570 Biowissenschaften; Biologie
Refine
Has Fulltext
- yes (97)
Is part of the Bibliography
- yes (97)
Year of publication
- 2010 (97) (remove)
Document Type
- Doctoral Thesis (78)
- Journal article (19)
Keywords
- Taufliege (8)
- Transforming Growth Factor beta (6)
- Biologie (4)
- Drosophila melanogaster (4)
- Escherichia coli (4)
- Knochen-Morphogenese-Proteine (4)
- Molekularbiologie (4)
- Signaltransduktion (4)
- Vaccinia-Virus (4)
- Ackerschmalwand (3)
- Assoziatives Gedächtnis (3)
- Bioinformatik (3)
- Genexpression (3)
- Genmutation (3)
- Genregulation (3)
- Krebs <Medizin> (3)
- Phylogenie (3)
- Synapsine (3)
- Tumor (3)
- Apoptosis (2)
- Arabidopsis (2)
- Aspergillus fumigatus (2)
- Biofilm (2)
- Bruchpilot (2)
- Calcium (2)
- DNS-Reparatur (2)
- DNS-Schädigung (2)
- Dendritische Zelle (2)
- Dopamine (2)
- Drosophila (2)
- EGFR (2)
- Epidermaler Wachstumsfaktor-Rezeptor (2)
- Evolution (2)
- Gehirn (2)
- Genetik (2)
- Geruchswahrnehmung (2)
- Guanylatcyclase (2)
- Immunologie (2)
- Immunreaktion (2)
- Immuntoleranz (2)
- Interferon (2)
- Kinasen (2)
- Knockout <Molekulargenetik> (2)
- Lernverhalten (2)
- Malaria (2)
- Massenspektrometrie (2)
- Melanom (2)
- Microarray (2)
- Myc (2)
- Neisseria meningitidis (2)
- Oxidativer Stress (2)
- Plasmodium falciparum (2)
- RNS-Spleißen (2)
- Raf (2)
- Raf <Biochemie> (2)
- Schließzelle (2)
- Schmalwand <Arabidopsis> (2)
- Shigella (2)
- Stammzelle (2)
- Synapsin (2)
- T-Lymphozyt (2)
- Therapie (2)
- Transkription <Genetik> (2)
- Tumorimmunologie (2)
- anti-parasitic (2)
- dendritic cell (2)
- leaf-cutting ants (2)
- learning (2)
- marine sponges (2)
- mass spectrometry (2)
- signal transduction (2)
- synapsin (2)
- 13C-isotopologue profiling (1)
- ACL (1)
- AMACR (1)
- APEC (1)
- Abscisinsäure (1)
- Abwehrreaktion (1)
- Acromyrmex heyeri (1)
- Actin (1)
- Actin cytoskeleton (1)
- Adenylatcyclase (1)
- Adhäsine (1)
- Aktionspotenzial (1)
- Aldosteron (1)
- Algen (1)
- Allgemeine Entzündungsreaktion (1)
- Allogene Zelle (1)
- Alpha-Methylacyl-CoA-Racemase (1)
- Altern (1)
- Alternatives Spleißen (1)
- Amine (1)
- Amino acids (1)
- Aminobisphosphonat (1)
- Aminobisphosphonate (1)
- Aminosäuren (1)
- Angewandte Mikrobiologie (1)
- Angiogenese (1)
- Anionenkanäle (1)
- Anionentranslokator (1)
- Anpassung (1)
- Arginin (1)
- Assembly (1)
- Atriales natriuretisches Hormon (1)
- Autoimmunität (1)
- Axon (1)
- Azospirillum brasilense (1)
- B. petrii-Isolate (1)
- B. petrii-Varianten (1)
- BLUF (1)
- BMP (1)
- BMP Rezeptoren (1)
- BMP receptos (1)
- BMP-2/6 (1)
- BMP-2/7 (1)
- BMPR-IA (1)
- BMPs (1)
- Bakterielle Infektion (1)
- Bildverarbeitung (1)
- Biochemie (1)
- Biologische Oxidation (1)
- Biosynthese (1)
- Blattschneiderameisen (1)
- Blutgefäß (1)
- Blutstillung (1)
- Bmi1 (1)
- Boden (1)
- Bodeneigenschaften (1)
- Bodenheterogenität (1)
- Bordetella (1)
- Bordetella bronchiseptica (1)
- Bordetella petrii (1)
- Borrelia (1)
- Bryophyta (1)
- BvgAS system (1)
- BvgAS-System (1)
- Bärtierchen (1)
- CCM3 (1)
- CD1d (1)
- CRE (1)
- Ca2+-Signal (1)
- Ca2+-signal (1)
