholtz-hzi.de:10033/142012019-08-30T11:35:39Zcom_10033_620636col_10033_620638
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms.
Van den Bulcke, Tim
Van Leemput, Koenraad
Naudts, Bart
van Remortel, Piet
Ma, Hongwu
Verschoren, Alain
De Moor, Bart
Marchal, Kathleen
BACKGROUND: The development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark data sets for which the underlying network is known. Since experimental data sets of the appropriate size and design are usually not available, there is a clear need to generate well-characterized synthetic data sets that allow thorough testing of learning algorithms in a fast and reproducible manner. RESULTS: In this paper we describe a network generator that creates synthetic transcriptional regulatory networks and produces simulated gene expression data that approximates experimental data. Network topologies are generated by selecting subnetworks from previously described regulatory networks. Interaction kinetics are modeled by equations based on Michaelis-Menten and Hill kinetics. Our results show that the statistical properties of these topologies more closely approximate those of genuine biological networks than do those of different types of random graph models. Several user-definable parameters adjust the complexity of the resulting data set with respect to the structure learning algorithms. CONCLUSION: This network generation technique offers a valid alternative to existing methods. The topological characteristics of the generated networks more closely resemble the characteristics of real transcriptional networks. Simulation of the network scales well to large networks. The generator models different types of biological interactions and produces biologically plausible synthetic gene expression data.
2007-10-23
2007-10-23
2006
Article
BMC Bioinformatics 2006, 7:43
1471-2105
16438721
10.1186/1471-2105-7-43
http://hdl.handle.net/10033/14201
en
oai:repository.helmholtz-hzi.de:10033/145552019-08-30T11:36:05Zcom_10033_620636col_10033_620638
Immune responses induced in cattle by vaccination with a recombinant adenovirus expressing Mycobacterial antigen 85A and Mycobacterium bovis BCG.
Vordermeier, H Martin
Huygen, Kris
Singh, Mahavir
Hewinson, R Glyn
Xing, Zhou
Cattle were vaccinated with an adenovirus expressing the mycobacterial antigen 85A (rAd85A), with Mycobacterium bovis BCG followed by rAd85A heterologous boosting, or with rAd85A followed by BCG boosting. BCG/rAd85A resulted in the highest direct gamma interferon responses. Cultured enzyme-linked immunospot assay analysis demonstrated that memory responses were induced by all three protocols but were strongest after BCG/rAd85A and rAd85A/BCG vaccination.
2007-11-13
2007-11-13
2006-02-01
Article
Infect. Immun. 2006, 74(2):1416-8
0019-9567
16428796
10.1128/IAI.74.2.1416-1418.2006
http://hdl.handle.net/10033/14555
en
oai:repository.helmholtz-hzi.de:10033/145752019-08-30T11:35:39Zcom_10033_620636col_10033_620638
Intranasal IFNgamma extends passive IgA antibody protection of mice against Mycobacterium tuberculosis lung infection.
Reljic, R
Clark, S O
Williams, A
Falero-Diaz, G
Singh, M
Challacombe, S
Marsh, P D
Ivanyi, J
Intranasal inoculation of mice with monoclonal IgA against the alpha-crystallin (acr1) antigen can diminish the tuberculous infection in the lungs. As this effect has been observed only over a short-term, we investigated if it could be extended by inoculation of IFNgamma 3 days before infection, and further co-inoculations with IgA, at 2 h before and 2 and 7 days after aerosol infection with Mycobacterium tuberculosis H37Rv. This treatment reduced the lung infection at 4 weeks more than either IgA or IFNgamma alone (i.e. 17-fold, from 4.2 x 10(7) to 2.5 x 10(6) CFU, P = 0.006), accompanied also by lower granulomatous infiltration of the lungs. IFNgamma added prior to infection of mouse peritoneal macrophages with IgA-opsonized bacilli resulted in a synergistic increase of nitric oxide and TNFalpha production and a 2-3 fold decrease in bacterial counts. Our improved results suggest, that combined treatment with IFNgamma and IgA could be developed towards prophylactic treatment of AIDS patients, or as an adjunct to chemotherapy.
2007-11-15
2007-11-15
2006-03-01
Article
Clin. Exp. Immunol. 2006, 143(3):467-73
0009-9104
16487246
10.1111/j.1365-2249.2006.03012.x
http://hdl.handle.net/10033/14575
en
oai:repository.helmholtz-hzi.de:10033/153722019-08-30T11:36:32Zcom_10033_620636col_10033_620638
The mycobacterial thioredoxin peroxidase can act as a one-cysteine peroxiredoxin.
Trujillo, Madia
Mauri, PierLuigi
Benazzi, Louise
Comini, Marcelo
De Palma, Antonella
Flohé, Leopold
Radi, Rafael
Stehr, Matthias
Singh, Mahavir
Ursini, Fulvio
Jaeger, Timo
Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, UY-11800 Montevideo, Uruguay.
Thioredoxin peroxidase (TPx) has been reported to dominate the defense against H(2)O(2), other hydroperoxides, and peroxynitrite at the expense of thioredoxin (Trx) B and C in Mycobacterium tuberculosis (Mt). By homology, the enzyme has been classified as an atypical 2-C-peroxiredoxin (Prx), with Cys(60) as the "peroxidatic" cysteine (C(P)) forming a complex catalytic center with Cys(93) as the "resolving" cysteine (C(R)). Site-directed mutagenesis confirms Cys(60) to be C(P) and Cys(80) to be catalytically irrelevant. Replacing Cys(93) with serine leads to fast inactivation as seen by conventional activity determination, which is associated with oxidation of Cys(60) to a sulfinic acid derivative. However, in comparative stopped-flow analysis, WT-MtTPx and MtTPx C93S reduce peroxynitrite and react with TrxB and -C similarly fast. Reduction of pre-oxidized WT-MtTPx and MtTPx C93S by MtTrxB is demonstrated by monitoring the redox-dependent tryptophan fluorescence of MtTrxB. Furthermore, MtTPx C93S remains stable for 10 min at a morpholinosydnonimine hydrochloride-generated low flux of peroxynitrite and excess MtTrxB in a dihydrorhodamine oxidation model. Liquid chromatography-tandem mass spectrometry analysis revealed disulfide bridges between Cys(60) and Cys(93) and between Cys(60) and Cys(80) in oxidized WT-MtTPx. Reaction of pre-oxidized WT-MtTPx and MtTPx C93S with MtTrxB C34S or MtTrxC C40S yielded dead-end intermediates in which the Trx mutants are preferentially linked via disulfide bonds to Cys(60) and never to Cys(93) of the TPx. It is concluded that neither Cys(80) nor Cys(93) is required for the catalytic cycle of the peroxidase. Instead, MtTPx can react as a 1-C-Prx with Cys(60) being the site of attack for both the oxidizing and the reducing substrate. The role of Cys(93) is likely to conserve the oxidation equivalents of the sulfenic acid state of C(P) as a disulfide bond to prevent overoxidation of Cys(60) under a restricted supply of reducing substrate.
2007-12-18
2007-12-18
2006-07-21
Article
The mycobacterial thioredoxin peroxidase can act as a one-cysteine peroxiredoxin. 2006, 281 (29):20555-66 J. Biol. Chem.
0021-9258
16682410
10.1074/jbc.M601008200
http://hdl.handle.net/10033/15372
The Journal of biological chemistry
en
oai:repository.helmholtz-hzi.de:10033/158682019-08-30T11:25:11Zcom_10033_620636col_10033_620638
A human-horse comparative map based on equine BAC end sequences.
Leeb, Tosso
Vogl, Claus
Zhu, Baoli
de Jong, Pieter J
Binns, Matthew M
Chowdhary, Bhanu P
Scharfe, Maren
Jarek, Michael
Nordsiek, Gabriele
Schrader, Frank
Blöcker, Helmut
Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany. Tosso.Leeb@itz.unibe.ch
In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E
2008-01-09
2008-01-09
2006-06
Article
A human-horse comparative map based on equine BAC end sequences. 2006, 87 (6):772-6 Genomics
0888-7543
16603334
10.1016/j.ygeno.2006.03.002
http://hdl.handle.net/10033/15868
Genomics
en
oai:repository.helmholtz-hzi.de:10033/177552019-08-30T11:26:13Zcom_10033_620636col_10033_620665
NK cell activation in visceral leishmaniasis requires TLR9, myeloid DCs, and IL-12, but is independent of plasmacytoid DCs.
Schleicher, Ulrike
Liese, Jan
Knippertz, Ilka
Kurzmann, Claudia
Hesse, Andrea
Heit, Antje
Fischer, Jens A A
Weiss, Siegfried
Kalinke, Ulrich
Kunz, Stefanie
Bogdan, Christian
Institute of Medical Microbiology and Hygiene, University of Freiburg, D-79104 Freiburg, Germany.
Natural killer (NK) cells are sentinel components of the innate response to pathogens, but the cell types, pathogen recognition receptors, and cytokines required for their activation in vivo are poorly defined. Here, we investigated the role of plasmacytoid dendritic cells (pDCs), myeloid DCs (mDCs), Toll-like receptors (TLRs), and of NK cell stimulatory cytokines for the induction of an NK cell response to the protozoan parasite Leishmania infantum. In vitro, pDCs did not endocytose Leishmania promastigotes but nevertheless released interferon (IFN)-alpha/beta and interleukin (IL)-12 in a TLR9-dependent manner. mDCs rapidly internalized Leishmania and, in the presence of TLR9, produced IL-12, but not IFN-alpha/beta. Depletion of pDCs did not impair the activation of NK cells in L. infantum-infected mice. In contrast, L. infantum-induced NK cell cytotoxicity and IFN-gamma production were abolished in mDC-depleted mice. The same phenotype was observed in TLR9(-/-) mice, which lacked IL-12 expression by mDCs, and in IL-12(-/-) mice, whereas IFN-alpha/beta receptor(-/-) mice showed only a minor reduction of NK cell IFN-gamma expression. This study provides the first direct evidence that mDCs are essential for eliciting NK cell cytotoxicity and IFN-gamma release in vivo and demonstrates that TLR9, mDCs, and IL-12 are functionally linked to the activation of NK cells in visceral leishmaniasis.
2008-02-08
2008-02-08
2007-04-16
Article
NK cell activation in visceral leishmaniasis requires TLR9, myeloid DCs, and IL-12, but is independent of plasmacytoid DCs. 2007, 204 (4):893-906 J. Exp. Med.
0022-1007
17389237
10.1084/jem.20061293
http://hdl.handle.net/10033/17755
The Journal of experimental medicine
en
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2118560
oai:repository.helmholtz-hzi.de:10033/188722019-08-30T11:36:04Zcom_10033_620636col_10033_620638
Antibodies against C-reactive protein cross-react with 60-kilodalton heat shock proteins.
Udvarnoki, Katalin
Cervenak, László
Uray, Katalin
Hudecz, Ferenc
Kacskovics, Imre
Spallek, Ralf
Singh, Mahavir
Füst, George
Prohászka, Zoltán
Third Department of Medicine, Semmelweis University, H-1125 Budapest, Kútvölgyi st. 4, Hungary.
C-reactive protein (CRP) is an acute-phase reactant frequently used in histochemistry as a marker of ongoing inflammation. Furthermore, CRP is a powerful biomarker for the prediction of coronary artery disease risk. Heat-shock protein 60 (Hsp60) and CRP are complement-activating molecules, and the effect of their interactions on the regulation of complement activation was studied. However, during the first experiments, we learned that polyclonal anti-CRP antibodies cross-react with Hsp60. Therefore, the aim of our present study was to analyze the cross-reactivity of anti-CRP antibodies (Ab) with Hsp60 in solid-phase enzyme immune assays, in epitope studies using a series of overlapping synthetic peptides, and in Ouchterlony analyses. We found that three different commercial rabbit polyclonal antibodies and two monoclonal (9C9 and CRP-8) anti-CRP antibodies specifically recognize recombinant human Hsp60 and recombinant Mycobacterium tuberculosis Hsp65, respectively. Hsp60 was found to inhibit the binding of anti-CRP polyclonal Ab to Hsp60. Six epitope regions of Hsp60 were recognized by the anti-CRP antibodies, and one region (amino acids [AA] 218 to 232) was recognized by monoclonal antibodies CRP-8 and 9C9. This epitope region of Hsp60 displays 26.6% amino acid identity to CRP AA region 77 to 90. These data suggest that the B-cell epitopes shared between CRP and Hsp60 give rise to a true mimicry-based cross-reaction and the induction of cross-reactive antibodies. Our study underlines the importance of thorough study design and careful interpretation of results while using polyclonal anti-CRP antibodies for histochemistry, especially at low dilutions. Furthermore, analytical interference with Hsp60 in CRP assays should also be tested.
2008-02-21
2008-02-21
2007-04
Article
Antibodies against C-reactive protein cross-react with 60-kilodalton heat shock proteins. 2007, 14 (4):335-41 Clin. Vaccine Immunol.
1556-6811
17301219
10.1128/CVI.00155-06
http://hdl.handle.net/10033/18872
Clinical and vaccine immunology : CVI
en
oai:repository.helmholtz-hzi.de:10033/197752019-08-30T11:37:44Zcom_10033_620636col_10033_620665
Synergistic and differential modulation of immune responses by Hsp60 and lipopolysaccharide.
Osterloh, Anke
Kalinke, Ulrich
Weiss, Siegfried
Fleischer, Bernhard
Breloer, Minka
Department of Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany. osterloh@bni.uni-hamburg.de
Activation of professional antigen-presenting cells (APC) is a crucial step in the initiation of an efficient immune response. In this study we show that Hsp60 mediates immune stimulation by different mechanisms, dependent and independent of lipopolysaccharide (LPS). We have demonstrated earlier that both, Hsp60 and LPS, increase antigen-specific interferon (IFN) gamma release in T cells. Here we show that in contrast to LPS Hsp60 induces IFNalpha production in professional APC. Neutralization of IFNalpha as well as the absence of functional IFNalphabeta receptor on APC and T cells interfered with Hsp60-mediated IFNgamma secretion in antigen-dependent T cell activation, strongly suggesting that IFNalpha represents one factor contributing to Hsp60-specific immune stimulation. On the other hand, we show that Hsp60 bound to the cell surface of APC colocalizes with the LPS co-receptor CD14 and LPS binding sites. Hsp60 specifically binds bacterial LPS and both molecules synergistically enhanced IL-12p40 production in APC and IFNgamma release in antigen-dependent T cell activation. This effect was Hsp60-specific and dependent on LPS-binding by Hsp60. Furthermore, we show that Hsp60 exclusively binds to macrophages and DC but not to T or B lymphocytes and that both, T cell stimulation by Hsp60 as well as Hsp60/LPS complexes, strictly depends on the presence of professional APC and is not mediated by B cells. Taken together, our data support an extension of the concept of Hsp60 as an endogenous danger signal: besides its function as a classical danger signal indicating unplanned tissue destruction to the innate immune system, in the incident of bacterial infection extracellular Hsp60 may bind LPS and facilitate microbe recognition by lowering the threshold of pathogen-associated molecular pattern (PAMP) detection and enhancing Toll-like receptor (TLR) signaling.
2008-03-05
2008-03-05
2007-02-16
Article
Synergistic and differential modulation of immune responses by Hsp60 and lipopolysaccharide. 2007, 282 (7):4669-80 J. Biol. Chem.
0021-9258
17164250
10.1074/jbc.M608666200
http://hdl.handle.net/10033/19775
The Journal of biological chemistry
en
oai:repository.helmholtz-hzi.de:10033/223132019-08-30T11:37:44Zcom_10033_620636col_10033_620638
Evaluation of latent tuberculosis infection in patients with inflammatory arthropathies before treatment with TNF-alpha blocking drugs using a novel flow-cytometric interferon-gamma release assay.
Dinser, R
Fousse, M
Sester, U
Albrecht, K
Singh, M
Köhler, H
Müller-Ladner, U
Sester, M
Department of Internal Medicine and Rheumatology, Justus-Liebig University of Giessen, Kerckhoff Clinic, Benekestrasse 2-8, D-61231 Bad Nauheim, Germany. r.dinser@kerckhoff-klinik.de
OBJECTIVE: To compare the efficacy of the conventional skin test and a novel flow cytometric whole blood assay in the diagnosis of latent tuberculosis infection (LTBI) in patients with rheumatological diseases evaluated for treatment with TNF-alpha-blocking agents. METHODS: Prospective study of 97 consecutively enrolled patients, who were assessed for the presence of LTBI through clinical history, Mendel-Mantoux skin testing and chest X-ray. In addition, T-cell reactivity towards tuberculin (PPD, purified protein derivative) and the Mycobacterium tuberculosis-specific proteins ESAT-6 and CFP-10 was determined ex vivo using a flow cytometric whole blood assay. RESULTS: After standard screening, 15% of patients receiving TNF-alpha-blocking therapy were pretreated with isoniazide (INH), another 5% of patients did not receive TNF-alpha-blocking therapy because of LTBI. PPD-reactivity in the skin was observed in 14% of patients compared with 39% with the whole blood test. Analysis of the M. tuberculosis-specific response to ESAT-6 and CFP-10 revealed positive results in 16% of patients. Using a decision tree incorporating history, chest X-ray and either skin-test or ESAT-6/CFP-10 results, 18 or 22% of the patients, respectively, were classified as latently infected with M. tuberculosis. Four patients treated with INH because of a positive skin reaction did not show reactivity to ESAT-6/CFP-10 in the whole blood assays. Another six patients not pretreated with INH because of negative skin tests would have received INH, had the results of the whole blood assay been taken into account. CONCLUSION: The Mendel-Mantoux skin test has a low sensitivity and specificity for the diagnosis of LTBI in this cohort of patients, potentially resulting in both over- and under-treatment with prophylactic INH when compared with the flow cytometric analysis of whole blood T-cell reactivity to proteins specific to M. tuberculosis. Use of T-cell based in vitro tests may help to refine diagnostic testing for LTBI.
2008-04-04
2008-04-04
2008-02
Article
Evaluation of latent tuberculosis infection in patients with inflammatory arthropathies before treatment with TNF-alpha blocking drugs using a novel flow-cytometric interferon-gamma release assay. 2008, 47 (2):212-8 Rheumatology (Oxford)
1462-0332
18208824
10.1093/rheumatology/kem351
http://hdl.handle.net/10033/22313
Rheumatology (Oxford, England)
en
oai:repository.helmholtz-hzi.de:10033/245132019-08-30T11:25:43Zcom_10033_620636col_10033_620638
Structural insights into catalysis and inhibition of O-acetylserine sulfhydrylase from Mycobacterium tuberculosis. Crystal structures of the enzyme alpha-aminoacrylate intermediate and an enzyme-inhibitor complex.
Schnell, Robert
Oehlmann, Wulf
Singh, Mahavir
Schneider, Gunter
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
Cysteine biosynthetic genes are up-regulated in the persistent phase of Mycobacterium tuberculosis, and the corresponding enzymes are therefore of interest as potential targets for novel antibacterial agents. cysK1 is one of these genes and has been annotated as coding for an O-acetylserine sulfhydrylase. Recombinant CysK1 is a pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the conversion of O-acetylserine to cysteine. The crystal structure of the enzyme was determined to 1.8A resolution. CysK1 belongs to the family of fold type II PLP enzymes and is similar in structure to other O-acetylserine sulfhydrylases. We were able to trap the alpha-aminoacrylate reaction intermediate and determine its structure by cryocrystallography. Formation of the aminoacrylate complex is accompanied by a domain rotation resulting in active site closure. The aminoacrylate moiety is bound in the active site via the covalent linkage to the PLP cofactor and by hydrogen bonds of its carboxyl group to several enzyme residues. The catalytic lysine residue is positioned such that it can protonate the Calpha-carbon atom of the aminoacrylate only from the si-face, resulting in the formation of L-cysteine. CysK1 is competitively inhibited by a four-residue peptide derived from the C-terminal of serine acetyl transferase. The crystallographic analysis reveals that the peptide binds to the enzyme active site, suggesting that CysK1 forms an bi-enzyme complex with serine acetyl transferase, in a similar manner to other bacterial and plant O-acetylserine sulfhydrylases. The structure of the enzyme-peptide complex provides a framework for the design of strong binding inhibitors.
2008-04-30
2008-04-30
2007-08-10
Article
Structural insights into catalysis and inhibition of O-acetylserine sulfhydrylase from Mycobacterium tuberculosis. Crystal structures of the enzyme alpha-aminoacrylate intermediate and an enzyme-inhibitor complex. 2007, 282 (32):23473-81 J. Biol. Chem.
0021-9258
17567578
10.1074/jbc.M703518200
http://hdl.handle.net/10033/24513
The Journal of biological chemistry
en
oai:repository.helmholtz-hzi.de:10033/282522019-08-30T11:25:43Zcom_10033_620636col_10033_620665
Listeria monocytogenes desensitizes immune cells to subsequent Ca2+ signaling via listeriolysin O-induced depletion of intracellular Ca2+ stores.
