An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats
Kaare Magne Nielsen
Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes.
Plasmid DNA with two resistance genes (nptI and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, were constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. No transformants were identified among 441 tested isolates.
The analyses showed that extensive ingestion of DNA (100 μg plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit < 1 transformant per 1,1 × 108 cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed. This study is consistent with other studies suggesting natural transformation is not detectable in the GIT of mammals.
Synthesis of szentiamide, a depsipeptide from entomopathogenic Xenorhabdus szentirmaii with activity against Plasmodium falciparum
Friederike I. Nollmann
Helge Björn Bode
- The synthesis of the recently characterized depsipeptide szentiamide (1), which is produced by the entomopathogenic bacterium Xenorhabdus szentirmaii, is described. Whereas no biological activity was previously identified for 1, the material derived from the efficient synthesis enabled additional bioactivity tests leading to the identification of a notable activity against insect cells and Plasmodium falciparum, the causative agent of malaria.
Ordnung der Fachbereiche Medizin, Biowissenschaften, Biochemie, Chemie und Pharmazie sowie Psychologie und Sportwissenschaften der Johann Wolfgang Goethe[-Universität] für den Masterstudiengang Interdisciplinary Neuroscience mit dem Abschluss "Master of Science" (M. Sc.) vom 30. März 2009 in der Fassung vom 22. April 2009, zuletzt geändert am 16. April 2012 : genehmigt vom Präsidium der Johann Wolfgang Goethe-Universität Frankfurt a. M. am 27. April 2010 ; hier: Änderungen vom 08.11.2012 ; genehmigt vom Präsidium der Johann Wolfgang Goethe-Universität Frankfurt a. M. am 18. Dezember 2012
Ordnung der Fachbereiche Medizin, Biowissenschaften, Biochemie, Chemie und Pharmazie sowie Psychologie und Sportwissenschaften der Johann Wolfgang Goethe-Universität für den Masterstudiengang Interdisciplinary Neuroscience mit dem Abschluss "Master of Science" (M.Sc.) vom 30. März 2009 in der Fassung vom 22. April 2009 : genehmigt durch das Präsidium am 11. Oktober 2011 ; hier: Änderung der Wahlpflichtmodule vom 16. April 2012 ; genehmigt durch das Präsidium am 11. September 2012
Ordnung des Fachbereichs Biowissenschaften der Johann Wolfgang Goethe-Universität für den Masterstudiengang Cell Biology and Physiology mit dem Abschluss Master of Science (M. Sc.) vom 18. Oktober 2011 : genehmigt vom Präsidium der Johann Wolfgang Goethe-Universität Frankfurt am Main am 29. November 2011 ; hier: Änderungen ; genehmigt vom Präsidium der Johann Wolfgang Goethe-Universität am 25. September 2012
Ordnung des Fachbereichs Biowissenschaften der Johann Wolfgang Goethe[-Universität] für den Masterstudiengang Ökologie und Evolution mit dem Abschluss "Master of Science" (M. Sc.) vom 16. Juni 2009 : Änderungen vom 04. Juni 2012 ; hier: Berichtigung der Bekanntmachung vom 25.September 2012
Gemeinsame Ordnung der Fachbereiche Biochemie, Chemie und Pharmazie, Biowissenschaften, Gesellschaftswissenschaften sowie Geowissenschaften, Geographie der Johann Wolfgang Goethe-Universität Frankfurt am Main für den Masterstudiengang Umweltwissenschaften mit dem Abschlussziel Master of Science (M.Sc.) vom 21.11.2011 : genehmigt durch das Präsidium der Johann Wolfgang Goethe-Universität Frankfurt am Main am 20.03.2012
AKT signaling mediates IGF-I survival actions on otic neural progenitors
Maria Rodriguez Aburto
- Background: Otic neurons and sensory cells derive from common progenitors whose transition into mature cells requires the coordination of cell survival, proliferation and differentiation programmes. Neurotrophic support and survival of post-mitotic otic neurons have been intensively studied, but the bases underlying the regulation of programmed cell death in immature proliferative otic neuroblasts remains poorly understood. The protein kinase AKT acts as a node, playing a critical role in controlling cell survival and cell cycle progression. AKT is activated by trophic factors, including insulin-like growth factor I (IGF-I), through the generation of the lipidic second messenger phosphatidylinositol 3-phosphate by phosphatidylinositol 3-kinase (PI3K). Here we have investigated the role of IGF-dependent activation of the PI3K-AKT pathway in maintenance of otic neuroblasts.
Methodology/Principal Findings: By using a combination of organotypic cultures of chicken (Gallus gallus) otic vesicles and acoustic-vestibular ganglia, Western blotting, immunohistochemistry and in situ hybridization, we show that IGF-I-activation of AKT protects neural progenitors from programmed cell death. IGF-I maintains otic neuroblasts in an undifferentiated and proliferative state, which is characterised by the upregulation of the forkhead box M1 (FoxM1) transcription factor. By contrast, our results indicate that post-mitotic p27Kip-positive neurons become IGF-I independent as they extend their neuronal processes. Neurons gradually reduce their expression of the Igf1r, while they increase that of the neurotrophin receptor, TrkC.
Conclusions/Significance: Proliferative otic neuroblasts are dependent on the activation of the PI3K-AKT pathway by IGF-I for survival during the otic neuronal progenitor phase of early inner ear development.
Bimodal activation of different neuron classes with the spectrally red-shifted channelrhodopsin chimera C1V1 in Caenorhabditis elegans
- The C. elegans nervous system is particularly well suited for optogenetic analyses of circuit function: Essentially all connections have been mapped, and light can be directed at the neuron of interest in the freely moving, transparent animals, while behavior is observed. Thus, different nodes of a neuronal network can be probed for their role in controlling a particular behavior, using different optogenetic tools for photo-activation or –inhibition, which respond to different colors of light. As neurons may act in concert or in opposing ways to affect a behavior, one would further like to excite these neurons concomitantly, yet independent of each other. In addition to the blue-light activated Channelrhodopsin-2 (ChR2), spectrally red-shifted ChR variants have been explored recently. Here, we establish the green-light activated ChR chimera C1V1 (from Chlamydomonas and Volvox ChR1′s) for use in C. elegans. We surveyed a number of red-shifted ChRs, and found that C1V1-ET/ET (E122T; E162T) works most reliable in C. elegans, with 540–580 nm excitation, which leaves ChR2 silent. However, as C1V1-ET/ET is very light sensitive, it still becomes activated when ChR2 is stimulated, even at 400 nm. Thus, we generated a highly efficient blue ChR2, the H134R; T159C double mutant (ChR2-HR/TC). Both proteins can be used in the same animal, in different neurons, to independently control each cell type with light, enabling a further level of complexity in circuit analyses.
De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
Jurgen F. Nijkamp
Marcel van den Broek
Stefan de Kok
Wilbert HM Heijne
Chris J. Paddon
Roeland C. van Ham
Marcel JT Reinders
Jack T. Pronk
Dick de Ridder
- Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN.PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN.PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.