- CaCo-2 cell (1)
- Camponotus floridanus (1)
- Candida albicans (1)
- Carbon Metabolism (1)
- Cell Biology (1)
- Cell adhesion (1)
- Channelrhodopsin (1)
- Chemokine (1)
- Chromosomenkondensation (1)
- Chronologisches Altern (1)
- Cirl (1)
- Colonkrebs (1)
- Cyclo-AMP (1)
- Cystein (1)
- Cystinknotenprotein (1)
- Cytokine (1)
- Cytologie (1)
- DAN modulator proteins (1)
- DAN-Modulatorproteine (1)
- DNA damage (1)
- DNA damage response (1)
- DNA-Schaden (1)
- DNS-Sequenz (1)
- Darmflora (1)
- Datenbank (1)
- Deformable models (1)
- Deutschland / Stammzellgesetz (1)
- Differenzierung (1)
- Dopamin (1)
- Dopaminerge Nervenzelle (1)
- Duplikation (1)
- EF-TU (1)
- EHEC (1)
- ESCRT (1)
- ESCRT-System (1)
- Efeu (1)
- Egfr (1)
- Eierstockkrebs (1)
- Embryonale Stammzelle (1)
- Embryonalentwicklung (1)
- Encephalomyelitis (1)
- Endothelzelle (1)
- Endothelzellen (1)
- Enterobacteriaceae (1)
- Enzym (1)
- Epigenetik (1)
- Erfahrung (1)
- Euglena gracilis (1)
- ExPEC (1)
- FRET (1)
- FURA (1)
- FarR (1)
- Farnesyl Pyrophosphate Synthase (1)
- Farnesylpyrophosphatsynthase (FPPS) (1)
- Furagierverhalten (1)
- Futterentzug (1)
- GAP (1)
- GAS2L3 (1)
- GDF-15 (1)
- GEF (1)
- GI-101A (1)
- Gag protein (1)
- Gag-Proteine (1)
- Galactosidase <beta-> (1)
- Gedächtnis (1)
- Gehirnanatomie (1)
- Gen (1)
- Genanalyse (1)
- Gene duplication (1)
- Gentherpie (1)
- Glatte Muskulatur (1)
- Glatter Krallenfrosch (1)
- Großhirnrinde (1)
- Guanosintriphosphatasen (1)
- Guanylyl cyclase A (1)
- H-ras (1)
- HMG-Proteine (1)
- HNPCC (1)
- HPLC-MS (1)
- HT-29 (1)
- Haemostasis (1)
- Harze (1)
- Heterodimer (1)
- High mobility group (1)
- Hydrathülle (1)
- Hyperoxide (1)
- Hypnales (1)
- ICEP (1)
- IFNAR (1)
- IL-10 (1)
- ITS2 (1)
- Immunmodulator (1)
- Immunology (1)
- Immunstimulation (1)
- Immunsuppression (1)
- Immunsystem (1)
- Imprinting (1)
- In-paralogs (1)
- Infektion (1)
- Inparanoid (1)
- Interferon Regulator Faktor 1 (1)
- Interferonrezeptor (1)
- Interleukin 10 (1)
- Intrazellulärraum (1)
- IronChip (1)
- Isopentenyl pyrophosphate (IPP) (1)
- Isopentenyl-pyrophosphat (IPP) (1)
- Isoprenoid Synthesis (1)
- Isoprenoide (1)
- Isoprenoidsynthese (1)
- Kernhülle (1)
- Kernhüllenbildung (1)
- Kernpore (1)
- Kernporenkomplex (1)
- Kernspindel (1)
- Kinase (1)
- Klassische Konditionierung (1)
- Knochenhomöostase (1)
- Kohlenstoffstoffwechsel (1)
- Konditionierung (1)
- Konfokalmikroskopie (1)
- Kontrolle (1)
- Kortikogenese (1)
- Krebsbildgebung (1)
- Krebstherapie (1)
- Kreuzband (1)
- Kutikula (1)
- LIN9 (1)
- LINC complexes (1)
- LPS (1)
- LRP5/6 (1)
- Lernen (1)
- Leukozyt (1)
- Ligand <Biochemie> (1)
- Listeria monocytogenes (1)
- Lungenentzündung (1)
- Lungenkrebs (1)
- MCP-1 (1)
- MLH1 (1)
- MRI (1)
- MSC (1)
- Mais (1)
- Major Vault Protein (1)
- Makrophage (1)
- Marker (1)
- Masernvirus (1)
- Mat Fimbrien (1)
- Mat fimbriae (1)
- Matrix-Protein (1)
- Matrixproteine (1)
- Mausmodell (1)
- Measles Virus release (1)
- Medizin (1)
- Medizinische Mikrobiologie (1)
- Mehrdimensionale NMR-Spektroskopie (1)
- Mensch (1)