Gekara, Nelson O
Groebe, Lothar
Viegas, Nuno
Weiss, Siegfried
Department of Molecular Immunology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany. nelson.gekara@helmholtz-hzi.de
Listeriolysin O (LLO), the pore-forming toxin of Listeria monocytogenes, is a prototype of the cholesterol-dependent cytolysins (CDCs) secreted by several pathogenic and nonpathogenic gram-positive bacteria. In addition to mediating the escape of the bacterium into the cytosol, this toxin is generally believed to be a central player in host-pathogen interactions during L. monocytogenes infection. LLO triggers the influx of Ca(2+) into host cells as well as the release of Ca(2+) from intracellular stores. Thus, many of the cellular responses induced by LLO are related to calcium signaling. Interestingly, in this study, we report that prolonged exposure to LLO desensitizes cells to Ca(2+) mobilization upon subsequent stimulations with LLO. Cells preexposed to LLO-positive L. monocytogenes but not to the LLO-deficient Deltahly mutant were found to be highly refractory to Ca(2+) induction in response to receptor-mediated stimulation. Such cells also exhibited diminished Ca(2+) signals in response to stimulation with LLO and thapsigargin. The presented results suggest that this phenomenon is due to the depletion of intracellular Ca(2+) stores. The ability of LLO to desensitize immune cells provides a significant hint about the possible role played by CDCs in the evasion of the immune system by bacterial pathogens.
2008-05-27
2008-05-27
2008-02
Article
Listeria monocytogenes desensitizes immune cells to subsequent Ca2+ signaling via listeriolysin O-induced depletion of intracellular Ca2+ stores. 2008, 76 (2):857-62 Infect. Immun.
1098-5522
18056478
10.1128/IAI.00622-07
http://hdl.handle.net/10033/28252
Infection and immunity
en
oai:repository.helmholtz-hzi.de:10033/303222019-08-30T11:29:47Zcom_10033_620636col_10033_620665
Liposome-encapsulated antigens induce a protective CTL response against Listeria monocytogenes independent of CD4+ T cell help.
Grenningloh, R
Darj, A
Bauer, H
zur Lage, S
Chakraborty, T
Jacobs, T
Weiss, S
Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Protection against intracellular pathogens is usually mediated by cytotoxic T lymphocytes (CTL). Induction of a protective CTL response for vaccination purposes has proven difficult because of the limited access of protein antigens or attenuated pathogens to the MHC class I presentation pathway. We show here that pH-sensitive PE/CHEMS liposomes can be used as a vehicle to efficiently deliver intact proteins for presentation by MHC class I. Mice immunized with listerial proteins encapsulated in such liposomes launched a strong CTL response and were protected against a subsequent challenge with L. monocytogenes. Remarkably, the CTL response was induced independently of detectable CD4(+) T cell help.
2008-06-23
2008-06-23
2008-06
Article
Liposome-encapsulated antigens induce a protective CTL response against Listeria monocytogenes independent of CD4+ T cell help. 2008, 67 (6):594-602 Scand. J. Immunol.
1365-3083
18433404
10.1111/j.1365-3083.2008.02112.x
http://hdl.handle.net/10033/30322
Scandinavian journal of immunology
en
oai:repository.helmholtz-hzi.de:10033/483732019-08-30T11:35:39Zcom_10033_620636col_10033_620665
Mast cells initiate early anti-Listeria host defences.
Gekara, Nelson O
Weiss, Siegfried
Helmholtz Centre for Infection Research, Department of Molecular Immunology, Inhoffenstrasse 7, 38124 Braunschweig, Germany. Nelson.Gekara@helmholtz-hzi.de
The Gram-positive bacterium Listeria monocytogenes (L. m.) is the aetiological agent of listeriosis. The early phase listeriosis is characterized by strong innate host responses that play a major role in bacterial clearance. This is emphasized by the fact that mice deficient in T and B cells have a remarkable ability to control infection. Mast cells, among the principal effectors of innate immunity, have largely been studied in the context of hyper-reactive conditions such as allergy and autoimmune diseases. In the present study, we evaluated the significance of mast cells during the early phase of listeriosis. Compared with controls, mice depleted of mast cells showed hundred-fold higher bacterial burden in spleen and liver and were significantly impaired in neutrophil mobilization. Although L. m. interacts with and triggers mast cell degranulation, bacteria were hardly found within such cells. Mainly neutrophils and macrophages phagozytosed L. m. Thus, mast cells control infection not via direct bacterial uptake, but by initiating neutrophils influx to the site of infection. We show that this is initiated by pre-synthesized TNF-alpha, rapidly secreted by mast cell upon activation by L. m. We also show that upon recruitment, neutrophils also become activated and additionally secrete TNF-alpha thus amplifying the anti-L. m. inflammatory response.
2009-02-03
2009-02-03
2008-01
Article
Mast cells initiate early anti-Listeria host defences. 2008, 10 (1):225-36 Cell. Microbiol.
1462-5822
17714516
10.1111/j.1462-5822.2007.01033.x
http://hdl.handle.net/10033/48373
Cellular microbiology
en
oai:repository.helmholtz-hzi.de:10033/711632019-08-30T11:33:05Zcom_10033_620636col_10033_620638
Three-dimensional structures of apo- and holo-L-alanine dehydrogenase from Mycobacterium tuberculosis reveal conformational changes upon coenzyme binding.
Agren, Daniel
Stehr, Matthias
Berthold, Catrine L
Kapoor, Shobhna
Oehlmann, Wulf
Singh, Mahavir
Schneider, Gunter
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
L-alanine dehydrogenase from Mycobacterium tuberculosis catalyzes the NADH-dependent reversible conversion of pyruvate and ammonia to L-alanine. Expression of the gene coding for this enzyme is up-regulated in the persistent phase of the organism, and alanine dehydrogenase is therefore a potential target for pathogen control by antibacterial compounds. We have determined the crystal structures of the apo- and holo-forms of the enzyme to 2.3 and 2.0 A resolution, respectively. The enzyme forms a hexamer of identical subunits, with the NAD-binding domains building up the core of the molecule and the substrate-binding domains located at the apical positions of the hexamer. Coenzyme binding stabilizes a closed conformation where the substrate-binding domains are rotated by about 16 degrees toward the dinucleotide-binding domains, compared to the open structure of the apo-enzyme. In the structure of the abortive ternary complex with NAD+ and pyruvate, the substrates are suitably positioned for hydride transfer between the nicotinamide ring and the C2 carbon atom of the substrate. The approach of the nucleophiles water and ammonia to pyruvate or the reaction intermediate iminopyruvate, respectively, is, however, only possible through conformational changes that make the substrate binding site more accessible. The crystal structures identified the conserved active-site residues His96 and Asp270 as potential acid/base catalysts in the reaction. Amino acid replacements of these residues by site-directed mutagenesis led to inactive mutants, further emphasizing their essential roles in the enzymatic reaction mechanism.
2009-06-22
2009-06-22
2008-04-04
Article
Three-dimensional structures of apo- and holo-L-alanine dehydrogenase from Mycobacterium tuberculosis reveal conformational changes upon coenzyme binding. 2008, 377 (4):1161-73 J. Mol. Biol.
1089-8638
18304579
10.1016/j.jmb.2008.01.091
http://hdl.handle.net/10033/71163
Journal of molecular biology
en
oai:repository.helmholtz-hzi.de:10033/909552019-08-30T11:36:05Zcom_10033_620636col_10033_620665
Strong interferon-inducing capacity of a highly virulent variant of influenza A virus strain PR8 with deletions in the NS1 gene.
Kochs, Georg
Martínez-Sobrido, Luis
Lienenklaus, Stefan
Weiss, Siegfried
García-Sastre, Adolfo
Staeheli, Peter
Department of Virology, University of Freiburg, D-79008 Freiburg, Germany. georg.kochs@uniklinik-freiburg.de
Influenza viruses lacking the interferon (IFN)-antagonistic non-structural NS1 protein are strongly attenuated. Here, we show that mutants of a highly virulent variant of A/PR/8/34 (H1N1) carrying either a complete deletion or C-terminal truncations of NS1 were far more potent inducers of IFN in infected mice than NS1 mutants derived from standard A/PR/8/34. Efficient induction of IFN correlated with successful initial virus replication in mouse lungs, indicating that the IFN response is boosted by enhanced viral activity. As the new NS1 mutants can be handled in standard biosafety laboratories, they represent convenient novel tools for studying virus-induced IFN expression in vivo.
2010-02-01
2010-02-01
2009-12
Article
Strong interferon-inducing capacity of a highly virulent variant of influenza A virus strain PR8 with deletions in the NS1 gene. 2009, 90 (Pt 12):2990-4 J. Gen. Virol.
1465-2099
19726611
10.1099/vir.0.015727-0
http://hdl.handle.net/10033/90955
The Journal of general virology
en
oai:repository.helmholtz-hzi.de:10033/929202019-08-30T11:33:05Zcom_10033_620636col_10033_620638
The mycolyltransferase 85A, a putative drug target of Mycobacterium tuberculosis: development of a novel assay and quantification of glycolipid-status of the mycobacterial cell wall.
Elamin, Ayssar A
Stehr, Matthias
Oehlmann, Wulf
Singh, Mahavir
Department of Genome Analysis, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.
The enzymes of the antigen 85 complex (Ag85A, B, and C) possess mycolyltransferase activity and catalyze the synthesis of the most abundant glycolipid of the mycobacterial cell wall, the cord factor. The cord factor (trehalose 6,6'-dimycolate, TDM) is essential for the integrity of the mycobacterial cell wall and pathogenesis of the bacillus. Thus, TDM biosynthesis is regarded as a potential drug target for control of Mycobacterium tuberculosis infections. Trehalose 6,6'-dimycolate (TDM) is synthesized from two molecules of trehalose-6'-monomycolate (TMM) by antigen 85A. We report here a novel enzyme assay using the natural substrate TMM. The novel colorimetric assay is based on the quantification of glucose from the degradation of trehalose, which is the product from catalytic activity of antigen 85A. Using the new assay, K(m) and K(cat) were determined with values of 129.6+/-8.1 microM and 65.4+/-4.1 min(-1), respectively. This novel assay is also suitable for robust high-throughput screening (HTS) for compound library screening against mycolyltransferase (antigen 85A). The assay is significantly faster and more convenient to use than all assays currently in use. The assay has a very low coefficient of variance (0.04) in 96-well plates and shows a Z' factor of 0.67-0.73, indicating the robustness of the assay. In addition, this new assay is highly suitable for the quantification of total TMM of the mycobacterial cell envelope.
2010-02-24
2010-02-24
2009-12
Article
The mycolyltransferase 85A, a putative drug target of Mycobacterium tuberculosis: development of a novel assay and quantification of glycolipid-status of the mycobacterial cell wall. 2009, 79 (3):358-63 J. Microbiol. Methods
1872-8359
19857528
10.1016/j.mimet.2009.10.010
http://hdl.handle.net/10033/92920
Journal of microbiological methods
en
oai:repository.helmholtz-hzi.de:10033/941732019-08-30T11:33:57Zcom_10033_620636col_10033_620638
Haplotypes of the porcine peroxisome proliferator-activated receptor delta gene are associated with backfat thickness.
Meidtner, Karina
Schwarzenbacher, Hermann
Scharfe, Maren
Severitt, Simone
Blöcker, Helmut
Fries, Ruedi
Chair of Animal Breeding, Technical University of Munich, Hochfeldweg 1, 85354 Freising - Weihenstephan, Germany. karina.meidtner@tierzucht.tum.de
BACKGROUND: Peroxisome proliferator-activated receptor delta belongs to the nuclear receptor superfamily of ligand-inducible transcription factors. It is a key regulator of lipid metabolism. The peroxisome proliferator-activated receptor delta gene (PPARD) has been assigned to a region on porcine chromosome 7, which harbours a quantitative trait locus for backfat. Thus, PPARD is considered a functional and positional candidate gene for backfat thickness. The purpose of this study was to test this candidate gene hypothesis in a cross of breeds that were highly divergent in lipid deposition characteristics. RESULTS: Screening for genetic variation in porcine PPARD revealed only silent mutations. Nevertheless, significant associations between PPARD haplotypes and backfat thickness were observed in the F2 generation of the Mangalitsa x Piétrain cross as well as a commercial German Landrace population. Haplotype 5 is associated with increased backfat in F2 Mangalitsa x Piétrain pigs, whereas haplotype 4 is associated with lower backfat thickness in the German Landrace population. Haplotype 4 and 5 carry the same alleles at all but one SNP. Interestingly, the opposite effects of PPARD haplotypes 4 and 5 on backfat thickness are reflected by opposite effects of these two haplotypes on PPAR-delta mRNA levels. Haplotype 4 significantly increases PPAR-delta mRNA levels, whereas haplotype 5 decreases mRNA levels of PPAR-delta. CONCLUSION: This study provides evidence for an association between PPARD and backfat thickness. The association is substantiated by mRNA quantification. Further studies are required to clarify, whether the observed associations are caused by PPARD or are the result of linkage disequilibrium with a causal variant in a neighbouring gene.
2010-03-12
2010-03-12
2009
Article
Haplotypes of the porcine peroxisome proliferator-activated receptor delta gene are associated with backfat thickness. 2009, 10:76 BMC Genet.
1471-2156
19943979
10.1186/1471-2156-10-76
http://hdl.handle.net/10033/94173
BMC genetics
en
oai:repository.helmholtz-hzi.de:10033/984572019-08-30T11:36:05Zcom_10033_620636col_10033_620665
Neutrophils responsive to endogenous IFN-beta regulate tumor angiogenesis and growth in a mouse tumor model.
Jablonska, Jadwiga
Leschner, Sara
Westphal, Kathrin
Lienenklaus, Stefan
Weiss, Siegfried
Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany. jja@gbf.de
Angiogenesis is a hallmark of malignant neoplasias, as the formation of new blood vessels is required for tumors to acquire oxygen and nutrients essential for their continued growth and metastasis. However, the signaling pathways leading to tumor vascularization are not fully understood. Here, using a transplantable mouse tumor model, we have demonstrated that endogenous IFN-beta inhibits tumor angiogenesis through repression of genes encoding proangiogenic and homing factors in tumor-infiltrating neutrophils. We determined that IFN-beta-deficient mice injected with B16F10 melanoma or MCA205 fibrosarcoma cells developed faster-growing tumors with better-developed blood vessels than did syngeneic control mice. These tumors displayed enhanced infiltration by CD11b+Gr1+ neutrophils expressing elevated levels of the genes encoding the proangiogenic factors VEGF and MMP9 and the homing receptor CXCR4. They also expressed higher levels of the transcription factors c-myc and STAT3, known regulators of VEGF, MMP9, and CXCR4. In vitro, treatment of these tumor-infiltrating neutrophils with low levels of IFN-beta restored expression of proangiogenic factors to control levels. Moreover, depletion of these neutrophils inhibited tumor growth in both control and IFN-beta-deficient mice. We therefore suggest that constitutively produced endogenous IFN-beta is an important mediator of innate tumor surveillance. Further, we believe our data help to explain the therapeutic effect of IFN treatment during the early stages of cancer development.
2010-05-11
2010-05-11
2010-04
Article
Neutrophils responsive to endogenous IFN-beta regulate tumor angiogenesis and growth in a mouse tumor model. 2010, 120 (4):1151-64 J. Clin. Invest.
1558-8238
20237412
10.1172/JCI37223
http://hdl.handle.net/10033/98457
The Journal of clinical investigation
en
oai:repository.helmholtz-hzi.de:10033/995552019-08-30T11:35:39Zcom_10033_620636col_10033_620665
Murine toll-like receptor 2 activation induces type I interferon responses from endolysosomal compartments.
Dietrich, Nicole
Lienenklaus, Stefan
Weiss, Siegfried
Gekara, Nelson O
Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
BACKGROUND: Toll-like receptors (TLRs) are among the first-line sentinels for immune detection and responsiveness to pathogens. The TLR2 subfamily of TLRs (TLR1, TLR2, TLR6) form heterodimers with each other and are thus able to recognize a broad range of components from several microbes such as yeast, Gram-positive bacteria and protozoa. Until now, TLR2 activation by bacterial ligands has long been associated with pro-inflammatory cytokines but not type I interferon responses. METHODOLOGY/PRINCIPAL FINDINGS: Using a variety of transgenic mice, here we provide in vivo and in vitro data showing that TLR2 activation does in fact induce interferon-beta and that this occurs via MyD88-IRF1 and -IRF7 pathways. Interestingly, by microscopy we demonstrate that although a cell surface receptor, TLR2 dependent induction of type I interferons occurs in endolysosomal compartments where it is translocated to upon ligand engagement. Furthermore, we could show that blocking receptor internalization or endolysosomal acidification inhibits the ability of TLR2 to trigger the induction type I interferon but not pro-inflammatory responses. CONCLUSION/SIGNIFICANCE: The results indicate that TLR2 activation induces pro-inflammatory and type I interferon responses from distinct subcellular sites: the plasma membrane and endolysosomal compartments respectively. Apart from identifying and characterizing a novel pathway for induction of type I interferons, the present study offers new insights into how TLR signaling discriminates and regulates the nature of responses to be elicited against extracellular and endocytosed microbes. These findings may also have clinical implication. Excessive production of pro-inflammatory cytokines and type I IFNs following activation of TLRs is a central pathologic event in several hyper-inflammatory conditions. The discovery that the induction of pro-inflammatory and type I IFN responses can be uncoupled through pharmacological manipulation of endolysosomal acidification suggests new avenues for potential therapeutic intervention against inflammations and sepsis.
2010-05-21
2010-05-21
2010
Article
Murine toll-like receptor 2 activation induces type I interferon responses from endolysosomal compartments. 2010, 5 (4):e10250 PLoS ONE
1932-6203
20422028
10.1371/journal.pone.0010250
http://hdl.handle.net/10033/99555
PloS one
en
oai:repository.helmholtz-hzi.de:10033/1262712019-08-30T11:25:11Zcom_10033_620636col_10033_620665
Listeria monocytogenes induces T cell receptor unresponsiveness through pore-forming toxin listeriolysin O.
Gekara, Nelson O
Zietara, Natalia
Geffers, Robert
Weiss, Siegfried
Molecular Immunology, Helmholtz Center for Infection Research, Braunschweig, Germany. nelson.gekara@mims.umu.se
The success of many pathogens relies on their ability to circumvent the innate and adaptive immune defenses. How bacterial pathogens subvert adaptive immune defenses is not clear. Cholesterol-dependent cytolysins (CDCs) represent an expansive family of homologous pore-forming toxins that are produced by more than 20 gram-positive bacterial species. Listeriolysin O (LLO), a prototype CDC, is the main virulence factor of Listeria monocytogenes.
2011-03-30
2011-03-30
2010-12-01
Article
Listeria monocytogenes induces T cell receptor unresponsiveness through pore-forming toxin listeriolysin O. 2010, 202 (11):1698-707 J. Infect. Dis.
1537-6613
20961225
10.1086/657145
http://hdl.handle.net/10033/126271
The Journal of infectious diseases
en
oai:repository.helmholtz-hzi.de:10033/1287912019-08-30T11:30:32Zcom_10033_620636col_10033_620638
Susceptibility to experimental biliary atresia linked to different hepatic gene expression profiles in two mouse strains.
Leonhardt, Johannes
Kuebler, Joachim F
Turowski, Carmen
Tschernig, Thomas
Geffers, Robert
Petersen, Claus
Department of Pediatric Surgery, Hannover Medical School, Hannover, Germany.
Aim: To compare hepatic gene expression during the development of experimental biliary atresia (BA) in two different mouse strains. Methods: Balb/c mice and C57Black/6 (Black/6) mice were infected with rhesus rotavirus (RRV) postpartum, clinical signs of BA and survival were noted. Liver sections were assessed for cluster of differentiation antigen (CD) 3, CD4 and CD8 expression, and the hepatic virus load was determined. Second, mice of both strains were sacrificed three days after infection. Isolated hepatic RNA was subjected to gene expression analysis using Affymetrix Gene Chip MOE 430 2.0. Results: The incidence of BA was significantly lower in Black/6 mice compared to Balb/c mice (13.5% vs. 67%, P < 0.05). The mean virus titers were higher in mice with BA compared to mice without BA. Different gene profiles three days after virus infection were noted, with differential expression of 201 genes, including those regulating apoptosis, nucleic acid binding, transport function and particularly the immune response (chemokine C-C motif ligand 2, toll-like receptor 3, CD antigen 14, chemokine (C-X-C motif) ligands 10 and 11). This correlated with a significant increase of CD4 positive cells only in Balb/c mice with BA compared to healthy mice (13.5 vs. 5.0; P < 0.05). Black/6 mice did not exhibit any significant increase of CD3 or CD4 leukocytes despite cholestasis. Conclusion: The different susceptibility to experimental BA was associated with an increase of CD4 T-cells in the liver of Balb/c mice, which is linked to different gene profiles at the onset of bile duct obstruction.
2011-04-27
2011-04-27
2010-02
Article
Susceptibility to experimental biliary atresia linked to different hepatic gene expression profiles in two mouse strains. 2010, 40 (2):196-203 Hepatol. Res.
1386-6346
19788687
10.1111/j.1872-034X.2009.00577.x
http://hdl.handle.net/10033/128791
Hepatology research : the official journal of the Japan Society of Hepatology
en
oai:repository.helmholtz-hzi.de:10033/1296852019-08-30T11:27:16Zcom_10033_620636col_10033_620665
Potentiation of epithelial innate host responses by intercellular communication.