- Mentale Retardierung (1)
- Mesenchymale Stammzellen (1)
- Metabolismus (1)
- Metagenom (1)
- Metastase (1)
- Midbody (1)
- Migration (1)
- Mikroarray (1)
- Mikrozephalie (1)
- Mimetika (1)
- Mimics (1)
- Missbildung (1)
- Mitose (1)
- Miz1 (1)
- Molekulare Biophysik (1)
- Molekulare Erkennung (1)
- Molekulargenetik (1)
- Moose (1)
- Motilität (1)
- Motoneuron (1)
- Mutation (1)
- NADPH-Oxidase (1)
- NKT (1)
- NLS-Sequenz (1)
- NMR-Tomographie (1)
- NSCLC (1)
- NTA Lipide (1)
- NTA lipids (1)
- NadA (1)
- Nahrungserwerb (1)
- Namibia (1)
- Natürliche Killerzelle (1)
- Neisseria gonorrhoeae (1)
- Neisseria meningitdis (1)
- Nephroblastom (1)
- Nephroblastoma (1)
- Nervensystem (1)
- Nervenzelle (1)
- Netzwerk (1)
- Neurogenese (1)
- Neurolucida (1)
- Neuromorphologie (1)
- Neurotrophine (1)
- Neutrophile Granulozyten (1)
- Nichtstrukturproteine (1)
- Nicotin (1)
- Nitratatmung (1)
- Nitrosativer Stress (1)
- Nuclear envelope assembly (1)
- Nuclear pore complex (1)
- Octopamine (1)
- Oktopamin (1)
- Optogenetic (1)
- Optogenetik (1)
- Osmolarität (1)
- Ovarialkarzinom (1)
- Oxidation (1)
- Oxidative Thiol Modifikationen (1)
- PAC (1)
- PAMPS (1)
- PCC-Syndrom (1)
- PVM (1)
- Pathogeninteraktion (1)
- Pathogens (1)
- Permeation (1)
- Peroxisom (1)
- Phosphatase (1)
- Phosphorylierung (1)
- Photoreceptor (1)
- Photorezeptor (1)
- Physiologische Chemie (1)
- Pilzkörper (1)
- Plasmamembran (1)
- Pluripotenz (1)
- Polycomb (1)
- Polyketid-Synthasen (1)
- Polyphosphate (1)
- Porins (1)
- Posttranslational (1)
- Primary Microcephaly (1)
- Primaten (1)
- Primärkultur (1)
- Proteasen (1)
- Protein Lipidierungen (1)
- Proteinfaltung (1)
- Proteininteraktion (1)
- Proteinkinasen (1)
- Proteinkristallographie (1)
- Proteinmodifikationen (1)
- Proteinsekretion (1)
- Proteom analysis (1)
- Proteomanalyse (1)
- Präsynapse (1)
- Pseudomonas (1)
- Pseudomonas syringae (1)
- Pseudomonas syringae tomato (1)
- ROS (1)
- RS-Virus (1)
- RSK2 (1)
- Racemase (1)
- Ras (1)
- Ratte (1)
- Reaktive Sauerstoffspezies (1)
- Repression <Genetik> (1)
- Retinoesaeure (1)
- Reversibel (1)
- Rezeptor (1)
- Rezeptor-Liganden-Interaktion (1)
- Rezeptormobilität (1)
- Rho GTPasen (1)
- Rho GTPases (1)
- Ribonucleoproteine (1)
- Ribosom (1)
- Ribosomale RNS (1)
- Rose (1)
- S-Typ Anionenkanal (1)
- S-typ anionchannel (1)
- SAP47 (1)
- SRPK79D (1)
- Saccharomyces cerevisiae (1)
- Salmonella (1)
- Salmonella enterica (1)
- Salmonella typhimurium (1)
- Salmonellose (1)
- Sap47 (1)
- Sauerstoffradikal (1)
- Schließzellen (1)
- Schwertkärpfling (1)
- Segmentierung (1)
- Sehne (1)
- Sekundärstruktur (1)
- Seneszenz (1)
- Serin (1)
- Serin-Arginin Proteinkinase (1)
- Serotonin (1)
- Shigella flexneri (1)
- Shikimatsynthese (1)
- Shikimisäure (1)
- Signal transduction (1)
- Signaling complex (1)
- Signalkomplex (1)
- Soziale Insekten (1)
- Sozialer Stress (1)
- Spaltöffnung (1)
- Speicheldrüse (1)
- Sperma (1)
- Spermatogenesis (1)
- Sphingolipide (1)
- Sphingolipids (1)
- Sphingolipidstoffwechsel (1)
- Spindelkontrollpunkt (1)
- Spleißen (1)
- Splicing (1)