Dolowschiak, Tamas
Chassin, Cécilia
Ben Mkaddem, Sanae
Fuchs, Thilo M
Weiss, Siegfried
Vandewalle, Alain
Hornef, Mathias W
Hannover Medical School, Hannover, Germany.
The epithelium efficiently attracts immune cells upon infection despite the low number of pathogenic microbes and moderate levels of secreted chemokines per cell. Here we examined whether horizontal intercellular communication between cells may contribute to a coordinated response of the epithelium. Listeria monocytogenes infection, transfection, and microinjection of individual cells within a polarized intestinal epithelial cell layer were performed and activation was determined at the single cell level by fluorescence microscopy and flow cytometry. Surprisingly, chemokine production after L. monocytogenes infection was primarily observed in non-infected epithelial cells despite invasion-dependent cell activation. Whereas horizontal communication was independent of gap junction formation, cytokine secretion, ion fluxes, or nitric oxide synthesis, NADPH oxidase (Nox) 4-dependent oxygen radical formation was required and sufficient to induce indirect epithelial cell activation. This is the first report to describe epithelial cell-cell communication in response to innate immune activation. Epithelial communication facilitates a coordinated infectious host defence at the very early stage of microbial infection.
2011-05-17
2011-05-17
2010
Article
Potentiation of epithelial innate host responses by intercellular communication. 2010, 6 (11):e1001194 PLoS Pathog.
1553-7374
21124989
10.1371/journal.ppat.1001194
http://hdl.handle.net/10033/129685
PLoS pathogens
en
oai:repository.helmholtz-hzi.de:10033/1417922019-08-30T11:28:23Zcom_10033_620636col_10033_620638
ATP inhibits the generation and function of regulatory T cells through the activation of purinergic P2X receptors.
Schenk, Ursula
Frascoli, Michela
Proietti, Michele
Geffers, Robert
Traggiai, Elisabetta
Buer, Jan
Ricordi, Camillo
Westendorf, Astrid M
Grassi, Fabio
Institute for Research in Biomedicine, Bellinzona, Switzerland.
Extracellular nucleotides are pleiotropic regulators of mammalian cell function. Adenosine triphosphate (ATP) released from CD4(+) helper T cells upon stimulation of the T cell receptor (TCR) contributes in an autocrine manner to the activation of mitogen-activated protein kinase (MAPK) signaling through purinergic P2X receptors. Increased expression of p2rx7, which encodes the purinergic receptor P2X7, is part of the transcriptional signature of immunosuppressive CD4(+)CD25(+) regulatory T cells (T(regs)). Here, we show that the activation of P2X7 by ATP inhibits the suppressive potential and stability of T(regs). The inflammatory cytokine interleukin-6 (IL-6) increased ATP synthesis and P2X7-mediated signaling in T(regs), which induced their conversion to IL-17-secreting T helper 17 (T(H)17) effector cells in vivo. Moreover, pharmacological antagonism of P2X receptors promoted the cell-autonomous conversion of naïve CD4(+) T cells into T(regs) after TCR stimulation. Thus, ATP acts as an autocrine factor that integrates stimuli from the microenvironment and cellular energetics to tune the developmental and immunosuppressive program of the T cell in adaptive immune responses.
2011-09-06
2011-09-06
2011
Article
ATP inhibits the generation and function of regulatory T cells through the activation of purinergic P2X receptors. 2011, 4 (162):ra12 Sci Signal
1937-9145
21364186
10.1126/scisignal.2001270
http://hdl.handle.net/10033/141792
Science signaling
en
oai:repository.helmholtz-hzi.de:10033/1819902019-08-30T11:31:23Zcom_10033_620636col_10033_620638
Genomewide analyses define different modes of transcriptional regulation by peroxisome proliferator-activated receptor-β/δ (PPARβ/δ).
Adhikary, Till
Kaddatz, Kerstin
Finkernagel, Florian
Schönbauer, Anne
Meissner, Wolfgang
Scharfe, Maren
Jarek, Michael
Blöcker, Helmut
Müller-Brüsselbach, Sabine
Müller, Rolf
Institute of Molecular Biology and Tumor Research, Philipps University, Marburg, Germany.
Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors with essential functions in lipid, glucose and energy homeostasis, cell differentiation, inflammation and metabolic disorders, and represent important drug targets. PPARs heterodimerize with retinoid X receptors (RXRs) and can form transcriptional activator or repressor complexes at specific DNA elements (PPREs). It is believed that the decision between repression and activation is generally governed by a ligand-mediated switch. We have performed genomewide analyses of agonist-treated and PPARβ/δ-depleted human myofibroblasts to test this hypothesis and to identify global principles of PPARβ/δ-mediated gene regulation. Chromatin immunoprecipitation sequencing (ChIP-Seq) of PPARβ/δ, H3K4me3 and RNA polymerase II enrichment sites combined with transcriptional profiling enabled the definition of 112 bona fide PPARβ/δ target genes showing either of three distinct types of transcriptional response: (I) ligand-independent repression by PPARβ/δ; (II) ligand-induced activation and/or derepression by PPARβ/δ; and (III) ligand-independent activation by PPARβ/δ. These data identify PPRE-mediated repression as a major mechanism of transcriptional regulation by PPARβ/δ, but, unexpectedly, also show that only a subset of repressed genes are activated by a ligand-mediated switch. Our results also suggest that the type of transcriptional response by a given target gene is connected to the structure of its associated PPRE(s) and the biological function of its encoded protein. These observations have important implications for understanding the regulatory PPAR network and PPARβ/δ ligand-based drugs.
2011-10-28
2011-10-28
2011
Article
Genomewide analyses define different modes of transcriptional regulation by peroxisome proliferator-activated receptor-β/δ (PPARβ/δ). 2011, 6 (1):e16344 PLoS ONE
1932-6203
21283829
10.1371/journal.pone.0016344
http://hdl.handle.net/10033/181990
PloS one
en
oai:repository.helmholtz-hzi.de:10033/2127092019-08-30T11:27:16Zcom_10033_620636col_10033_620665
In-vivo expression profiling of Pseudomonas aeruginosa infections reveals niche-specific and strain-independent transcriptional programs.
Bielecki, Piotr
Puchałka, Jacek
Wos-Oxley, Melissa L
Loessner, Holger
Glik, Justyna
Kawecki, Marek
Nowak, Mariusz
Tümmler, Burkhard
Weiss, Siegfried
dos Santos, Vítor A P Martins
Systems and Synthetic Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
Pseudomonas aeruginosa is a threatening, opportunistic pathogen causing disease in immunocompromised individuals. The hallmark of P. aeruginosa virulence is its multi-factorial and combinatorial nature. It renders such bacteria infectious for many organisms and it is often resistant to antibiotics. To gain insights into the physiology of P. aeruginosa during infection, we assessed the transcriptional programs of three different P. aeruginosa strains directly after isolation from burn wounds of humans. We compared the programs to those of the same strains using two infection models: a plant model, which consisted of the infection of the midrib of lettuce leaves, and a murine tumor model, which was obtained by infection of mice with an induced tumor in the abdomen. All control conditions of P. aeruginosa cells growing in suspension and as a biofilm were added to the analysis. We found that these different P. aeruginosa strains express a pool of distinct genetic traits that are activated under particular infection conditions regardless of their genetic variability. The knowledge herein generated will advance our understanding of P. aeruginosa virulence and provide valuable cues for the definition of prospective targets to develop novel intervention strategies.
2012-02-24
2012-02-24
2011
Article
In-vivo expression profiling of Pseudomonas aeruginosa infections reveals niche-specific and strain-independent transcriptional programs. 2011, 6 (9):e24235 PLoS ONE
1932-6203
21931663
10.1371/journal.pone.0024235
http://hdl.handle.net/10033/212709
PloS one
en
oai:repository.helmholtz-hzi.de:10033/2139692019-08-30T11:29:47Zcom_10033_620636col_10033_620638
Genome sequence of the thermophilic strain Bacillus coagulans 2-6, an efficient producer of high-optical-purity L-lactic acid.
Su, Fei
Yu, Bo
Sun, Jibin
Ou, Hong-Yu
Zhao, Bo
Wang, Limin
Qin, Jiayang
Tang, Hongzhi
Tao, Fei
Jarek, Michael
Scharfe, Maren
Ma, Cuiqing
Ma, Yanhe
Xu, Ping
State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China.
Bacillus coagulans 2-6 is an efficient producer of lactic acid. The genome of B. coagulans 2-6 has the smallest genome among the members of the genus Bacillus known to date. The frameshift mutation at the start of the d-lactate dehydrogenase sequence might be responsible for the production of high-optical-purity l-lactic acid.
2012-03-02
2012-03-02
2011-09
Article
Genome sequence of the thermophilic strain Bacillus coagulans 2-6, an efficient producer of high-optical-purity L-lactic acid. 2011, 193 (17):4563-4 J. Bacteriol.
1098-5530
21705584
10.1128/JB.05378-11
http://hdl.handle.net/10033/213969
Journal of bacteriology
en
oai:repository.helmholtz-hzi.de:10033/2266512019-08-30T11:34:22Zcom_10033_620636col_10033_620638
Cellular retinaldehyde-binding protein (CRALBP) is a direct downstream target of transcription factor Pax6.
Boppana, Sridhar
Scheglov, Alexander
Geffers, Robert
Tarabykin, Victor
Max-Planck-Institute for Experimental Medicine, Hermann-Rein Strasse 3, 37075 Göttingen, Germany. boppansr@umdnj.edu
Transcription factor Pax6 plays an essential role in the expression of other transcription factors, cell adhesion molecules and is crucial for neurogenesis in the developing forebrain. Analysis of gene expression profiles through microarray experiments in Pax6 mutants allowed us to focus on CRALBP, one of the many genes that were downregulated.
2012-05-30
2012-05-30
2012-02
Article
Cellular retinaldehyde-binding protein (CRALBP) is a direct downstream target of transcription factor Pax6. 2012, 1820 (2):151-6 Biochim. Biophys. Acta
0006-3002
21996446
10.1016/j.bbagen.2011.09.015
http://hdl.handle.net/10033/226651
Biochimica et biophysica acta
en
Archived with thanks to Biochimica et biophysica acta
oai:repository.helmholtz-hzi.de:10033/2295732019-08-30T11:25:43Zcom_10033_620636col_10033_620637
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.
Gabdoulline, R
Eckweiler, D
Kel, A
Stegmaier, P
Heinrich-Heine University of Duesseldorf, Universitaetstr. 1, 40225 Duesseldorf, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38234 Braunschweig, GeneXplain GmbH, Am Exer 10 b, 38302 Wolfenbüttel, BIOBASE GmbH, Halchtersche Str. 33, 38304 Wolfenbüttel, Germany and Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Science, 10 Lavrentyev Ave, 630090 Novosibirsk, Russia.
We present the webserver 3D transcription factor (3DTF) to compute position-specific weight matrices (PWMs) of transcription factors using a knowledge-based statistical potential derived from crystallographic data on protein-DNA complexes. Analysis of available structures that can be used to construct PWMs shows that there are hundreds of 3D structures from which PWMs could be derived, as well as thousands of proteins homologous to these. Therefore, we created 3DTF, which delivers binding matrices given the experimental or modeled protein-DNA complex. The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/.
2012-06-19
2012-06-19
2012-06-11
Article
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. 2012:notNucleic Acids Res
1362-4962
22693215
10.1093/nar/gks551
http://hdl.handle.net/10033/229573
Nucleic acids research
Archived with thanks to Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/2296722019-08-30T11:27:16Zcom_10033_620636col_10033_620665
Identification of tumor-specific Salmonella Typhimurium promoters and their regulatory logic.
Leschner, Sara
Deyneko, Igor V
Lienenklaus, Stefan
Wolf, Kathrin
Bloecker, Helmut
Bumann, Dirk
Loessner, Holger
Weiss, Siegfried
Molecular Immunology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany. sara.leschner@helmholtz-hzi.de
Conventional cancer therapies are often limited in effectiveness and exhibit strong side effects. Therefore, alternative therapeutic strategies are demanded. The employment of tumor-colonizing bacteria that exert anticancer effects is such a novel approach that attracts increasing attention. For instance, Salmonella enterica serovar Typhimurium has been used in many animal tumor models as well as in first clinical studies. These bacteria exhibit inherent tumoricidal effects. In addition, they can be used to deliver therapeutic agents. However, bacterial expression has to be restricted to the tumor to prevent toxic substances from harming healthy tissue. Therefore, we screened an S. Typhimurium promoter-trap library to identify promoters that exclusively drive gene expression in the cancerous tissue. Twelve elements could be detected that show reporter gene expression in tumors but not in spleen and liver. In addition, a DNA motif was identified that appears to be necessary for tumor specificity. Now, such tumor-specific promoters can be used to safely express therapeutic proteins by tumor-colonizing S. Typhimurium directly in the neoplasia.
2012-06-19
2012-06-19
2012-04
Article
Identification of tumor-specific Salmonella Typhimurium promoters and their regulatory logic. 2012, 40 (7):2984-94 Nucleic Acids Res.
1362-4962
22140114
10.1093/nar/gkr1041
http://hdl.handle.net/10033/229672
Nucleic acids research
en
Archived with thanks to Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/2334552019-08-30T11:33:57Zcom_10033_620636col_10033_620638
Neoplastic MiR-17~92 deregulation at a DNA fragility motif (SIDD).
Schneider, Björn
Nagel, Stefan
Ehrentraut, Stefan
Kaufmann, Maren
Meyer, Corinna
Geffers, Robert
Drexler, Hans G
MacLeod, Roderick A F
Department of Human and Animal Cell Cultures, DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7b, 38124 Braunschweig, Germany. bjoern.schneider@med.uni-rostock.de
Chromosomal or mutational activation of BCL6 (at 3q27) typifies diffuse large B-cell lymphoma (DLBCL) which in the germinal center subtype may be accompanied by focal amplification of chromosome band 13q31 effecting upregulation of miR-17~92. Using long distance inverse-polymerase chain reaction, we mapped and sequenced six breakpoints of a complex BCL6 rearrangement t(3;13)(q27;q31)t(12;13)(p11;q31) in DLBCL cells, which places miR-17~92 antisense within the resulting ITPR2-BCL6 chimeric fusion gene rearrangement. MiR-17~92 members were upregulated ~15-fold over controls in a copy number independent manner consistent with structural deregulation. MIR17HG and ITPR2-BCL6 were, despite their close configuration, independently expressed, discounting antisense regulation. MIR17HG in t(3;13)t(12;13) cells proved highly responsive to treatment with histone deacetylase inhibitors implicating epigenetic deregulation, consistent with which increased histone-H3 acetylation was detected by chromatin immunoprecipitation near the upstream MIR17HG breakpoint. Remarkably, 5/6 DNA breaks in the t(3;13)t(12;13) precisely cut at stress-induced DNA duplex destabilization (SIDD) peaks reminiscent of chromosomal fragile sites, while the sixth lay 150 bp distant. Extended SIDD profiling showed that additional oncomiRs also map to SIDD peaks. Fluorescence in situ hybridization analysis showed that 11 of 52 (21%) leukemia-lymphoma (L-L) cell lines with 13q31 involvement bore structural rearrangements at/near MIR17HG associated with upregulation. As well as fueling genome instability, SIDD peaks mark regulatory nuclear-scaffold matrix attachment regions open to nucleosomal acetylation. Collectively, our data indict a specific DNA instability motif (SIDD) in chromosome rearrangement, specifically alterations activating miR-17~92 epigenetically via promoter hyperacetylation, and supply a model for the clustering of oncomiRs near cancer breakpoints.
2012-07-12
2012-07-12
2012-03
Article
Neoplastic MiR-17~92 deregulation at a DNA fragility motif (SIDD). 2012, 51 (3):219-28 Genes Chromosomes Cancer
1098-2264
22072491
10.1002/gcc.20946
http://hdl.handle.net/10033/233455
Genes, chromosomes & cancer
en
Archived with thanks to Genes, chromosomes & cancer
oai:repository.helmholtz-hzi.de:10033/2369892019-08-30T11:25:43Zcom_10033_311624com_10033_6839com_10033_620636col_10033_311625col_10033_620638
More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli.
Göhler, Anna-Katharina
Kökpinar, Öznur
Schmidt-Heck, Wolfgang
Geffers, Robert
Guthke, Reinhard
Rinas, Ursula
Schuster, Stefan
Jahreis, Knut
Kaleta, Christoph
Department of Genetics, University of Osnabrück, Osnabrück, Germany.
The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon has not yet been uncovered. To achieve an extended understanding of its gene regulatory network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach.
2012-08-02
2012-08-02
2011
Article
More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli. 2011, 5:197 BMC Syst Biol
1752-0509
22168595
10.1186/1752-0509-5-197
http://hdl.handle.net/10033/236989
BMC systems biology
en
Archived with thanks to BMC systems biology
oai:repository.helmholtz-hzi.de:10033/2399312019-08-30T11:28:51Zcom_10033_620636col_10033_620638
FMNL2 drives actin-based protrusion and migration downstream of Cdc42.
Block, Jennifer
Breitsprecher, Dennis
Kühn, Sonja
Winterhoff, Moritz
Kage, Frieda
Geffers, Robert
Duwe, Patrick
Rohn, Jennifer L
Baum, Buzz
Brakebusch, Cord
Geyer, Matthias
Stradal, Theresia E B
Faix, Jan
Rottner, Klemens
Institute of Genetics, University of Bonn, Karlrobert-Kreiten-Strasse 13, 53115 Bonn, Germany.
Cell migration entails protrusion of lamellipodia, densely packed networks of actin filaments at the cell front. Filaments are generated by nucleation, likely mediated by Arp2/3 complex and its activator Scar/WAVE. It is unclear whether formins contribute to lamellipodial actin filament nucleation or serve as elongators of filaments nucleated by Arp2/3 complex. Here we show that the Diaphanous-related formin FMNL2, also known as FRL3 or FHOD2, accumulates at lamellipodia and filopodia tips. FMNL2 is cotranslationally modified by myristoylation and regulated by interaction with the Rho-guanosine triphosphatase Cdc42. Abolition of myristoylation or Cdc42 binding interferes with proper FMNL2 activation, constituting an essential prerequisite for subcellular targeting. In vitro, C-terminal FMNL2 drives elongation rather than nucleation of actin filaments in the presence of profilin. In addition, filament ends generated by Arp2/3-mediated branching are captured and efficiently elongated by the formin. Consistent with these biochemical properties, RNAi-mediated silencing of FMNL2 expression decreases the rate of lamellipodia protrusion and, accordingly, the efficiency of cell migration. Our data establish that the FMNL subfamily member FMNL2 is a novel elongation factor of actin filaments that constitutes the first Cdc42 effector promoting cell migration and actin polymerization at the tips of lamellipodia.
2012-08-24
2012-08-24
2012-06-05
Article
FMNL2 drives actin-based protrusion and migration downstream of Cdc42. 2012, 22 (11):1005-12 Curr. Biol.
1879-0445
22608513
10.1016/j.cub.2012.03.064
http://hdl.handle.net/10033/239931
Current biology : CB
en
Archived with thanks to Current biology : CB
oai:repository.helmholtz-hzi.de:10033/2416972019-08-30T11:25:43Zcom_10033_620636col_10033_620638
LINT, a novel dL(3)mbt-containing complex, represses malignant brain tumour signature genes.
Meier, Karin
Mathieu, Eve-Lyne
Finkernagel, Florian
Reuter, L Maximilian
Scharfe, Maren
Doehlemann, Gunther
Jarek, Michael
Brehm, Alexander
Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany.
Mutations in the l(3)mbt tumour suppressor result in overproliferation of Drosophila larval brains. Recently, the derepression of different gene classes in l(3)mbt mutants was shown to be causal for transformation. However, the molecular mechanisms of dL(3)mbt-mediated gene repression are not understood. Here, we identify LINT, the major dL(3)mbt complex of Drosophila. LINT has three core subunits-dL(3)mbt, dCoREST, and dLint-1-and is expressed in cell lines, embryos, and larval brain. Using genome-wide ChIP-Seq analysis, we show that dLint-1 binds close to the TSS of tumour-relevant target genes. Depletion of the LINT core subunits results in derepression of these genes. By contrast, histone deacetylase, histone methylase, and histone demethylase activities are not required to maintain repression. Our results support a direct role of LINT in the repression of brain tumour-relevant target genes by restricting promoter access.
2012-09-06
2012-09-06
2012-05
Article
LINT, a novel dL(3)mbt-containing complex, represses malignant brain tumour signature genes. 2012, 8 (5):e1002676 PLoS Genet.
1553-7404
22570633
10.1371/journal.pgen.1002676
http://hdl.handle.net/10033/241697
PLoS genetics
en
Archived with thanks to PLoS genetics
oai:repository.helmholtz-hzi.de:10033/2442982019-08-30T11:33:30Zcom_10033_620636col_10033_620665
Priming of natural killer cells by nonmucosal mononuclear phagocytes requires instructive signals from commensal microbiota.
Ganal, Stephanie C
Sanos, Stephanie L
Kallfass, Carsten
Oberle, Karin
Johner, Caroline
Kirschning, Carsten
Lienenklaus, Stefan
Weiss, Siegfried
Staeheli, Peter
Aichele, Peter
Diefenbach, Andreas
IMMH, Institute of Medical Microbiology and Hygiene, University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine, Albertstrasse 19A, 79104 Freiburg, Germany.