- Spumaviren (1)
- Spumaviruses (1)
- Src (1)
- Stickstoffmetabolismus (1)
- Stickstoffoxidsynthase (1)
- Stickstoffwechsel (1)
- Stomata (1)
- Streptomyces (1)
- Stress (1)
- Stressreaktion (1)
- Struktur-Aktivitäts-B (1)
- Strukturaufklärung (1)
- Synthese (1)
- T-Zell-Lymphom (1)
- T3SS (1)
- TGF-ß (1)
- Tabak (1)
- Tardigraden (1)
- Tardigrades (1)
- Termiten (1)
- Terpene (1)
- Thiol:Disulfid-Redox-Metabolismus (1)
- Thiole (1)
- Thiolgruppe (1)
- Thrombosis (1)
- Tiermodell (1)
- Tissue Engineering (1)
- Toll-like-Rezeptoren (1)
- Transfektion (1)
- Transforming Growth Factor (1)
- Transkriptionsfaktoren (1)
- Transkriptionsregulation (1)
- Transplantation (1)
- TrkB (1)
- Tumor detection (1)
- Tumordetektion (1)
- Tumorinduktion (1)
- Tumorregression (1)
- Tumorwachstum (1)
- Tyrosin (1)
- Ubiquitinierung (1)
- Vaccinia Virus (1)
- Vault (1)
- Vegetation (1)
- Venusfliegenfalle (1)
- Verhaltensforschung (1)
- Vermehrung (1)
- Vg9Vd2 T Zellaktivierung (1)
- Vg9Vd2 T cell (1)
- Virulenzfaktor (1)
- Vitamin B6 (1)
- WTX (1)
- Wachstum (1)
- Wasserstoffperoxid (1)
- Waterbear (1)
- Wechselwirkung (1)
- Wilms Tumor (1)
- Wilms tumor (1)
- Wirkstoff-Rezeptor-Bindung (1)
- Wnt-Proteine (1)
- Würzburg / Universität / Lehrstuhl für Bioinformatik (1)
- Xenopus laevis (1)
- Yersinia enterocolitica (1)
- Zell-basierte Therapie (1)
- Zelle (1)
- Zellzyklus (1)
- Zoonotisches Risiko (1)
- Zytokinese (1)
- actinomycetes (1)
- aldosterone (1)
- aliphatic glucosinolates (1)
- allogen (1)
- allogenic (1)
- alternative splicing (1)
- amacr (1)
- androgenetic (1)
- androgenetisch (1)
- angiogenesis (1)
- anion channel (1)
- anti-infective (1)
- apoptosis (1)
- aqueous pathways (1)
- arabidopsis (1)
- atrial natriuretic peptide (1)
- autoimmunity (1)
- bacterial cancer therapy (1)
- bacterial tumor targeting (1)
- biochemistry (1)
- biofilm (1)
- bone homeostasis (1)
- brain anatomy (1)
- building behaviour (1)
- butenolide (1)
- cAMP (1)
- calcium (1)
- cancer (1)
- cancer therapy (1)
- carpenter ant (1)
- cell-based therapy (1)
- chromosome condensation (1)
- chronological aging (1)
- classical conditioning (1)
- comparative metagenomics (1)
- computational analysis (1)
- confocal microscopy (1)
- corticogenesis (1)
- cystin knot protein (1)
- cytokinesis (1)
- deformable models (1)
- differentiation (1)
- dmrt1 (1)
- embryonic stem cell (1)
- endothelial cells (1)
- enteroinvasive (1)
- epidermal growth factor receptor (1)
- epigenetic (1)
- experience (1)
- fish model (1)
- food deprivation (1)
- foraging behavior (1)
- geneexpression (1)
- genetherapy (1)
- guard cell (1)
- heat transfer (1)
- heterodimer (1)
- host-pathogen-interaction (1)
- human gut microbiome (1)
- hydration (1)
- immune modulator (1)
- immune sytem (1)
- imprinting (1)
- inflammation (1)
- innate immunity (1)
- interferon (1)
- isolates of B. petrii (1)
- klassische Konditionierung (1)
- kollektive Muster (1)
- leukocyte (1)
- localisation (1)
- maize (1)
- malaria (1)
- melanoma (1)
- memory (1)
- metagenomics (1)
- metastasis (1)
- microarray (1)