Mononuclear phagocytes are an important component of an innate immune system perceived as a system ready to react upon encounter of pathogens. Here, we show that in response to microbial stimulation, mononuclear phagocytes residing in nonmucosal lymphoid organs of germ-free mice failed to induce expression of a set of inflammatory response genes, including those encoding the various type I interferons (IFN-I). Consequently, NK cell priming and antiviral immunity were severely compromised. Whereas pattern recognition receptor signaling and nuclear translocation of the transcription factors NF-κB and IRF3 were normal in mononuclear phagocytes of germ-free mice, binding to their respective cytokine promoters was impaired, which correlated with the absence of activating histone marks. Our data reveal a previously unrecognized role for postnatally colonizing microbiota in the introduction of chromatin level changes in the mononuclear phagocyte system, thereby poising expression of central inflammatory genes to initiate a powerful systemic immune response during viral infection.
2012-09-17
2012-09-17
2012-07-27
Article
Priming of natural killer cells by nonmucosal mononuclear phagocytes requires instructive signals from commensal microbiota. 2012, 37 (1):171-86 Immunity
1097-4180
22749822
10.1016/j.immuni.2012.05.020
http://hdl.handle.net/10033/244298
Immunity
en
Archived with thanks to Immunity
oai:repository.helmholtz-hzi.de:10033/2446912019-08-30T11:33:05Zcom_10033_620636col_10033_620637
A chemical proteomics approach to identify c-di-GMP binding proteins in Pseudomonas aeruginosa.
Düvel, Juliane
Bertinetti, Daniela
Möller, Stefan
Schwede, Frank
Morr, Michael
Wissing, Josef
Radamm, Lena
Zimmermann, Bastian
Genieser, Hans-Gottfried
Jänsch, Lothar
Herberg, Friedrich W
Häussler, Susanne
Department of Cell Biology, Helmholtz Center for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
In many bacteria, high levels of the ubiquitous second messenger c-di-GMP have been demonstrated to suppress motility and to promote the establishment of surface-adherent biofilm communities. While molecular mechanisms underlying the synthesis and degradation of c-di-GMP have been comprehensively characterized, little is known about how c-di-GMP mediates its regulatory effects. In this study, we have established a chemical proteomics approach to identify c-di-GMP interacting proteins in the opportunistic pathogen Pseudomonas aeruginosa. A functionalized c-di-GMP analog, 2'-aminohexylcarbamoyl-c-di-GMP (2'-AHC-c-di-GMP), was chemically synthesized and following its immobilization used to perform affinity pull down experiments. Enriched proteins were subsequently identified by high-resolution mass spectrometry. 2'-AHC-c-di-GMP was also employed in surface plasmon resonance studies to evaluate and quantify the interaction of c-di-GMP with its potential target molecules in vitro. The biochemical tools presented here may serve the identification of novel classes of c-di-GMP effectors and thus contribute to a better characterization and understanding of the complex c-di-GMP signaling network.
2012-09-18
2012-09-18
2012-02
Article
A chemical proteomics approach to identify c-di-GMP binding proteins in Pseudomonas aeruginosa. 2012, 88 (2):229-36 J. Microbiol. Methods
1872-8359
22178430
10.1016/j.mimet.2011.11.015
http://hdl.handle.net/10033/244691
Journal of microbiological methods
en
Archived with thanks to Journal of microbiological methods
oai:repository.helmholtz-hzi.de:10033/2451832019-08-30T11:28:24Zcom_10033_620636col_10033_620638
Recruitment of the ATP-dependent chromatin remodeler dMi-2 to the transcribed region of active heat shock genes.
Mathieu, Eve-Lyne
Finkernagel, Florian
Murawska, Magdalena
Scharfe, Maren
Jarek, Michael
Brehm, Alexander
Institute for Molecular Biology and Tumor Research, Philipps-University, Emil-Mannkopff-Strasse 2, 35037 Marburg, Germany.
The ATP-dependent chromatin remodeler dMi-2 can play both positive and negative roles in gene transcription. Recently, we have shown that dMi-2 is recruited to the hsp70 gene in a heat shock-dependent manner, and is required to achieve high transcript levels. Here, we use chromatin immunoprecipitation sequencing (ChIP-Seq) to identify other chromatin regions displaying increased dMi-2 binding upon heat shock and to characterize the distribution of dMi-2 over heat shock genes. We show that dMi-2 is recruited to the body of at least seven heat shock genes. Interestingly, dMi-2 binding extends several hundred base pairs beyond the polyadenylation site into the region where transcriptional termination occurs. We find that dMi-2 does not associate with the entire nucleosome-depleted hsp70 locus 87A. Rather, dMi-2 binding is restricted to transcribed regions. Our results suggest that dMi-2 distribution over active heat shock genes are determined by transcriptional activity.
2012-09-20
2012-09-20
2012-06
Article
Recruitment of the ATP-dependent chromatin remodeler dMi-2 to the transcribed region of active heat shock genes. 2012, 40 (11):4879-91 Nucleic Acids Res.
1362-4962
22362736
10.1093/nar/gks178
http://hdl.handle.net/10033/245183
Nucleic acids research
en
Archived with thanks to Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/2471392019-08-30T11:24:31Zcom_10033_620636col_10033_620637
The YfiBNR signal transduction mechanism reveals novel targets for the evolution of persistent Pseudomonas aeruginosa in cystic fibrosis airways.
Malone, Jacob G
Jaeger, Tina
Manfredi, Pablo
Dötsch, Andreas
Blanka, Andrea
Bos, Raphael
Cornelis, Guy R
Häussler, Susanne
Jenal, Urs
Biozentrum of the University of Basel, Basel, Switzerland.
The genetic adaptation of pathogens in host tissue plays a key role in the establishment of chronic infections. While whole genome sequencing has opened up the analysis of genetic changes occurring during long-term infections, the identification and characterization of adaptive traits is often obscured by a lack of knowledge of the underlying molecular processes. Our research addresses the role of Pseudomonas aeruginosa small colony variant (SCV) morphotypes in long-term infections. In the lungs of cystic fibrosis patients, the appearance of SCVs correlates with a prolonged persistence of infection and poor lung function. Formation of P. aeruginosa SCVs is linked to increased levels of the second messenger c-di-GMP. Our previous work identified the YfiBNR system as a key regulator of the SCV phenotype. The effector of this tripartite signaling module is the membrane bound diguanylate cyclase YfiN. Through a combination of genetic and biochemical analyses we first outline the mechanistic principles of YfiN regulation in detail. In particular, we identify a number of activating mutations in all three components of the Yfi regulatory system. YfiBNR is shown to function via tightly controlled competition between allosteric binding sites on the three Yfi proteins; a novel regulatory mechanism that is apparently widespread among periplasmic signaling systems in bacteria. We then show that during long-term lung infections of CF patients, activating mutations invade the population, driving SCV formation in vivo. The identification of mutational "scars" in the yfi genes of clinical isolates suggests that Yfi activity is both under positive and negative selection in vivo and that continuous adaptation of the c-di-GMP network contributes to the in vivo fitness of P. aeruginosa during chronic lung infections. These experiments uncover an important new principle of in vivo persistence, and identify the c-di-GMP network as a valid target for novel anti-infectives directed against chronic infections.
2012-10-05
2012-10-05
2012-06
Article
The YfiBNR signal transduction mechanism reveals novel targets for the evolution of persistent Pseudomonas aeruginosa in cystic fibrosis airways. 2012, 8 (6):e1002760 PLoS Pathog.
1553-7374
22719254
10.1371/journal.ppat.1002760
http://hdl.handle.net/10033/247139
PLoS pathogens
en
Archived with thanks to PLoS pathogens
oai:repository.helmholtz-hzi.de:10033/2493552019-08-30T11:27:16Zcom_10033_620636col_10033_620638
Transcriptional activation of prostate specific homeobox gene NKX3-1 in subsets of T-cell lymphoblastic leukemia (T-ALL).
Nagel, Stefan
Ehrentraut, Stefan
Tomasch, Jürgen
Lienenklaus, Stefan
Schneider, Björn
Geffers, Robert
Meyer, Corinna
Kaufmann, Maren
Drexler, Hans G
MacLeod, Roderick A F
Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany. sna@dsmz.de
Homeobox genes encode transcription factors impacting key developmental processes including embryogenesis, organogenesis, and cell differentiation. Reflecting their tight transcriptional control, homeobox genes are often embedded in large non-coding, cis-regulatory regions, containing tissue specific elements. In T-cell acute lymphoblastic leukemia (T-ALL) homeobox genes are frequently deregulated by chromosomal aberrations, notably translocations adding T-cell specific activatory elements. NKX3-1 is a prostate specific homeobox gene activated in T-ALL patients expressing oncogenic TAL1 or displaying immature T-cell characteristics. After investigating regulation of NKX3-1 in primary cells and cell lines, we report its ectopic expression in T-ALL cells independent of chromosomal rearrangements. Using siRNAs and expression profiling, we exploited NKX3-1 positive T-ALL cell lines as tools to investigate aberrant activatory mechanisms. Our data confirmed NKX3-1 activation by TAL1/GATA3/LMO and identified LYL1 as an alternative activator in immature T-ALL cells devoid of GATA3. Moreover, we showed that NKX3-1 is directly activated by early T-cell homeodomain factor MSX2. These activators were regulated by MLL and/or by IL7-, BMP4- and IGF2-signalling. Finally, we demonstrated homeobox gene SIX6 as a direct leukemic target of NKX3-1 in T-ALL. In conclusion, we identified three major mechanisms of NKX3-1 regulation in T-ALL cell lines which are represented by activators TAL1, LYL1 and MSX2, corresponding to particular T-ALL subtypes described in patients. These results may contribute to the understanding of leukemic transcriptional networks underlying disturbed T-cell differentiation in T-ALL.
2012-10-18
2012-10-18
2012
Article
Transcriptional activation of prostate specific homeobox gene NKX3-1 in subsets of T-cell lymphoblastic leukemia (T-ALL). 2012, 7 (7):e40747 PLoS ONE
1932-6203
22848398
10.1371/journal.pone.0040747
http://hdl.handle.net/10033/249355
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/2648942019-08-30T11:30:32Zcom_10033_620636col_10033_620638
Genome-wide localization and expression profiling establish Sp2 as a sequence-specific transcription factor regulating vitally important genes.
Terrados, Gloria
Finkernagel, Florian
Stielow, Bastian
Sadic, Dennis
Neubert, Juliane
Herdt, Olga
Krause, Michael
Scharfe, Maren
Jarek, Michael
Suske, Guntram
Institute of Molecular Biology and Tumor Research, Philipps-University, Emil-Mannkopff-Str. 2, D-35032 Marburg, Germany.
The transcription factor Sp2 is essential for early mouse development and for proliferation of mouse embryonic fibroblasts in culture. Yet its mechanisms of action and its target genes are largely unknown. In this study, we have combined RNA interference, in vitro DNA binding, chromatin immunoprecipitation sequencing and global gene-expression profiling to investigate the role of Sp2 for cellular functions, to define target sites and to identify genes regulated by Sp2. We show that Sp2 is important for cellular proliferation that it binds to GC-boxes and occupies proximal promoters of genes essential for vital cellular processes including gene expression, replication, metabolism and signalling. Moreover, we identified important key target genes and cellular pathways that are directly regulated by Sp2. Most significantly, Sp2 binds and activates numerous sequence-specific transcription factor and co-activator genes, and represses the whole battery of cholesterol synthesis genes. Our results establish Sp2 as a sequence-specific regulator of vitally important genes.
2013-01-11
2013-01-11
2012-09
Article
Genome-wide localization and expression profiling establish Sp2 as a sequence-specific transcription factor regulating vitally important genes. 2012, 40 (16):7844-57 Nucleic Acids Res.
1362-4962
22684502
10.1093/nar/gks544
http://hdl.handle.net/10033/264894
Nucleic acids research
en
Archived with thanks to Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/2672722019-08-30T11:29:17Zcom_10033_620636col_10033_620638
Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors.
Neumann, Olaf
Kesselmeier, Miriam
Geffers, Robert
Pellegrino, Rossella
Radlwimmer, Bernhard
Hoffmann, Katrin
Ehemann, Volker
Schemmer, Peter
Schirmacher, Peter
Lorenzo Bermejo, Justo
Longerich, Thomas
Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
To identify new tumor-suppressor gene candidates relevant for human hepatocarcinogenesis, we performed genome-wide methylation profiling and vertical integration with array-based comparative genomic hybridization (aCGH), as well as expression data from a cohort of well-characterized human hepatocellular carcinomas (HCCs). Bisulfite-converted DNAs from 63 HCCs and 10 healthy control livers were analyzed for the methylation status of more than 14,000 genes. After defining the differentially methylated genes in HCCs, we integrated their DNA copy-number alterations as determined by aCGH data and correlated them with gene expression to identify genes potentially silenced by promoter hypermethylation. Aberrant methylation of candidates was further confirmed by pyrosequencing, and methylation dependency of silencing was determined by 5-aza-2'-deoxycytidine (5-aza-dC) treatment. Methylation profiling revealed 2,226 CpG sites that showed methylation differences between healthy control livers and HCCs. Of these, 537 CpG sites were hypermethylated in the tumor DNA, whereas 1,689 sites showed promoter hypomethylation. The hypermethylated set was enriched for genes known to be inactivated by the polycomb repressive complex 2, whereas the group of hypomethylated genes was enriched for imprinted genes. We identified three genes matching all of our selection criteria for a tumor-suppressor gene (period homolog 3 [PER3], insulin-like growth-factor-binding protein, acid labile subunit [IGFALS], and protein Z). PER3 was down-regulated in human HCCs, compared to peritumorous and healthy liver tissues. 5-aza-dC treatment restored PER3 expression in HCC cell lines, indicating that promoter hypermethylation was indeed responsible for gene silencing. Additionally, functional analysis supported a tumor-suppressive function for PER3 and IGFALS in vitro. CONCLUSION: The present study illustrates that vertical integration of methylation data with high-resolution genomic and transcriptomic data facilitates the identification of new tumor-suppressor gene candidates in human HCC.
2013-01-28
2013-01-28
2012-11
Article
Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors. 2012, 56 (5):1817-27 Hepatology
1527-3350
22689435
10.1002/hep.25870
http://hdl.handle.net/10033/267272
Hepatology (Baltimore, Md.)
en
Archived with thanks to Hepatology (Baltimore, Md.)
oai:repository.helmholtz-hzi.de:10033/2678322019-08-30T11:29:17Zcom_10033_620636col_10033_620638
Differential gene expression from genome-wide microarray analyses distinguishes Lohmann Selected Leghorn and Lohmann Brown layers.
Habig, Christin
Geffers, Robert
Distl, Ottmar
Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), Hannover, Germany.
The Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) layer lines have been selected for high egg production since more than 50 years and belong to the worldwide leading commercial layer lines. The objectives of the present study were to characterize the molecular processes that are different among these two layer lines using whole genome RNA expression profiles. The hens were kept in the newly developed small group housing system Eurovent German with two different group sizes. Differential expression was observed for 6,276 microarray probes (FDR adjusted P-value <0.05) among the two layer lines LSL and LB. A 2-fold or greater change in gene expression was identified on 151 probe sets. In LSL, 72 of the 151 probe sets were up- and 79 of them were down-regulated. Gene ontology (GO) enrichment analysis accounting for biological processes evinced 18 GO-terms for the 72 probe sets with higher expression in LSL, especially those taking part in immune system processes and membrane organization. A total of 32 enriched GO-terms were determined among the 79 down-regulated probe sets of LSL. Particularly, these terms included phosphorus metabolic processes and signaling pathways. In conclusion, the phenotypic differences among the two layer lines LSL and LB are clearly reflected in their gene expression profiles of the cerebrum. These novel findings provide clues for genes involved in economically important line characteristics of commercial laying hens.
2013-01-31
2013-01-31
2012
Article
Differential gene expression from genome-wide microarray analyses distinguishes Lohmann Selected Leghorn and Lohmann Brown layers. 2012, 7 (10):e46787 PLoS ONE
1932-6203
23056453
10.1371/journal.pone.0046787
http://hdl.handle.net/10033/267832
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/2696952019-08-30T11:26:42Zcom_10033_620636col_10033_620665
Visualizing production of beta interferon by astrocytes and microglia in brain of La Crosse virus-infected mice.
Kallfass, Carsten
Ackerman, Andreas
Lienenklaus, Stefan
Weiss, Siegfried
Heimrich, Bernd
Staeheli, Peter
Department of Virology, University of Freiburg, Freiburg, Germany.
Beta interferon (IFN-β) is a major component of innate immunity in mammals, but information on the in vivo source of this cytokine after pathogen infection is still scarce. To identify the cell types responsible for IFN-β production during viral encephalitis, we used reporter mice that express firefly luciferase under the control of the IFN-β promoter and stained organ sections with luciferase-specific antibodies. Numerous luciferase-positive cells were detected in regions of La Crosse virus (LACV)-infected mouse brains that contained many infected cells. Double-staining experiments with cell-type-specific markers revealed that similar numbers of astrocytes and microglia of infected brains were luciferase positive, whereas virus-infected neurons rarely contained detectable levels of luciferase. Interestingly, if a mutant LACV unable of synthesizing the IFN-antagonistic factor NSs was used for challenge, the vast majority of the IFN-β-producing cells in infected brains were astrocytes rather than microglia. Similar conclusions were reached in a second series of experiments in which conditional reporter mice expressing the luciferase reporter gene solely in defined cell types were infected with wild-type or mutant LACV. Collectively, our data suggest that glial cells rather than infected neurons represent the major source of IFN-β in LACV-infected mouse brains. They further indicate that IFN-β synthesis in astrocytes and microglia is differentially affected by the viral IFN antagonist, presumably due to differences in LACV susceptibility of these two cell types.
2013-02-18
2013-02-18
2012-10
Article
Visualizing production of beta interferon by astrocytes and microglia in brain of La Crosse virus-infected mice. 2012, 86 (20):11223-30 J. Virol.
1098-5514
22875966
10.1128/JVI.01093-12
http://hdl.handle.net/10033/269695
Journal of virology
en
Archived with thanks to Journal of virology
oai:repository.helmholtz-hzi.de:10033/2703752019-08-30T11:34:22Zcom_10033_620636col_10033_620638
Impact of SO(2) on Arabidopsis thaliana transcriptome in wildtype and sulfite oxidase knockout plants analyzed by RNA deep sequencing.
Hamisch, Domenica
Randewig, Dörte
Schliesky, Simon
Bräutigam, Andrea
Weber, Andreas P M
Geffers, Robert
Herschbach, Cornelia
Rennenberg, Heinz
Mendel, Ralf R
Hänsch, Robert
Institut für Pflanzenbiologie, Technische Universität Braunschweig, Braunschweig, Germany.
High concentrations of sulfur dioxide (SO(2) ) as an air pollutant, and its derivative sulfite, cause abiotic stress that can lead to cell death. It is currently unknown to what extent plant fumigation triggers specific transcriptional responses. To address this question, and to test the hypothesis that sulfite oxidase (SO) is acting in SO(2) detoxification, we compared Arabidopsis wildtype (WT) and SO knockout lines (SO-KO) facing the impact of 600 nl l(-1) SO(2) , using RNAseq to quantify absolute transcript abundances. These transcriptome data were correlated to sulfur metabolism-related enzyme activities and metabolites obtained from identical samples in a previous study. SO-KO plants exhibited remarkable and broad regulative responses at the mRNA level, especially in transcripts related to sulfur metabolism enzymes, but also in those related to stress response and senescence. Focusing on SO regulation, no alterations were detectable in the WT, whereas in SO-KO plants we found up-regulation of two splice variants of the SO gene, although this gene is not functional in this line. Our data provide evidence for the highly specific coregulation between SO and sulfur-related enzymes like APS reductase, and suggest two novel candidates for involvement in SO(2) detoxification: an apoplastic peroxidase, and defensins as putative cysteine mass storages.
2013-02-25
2013-02-25
2012-12
Article
Impact of SO(2) on Arabidopsis thaliana transcriptome in wildtype and sulfite oxidase knockout plants analyzed by RNA deep sequencing. 2012, 196 (4):1074-85 New Phytol.
1469-8137
23025405
10.1111/j.1469-8137.2012.04331.x
http://hdl.handle.net/10033/270375
The New phytologist
en
Archived with thanks to The New phytologist
oai:repository.helmholtz-hzi.de:10033/2713042019-08-30T11:31:23Zcom_10033_620636col_10033_620638
t(8;9)(p22;p24)/PCM1-JAK2 Activates SOCS2 and SOCS3 via STAT5.
Ehrentraut, Stefan
Nagel, Stefan
Scherr, Michaela E
Schneider, Björn
Quentmeier, Hilmar
Geffers, Robert
Kaufmann, Maren
Meyer, Corinna
Prochorec-Sobieszek, Monika
Ketterling, Rhett P
Knudson, Ryan A
Feldman, Andrew L
Kadin, Marshall E
Drexler, Hans G
Macleod, Roderick A F
Leibniz Institute, DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Cultures, Braunschweig, Germany.