- microarrays (1)
- microinjection (1)
- migration (1)
- mitosis (1)
- mousemodell (1)
- mushroom body (1)
- mutation (1)
- nest material (1)
- neurolucida (1)
- neuromorphology (1)
- neurotrophins (1)
- neutrophile Granulozyten (1)
- neutrophils (1)
- niche adaptation (1)
- nicotine (1)
- nitrosative stress (1)
- olfaction (1)
- olfactory learning (1)
- olfactory memory (1)
- olfaktorisches Gedächtnis (1)
- olfaktorisches Lernen (1)
- oligopeptide transport (1)
- ovarian cancer (1)
- oxidative stress (1)
- oxidative thiol modification (1)
- p15Ink4b (1)
- pH-Wert (1)
- permeability (1)
- phosphorylation sites (1)
- photoaktiviert (1)
- phylogenetic (1)
- phylogenetics (1)
- phylogeny evolution (1)
- plant cuticle (1)
- pluripotency (1)
- polyketide synthases (1)
- presynapse (1)
- primary cell culture (1)
- protease; Indinavir; lead expansion; docking; pharmacophore (1)
- protein crystallography (1)
- protein lipidations (1)
- protein modifications (1)
- protein-interaction networks (1)
- rRNA (1)
- racemase (1)
- rat (1)
- reactive oxygen species (1)
- receptor (1)
- receptor mobility (1)
- receptor-ligand-interaction (1)
- regulatorische T-Zellen (1)
- regulatory T cells (1)
- resin (1)
- retinoic acid (1)
- salivary gland (1)
- secondary structure (1)
- senescence (1)
- sequence (1)
- serine-arginine protein kinase (1)
- sex-determining gene (1)
- shikimate pathway (1)
- sifA (1)
- social insects (1)
- soil heterogeneity (1)
- spindle assembly checkpoint (1)
- splicing (1)
- stachellose Biene (1)
- stachellose Bienen (1)
- starvation (1)
- staurosporine (1)
- stem (1)
- stingless bees (1)
- stomata (1)
- sugar-conditioned behaviour (1)
- synaptic proteins (1)
- synaptisch protein (1)
- teleost fishes (1)
- tendon (1)
- termites (1)
- terpenes (1)
- thermal biology (1)
- thioredoxin reductase (1)
- tissue-specific destruction (1)
- tolerance (1)
- tolerogen (1)
- tolerogenic (1)
- transcription factors (1)
- transcriptional regulation (1)
- transplantation (1)
- trkB (1)
- tubulin binding chaperone E-like (1)
- tumor immunology (1)
- ubiquitination (1)
- valinomycin (1)
- variants of B. petrii (1)
- vascular smooth muscle cells (1)
- vaskuläre glatte Muskelzellen (1)
- vitamin B6 synthesis (1)
- zoonotic risk (1)
- zuckerkonditioniertes Verhalten (1)
- ß-Galaktosidase (1)
- ß-galactosidase (1)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (52)
- Graduate School of Life Sciences (13)
- Julius-von-Sachs-Institut für Biowissenschaften (9)
- Institut für Virologie und Immunbiologie (8)
- Institut für Medizinische Strahlenkunde und Zellforschung (7)
- Institut für Molekulare Infektionsbiologie (5)
- Institut für Pharmakologie und Toxikologie (3)
- Institut für Humangenetik (2)
- Institut für Hygiene und Mikrobiologie (2)
- Institut für Klinische Biochemie und Pathobiochemie (2)
The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps .biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160 000 correct full ength and more than 50 000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses.