Fusions of the tyrosine kinase domain of JAK2 with multiple partners occur in leukemia/lymphoma where they reportedly promote JAK2-oligomerization and autonomous signalling, Affected entities are promising candidates for therapy with JAK2 signalling inhibitors. While JAK2-translocations occur in myeloid, B-cell and T-cell lymphoid neoplasms, our findings suggest their incidence among the last group is low. Here we describe the genomic, transcriptional and signalling characteristics of PCM1-JAK2 formed by t(8;9)(p22;p24) in a trio of cell lines established at indolent (MAC-1) and aggressive (MAC-2A/2B) phases of a cutaneous T-cell lymphoma (CTCL). To investigate signalling, PCM1-JAK2 was subjected to lentiviral knockdown which inhibited 7 top upregulated genes in t(8;9) cells, notably SOCS2/3. SOCS3, but not SOCS2, was also upregulated in a chronic eosinophilic leukemia bearing PCM1-JAK2, highlighting its role as a central signalling target of JAK2 translocation neoplasia. Conversely, expression of GATA3, a key T-cell developmental gene silenced in aggressive lymphoma cells, was partially restored by PCM1-JAK2 knockdown. Treatment with a selective JAK2 inhibitor (TG101348) to which MAC-1/2A/2B cells were conspicuously sensitive confirmed knockdown results and highlighted JAK2 as the active moiety. PCM1-JAK2 signalling required pSTAT5, supporting a general paradigm of STAT5 activation by JAK2 alterations in lymphoid malignancies. MAC-1/2A/2B - the first JAK2-translocation leukemia/lymphoma cell lines described - display conspicuous JAK/STAT signalling accompanied by T-cell developmental and autoimmune disease gene expression signatures, confirming their fitness as CTCL disease models. Our data support further investigation of SOCS2/3 as signalling effectors, prognostic indicators and potential therapeutic targets in cancers with JAK2 rearrangements.
2013-03-06
2013-03-06
2013
Article
t(8;9)(p22;p24)/PCM1-JAK2 Activates SOCS2 and SOCS3 via STAT5. 2013, 8 (1):e53767 PLoS ONE
1932-6203
23372669
10.1371/journal.pone.0053767
http://hdl.handle.net/10033/271304
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/2743182019-08-30T11:29:17Zcom_10033_620636col_10033_620638
Efficient Replication of the Novel Human Betacoronavirus EMC on Primary Human Epithelium Highlights Its Zoonotic Potential.
Kindler, Eveline
Jónsdóttir, Hulda R
Muth, Doreen
Hamming, Ole J
Hartmann, Rune
Rodriguez, Regulo
Geffers, Robert
Fouchier, Ron A M
Drosten, Christian
Müller, Marcel A
Dijkman, Ronald
Thiel, Volker
Institute of Immunobiology, Kantonal Hospital, St. Gallen, Switzerland.
ABSTRACT The recent emergence of a novel human coronavirus (HCoV-EMC) in the Middle East raised considerable concerns, as it is associated with severe acute pneumonia, renal failure, and fatal outcome and thus resembles the clinical presentation of severe acute respiratory syndrome (SARS) observed in 2002 and 2003. Like SARS-CoV, HCoV-EMC is of zoonotic origin and closely related to bat coronaviruses. The human airway epithelium (HAE) represents the entry point and primary target tissue for respiratory viruses and is highly relevant for assessing the zoonotic potential of emerging respiratory viruses, such as HCoV-EMC. Here, we show that pseudostratified HAE cultures derived from different donors are highly permissive to HCoV-EMC infection, and by using reverse transcription (RT)-PCR and RNAseq data, we experimentally determined the identity of seven HCoV-EMC subgenomic mRNAs. Although the HAE cells were readily responsive to type I and type III interferon (IFN), we observed neither a pronounced inflammatory cytokine nor any detectable IFN responses following HCoV-EMC, SARS-CoV, or HCoV-229E infection, suggesting that innate immune evasion mechanisms and putative IFN antagonists of HCoV-EMC are operational in the new host. Importantly, however, we demonstrate that both type I and type III IFN can efficiently reduce HCoV-EMC replication in HAE cultures, providing a possible treatment option in cases of suspected HCoV-EMC infection. IMPORTANCE A novel human coronavirus, HCoV-EMC, has recently been described to be associated with severe respiratory tract infection and fatalities, similar to severe acute respiratory syndrome (SARS) observed during the 2002-2003 epidemic. Closely related coronaviruses replicate in bats, suggesting that, like SARS-CoV, HCoV-EMC is of zoonotic origin. Since the animal reservoir and circumstances of zoonotic transmission are yet elusive, it is critically important to assess potential species barriers of HCoV-EMC infection. An important first barrier against invading respiratory pathogens is the epithelium, representing the entry point and primary target tissue of respiratory viruses. We show that human bronchial epithelia are highly susceptible to HCoV-EMC infection. Furthermore, HCoV-EMC, like other coronaviruses, evades innate immune recognition, reflected by the lack of interferon and minimal inflammatory cytokine expression following infection. Importantly, type I and type III interferon treatment can efficiently reduce HCoV-EMC replication in the human airway epithelium, providing a possible avenue for treatment of emerging virus infections.
2013-03-20
2013-03-20
2013
Article
Efficient Replication of the Novel Human Betacoronavirus EMC on Primary Human Epithelium Highlights Its Zoonotic Potential. 2013, 4 (1): MBio
2150-7511
23422412
10.1128/mBio.00611-12
http://hdl.handle.net/10033/274318
mBio
en
Archived with thanks to mBio
oai:repository.helmholtz-hzi.de:10033/2756122019-08-30T11:32:41Zcom_10033_306379com_10033_620636col_10033_306382col_10033_620637
Quantitative Contributions of Target Alteration and Decreased Drug Accumulation to Pseudomonas aeruginosa Fluoroquinolone Resistance.
Bruchmann, Sebastian
Dötsch, Andreas
Nouri, Bianka
Chaberny, Iris F
Häussler, Susanne
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Quinolone antibiotics constitute a clinically successful and widely used class of broad-spectrum antibiotics; however, the emergence and spread of resistance increasingly limits the use of fluoroquinolones in the treatment and management of microbial disease. In this study, we evaluated the quantitative contributions of quinolone target alteration and efflux pump expression to fluoroquinolone resistance in Pseudomonas aeruginosa. We generated isogenic mutations in hot spots of the quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, and parC and inactivated the efflux regulator genes so as to overexpress the corresponding multidrug resistance (MDR) efflux pumps. We then introduced the respective mutations into the reference strain PA14 singly and in various combinations. Whereas the combined inactivation of two efflux regulator-encoding genes did not lead to resistance levels higher than those obtained by inactivation of only one efflux regulator-encoding gene, the combination of mutations leading to increased efflux and target alteration clearly exhibited an additive effect. This combination of target alteration and overexpression of efflux pumps was commonly observed in clinical P. aeruginosa isolates; however, these two mechanisms were frequently found not to be sufficient to explain the level of fluoroquinolone resistance. Our results suggest that there are additional mechanisms, independent of the expression of the MexAB-OprM, MexCD-OprJ, MexEF-OprN, and/or MexXY-OprM efflux pump, that increase ciprofloxacin resistance in isolates with mutations in the QRDRs.
2013-03-21
2013-03-21
2013-03
Article
Quantitative Contributions of Target Alteration and Decreased Drug Accumulation to Pseudomonas aeruginosa Fluoroquinolone Resistance. 2013, 57 (3):1361-8 Antimicrob. Agents Chemother.
1098-6596
23274661
10.1128/AAC.01581-12
http://hdl.handle.net/10033/275612
Antimicrobial agents and chemotherapy
en
info:eu-repo/grantAgreement/EC/FP7/260276/
Archived with thanks to Antimicrobial agents and chemotherapy
openAccess
oai:repository.helmholtz-hzi.de:10033/2795122019-08-30T11:27:16Zcom_10033_620636col_10033_620637
Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites.
Bielecki, Piotr
Komor, Uliana
Bielecka, Agata
Müsken, Mathias
Puchałka, Jacek
Pletz, Mathias W
Ballmann, Manfred
Martins dos Santos, Vítor A P
Weiss, Siegfried
Häussler, Susanne
Bielecki, Piotr
Komor, Uliana
Bielecka, Agata
Müsken, Mathias
Puchałka, Jacek
Pletz, Mathias W
Ballmann, Manfred
Martins dos Santos, Vítor A P
Weiss, Siegfried
Häussler, Susanne
Institute for Molecular Bacteriology, Twincore, Center for Clinical and Experimental Infection Research, a joint venture of the Helmholtz Center of Infection Research and the Hannover Medical School, Hannover, 30625, Germany.
Institute for Molecular Bacteriology, Twincore, Center for Clinical and Experimental Infection Research, a joint venture of the Helmholtz Center of Infection Research and the Hannover Medical School, Hannover, 30625, Germany.
The opportunistic bacterium Pseudomonas aeruginosa is a major nosocomial pathogen causing both devastating acute and chronic persistent infections. During the course of an infection, P. aeruginosa rapidly adapts to the specific conditions within the host. In the present study, we aimed at the identification of genes that are highly expressed during biofilm infections such as in chronically infected lungs of patients with cystic fibrosis (CF), burn wounds and subcutaneous mouse tumours. We found a common subset of differentially regulated genes in all three in vivo habitats and evaluated whether their inactivation impacts on the bacterial capability to form biofilms in vitro and to establish biofilm-associated infections in a murine model. Additive effects on biofilm formation and host colonization were discovered by the combined inactivation of several highly expressed genes. However, even combined inactivation was not sufficient to abolish the establishment of an infection completely. These findings can be interpreted as evidence that either redundant traits encode functions that are essential for in vivo survival and chronic biofilm infections and/or bacterial adaptation is considerably achieved independently of transcription levels. Supplemental screens, will have to be applied in order to identify the minimal set of key genes essential for the establishment of chronic infectious diseases.
The opportunistic bacterium Pseudomonas aeruginosa is a major nosocomial pathogen causing both devastating acute and chronic persistent infections. During the course of an infection, P. aeruginosa rapidly adapts to the specific conditions within the host. In the present study, we aimed at the identification of genes that are highly expressed during biofilm infections such as in chronically infected lungs of patients with cystic fibrosis (CF), burn wounds and subcutaneous mouse tumours. We found a common subset of differentially regulated genes in all three in vivo habitats and evaluated whether their inactivation impacts on the bacterial capability to form biofilms in vitro and to establish biofilm-associated infections in a murine model. Additive effects on biofilm formation and host colonization were discovered by the combined inactivation of several highly expressed genes. However, even combined inactivation was not sufficient to abolish the establishment of an infection completely. These findings can be interpreted as evidence that either redundant traits encode functions that are essential for in vivo survival and chronic biofilm infections and/or bacterial adaptation is considerably achieved independently of transcription levels. Supplemental screens, will have to be applied in order to identify the minimal set of key genes essential for the establishment of chronic infectious diseases.
2013-04-09
2013-04-09
2013-02
Article
Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites. 2013, 15 (2):570-87 Environ. Microbiol.
Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites. 2013, 15 (2):570-87 Environ. Microbiol.
1462-2920
23145907
10.1111/1462-2920.12024
http://hdl.handle.net/10033/279512
Environmental microbiology
Environmental microbiology
en
eu-repo/grantAgreement/EC/FP7/260276
Archived with thanks to Environmental microbiology
openAccess
oai:repository.helmholtz-hzi.de:10033/2798712019-08-30T11:25:11Zcom_10033_620636col_10033_620637
Recycling of Peptidyl-tRNAs by Peptidyl-tRNA Hydrolase Counteracts Azithromycin-Mediated Effects on Pseudomonas aeruginosa.
Gödeke, Julia
Pustelny, Christian
Häussler, Susanne
Gödeke, Julia
Pustelny, Christian
Häussler, Susanne
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.
Acute and chronic infections caused by the opportunistic pathogen Pseudomonas aeruginosa pose a serious threat to human health worldwide, and its increasing resistance to antibiotics requires alternative treatments that are more effective than available strategies. Clinical studies have clearly demonstrated that cystic fibrosis (CF) patients with chronic P. aeruginosa infections benefit from long-term low-dose azithromycin (AZM) treatment. Immunomodulating activity, the impact of AZM on the expression of quorum-sensing-dependent virulence factors, type three secretion, and motility in P. aeruginosa seem to contribute to the therapeutic response. However, to date, the molecular mechanisms underlying these AZM effects have remained elusive. Our data indicate that the AZM-mediated phenotype is caused by a depletion of the intracellular pools of tRNAs available for protein synthesis. Overexpression of the P. aeruginosa peptidyl-tRNA hydrolase, which recycles the tRNA from peptidyl-tRNA drop-off during translation, counteracted the effects of AZM on stationary-phase cell killing, cytotoxicity, and the production of rhamnolipids and partially restored swarming motility. Intriguingly, the exchange of a rare for a frequent codon in rhlR also explicitly diminished the AZM-mediated decreased production of rhamnolipids. These results indicate that depletion of the tRNA pools by AZM seems to affect the translation of genes that use rare aminoacyl-tRNA isoacceptors to a great extent and might explain the selective activity of AZM on the P. aeruginosa proteome and possibly also on the protein expression profiles of other bacterial pathogens.
Acute and chronic infections caused by the opportunistic pathogen Pseudomonas aeruginosa pose a serious threat to human health worldwide, and its increasing resistance to antibiotics requires alternative treatments that are more effective than available strategies. Clinical studies have clearly demonstrated that cystic fibrosis (CF) patients with chronic P. aeruginosa infections benefit from long-term low-dose azithromycin (AZM) treatment. Immunomodulating activity, the impact of AZM on the expression of quorum-sensing-dependent virulence factors, type three secretion, and motility in P. aeruginosa seem to contribute to the therapeutic response. However, to date, the molecular mechanisms underlying these AZM effects have remained elusive. Our data indicate that the AZM-mediated phenotype is caused by a depletion of the intracellular pools of tRNAs available for protein synthesis. Overexpression of the P. aeruginosa peptidyl-tRNA hydrolase, which recycles the tRNA from peptidyl-tRNA drop-off during translation, counteracted the effects of AZM on stationary-phase cell killing, cytotoxicity, and the production of rhamnolipids and partially restored swarming motility. Intriguingly, the exchange of a rare for a frequent codon in rhlR also explicitly diminished the AZM-mediated decreased production of rhamnolipids. These results indicate that depletion of the tRNA pools by AZM seems to affect the translation of genes that use rare aminoacyl-tRNA isoacceptors to a great extent and might explain the selective activity of AZM on the P. aeruginosa proteome and possibly also on the protein expression profiles of other bacterial pathogens.
2013-04-11
2013-04-11
2013-04
Article
Recycling of Peptidyl-tRNAs by Peptidyl-tRNA Hydrolase Counteracts Azithromycin-Mediated Effects on Pseudomonas aeruginosa. 2013, 57 (4):1617-24 Antimicrob. Agents Chemother.
Recycling of Peptidyl-tRNAs by Peptidyl-tRNA Hydrolase Counteracts Azithromycin-Mediated Effects on Pseudomonas aeruginosa. 2013, 57 (4):1617-24 Antimicrob. Agents Chemother.
1098-6596
23318806
10.1128/AAC.02582-12
http://hdl.handle.net/10033/279871
Antimicrobial agents and chemotherapy
Antimicrobial agents and chemotherapy
en
eu-repo/grantAgreement/EC/FP7/260276
Archived with thanks to Antimicrobial agents and chemotherapy
openAccess
oai:repository.helmholtz-hzi.de:10033/2884072019-08-30T11:30:32Zcom_10033_620636col_10033_620638
Lentivirus-induced dendritic cells for immunization against high-risk WT1(+) acute myeloid leukemia.
Sundarasetty, Bala Sai
Singh, Vijay Kumar
Salguero, Gustavo
Geffers, Robert
Rickmann, Mareike
Macke, Laura
Borchers, Sylvia
Figueiredo, Constanca
Schambach, Axel
Gullberg, Urban
Provasi, Elena
Bonini, Chiara
Ganser, Arnold
Woelfel, Thomas
Stripecke, Renata
Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany.
Wilms' tumor 1 antigen (WT1) is overexpressed in acute myeloid leukemia (AML), a high-risk neoplasm warranting development of novel immunotherapeutic approaches. Unfortunately, clinical immunotherapeutic use of WT1 peptides against AML has been inconclusive. With the rationale of stimulating multiantigenic responses against WT1, we genetically programmed long-lasting dendritic cells capable of producing and processing endogenous WT1 epitopes. A tricistronic lentiviral vector co-expressing a truncated form of WT1 (lacking the DNA-binding domain), granulocyte-macrophage colony-stimulating factor (GM-CSF), and interleukin-4 (IL-4) was used to transduce human monocytes ex vivo. Overnight transduction induced self-differentiation of monocytes into immunophenotypically stable "SmartDC/tWT1" (GM-CSF(+), IL-4(+), tWT1(+), IL-6(+), IL-8(+), TNF-α(+), MCP-1(+), HLA-DR(+), CD86(+), CCR2(+), CCR5(+)) that were viable for 3 weeks in vitro. SmartDC/tWT1 were produced with peripheral blood mononuclear cells (PBMC) obtained from an FLT3-ITD(+) AML patient and surplus material from a donor lymphocyte infusion (DLI) and used to expand CD8(+) T cells in vitro. Expanded cytotoxic T lymphocytes (CTLs) showed antigen-specific reactivity against WT1 and against WT1(+) leukemia cells. SmartDC/tWT1 injected s.c. into Nod.Rag1(-/-).IL2rγc(-/-) mice were viable in vivo for more than three weeks. Migration of human T cells (huCTLs) to the immunization site was demonstrated following adoptive transfer of huCTLs into mice immunized with SmartDC/tWT1. Furthermore, SmartDC/tWT1 immunization plus adoptive transfer of T cells reactive against WT1 into mice resulted in growth arrest of a WT1(+) tumor. Gene array analyses of SmartDC/tWT1 demonstrated upregulation of several genes related to innate immunity. Thus, SmartDC/tWT1 can be produced in a single day of ex vivo gene transfer, are highly viable in vivo, and have great potential for use as immunotherapy against malignant transformation overexpressing WT1.
2013-05-02
2013-05-02
2013-02
Article
Lentivirus-induced dendritic cells for immunization against high-risk WT1(+) acute myeloid leukemia. 2013, 24 (2):220-37 Hum. Gene Ther.
1557-7422
23311414
10.1089/hum.2012.128
http://hdl.handle.net/10033/288407
Human gene therapy
en
Archived with thanks to Human gene therapy
oai:repository.helmholtz-hzi.de:10033/2930252019-08-30T11:30:58Zcom_10033_620636col_10033_620665
Immunoglobulins drive terminal maturation of splenic dendritic cells.
Zietara, Natalia
Łyszkiewicz, Marcin
Puchałka, Jacek
Pei, Gang
Gutierrez, Maximiliano Gabriel
Lienenklaus, Stefan
Hobeika, Elias
Reth, Michael
Martins dos Santos, Vitor A P
Krueger, Andreas
Weiss, Siegfried
Department of Molecular Immunology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany. zietara.natalia@mh-hannover.de
Nature and physiological status of antigen-presenting cells, such as dendritic cells DCs, are decisive for the immune reactions elicited. Multiple factors and cell interactions have been described that affect maturation of DCs. Here, we show that DCs arising in the absence of immunoglobulins (Ig) in vivo are impaired in cross-presentation of soluble antigen. This deficiency was due to aberrant cellular targeting of antigen to lysosomes and its rapid degradation. Function of DCs could be restored by transfer of Ig irrespective of antigen specificity and isotype. Modulation of cross-presentation by Ig was inhibited by coapplication of mannan and, thus, likely to be mediated by C-type lectin receptors. This unexpected dependency of splenic DCs on Ig to cross-present antigen provides insights into the interplay between cellular and humoral immunity and the immunomodulatory capacity of Ig.
2013-05-30
2013-05-30
2013-02-05
Article
Immunoglobulins drive terminal maturation of splenic dendritic cells. 2013, 110 (6):2282-7 Proc. Natl. Acad. Sci. U.S.A.
1091-6490
23345431
10.1073/pnas.1210654110
http://hdl.handle.net/10033/293025
Proceedings of the National Academy of Sciences of the United States of America
en
Archived with thanks to Proceedings of the National Academy of Sciences of the United States of America
oai:repository.helmholtz-hzi.de:10033/2930722019-08-30T11:32:41Zcom_10033_6815com_10033_6814com_10033_620636col_10033_6886col_10033_620665
Influence of internalin a murinisation on host resistance to orally acquired listeriosis in mice.
Bergmann, Silke
Beard, Philippa M
Pasche, Bastian
Lienenklaus, Stefan
Weiss, Siegfried
Gahan, Cormac G M
Schughart, Klaus
Lengeling, Andreas
Infection and Immunity Division, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Veterinary Campus, Edinburgh EH25 9RG, UK. andreas.lengeling@roslin.ed.ac.uk.