Chlamydia trachomatis is an obligate intracellular pathogenic bacterium that has been refractory to genetic manipulations. Although the genomes of several strains have been sequenced, very little information is available on the gene structure of these bacteria. We used deep sequencing to define the transcriptome of purified elementary bodies (EB) and reticulate bodies (RB) of C. trachomatis L2b, respectively. Using an RNAseq approach, we have mapped 363 transcriptional start sites (TSS) of annotated genes. Semiquantitative analysis of mapped cDNA reads revealed differences in the RNA levels of 84 genes isolated from EB and RB, respectively. We have identified and in part confirmed 42 genome- and 1 plasmid-derived novel non-coding RNAs. The genome encoded non-coding RNA, ctrR0332 was one of the most abundantly and differentially expressed RNA in EB and RB, implying an important role in the developmental cycle of C. trachomatis. The detailed map of TSS in a thus far unprecedented resolution as a complement to the genome sequence will help to understand the organization, control and function of genes of this important pathogen.
Background: Melanoma cells are usually characterized by a strong proliferative potential and efficient invasive migration. Among the multiple molecular changes that are recorded during progression of this disease, aberrant activation of receptor tyrosine kinases (RTK) is often observed. Activation of matrix metalloproteases goes along with RTK activation and usually enhances RTK-driven migration. The purpose of this study was to examine RTKdriven three-dimensional migration of melanocytes and the pro-tumorigenic role of matrix metalloproteases for melanocytes and melanoma cells. Results: Using experimental melanocyte dedifferentiation as a model for early melanomagenesis we show that an activated EGF receptor variant potentiates migration through three-dimensional fibrillar collagen. EGFR stimulation also resulted in a strong induction of matrix metalloproteases in a MAPK-dependent manner. However, neither MAPK nor MMP activity were required for migration, as the cells migrated in an entirely amoeboid mode. Instead, MMPs fulfilled a function in cell cycle regulation, as their inhibition resulted in strong growth inhibition of melanocytes. The same effect was observed in the human melanoma cell line A375 after stimulation with FCS. Using sh- and siRNA techniques, we could show that MMP13 is the protease responsible for this effect. Along with decreased proliferation, knockdown of MMP13 strongly enhanced pigmentation of melanocytes. Conclusions: Our data show for the first time that growth stimuli are mediated via MMP13 in melanocytes and melanoma, suggesting an autocrine MMP13-driven loop. Given that MMP13-specific inhibitors are already developed, these results support the evaluation of these inhibitors in the treatment of melanoma.
Actinomycetes are prolific producers of pharmacologically important compounds accounting for about 70% of the naturally derived antibiotics that are currently in clinical use. In this study, we report on the isolation of Streptomyces sp. strains from Mediterranean sponges, on their secondary metabolite production and on their screening for anti-infective activities. Bioassay-guided isolation and purification yielded three previously known compounds namely, cyclic depsipeptide valinomycin, indolocarbazole alkaloid staurosporine and butenolide. This is the first report of the isolation of valinomycin from a marine source. These compounds exhibited novel anti-parasitic activities specifically against Leishmania major (valinomycin IC50 < 0.11 μM; staurosporine IC50 5.30 μM) and Trypanosoma brucei brucei (valinomycin IC50 0.0032 μM; staurosporine IC50 0.022 μM; butenolide IC50 31.77 μM). These results underscore the potential of marine actinomycetes to produce bioactive compounds as well as the re-evaluation of previously known compounds for novel anti-infective activities.
Terrestrial actinomycetes are noteworthy producers of a multitude of antibiotics, however the marine representatives are much less studied in this regard. In this study, 90 actinomycetes were isolated from 11 different species of marine sponges that had been collected from offshore Ras Mohamed (Egypt) and from Rovinj (Croatia). Phylogenetic characterization of the isolates based on 16S rRNA gene sequencing supported their assignment to 18 different actinomycete genera representing seven different suborders. Fourteen putatively novel species were identified based on sequence similarity values below 98.2% to other strains in the NCBI database. A putative new genus related to Rubrobacter was isolated on M1 agar that had been amended with sponge extract, thus highlighting the need for innovative cultivation protocols. Testing for anti-infective activities was performed against clinically relevant, Gram-positive (Enterococcus faecalis, Staphylococcus aureus) and Gram-negative (Escherichia coli, Pseudomonas aeruginosa) bacteria, fungi (Candida albicans) and human parasites (Leishmania major, Trypanosoma brucei). Bioactivities against these pathogens were documented for 10 actinomycete isolates. These results show a high diversity of actinomycetes associated with marine sponges as well as highlight their potential to produce anti-infective agents.
The construction of mound-shaped nests by ants is considered as a behavioral adaptation to low environmental temperatures, i.e., colonies achieve higher and more stables temperatures than those of the environment. Besides the well-known nests of boreal Formica wood-ants, several species of South American leaf-cutting ants of the genus Acromyrmex construct thatched nests. Acromyrmex workers import plant fragments as building material, and arrange them so as to form a thatch covering a central chamber, where the fungus garden is located. Thus, the degree of thermoregulation attained by the fungus garden inside the thatched nest largely depends on how the thatch affects the thermal relations between the fungus and the environment. This work was aimed at studying the thermoregulatory function of the thatched nests built by the grass-cutting ant Acromyrmex heyeri Forel (Hymenoptera: Formicidae: Myrmicinae). Nest and environmental temperatures were measured as a function of solar radiation on the long-term. The thermal diffusivity of the nest thatch was measured and compared to that of the surrounding soil, in order to assess the influence of the building material on the nest’s thermoregulatory ability. The results showed that the average core temperature of thatched nests was higher than that of the environment, but remained below values harmful for the fungus. This thermoregulation was brought about by the low thermal diffusivity of the nest thatch built by workers with plant fragments, instead of the readily-available soil particles that have a higher thermal diffusivity. The thatch prevented diurnal nest overheating by the incoming solar radiation, and avoided losses of the accumulated daily heat into the cold air during the night. The adaptive value of thatching behavior in Acromyrmex leaf-cutting ants occurring in the southernmost distribution range is discussed.
Background: In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results: This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions: Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers: This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Open peer review: Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers’ comments section.
Indinavir (Crivaxan®) is a potent inhibitor of the HIV (human immunodeficiency virus) protease. This enzyme has an important role in viral replication and is considered to be very attractive target for new antiretroviral drugs. However, it becomes less effective due to highly resistant new viral strains of HIV, which have multiple mutations in their proteases. For this reason, we used a lead expansion method to create a new set of compounds with a new mode of action to protease binding site. 1300 compounds chemically diverse from the initial hit were generated and screened to determine their ability to interact with protease and establish their QSAR properties. Further computational analyses revealed one unique compound with different protease binding ability from the initial hit and its role for possible new class of protease inhibitors is discussed in this report.