The bacterial surface protein internalin (InlA) is a major virulence factor of the food-born pathogen Listeria monocytogenes. It plays a critical role in the bacteria crossing the host intestinal barrier by a species-specific interaction with the cell adhesion molecule E-cadherin. In mice, the interaction of InlA with murine E-cadherin is impaired due to sequence-specific binding incompatibilities. We have previously used the approach of 'murinisation' to establish an oral listeriosis infection model in mice by exchanging two amino acid residues in InlA. This dramatically increases binding to mouse E-cadherin. In the present study, we have used bioluminescent murinised and non-murinised Listeria strains to examine the spatiotemporal dissemination of Listeria in four diverse mouse genetic backgrounds after oral inoculation.
2013-05-30
2013-05-30
2013
Article
Influence of internalin a murinisation on host resistance to orally acquired listeriosis in mice. 2013, 13:90 BMC Microbiol.
1471-2180
23617550
10.1186/1471-2180-13-90
http://hdl.handle.net/10033/293072
BMC microbiology
en
Archived with thanks to BMC microbiology
oai:repository.helmholtz-hzi.de:10033/2931492019-08-30T11:25:11Zcom_10033_620636col_10033_620637
The peptide chain release factor methyltransferase PrmC is essential for pathogenicity and environmental adaptation of Pseudomonas aeruginosa PA14.
Pustelny, Christian
Brouwer, Stephan
Müsken, Mathias
Bielecka, Agata
Dötsch, Andreas
Nimtz, Manfred
Häussler, Susanne
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany. Christian.pustelny@helmholtz-hzi.de
Pseudomonas aeruginosa pathogenicity and its capability to adapt to multiple environments are dependent on the production of diverse virulence factors, controlled by the sophisticated quorum sensing (QS) network of P. aeruginosa. To better understand the molecular mechanisms that underlie this adaptation we searched for novel key regulators of virulence factor production by screening a PA14 transposon mutant library for potential candidates acting downstream of the unique 2-alkyl-4-quinolone (AQ) QS system of P. aeruginosa. We focused the work on a protein named HemK with high homology to PrmC of Escherichia coli displaying a similar enzymatic activity (therefore also referred to as PrmC). In this study, we demonstrate that PrmC is an S-adenosyl-l-methionine (AdoMet)-dependent methyltransferase of peptide chain release factors (RFs) essential for the expression of several virulence factors, such as pyocyanin, rhamnolipids and the type III-secreted toxin ExoT. Furthermore, the PA14_prmC mutant strain is unable to grow under anoxic conditions and has a significantly reduced pathogenicity in the infection model Galleria mellonella. Along with transcriptomic and proteomic analyses, the presented data indicate that the methylation of RFs in P. aeruginosa seems to have a global effect on cellular processes related to the virulence of this nosocomial pathogen.
2013-05-31
2013-05-31
2013-02
Article
The peptide chain release factor methyltransferase PrmC is essential for pathogenicity and environmental adaptation of Pseudomonas aeruginosa PA14. 2013, 15 (2):597-609 Environ. Microbiol.
1462-2920
23278968
10.1111/1462-2920.12040
http://hdl.handle.net/10033/293149
Environmental microbiology
en
info:eu-repo/grantAgreement/EC/FP7/260276/
Archived with thanks to Environmental microbiology
openAccess
oai:repository.helmholtz-hzi.de:10033/2979092019-08-30T11:28:23Zcom_10033_620636col_10033_620665
Visualizing the beta interferon response in mice during infection with influenza A viruses expressing or lacking nonstructural protein 1.
Kallfass, Carsten
Lienenklaus, Stefan
Weiss, Siegfried
Staeheli, Peter
Department of Virology, University of Freiburg, Freiburg, Germany.
The innate host defense against influenza virus is largely dependent on the type I interferon (IFN) system. However, surprisingly little is known about the cellular source of IFN in the infected lung. To clarify this question, we employed a reporter mouse that contains the firefly luciferase gene in place of the IFN-β-coding region. IFN-β-producing cells were identified either by simultaneous immunostaining of lungs for luciferase and cellular markers or by generating conditional reporter mice that express luciferase exclusively in defined cell types. Two different strains of influenza A virus were employed that either do or do not code for nonstructural protein 1 (NS1), which strongly suppresses innate immune responses of infected cells. We found that epithelial cells and lung macrophages, which represent the prime host cells for influenza viruses, showed vigorous IFN-β responses which, however, were severely reduced and delayed if the infecting virus was able to produce NS1. Interestingly, CD11c(+) cell populations that were either expressing or lacking macrophage markers produced the bulk of IFN-β at 48 h after infection with wild-type influenza A virus. Our results demonstrate that the virus-encoded IFN-antagonistic factor NS1 disarms specifically epithelial cells and lung macrophages, which otherwise would serve as main mediators of the early response against infection by influenza virus.
2013-08-12
2013-08-12
2013-06
Article
Visualizing the beta interferon response in mice during infection with influenza A viruses expressing or lacking nonstructural protein 1. 2013, 87 (12):6925-30 J. Virol.
1098-5514
23576514
10.1128/JVI.00283-13
http://hdl.handle.net/10033/297909
Journal of virology
en
Archived with thanks to Journal of virology
oai:repository.helmholtz-hzi.de:10033/2980862019-08-30T11:25:43Zcom_10033_620636col_10033_620637
Biofilms 2012: new discoveries and significant wrinkles in a dynamic field.
Haussler, Susanne
Fuqua, Clay
Twincore, Center for Clinical and Experimental Infection Research, a joint venture of the Helmholtz Center of Infection Research, Braunschweig, and the Hannover Medical School, Hannover, Germany.
The ASM 6th Conference on Biofilms was held in Miami, Florida, 29 September to 4 October, 2012. The conference provided an opportunity for the exchange of new findings and ideas with regard to biofilm research. A wide range of findings, spanning applied biology, evolution, ecology, physiology, and molecular biology, were presented at the conference. This review summarizes the presentations with regard to emerging biofilm-related themes.
2013-08-13
2013-08-13
2013-07
Article
Biofilms 2012: new discoveries and significant wrinkles in a dynamic field. 2013, 195 (13):2947-58 J. Bacteriol.
1098-5530
23625847
10.1128/JB.00239-13
http://hdl.handle.net/10033/298086
Journal of bacteriology
en
Archived with thanks to Journal of bacteriology
oai:repository.helmholtz-hzi.de:10033/2982452019-08-30T11:31:23Zcom_10033_620636col_10033_620665
An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters.
Deyneko, Igor V
Weiss, Siegfried
Leschner, Sara
Molecular Immunology, Helmholtz Centre for Infection Research, Inhoffenstr, 7, 38124 Braunschweig, Germany. Igor.Deyneko@helmholtz-hzi.de
Transcriptional activity of genes depends on many factors like DNA motifs, conformational characteristics of DNA, melting etc. and there are computational approaches for their identification. However, in real applications, the number of predicted, for example, DNA motifs may be considerably large. In cases when various computational programs are applied, systematic experimental knock out of each of the potential elements obviously becomes nonproductive. Hence, one needs an approach that is able to integrate many heterogeneous computational methods and upon that suggest selected regulatory elements for experimental verification.
2013-08-14
2013-08-14
2012
Article
An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters. 2012, 13:202 BMC Bioinformatics
1471-2105
22897887
10.1186/1471-2105-13-202
http://hdl.handle.net/10033/298245
BMC bioinformatics
en
Archived with thanks to BMC bioinformatics
oai:repository.helmholtz-hzi.de:10033/2989022019-08-30T11:33:57Zcom_10033_620636col_10033_620638
Mycobacterium tuberculosis isolates from Rio de Janeiro reveal unusually low correlation between pyrazinamide resistance and mutations in the pncA gene.
Bhuju, Sabin
Fonseca, Leila de Souza
Marsico, Anna Grazia
de Oliveira Vieira, Gisele Betzler
Sobral, Luciana Fonseca
Stehr, Matthias
Singh, Mahavir
Saad, Maria Helena Féres
Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany.
It has been widely accepted, that pyrazinamide (PZA) resistance in Mycobacterium tuberculosis is correlated with mutations in the pncA gene. But since years researchers have been puzzled by the fact that up to 30% of PZA resistant strains do not show any correlation between PZA resistance and mutations in the pncA gene, and thus may vary with geographic area. The objective of the study was to investigate the correlation between PZA susceptibility and mutations in pncA gene in M. tuberculosis isolates from individuals living in a highly endemic area. Therefore we analyzed drug resistant and multidrug resistant (MDR) isolates from patients in Rio de Janeiro, Brazil. From a total of 97 clinical isolates of M. tuberculosis 35 were identified as PZA resistant, 24/35 strains did not show PZase activity and 15/24 (62.5%) strains possess mutation in the pncA gene. This is a low correlation between PZA resistance and PZase activity (68.6%) and even lower correlation between PZA resistance and the presence of mutation in pncA gene (45.7%). Most of the mutations found were conserved near the active site or metal binding site of PZase. The 146A>C mutation was found both in PZA resistant and susceptible isolates, suggesting that this mutation may not fully associated with PZA resistance. Of the mutations found, three have not been previously described. The insertions 192-193 TCCTCGTC and 388-389 AGGTCGATG, although found before, here was found to be a short tandem repeat and in one strain, insertion of the IS6110 was observed 55nt upstream of the gene. All PZA resistant isolates had no mutation in the gene coding ribosomal protein S1 (rpsA), which has recently been proposed as alternate target for pyrazinoic acid (POA). The results show a low association of PZA resistance and pncA gene mutations in a selected patient group from an highly endemic area. Our findings point out that the phenotypic susceptibility testing remains important for the detection of PZA-resistant M. tuberculosis.
2013-08-15
2013-08-15
2013-06-14
Article
Mycobacterium tuberculosis isolates from Rio de Janeiro reveal unusually low correlation between pyrazinamide resistance and mutations in the pncA gene. 2013, 19C:1-6 Infect. Genet. Evol.
1567-7257
23770140
10.1016/j.meegid.2013.06.008
http://hdl.handle.net/10033/298902
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
Archived with thanks to Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
oai:repository.helmholtz-hzi.de:10033/2995072019-08-30T11:27:16Zcom_10033_620636col_10033_620638
Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences.
Günther, Katharina
Rust, Mareike
Leers, Joerg
Boettger, Thomas
Scharfe, Maren
Jarek, Michael
Bartkuhn, Marek
Renkawitz, Rainer
Institute for Genetics, Justus-Liebig-University, D35392 Giessen, Germany.
The heterogeneous collection of nucleosome remodelling and deacetylation (NuRD) complexes can be grouped into the MBD2- or MBD3-containing complexes MBD2-NuRD and MBD3-NuRD. MBD2 is known to bind to methylated CpG sequences in vitro in contrast to MBD3. Although functional differences have been described, a direct comparison of MBD2 and MBD3 in respect to genome-wide binding and function has been lacking. Here, we show that MBD2-NuRD, in contrast to MBD3-NuRD, converts open chromatin with euchromatic histone modifications into tightly compacted chromatin with repressive histone marks. Genome-wide, a strong enrichment for MBD2 at methylated CpG sequences is found, whereas CpGs bound by MBD3 are devoid of methylation. MBD2-bound genes are generally lower expressed as compared with MBD3-bound genes. When depleting cells for MBD2, the MBD2-bound genes increase their activity, whereas MBD2 plus MBD3-bound genes reduce their activity. Most strikingly, MBD3 is enriched at active promoters, whereas MBD2 is bound at methylated promoters and enriched at exon sequences of active genes.
2013-08-22
2013-08-22
2013-03-01
Article
Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences. 2013, 41 (5):3010-21 Nucleic Acids Res.
1362-4962
23361464
10.1093/nar/gkt035
http://hdl.handle.net/10033/299507
Nucleic acids research
en
Archived with thanks to Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/2996382019-08-30T11:27:46Zcom_10033_620636col_10033_620665
Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production.
Michelucci, Alessandro
Cordes, Thekla
Ghelfi, Jenny
Pailot, Arnaud
Reiling, Norbert
Goldmann, Oliver
Binz, Tina
Wegner, André
Tallam, Aravind
Rausell, Antonio
Buttini, Manuel
Linster, Carole L
Medina, Eva
Balling, Rudi
Hiller, Karsten
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-Belval, Luxembourg.
Immunoresponsive gene 1 (Irg1) is highly expressed in mammalian macrophages during inflammation, but its biological function has not yet been elucidated. Here, we identify Irg1 as the gene coding for an enzyme producing itaconic acid (also known as methylenesuccinic acid) through the decarboxylation of cis-aconitate, a tricarboxylic acid cycle intermediate. Using a gain-and-loss-of-function approach in both mouse and human immune cells, we found Irg1 expression levels correlating with the amounts of itaconic acid, a metabolite previously proposed to have an antimicrobial effect. We purified IRG1 protein and identified its cis-aconitate decarboxylating activity in an enzymatic assay. Itaconic acid is an organic compound that inhibits isocitrate lyase, the key enzyme of the glyoxylate shunt, a pathway essential for bacterial growth under specific conditions. Here we show that itaconic acid inhibits the growth of bacteria expressing isocitrate lyase, such as Salmonella enterica and Mycobacterium tuberculosis. Furthermore, Irg1 gene silencing in macrophages resulted in significantly decreased intracellular itaconic acid levels as well as significantly reduced antimicrobial activity during bacterial infections. Taken together, our results demonstrate that IRG1 links cellular metabolism with immune defense by catalyzing itaconic acid production.
2013-08-23
2013-08-23
2013-05-07
Article
Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production. 2013, 110 (19):7820-5 Proc. Natl. Acad. Sci. U.S.A.
1091-6490
23610393
10.1073/pnas.1218599110
http://hdl.handle.net/10033/299638
Proceedings of the National Academy of Sciences of the United States of America
en
Archived with thanks to Proceedings of the National Academy of Sciences of the United States of America
oai:repository.helmholtz-hzi.de:10033/3021632019-08-30T11:25:43Zcom_10033_620636col_10033_620665
B-1-cell subpopulations contribute differently to gut immunity.
Roy, Bishnudeo
Agarwal, Shiwani
Brennecke, Anne-Margarete
Krey, Martina
Pabst, Oliver
Düber, Sandra
Weiss, Siegfried
Molecular Immunology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
In mice, B-1 (B1a/B1b) cells are mainly located in the peritoneal cavity. B-1 cells are well known for their role in the early stages of Ab-mediated immune responses against pathogenic invasion as well as for the production of natural IgM antibodies. Although such B cells have been claimed to give rise to intestinal plasma cells producing IgA, a clear role of B-1 cells in IgA production in the gut-associated tissues is still not defined. Here, we employed the transgenic L2 mouse model characterized by the lack of B-2 cells and presence of B-1 cells as major B-cell subpopulation. The oligoclonality of the Ab repertoire in this mouse allowed us to take typical B1a cell VH sequences as indicators of the presence of IgM-producing B-1a cells in Peyer's patches as well as in lamina propria. However, amongst the IgAVH sequences recovered from the same tissues, none of the sequences showed B1a-cell specificity. Interestingly, all IgAVH sequences derived from the lamina propria of L2 mice displayed extensive numbers of nucleotide exchanges, indicating somatic hypermutation, and affinity maturation. This suggests that the contribution of natural unmutated IgA by B-1a cells to intestinal immunity is negligible.
2013-09-24
2013-09-24
2013-08
Article
B-1-cell subpopulations contribute differently to gut immunity. 2013, 43 (8):2023-32 Eur. J. Immunol.
1521-4141
23677546
10.1002/eji.201243070
http://hdl.handle.net/10033/302163
European journal of immunology
en
Archived with thanks to European journal of immunology
oai:repository.helmholtz-hzi.de:10033/3029672019-08-30T11:28:23Zcom_10033_620636col_10033_620665
MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters.
Deyneko, Igor V
Kel, Alexander E
Kel-Margoulis, Olga V
Deineko, Elena V
Wingender, Edgar
Weiss, Siegfried
Department of Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany. Igor.Deyneko@helmholtz-hzi.de
Accurate recognition of regulatory elements in promoters is an essential prerequisite for understanding the mechanisms of gene regulation at the level of transcription. Composite regulatory elements represent a particular type of such transcriptional regulatory elements consisting of pairs of individual DNA motifs. In contrast to the present approach, most available recognition techniques are based purely on statistical evaluation of the occurrence of single motifs. Such methods are limited in application, since the accuracy of recognition is greatly dependent on the size and quality of the sequence dataset. Methods that exploit available knowledge and have broad applicability are evidently needed.
2013-10-08
2013-10-08
2013
Article
MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters. 2013, 14:241 BMC Bioinformatics
1471-2105
23924163
10.1186/1471-2105-14-241
http://hdl.handle.net/10033/302967
BMC bioinformatics
en
Archived with thanks to BMC bioinformatics
oai:repository.helmholtz-hzi.de:10033/3030642019-08-30T11:33:57Zcom_10033_620636col_10033_620665
Mouse SAMHD1 Has Antiretroviral Activity and Suppresses a Spontaneous Cell-Intrinsic Antiviral Response.
Behrendt, Rayk
Schumann, Tina
Gerbaulet, Alexander
Nguyen, Laura A
Schubert, Nadja
Alexopoulou, Dimitra
Berka, Ursula
Lienenklaus, Stefan
Peschke, Katrin
Gibbert, Kathrin
Wittmann, Sabine
Lindemann, Dirk
Weiss, Siegfried
Dahl, Andreas
Naumann, Ronald
Dittmer, Ulf
Kim, Baek
Mueller, Werner
Gramberg, Thomas
Roers, Axel
Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Fetscherstrasse 74, 01307 Dresden, Germany.
Aicardi-Goutières syndrome (AGS), a hereditary autoimmune disease, clinically and biochemically overlaps with systemic lupus erythematosus (SLE) and, like SLE, is characterized by spontaneous type I interferon (IFN) production. The finding that defects of intracellular nucleases cause AGS led to the concept that intracellular accumulation of nucleic acids triggers inappropriate production of type I IFN and autoimmunity. AGS can also be caused by defects of SAMHD1, a 3' exonuclease and deoxynucleotide (dNTP) triphosphohydrolase. Human SAMHD1 is an HIV-1 restriction factor that hydrolyzes dNTPs and decreases their concentration below the levels required for retroviral reverse transcription. We show in gene-targeted mice that also mouse SAMHD1 reduces cellular dNTP concentrations and restricts retroviral replication in lymphocytes, macrophages, and dendritic cells. Importantly, the absence of SAMHD1 triggered IFN-β-dependent transcriptional upregulation of type I IFN-inducible genes in various cell types indicative of spontaneous IFN production. SAMHD1-deficient mice may be instrumental for elucidating the mechanisms that trigger pathogenic type I IFN responses in AGS and SLE.
2013-10-09
2013-10-09
2013-08-29
Article
Mouse SAMHD1 Has Antiretroviral Activity and Suppresses a Spontaneous Cell-Intrinsic Antiviral Response. 2013, 4 (4):689-96 Cell Rep
2211-1247
23972988
10.1016/j.celrep.2013.07.037
http://hdl.handle.net/10033/303064
Cell reports
en
Archived with thanks to Cell reports
oai:repository.helmholtz-hzi.de:10033/3034622019-08-30T11:30:58Zcom_10033_620636col_10033_620638
The degree of liver injury determines the role of p21 in liver regeneration and hepatocarcinogenesis in mice.
Buitrago-Molina, Laura Elisa
Marhenke, Silke
Longerich, Thomas
Sharma, Amar Deep
Boukouris, Aristeidis E
Geffers, Robert
Guigas, Bruno
Manns, Michael P
Vogel, Arndt
Department of Gastroenterology, Hepatology and Endocrinology, Medical School Hannover, Hannover, Germany.
Hepatocellular carcinoma (HCC) frequently arises in the context of chronic injury that promotes DNA damage and chromosomal aberrations. The cyclin-dependent kinase inhibitor p21 is an important transcriptional target of several tumor suppressors, which promotes cell cycle arrest in response to many stimuli. The aim of this study was to further delineate the role of p21 in the liver during moderate and severe injury and to specify its role in the initiation and progression of HCC. Deletion of p21 led to continuous hepatocyte proliferation in mice with severe injury allowing animal survival but also facilitated rapid tumor development, suggesting that control of compensatory proliferation by high levels of p21 is critical to the prevention of tumor development. Unexpectedly, however, liver regeneration and hepatocarcinogenesis was impaired in p21-deficient mice with moderate injury. Mechanistically, loss of p21 was compensated by activation of Sestrin2, which impaired mitogenic mammalian target of rapamycin (mTOR) signaling and activated cytoprotective Nrf2 signaling. Conclusion: The degree of liver injury and the strength of p21 activation determine its effects on liver regeneration and tumor development in the liver. Moreover, our data uncover a molecular link in the complex mTOR, Nrf2, and p53/p21-signaling network through activation of Sestrin2, which regulates hepatocyte proliferation and tumor development in mice with liver injury. (Hepatology 2013;53:1143-1152).
2013-10-15
2013-10-15
2013-09
Article
The degree of liver injury determines the role of p21 in liver regeneration and hepatocarcinogenesis in mice. 2013, 58 (3):1143-52 Hepatology
1527-3350
23526443
10.1002/hep.26412
http://hdl.handle.net/10033/303462
Hepatology (Baltimore, Md.)
en
Archived with thanks to Hepatology (Baltimore, Md.)
oai:repository.helmholtz-hzi.de:10033/3046762019-08-30T11:34:18Zcom_10033_620636col_10033_620638
Archival bone marrow trephines are suitable for high-throughput mutation analysis using next generation sequencing technology.