The present study was aimed at revealing the early signalling events during the interaction of the diazotrophic soil bacterium Azospirillum brasilense with its host plant Arabidopsis thaliana. Furthermore, taking advantage of the micro array technique, a comprehensive overview of Arabidopsis genes has been undertaken which are affected upon association with A. brasilense The characterization of the early responses of Arabidopsis plants upon inoculation with Azospirillum brasilense strain Sp7 clearly indicated parallels with the initial events in plant pathogen interaction. For instance, not only bacterial preprations (lysates) form Azospirillum elicited an apoplastic alkalinization of the culture medium, but also the live bacteria, which were even more effective. Besides, in a luminol based assay, the bacterial lysates triggered production of the reactive oxygen species (ROS) in the Arabidopsis leaf discs. Interestingly, the elongation factor receptor mutants (efr) were completely insensitive to Azospirillum, suggesting elongation factor Tu (EF-TU) recognition as elicitor by Arabidopsis. This hypothesis was further validated with a bioinformatic approach. The N terminus initial 26 amino acids from Azospirillum EF-TU gene (elf26) showed more similarity to the elf26 sequences of bacteria like Agrobacterium tumefaciens which elicit responses in the plants through EF-TU rather than Pseudomonas syringae where the potent elicitor is flagellin 22. Universal transcriptome profiling of Arabidopsis thaliana seedlings upon inoculation with Azospirillum brasilense over a time course of six, twenty four and ninty six hours revealed very little genetic responses in the early time points. However, a bulk of genes was differentially regulated in 96 hours post inoculation (96hpi). The nature of these genes indicated that the bacterial treatment, among others, greatly affect the processes like cell wall modification, hormone metabolism, stress and secondary metabolism. Additionally expression levels of a numer of transcription factors (TFs) related to basic helix loop helix (BHLH) and MYB domain containing TF families were altered with Azospirillum inoculation. Particularly the BHLH TFs were among the most highly regulated genes. The array results from Azospirillum treated plants were further compared with the already available data emnating from treatment with flagellin 22 (flg22), oligogalacturonides (OGs) and Agrobacterium tumefaciens. Noteworthy, very different set of genes were affected upon inoculation with Azospirillum in relation to other treatments. Secondly a cluster of proteins involved in the biosynthesis of aliphatic glucosinolates (GSL) were uniquely induced upon Sp7 exposure. Genes operating in flavonoid biosynthesis also showed a distinct regulation trend in the comparative analysis. Taken together, the study in question provides insights into the early signalling events in the context of Azospirillum-Arabidopsis association and the bacterial signals recognized by the plants. The array data, at the same time, elucidates the genetic factors of Arabidopsis triggered upon association with Azospirillum brasilense.
The phylum Tardigrada consists of about 1000 described species to date. The animals live in habitats within marine, freshwater and terrestrial ecosystems allover the world. Tardigrades are polyextremophiles. They are capable to resist extreme temperature, pressure or radiation. In the event of desiccation, tardigrades enter a so-called tun stage. The reason for their great tolerance capabilities against extreme environmental conditions is not discovered yet. Our Funcrypta project aims at finding answers to the question what mechanisms underlie these adaption capabilities particularly with regard to the species Milnesium tardigradum. The first part of this thesis describes the establishment of expressed sequence tags (ESTs) libraries for different stages of M. tardigradum. From proteomics data we bioinformatically identified 144 proteins with a known function and additionally 36 proteins which seemed to be specific for M. tardigradum. The generation of a comprehensive web-based database allows us to merge the proteome and transcriptome data. Therefore we created an annotation pipeline for the functional annotation of the protein and nucleotide sequences. Additionally, we clustered the obtained proteome dataset and identified some tardigrade-specific proteins (TSPs) which did not show homology to known proteins. Moreover, we examined the heat shock proteins of M. tardigradum and their different expression levels depending on the actual state of the animals. In further bioinformatical analyses of the whole data set, we discovered promising proteins and pathways which are described to be correlated with the stress tolerance, e.g. late embryogenesis abundant (LEA) proteins. Besides, we compared the tardigrades with nematodes, rotifers, yeast and man to identify shared and tardigrade specific stress pathways. An analysis of the 50 and 30 untranslated regions (UTRs) demonstrates a strong usage of stabilising motifs like the 15-lipoxygenase differentiation control element (15-LOX-DICE) but also reveals a lack of other common UTR motifs normally used, e.g. AU rich elements. The second part of this thesis focuses on the relatedness between several cryptic species within the tardigrade genus Paramacrobiotus. Therefore for the first time, we used the sequence-structure information of the internal transcribed spacer 2 (ITS2) as a phylogenetic marker in tardigrades. This allowed the description of three new species which were indistinguishable using morphological characters or common molecular markers like the 18S ribosomal ribonucleic acid (rRNA) or the Cytochrome c oxidase subunit I (COI). In a large in silico simulation study we also succeeded to show the benefit for the phylogenetic tree reconstruction by adding structure information to the ITS2 sequence. Next to the genus Paramacrobiotus we used the ITS2 to corroborate a monophyletic DO-group (Sphaeropleales) within the Chlorophyceae. Additionally we redesigned another comprehensive database—the ITS2 database resulting in a doubled number of sequence-structure pairs of the ITS2. In conclusion, this thesis shows the first insights (6 first author publications and 4 coauthor publications) into the reasons for the enormous adaption capabilities of tardigrades and offers a solution to the debate on the phylogenetic relatedness within the tardigrade genus Paramacrobiotus.