Hasemeier, Britta
Geffers, Robert
Bartels, Stephan
Schlegelberger, Brigitte
Kreipe, Hans
Lehmann, Ulrich
Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
2013-10-29
2013-10-29
2013-09
Article
Archival bone marrow trephines are suitable for high-throughput mutation analysis using next generation sequencing technology. 2013, 98 (9):e115-6 Haematologica
1592-8721
24006411
10.3324/haematol.2013.091652
http://hdl.handle.net/10033/304676
Haematologica
en
Archived with thanks to Haematologica
Ferrata Storti Foundation
oai:repository.helmholtz-hzi.de:10033/3058762019-08-30T11:30:58Zcom_10033_620636col_10033_620638
Characterization of the p53 cistrome--DNA binding cooperativity dissects p53's tumor suppressor functions.
Schlereth, Katharina
Heyl, Charlotte
Krampitz, Anna-Maria
Mernberger, Marco
Finkernagel, Florian
Scharfe, Maren
Jarek, Michael
Leich, Ellen
Rosenwald, Andreas
Stiewe, Thorsten
Molecular Oncology, Philipps-University, Marburg, Germany.
p53 protects us from cancer by transcriptionally regulating tumor suppressive programs designed to either prevent the development or clonal expansion of malignant cells. How p53 selects target genes in the genome in a context- and tissue-specific manner remains largely obscure. There is growing evidence that the ability of p53 to bind DNA in a cooperative manner prominently influences target gene selection with activation of the apoptosis program being completely dependent on DNA binding cooperativity. Here, we used ChIP-seq to comprehensively profile the cistrome of p53 mutants with reduced or increased cooperativity. The analysis highlighted a particular relevance of cooperativity for extending the p53 cistrome to non-canonical binding sequences characterized by deletions, spacer insertions and base mismatches. Furthermore, it revealed a striking functional separation of the cistrome on the basis of cooperativity; with low cooperativity genes being significantly enriched for cell cycle and high cooperativity genes for apoptotic functions. Importantly, expression of high but not low cooperativity genes was correlated with superior survival in breast cancer patients. Interestingly, in contrast to most p53-activated genes, p53-repressed genes did not commonly contain p53 binding elements. Nevertheless, both the degree of gene activation and repression were cooperativity-dependent, suggesting that p53-mediated gene repression is largely indirect and mediated by cooperativity-dependently transactivated gene products such as CDKN1A, E2F7 and non-coding RNAs. Since both activation of apoptosis genes with non-canonical response elements and repression of pro-survival genes are crucial for p53's apoptotic activity, the cistrome analysis comprehensively explains why p53-induced apoptosis, but not cell cycle arrest, strongly depends on the intermolecular cooperation of p53 molecules as a possible safeguard mechanism protecting from accidental cell killing.
2013-11-28
2013-11-28
2013-08
Article
Characterization of the p53 cistrome--DNA binding cooperativity dissects p53's tumor suppressor functions. 2013, 9 (8):e1003726 PLoS Genet.
1553-7404
23966881
10.1371/journal.pgen.1003726
http://hdl.handle.net/10033/305876
PLoS genetics
en
Archived with thanks to PLoS genetics
oai:repository.helmholtz-hzi.de:10033/3062712019-08-30T11:25:43Zcom_10033_620636col_10033_620638
Planning the human variome project: the Spain report.
Kaput, Jim
Cotton, Richard G H
Hardman, Lauren
Watson, Michael
Al Aqeel, Aida I
Al-Aama, Jumana Y
Al-Mulla, Fahd
Alonso, Santos
Aretz, Stefan
Auerbach, Arleen D
Bapat, Bharati
Bernstein, Inge T
Bhak, Jong
Bleoo, Stacey L
Blöcker, Helmut
Brenner, Steven E
Burn, John
Bustamante, Mariona
Calzone, Rita
Cambon-Thomsen, Anne
Cargill, Michele
Carrera, Paola
Cavedon, Lawrence
Cho, Yoon Shin
Chung, Yeun-Jun
Claustres, Mireille
Cutting, Garry
Dalgleish, Raymond
den Dunnen, Johan T
Díaz, Carlos
Dobrowolski, Steven
dos Santos, M Rosário N
Ekong, Rosemary
Flanagan, Simon B
Flicek, Paul
Furukawa, Yoichi
Genuardi, Maurizio
Ghang, Ho
Golubenko, Maria V
Greenblatt, Marc S
Hamosh, Ada
Hancock, John M
Hardison, Ross
Harrison, Terence M
Hoffmann, Robert
Horaitis, Rania
Howard, Heather J
Barash, Carol Isaacson
Izagirre, Neskuts
Jung, Jongsun
Kojima, Toshio
Laradi, Sandrine
Lee, Yeon-Su
Lee, Jong-Young
Gil-da-Silva-Lopes, Vera L
Macrae, Finlay A
Maglott, Donna
Marafie, Makia J
Marsh, Steven G E
Matsubara, Yoichi
Messiaen, Ludwine M
Möslein, Gabriela
Netea, Mihai G
Norton, Melissa L
Oefner, Peter J
Oetting, William S
O'Leary, James C
de Ramirez, Ana Maria Oller
Paalman, Mark H
Parboosingh, Jillian
Patrinos, George P
Perozzi, Giuditta
Phillips, Ian R
Povey, Sue
Prasad, Suyash
Qi, Ming
Quin, David J
Ramesar, Rajkumar S
Richards, C Sue
Savige, Judith
Scheible, Dagmar G
Scott, Rodney J
Seminara, Daniela
Shephard, Elizabeth A
Sijmons, Rolf H
Smith, Timothy D
Sobrido, María-Jesús
Tanaka, Toshihiro
Tavtigian, Sean V
Taylor, Graham R
Teague, Jon
Töpel, Thoralf
Ullman-Cullere, Mollie
Utsunomiya, Joji
van Kranen, Henk J
Vihinen, Mauno
Webb, Elizabeth
Weber, Thomas K
Yeager, Meredith
Yeom, Young I
Yim, Seon-Hee
Yoo, Hyang-Sook
Division of Personalised Nutrition and Medicine, FDA/National Center for Toxicological Research, Jefferson, Arkansas 72079, USA. James.kaput@fda.hhs.gov
The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.
2013-12-04
2013-12-04
2009-04
Article
Planning the human variome project: the Spain report. 2009, 30 (4):496-510 Hum. Mutat.
1098-1004
19306394
10.1002/humu.20972
http://hdl.handle.net/10033/306271
Human mutation
en
Archived with thanks to Human mutation
oai:repository.helmholtz-hzi.de:10033/3066562019-08-30T11:31:49Zcom_10033_620636col_10033_620638
Inverse PPARβ/δ agonists suppress oncogenic signaling to the ANGPTL4 gene and inhibit cancer cell invasion.
Adhikary, T
Brandt, D T
Kaddatz, K
Stockert, J
Naruhn, S
Meissner, W
Finkernagel, F
Obert, J
Lieber, S
Scharfe, M
Jarek, M
Toth, P M
Scheer, F
Diederich, W E
Reinartz, S
Grosse, R
Müller-Brüsselbach, S
Müller, R
Institute of Molecular Biology and Tumor Research (IMT), Philipps University, Marburg, Germany.
Besides its established functions in intermediary metabolism and developmental processes, the nuclear receptor peroxisome proliferator-activated receptor β/δ (PPARβ/δ) has a less defined role in tumorigenesis. In the present study, we have identified a function for PPARβ/δ in cancer cell invasion. We show that two structurally divergent inhibitory ligands for PPARβ/δ, the inverse agonists ST247 and DG172, strongly inhibit the serum- and transforming growth factor β (TGFβ)-induced invasion of MDA-MB-231 human breast cancer cells into a three-dimensional matrigel matrix. To elucidate the molecular basis of this finding, we performed chromatin immunoprecipitation sequencing (ChIP-Seq) and microarray analyses, which identified the gene encoding angiopoietin-like 4 (ANGPTL4) as the major transcriptional PPARβ/δ target in MDA-MB-231 cells, previously implicated in TGFβ-mediated tumor progression and metastatic dissemination. We show that the induction of ANGPTL4 by TGFβ and other oncogenic signals is strongly repressed by ST247 and DG172 in a PPARβ/δ-dependent fashion, resulting in the inhibition of ANGPTL4 secretion. This effect is attributable to these ligands' ability to induce a dominant transcriptional repressor complex at the site of transcription initiation that blocks preinitiation complex formation through an histone deacetylase-independent, non-canonical mechanism. Repression of ANGPTL4 transcription by inverse PPARβ/δ agonists is functionally linked to the inhibition of cancer cell invasion into a three-dimensional matrix, as (i) invasion of MDA-MB-231 cells is critically dependent on ANGPTL4 expression, (ii) recombinant ANGPTL4 stimulates invasion, and (iii) reverses the inhibitory effect of ST247 and DG172. These findings indicate that a PPARβ/δ-ANGPTL4 pathway is involved in the regulation of tumor cell invasion and that its pharmacological manipulation by inverse PPARβ/δ agonists is feasible.
2013-12-10
2013-12-10
2013-10-31
Article
Inverse PPARβ/δ agonists suppress oncogenic signaling to the ANGPTL4 gene and inhibit cancer cell invasion. 2013, 32 (44):5241-52 Oncogene
1476-5594
23208498
10.1038/onc.2012.549
http://hdl.handle.net/10033/306656
Oncogene
en
Archived with thanks to Oncogene
oai:repository.helmholtz-hzi.de:10033/3109112019-08-30T11:30:31Zcom_10033_620636col_10033_620665
An Intrinsic Propensity of Murine Peritoneal B1b Cells to Switch to IgA in Presence of TGF-β and Retinoic Acid.
Roy, Bishnudeo
Brennecke, Anne-Margarete
Agarwal, Shiwani
Krey, Martina
Düber, Sandra
Weiss, Siegfried
In the present study we have investigated the comparative switching propensity of murine peritoneal and splenic B cell subpopulations to IgA in presence of retinoic acid (RA) and TGF-β.
2014-01-06
2014-01-06
2013
Article
An Intrinsic Propensity of Murine Peritoneal B1b Cells to Switch to IgA in Presence of TGF-β and Retinoic Acid. 2013, 8 (12):e82121 PLoS ONE
1932-6203
24324757
10.1371/journal.pone.0082121
http://hdl.handle.net/10033/310911
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3109752019-08-30T11:25:11Zcom_10033_620636col_10033_620638
SUMOylation of the polycomb group protein L3MBTL2 facilitates repression of its target genes.
Stielow, Christina
Stielow, Bastian
Finkernagel, Florian
Scharfe, Maren
Jarek, Michael
Suske, Guntram
Lethal(3) malignant brain tumour like 2 (L3MBTL2) is an integral component of the polycomb repressive complex 1.6 (PRC1.6) and has been implicated in transcriptional repression and chromatin compaction. Here, we show that L3MBTL2 is modified by SUMO2/3 at lysine residues 675 and 700 close to the C-terminus. SUMOylation of L3MBTL2 neither affected its repressive activity in reporter gene assays nor it's binding to histone tails in vitro. In order to analyse whether SUMOylation affects binding of L3MBTL2 to chromatin, we performed ChIP-Seq analysis with chromatin of wild-type HEK293 cells and with chromatin of HEK293 cells stably expressing either FLAG-tagged SUMOylation-competent or SUMOylation-defective L3MBTL2. Wild-type FLAG-L3MBTL2 and the SUMOylation-defective FLAG-L3MBTL2 K675/700R mutant essentially occupied the same sites as endogenous L3MBTL2 suggesting that SUMOylation of L3MBTL2 does not affect chromatin binding. However, a subset of L3MBTL2-target genes, particularly those with low L3MBTL2 occupancy including pro-inflammatory genes, was de-repressed in cells expressing the FLAG-L3MBTL2 K675/700R mutant. Finally, we provide evidence that SUMOylation of L3MBTL2 facilitates repression of these PRC1.6-target genes by balancing the local H2Aub1 levels established by the ubiquitinating enzyme RING2 and the de-ubiquitinating PR-DUB complex.
2014-01-07
2014-01-07
2013-12-24
Article
SUMOylation of the polycomb group protein L3MBTL2 facilitates repression of its target genes. 2013: Nucleic Acids Res.
1362-4962
24369422
10.1093/nar/gkt1317
http://hdl.handle.net/10033/310975
Nucleic acids research
Archived with thanks to Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/3110232019-08-30T11:25:43Zcom_10033_620636col_10033_620638
Human Host Defense Peptide LL-37 Stimulates Virulence Factor Production and Adaptive Resistance in Pseudomonas aeruginosa.
Strempel, Nikola
Neidig, Anke
Nusser, Michael
Geffers, Robert
Vieillard, Julien
Lesouhaitier, Olivier
Brenner-Weiss, Gerald
Overhage, Joerg
Research group genomeanalytics, Helmholtz Centre for infection research, Braunschweig, Germany
A multitude of different virulence factors as well as the ability to rapidly adapt to adverse environmental conditions are important features for the high pathogenicity of Pseudomonas aeruginosa. Both virulence and adaptive resistance are tightly controlled by a complex regulatory network and respond to external stimuli, such as host signals or antibiotic stress, in a highly specific manner. Here, we demonstrate that physiological concentrations of the human host defense peptide LL-37 promote virulence factor production as well as an adaptive resistance against fluoroquinolone and aminoglycoside antibiotics in P. aeruginosa PAO1. Microarray analyses of P. aeruginosa cells exposed to LL-37 revealed an upregulation of gene clusters involved in the production of quorum sensing molecules and secreted virulence factors (PQS, phenazine, hydrogen cyanide (HCN), elastase and rhamnolipids) and in lipopolysaccharide (LPS) modification as well as an induction of genes encoding multidrug efflux pumps MexCD-OprJ and MexGHI-OpmD. Accordingly, we detected significantly elevated levels of toxic metabolites and proteases in bacterial supernatants after LL-37 treatment. Pre-incubation of bacteria with LL-37 for 2 h led to a decreased susceptibility towards gentamicin and ciprofloxacin. Quantitative Realtime PCR results using a PAO1-pqsE mutant strain present evidence that the quinolone response protein and virulence regulator PqsE may be implicated in the regulation of the observed phenotype in response to LL-37. Further experiments with synthetic cationic antimicrobial peptides IDR-1018, 1037 and HHC-36 showed no induction of pqsE expression, suggesting a new role of PqsE as highly specific host stress sensor.
2014-01-07
2014-01-07
2013
Article
Human Host Defense Peptide LL-37 Stimulates Virulence Factor Production and Adaptive Resistance in Pseudomonas aeruginosa. 2013, 8 (12):e82240 PLoS ONE
1932-6203
24349231
10.1371/journal.pone.0082240
http://hdl.handle.net/10033/311023
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3113322019-08-30T11:27:16Zcom_10033_620636col_10033_620638
Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1).
Hämmerle, Monika
Gutschner, Tony
Uckelmann, Hannah
Ozgur, Sevim
Fiskin, Evgenij
Gross, Matthias
Skawran, Britta
Geffers, Robert
Longerich, Thomas
Breuhahn, Kai
Schirmacher, Peter
Stoecklin, Georg
Diederichs, Sven
AG Genomanalytic, Hemholtz Centre for Infection research, D38124 Braunschweig, Germany
Selected long noncoding RNAs (lncRNAs) have been shown to play important roles in carcinogenesis. Although the cellular functions of these transcripts can be diverse, many lncRNAs regulate gene expression. In contrast, factors that control the expression of lncRNAs remain largely unknown. Here we investigated the impact of RNA binding proteins on the expression of the liver cancer-associated lncRNA HULC (highly up-regulated in liver cancer). First, we validated the strong up-regulation of HULC in human hepatocellular carcinoma. To elucidate posttranscriptional regulatory mechanisms governing HULC expression, we applied an RNA affinity purification approach to identify specific protein interaction partners and potential regulators. This method identified the family of IGF2BPs (IGF2 mRNA-binding proteins) as specific binding partners of HULC. Depletion of IGF2BP1, also known as IMP1, but not of IGF2BP2 or IGF2BP3, led to an increased HULC half-life and higher steady-state expression levels, indicating a posttranscriptional regulatory mechanism. Importantly, HULC represents the first IGF2BP substrate that is destabilized. To elucidate the mechanism by which IGF2BP1 destabilizes HULC, the CNOT1 protein was identified as a novel interaction partner of IGF2BP1. CNOT1 is the scaffold of the human CCR4-NOT deadenylase complex, a major component of the cytoplasmic RNA decay machinery. Indeed, depletion of CNOT1 increased HULC half-life and expression. Thus, IGF2BP1 acts as an adaptor protein that recruits the CCR4-NOT complex and thereby initiates the degradation of the lncRNA HULC. Conclusion: Our findings provide important insights into the regulation of lncRNA expression and identify a novel function for IGF2BP1 in RNA metabolism. (Hepatology 2013).
2014-01-15
2014-01-15
2013-05-31
Article
Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1). 2013: Hepatology
1527-3350
23728852
10.1002/hep.26537
http://hdl.handle.net/10033/311332
Hepatology (Baltimore, Md.)
Archived with thanks to Hepatology (Baltimore, Md.)
oai:repository.helmholtz-hzi.de:10033/3119392019-08-30T11:25:11Zcom_10033_620636col_10033_620637
Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265.
Eckweiler, Denitsa
Bunk, Boyke
Spröer, Cathrin
Overmann, Jörg
Häussler, Susanne
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
The evolution of small-colony variants within Pseudomonas aeruginosa populations chronically infecting the cystic fibrosis lung is one example of the emergence of adapted subpopulations. Here, we present the complete genome sequence of the autoaggregative and hyperpiliated P. aeruginosa small-colony variant SCV20265, which was isolated from a cystic fibrosis (CF) patient.
2014-01-28
2014-01-28
2014
Article
Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265. 2014, 2 (1): Genome Announc
2169-8287
24459283
10.1128/genomeA.01232-13
http://hdl.handle.net/10033/311939
Genome announcements
en
info:eu-repo/grantAgreement/EC/FP7/260276
openAccess
oai:repository.helmholtz-hzi.de:10033/3170632019-08-30T11:30:58Zcom_10033_620636col_10033_620665
Systemic and Mucosal Immune Reactivity upon Mycobacterium avium ssp. paratuberculosis Infection in Mice.
Koc, Arzu
Bargen, Imke
Suwandi, Abdulhadi
Roderfeld, Martin
Tschuschner, Annette
Rath, Timo
Gerlach, Gerald F
Hornef, Mathias
Goethe, Ralph
Weiss, Siegfried
Roeb, Elke
RG molecular immunology, Helmholtz Centre for infection research, D-38124 Braunschweig, Germany.
Mycobacterium avium ssp. paratuberculosis (MAP) is the cause of Johne's disease, an inflammatory bowel disorder of ruminants. Due to the similar pathology, MAP was also suggested to cause Crohn's disease (CD). Despite of intensive research, this question is still not settled, possibly due to the lack of versatile mouse models. The aim of this study was to identify basic immunologic mechanisms in response to MAP infection. Immune compromised C57BL/6 Rag2-/- mice were infected with MAP intraperitoneally. Such chronically infected mice were then reconstituted with CD4+ and CD8+ T cells 28 days after infection. A systemic inflammatory response, detected as enlargement of the spleen and granuloma formation in the liver, was observed in mice infected and reconstituted with CD4+ T cells. Whereby inflammation in infected and CD4+CD45RBhi T cell reconstituted animals was always higher than in the other groups. Reconstitution of infected animals with CD8+ T cells did not result in any inflammatory signs. Interestingly, various markers of inflammation were strongly up-regulated in the colon of infected mice reconstituted with CD4+CD45RBlo/int T cells. We propose, the usual non-colitogenic CD4+CD45RBlo/int T cells were converted into inflammatory T cells by the interaction with MAP. However, the power of such cells might be not sufficient for a fully established inflammatory response in the colon. Nevertheless, our model system appears to mirror aspects of an inflammatory bowel disease (IBD) like CD and Johne's diseases. Thus, it will provide an experimental platform on which further knowledge on IBD and the involvement of MAP in the induction of CD could be acquired.
2014-05-16
2014-05-16
2014
Article
Systemic and Mucosal Immune Reactivity upon Mycobacterium avium ssp. paratuberculosis Infection in Mice. 2014, 9 (4):e94624 PLoS ONE
1932-6203
24728142
10.1371/journal.pone.0094624
http://hdl.handle.net/10033/317063
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3172372019-08-30T11:25:43Zcom_10033_620636col_10033_620638
From Human Monocytes to Genome-Wide Binding Sites - A Protocol for Small Amounts of Blood: Monocyte Isolation/ChIP-Protocol/Library Amplification/Genome Wide Computational Data Analysis.
Weiterer, Sebastian
Uhle, Florian
Bhuju, Sabin
Jarek, Michael
Weigand, Markus A
Bartkuhn, Marek
Chromatin immunoprecipitation in combination with a genome-wide analysis via high-throughput sequencing is the state of the art method to gain genome-wide representation of histone modification or transcription factor binding profiles. However, chromatin immunoprecipitation analysis in the context of human experimental samples is limited, especially in the case of blood cells. The typically extremely low yields of precipitated DNA are usually not compatible with library amplification for next generation sequencing. We developed a highly reproducible protocol to present a guideline from the first step of isolating monocytes from a blood sample to analyse the distribution of histone modifications in a genome-wide manner. Conclusion: The protocol describes the whole work flow from isolating monocytes from human blood samples followed by a high-sensitivity and small-scale chromatin immunoprecipitation assay with guidance for generating libraries compatible with next generation sequencing from small amounts of immunoprecipitated DNA.
2014-05-21
2014-05-21
2014
Article
From Human Monocytes to Genome-Wide Binding Sites - A Protocol for Small Amounts of Blood: Monocyte Isolation/ChIP-Protocol/Library Amplification/Genome Wide Computational Data Analysis. 2014, 9 (4):e94164 PLoS ONE
1932-6203
24732314
10.1371/journal.pone.0094164
http://hdl.handle.net/10033/317237
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3173872019-08-30T11:36:05Zcom_10033_620636col_10033_620637
Effects of green tea compound epigallocatechin-3-gallate against Stenotrophomonas maltophilia infection and biofilm.
Vidigal, Pedrina G
Müsken, Mathias
Becker, Katrin A
Häussler, Susanne
Wingender, Jost
Steinmann, Eike
Kehrmann, Jan
Gulbins, Erich
Buer, Jan
Rath, Peter Michael
Steinmann, Jörg
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
We investigated the in vitro and in vivo activities of epigallocatechin-3-gallate (EGCg), a green tea component, against Stenotrophomonas maltophilia (Sm) isolates from cystic fibrosis (CF) patients. In vitro effects of EGCg and the antibiotic colistin (COL) on growth inhibition, survival, and also against young and mature biofilms of S. maltophilia were determined. Qualitative and quantitative changes on the biofilms were assessed by confocal laser scanning microscopy (CLSM). Further, in vivo effects of nebulized EGCg in C57BL/6 and Cftr mutant mice during acute Sm lung infection were evaluated. Subinhibitory concentrations of EGCg significantly reduced not only biofilm formation, but also the quantity of viable cells in young and mature biofilms. CLSM showed that EGCg-exposed biofilms exhibited either a change in total biofilm biovolume or an increase of the fraction of dead cells contained within the biofilm in a dose depended manner. Sm infected wild-type and Cftr mutant mice treated with 1,024 mg/L EGCg by inhalation exhibited significantly lower bacterial counts than those undergoing no treatment or treated with COL. EGCg displayed promising inhibitory and anti-biofilm properties against CF Sm isolates in vitro and significantly reduced Sm bacterial counts in an acute infection model with wild type and CF mice. This natural compound may represent a novel therapeutic agent against Sm infection in CF.
2014-05-23
2014-05-23
2014
Article
Effects of green tea compound epigallocatechin-3-gallate against Stenotrophomonas maltophilia infection and biofilm. 2014, 9 (4):e92876 PLoS ONE
1932-6203
24690894
10.1371/journal.pone.0092876
http://hdl.handle.net/10033/317387
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3219712019-08-30T11:36:33Zcom_10033_620636col_10033_620638
A replication study for genome-wide gene expression levels in two layer lines elucidates differentially expressed genes of pathways involved in bone remodeling and immune responsiveness.
Habig, Christin
Geffers, Robert
Distl, Ottmar
The current replication study confirmed significant differences in gene expression profiles of the cerebrum among the two commercial layer lines Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB). Microarray analyses were performed for 30 LSL and another 30 LB laying hens kept in the small group housing system Eurovent German. A total of 14,103 microarray probe sets using customized Affymetrix ChiGene-1_0-st Arrays with 20,399 probe sets were differentially expressed among the two layer lines LSL and LB (FDR adjusted P-value <0.05). An at least 2-fold change in expression levels could be observed for 388 of these probe sets. In LSL, 214 of the 388 probe sets were down- and 174 were up-regulated and vice versa for the LB layer line. Among the 174 up-regulated probe sets in LSL, we identified 51 significantly enriched Gene ontology (GO) terms of the biological process category. A total of 63 enriched GO-terms could be identified for the 214 down-regulated probe sets of the layer line LSL. We identified nine genes significantly differentially expressed between the two layer lines in both microarray experiments. These genes play a crucial role in protection of neuronal cells from oxidative stress, bone mineral density and immune response among the two layer lines LSL and LB. Thus, the different regulation of these genes may significantly contribute to phenotypic trait differences among these layer lines. In conclusion, these novel findings provide a basis for further research to improve animal welfare in laying hens and these layer lines may be of general interest as an animal model.
2014-06-19
2014-06-19
2014
Article
A replication study for genome-wide gene expression levels in two layer lines elucidates differentially expressed genes of pathways involved in bone remodeling and immune responsiveness. 2014, 9 (6):e98350 PLoS ONE
1932-6203
24922511
10.1371/journal.pone.0098350
http://hdl.handle.net/10033/321971
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3219732019-08-30T11:32:17Zcom_10033_620636col_10033_620638
Impact of MLL5 expression on decitabine efficacy and DNA methylation in acute myeloid leukemia.
Yun, Haiyang
Damm, Frederik
Yap, Damian
Schwarzer, Adrian
Chaturvedi, Anuhar
Jyotsana, Nidhi
Lübbert, Michael
Bullinger, Lars
Döhner, Konstanze
Geffers, Robert
Aparicio, Samuel
Humphries, R Keith
Ganser, Arnold
Heuser, Michael
Hypomethylating agents are widely used in patients with myelodysplastic syndromes and unfit patients with acute myeloid leukemia. However, it is not well understood why only some patients respond to hypomethylating agents. We found previously that the effect of decitabine on hematopoietic stem cell viability differed between Mll5 wildtype and null cells. We therefore investigated the role of MLL5 expression levels on outcome of acute myeloid leukemia patients who were treated with decitabine. MLL5 above the median expression level predicted longer overall survival independent of DNMT3A mutation status in bivariate analysis (median overall survival for high vs. low MLL5 expression, 292 vs. 167 days, P=.026). In patients who received 3 or more courses decitabine, high MLL5 expression and wildtype DNMT3A independently predicted improved overall survival (median overall survival for high vs. low MLL5 expression, 468 vs. 243 days, P=.012). In transformed murine cells, loss of Mll5 was associated with resistance to low-dose decitabine, less global DNA methylation in promoter regions, and reduced DNA demethylation upon decitabine treatment. Together, these data support our clinical observation of improved outcome in decitabine treated patients who express MLL5 at high levels, and suggest a mechanistic role of MLL5 in the regulation of DNA methylation.
2014-06-19
2014-06-19
2014-06-03
Article
Impact of MLL5 expression on decitabine efficacy and DNA methylation in acute myeloid leukemia. 2014: Haematologica
1592-8721
24895338
10.3324/haematol.2013.101386
http://hdl.handle.net/10033/321973
Haematologica
Archived with thanks to Haematologica
oai:repository.helmholtz-hzi.de:10033/3235142019-08-30T11:32:16Zcom_10033_620636col_10033_620638
Chromera velia, endosymbioses and the rhodoplex hypothesis--plastid evolution in cryptophytes, alveolates, stramenopiles, and haptophytes (CASH lineages).
Petersen, Jörn
Ludewig, Ann-Kathrin
Michael, Victoria
Bunk, Boyke
Jarek, Michael
Baurain, Denis
Brinkmann, Henner
The discovery of Chromera velia, a free-living photosynthetic relative of apicomplexan pathogens, has provided an unexpected opportunity to study the algal ancestry of malaria parasites. In this work, we compared the molecular footprints of a eukaryote-to-eukaryote endosymbiosis in C. velia to their equivalents in peridinin-containing dinoflagellates (PCD) to reevaluate recent claims in favor of a common ancestry of their plastids. To this end, we established the draft genome and a set of full-length cDNA sequences from C. velia via next-generation sequencing. We documented the presence of a single coxI gene in the mitochondrial genome, which thus represents the genetically most reduced aerobic organelle identified so far, but focused our analyses on five "lucky genes" of the Calvin cycle. These were selected because of their known support for a common origin of complex plastids from cryptophytes, alveolates (represented by PCDs), stramenopiles, and haptophytes (CASH) via a single secondary endosymbiosis with a red alga. As expected, our broadly sampled phylogenies of the nuclear-encoded Calvin cycle markers support a rhodophycean origin for the complex plastid of Chromera. However, they also suggest an independent origin of apicomplexan and dinophycean (PCD) plastids via two eukaryote-to-eukaryote endosymbioses. Although at odds with the current view of a common photosynthetic ancestry for alveolates, this conclusion is nonetheless in line with the deviant plastome architecture in dinoflagellates and the morphological paradox of four versus three plastid membranes in the respective lineages. Further support for independent endosymbioses is provided by analysis of five additional markers, four of them involved in the plastid protein import machinery. Finally, we introduce the "rhodoplex hypothesis" as a convenient way to designate evolutionary scenarios where CASH plastids are ultimately the product of a single secondary endosymbiosis with a red alga but were subsequently horizontally spread via higher-order eukaryote-to-eukaryote endosymbioses.
2014-07-21
2014-07-21
2014-03
Article
Chromera velia, endosymbioses and the rhodoplex hypothesis--plastid evolution in cryptophytes, alveolates, stramenopiles, and haptophytes (CASH lineages). 2014, 6 (3):666-84 Genome Biol Evol
1759-6653
24572015
10.1093/gbe/evu043
http://hdl.handle.net/10033/323514
Genome biology and evolution
en
Archived with thanks to Genome biology and evolution
oai:repository.helmholtz-hzi.de:10033/3247642019-08-30T11:30:32Zcom_10033_620636col_10033_620665
Influence of infection route and virulence factors on colonization of solid tumors by Salmonella enterica serovar Typhimurium.
Crull, Katja
Bumann, Dirk
Weiss, Siegfried
Dept. Molecular Immunology, Helmholtz Centre for infection research, Inhoffenstr. 7, D38124 Braunschweig, Germany.
Administration of facultative anaerobic bacteria such as Salmonella enterica serovar Typhimurium as anticancer treatment holds a great therapeutic potential. Here, we tested different routes of application of S. typhimurium with regard to tumor colonization and therapeutic efficacy. No differences between intravenous and intraperitoneal infection were observed, often leading to a complete tumor clearance. In contrast, after oral application, tumor colonization was inefficient and delayed. No therapeutic effect was observed under such conditions. We also showed that tumor invasion and colonization were independent of functional Salmonella pathogenicity island (SPI) 1 and SPI 2. Furthermore, tumor invasion and colonization did not require bacterial motility or chemotactic responsiveness. The distribution of the bacteria within the tumor was independent of such functions.
2014-08-13
2014-08-13
2011-06
Article
Influence of infection route and virulence factors on colonization of solid tumors by Salmonella enterica serovar Typhimurium. 2011, 62 (1):75-83 FEMS Immunol. Med. Microbiol.
1574-695X
21314734
10.1111/j.1574-695X.2011.00790.x
http://hdl.handle.net/10033/324764
FEMS immunology and medical microbiology
en
Archived with thanks to FEMS immunology and medical microbiology
oai:repository.helmholtz-hzi.de:10033/3260562019-08-30T11:31:23Zcom_10033_620636col_10033_620665
Tumor invasion of Salmonella enterica serovar Typhimurium is accompanied by strong hemorrhage promoted by TNF-alpha.
Leschner, Sara
Westphal, Kathrin
Dietrich, Nicole
Viegas, Nuno
Jablonska, Jadwiga
Lyszkiewicz, Marcin
Lienenklaus, Stefan
Falk, Werner
Gekara, Nelson
Loessner, Holger
Weiss, Siegfried
Several facultative anaerobic bacteria with potential therapeutic abilities are known to preferentially colonize solid tumors after systemic administration. How they efficiently find and invade the tumors is still unclear. However, this is an important issue to be clarified when bacteria should be tailored for application in cancer therapy.
2014-09-11
2014-09-11
2009
Article
Tumor invasion of Salmonella enterica serovar Typhimurium is accompanied by strong hemorrhage promoted by TNF-alpha. 2009, 4 (8):e6692 PLoS ONE
1932-6203
19693266
10.1371/journal.pone.0006692
http://hdl.handle.net/10033/326056
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3344052019-08-30T11:31:23Zcom_10033_620636col_10033_620665
The arginine-ornithine antiporter ArcD contributes to biological fitness of Streptococcus suis.
Fulde, Marcus
Willenborg, Joerg
Huber, Claudia
Hitzmann, Angela
Willms, Daniela
Seitz, Maren
Eisenreich, Wolfgang
Valentin-Weigand, Peter
Goethe, Ralph
Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover, Germany ; Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI) Braunschweig, Germany.
The arginine-ornithine antiporter (ArcD) is part of the Arginine Deiminase System (ADS), a catabolic, energy-providing pathway found in a variety of different bacterial species, including the porcine zoonotic pathogen Streptococcus suis. The ADS has recently been shown to play a role in the pathogenicity of S. suis, in particular in its survival in host cells. The contribution of arginine and arginine transport mediated by ArcD, however, has yet to be clarified. In the present study, we showed by experiments using [U-(13)C6]arginine as a tracer molecule that S. suis is auxotrophic for arginine and that bacterial growth depends on the uptake of extracellular arginine. To further study the role of ArcD in arginine metabolism, we generated an arcD-specific mutant strain and characterized its growth compared to the wild-type (WT) strain, a virulent serotype 2 strain. The mutant strain showed a markedly reduced growth in chemically defined media supplemented with arginine when compared to the WT strain, suggesting that ArcD promotes arginine uptake. To further evaluate the in vivo relevance of ArcD, we studied the intracellular bacterial survival of the arcD mutant strain in an epithelial cell culture infection model. The mutant strain was substantially attenuated, and its reduced intracellular survival rate correlated with a lower ability to neutralize the acidified environment. Based on these results, we propose that ArcD, by its function as an arginine-ornithine antiporter, is important for supplying arginine as substrate of the ADS and, thereby, contributes to biological fitness and virulence of S. suis in the host.
2014-11-10
2014-11-10
2014
Article
The arginine-ornithine antiporter ArcD contributes to biological fitness of Streptococcus suis. 2014, 4:107 Front Cell Infect Microbiol
2235-2988
25161959
10.3389/fcimb.2014.00107
http://hdl.handle.net/10033/334405
Frontiers in cellular and infection microbiology
en
oai:repository.helmholtz-hzi.de:10033/3344792019-08-30T11:31:23Zcom_10033_620636col_10033_620665
The Mycobacterium avium ssp. paratuberculosis specific mptD gene is required for maintenance of the metabolic homeostasis necessary for full virulence in mouse infections.
Meißner, Thorsten
Eckelt, Elke
Basler, Tina
Meens, Jochen
Heinzmann, Julia
Suwandi, Abdulhadi
Oelemann, Walter M R
Trenkamp, Sandra
Holst, Otto
Weiss, Siegfried
Bunk, Boyke
Spröer, Cathrin
Gerlach, Gerald-F
Goethe, Ralph
Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover Hannover, Germany.
Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne's disease, a chronic granulomatous enteritis in ruminants. Furthermore, infections of humans with MAP have been reported and a possible association with Crohn's disease and diabetes type I is currently discussed. MAP owns large sequence polymorphisms (LSPs) that were exclusively found in this mycobacteria species. The relevance of these LSPs in the pathobiology of MAP is still unclear. The mptD gene (MAP3733c) of MAP belongs to a small group of functionally uncharacterized genes, which are not present in any other sequenced mycobacteria species. mptD is part of a predicted operon (mptABCDEF), encoding a putative ATP binding cassette-transporter, located on the MAP-specific LSP14. In the present study, we generated an mptD knockout strain (MAPΔmptD) by specialized transduction. In order to investigate the potential role of mptD in the host, we performed infection experiments with macrophages. By this, we observed a significantly reduced cell number of MAPΔmptD early after infection, indicating that the mutant was hampered with respect to adaptation to the early macrophage environment. This important role of mptD was supported in mouse infection experiments where MAPΔmptD was significantly attenuated after peritoneal challenge. Metabolic profiling was performed to determine the cause for the reduced virulence and identified profound metabolic disorders especially in the lipid metabolism of MAPΔmptD. Overall our data revealed the mptD gene to be an important factor for the metabolic adaptation of MAP required for persistence in the host.
2014-11-11
2014-11-11
2014
Article
The Mycobacterium avium ssp. paratuberculosis specific mptD gene is required for maintenance of the metabolic homeostasis necessary for full virulence in mouse infections. 2014, 4:110 Front Cell Infect Microbiol
2235-2988
25177550
10.3389/fcimb.2014.00110
http://hdl.handle.net/10033/334479
Frontiers in cellular and infection microbiology
en
oai:repository.helmholtz-hzi.de:10033/3379622019-08-30T11:32:17Zcom_10033_620636col_10033_620638
A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking.
Bohla, Dorte
Herold, Martin
Panzer, Imke
Buxa, Melanie K
Ali, Tamer
Demmers, Jeroen
Krüger, Marcus
Scharfe, Maren
Jarek, Michael
Bartkuhn, Marek
Renkawitz, Rainer
Helmholtz Centre for ifection research, Innhoffenstr. 7, D38124 Braunschweig, Germany.
Chromatin insulators of higher eukaryotes functionally divide the genome into active and inactive domains. Furthermore, insulators regulate enhancer/promoter communication, which is evident from the Drosophila bithorax locus in which a multitude of regulatory elements control segment specific gene activity. Centrosomal protein 190 (CP190) is targeted to insulators by CTCF or other insulator DNA-binding factors. Chromatin analyses revealed that insulators are characterized by open and nucleosome depleted regions. Here, we wanted to identify chromatin modification and remodelling factors required for an enhancer blocking function. We used the well-studied Fab-8 insulator of the bithorax locus to apply a genome-wide RNAi screen for factors that contribute to the enhancer blocking function of CTCF and CP190. Among 78 genes required for optimal Fab-8 mediated enhancer blocking, all four components of the NURF complex as well as several subunits of the dREAM complex were most evident. Mass spectrometric analyses of CTCF or CP190 bound proteins as well as immune precipitation confirmed NURF and dREAM binding. Both co-localise with most CP190 binding sites in the genome and chromatin immune precipitation showed that CP190 recruits NURF and dREAM. Nucleosome occupancy and histone H3 binding analyses revealed that CP190 mediated NURF binding results in nucleosomal depletion at CP190 binding sites. Thus, we conclude that CP190 binding to CTCF or to other DNA binding insulator factors mediates recruitment of NURF and dREAM. Furthermore, the enhancer blocking function of insulators is associated with nucleosomal depletion and requires NURF and dREAM.
2015-01-09
2015-01-09
2014
Article
A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking. 2014, 9 (9):e107765 PLoS ONE
1932-6203
25247414
10.1371/journal.pone.0107765
http://hdl.handle.net/10033/337962
PloS one
en
oai:repository.helmholtz-hzi.de:10033/3380202019-08-30T11:25:11Zcom_10033_620636col_10033_620637
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles.
Bielecki, Piotr
Muthukumarasamy, Uthayakumar
Eckweiler, Denitsa
Bielecka, Agata
Pohl, Sarah
Schanz, Ansgar
Niemeyer, Ute
Oumeraci, Tonio
von Neuhoff, Nils
Ghigo, Jean-Marc
Häussler, Susanne
Helmholtz Centre for infection research; Inhoffenstr. 7; D-38124 Braunschweig; Germany.
mRNA profiling of pathogens during the course of human infections gives detailed information on the expression levels of relevant genes that drive pathogenicity and adaptation and at the same time allows for the delineation of phylogenetic relatedness of pathogens that cause specific diseases. In this study, we used mRNA sequencing to acquire information on the expression of Escherichia coli pathogenicity genes during urinary tract infections (UTI) in humans and to assign the UTI-associated E. coli isolates to different phylogenetic groups. Whereas the in vivo gene expression profiles of the majority of genes were conserved among 21 E. coli strains in the urine of elderly patients suffering from an acute UTI, the specific gene expression profiles of the flexible genomes was diverse and reflected phylogenetic relationships. Furthermore, genes transcribed in vivo relative to laboratory media included well-described virulence factors, small regulatory RNAs, as well as genes not previously linked to bacterial virulence. Knowledge on relevant transcriptional responses that drive pathogenicity and adaptation of isolates to the human host might lead to the introduction of a virulence typing strategy into clinical microbiology, potentially facilitating management and prevention of the disease. Importance: Urinary tract infections (UTI) are very common; at least half of all women experience UTI, most of which are caused by pathogenic Escherichia coli strains. In this study, we applied massive parallel cDNA sequencing (RNA-seq) to provide unbiased, deep, and accurate insight into the nature and the dimension of the uropathogenic E. coli gene expression profile during an acute UTI within the human host. This work was undertaken to identify key players in physiological adaptation processes and, hence, potential targets for new infection prevention and therapy interventions specifically aimed at sabotaging bacterial adaptation to the human host.
2015-01-12
2015-01-12
2014
Article
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles. 2014, 5 (4):e01075-14 MBio
2150-7511
25096872
10.1128/mBio.01075-14
http://hdl.handle.net/10033/338020
mBio
en
eu-repo/grantAgreement/EC/FP7/260276
openAccess
etdms///com_10033_620636/100