Taxonomische und nomenklatorische Neuigkeiten zur Flora Deutschlands 2
Karl Peter Buttler
- Im Abschnitt "Taxonomie" werden folgende Sippen besprochen: Festuca ser. Psammophilae, Hierochloë, Orchis ustalata, Sorbus und Viola. Es folgt ein Abschnitt "Molekulare Phylogenetik" mit Hinweisen betreffend Alisma, Betula, Brassicaceae, Coeloglossum/Dactylorhiza, Crataegus/Mespilus, Helichrysum/Pseudognaphalium, Loteae, Plantaginaceae und Salsoleae. Den Abschluss bilden Nachrichten zur Noenklatur.
Erigeron sumatrensis, das Sumatra-Berufkraut, in Frankfurt am Main
Karl Peter Buttler
- Erigeron sumatrensis ist seit 1981 in Frankfurt am Main als Neophyt
bekannt. Das gegenwärtige Verbreitungsmuster deutet darauf hin, dass die Art sich
langsam ausbreitet. Um ihr Erkennen zu erleichtern, wird ein Bestimmungsschlüssel für
die in Europa vorkommenden annuellen Adventivarten der Sektion Conyza beigegeben,
ergänzt durch einige Anmerkungen zu noch offenen taxonomischen Fragen. Für drei
Herkünfte aus Frankreich wurde die hexaploide Chromosomenzahl 2n = 54 ermittelt.
Die Felsen-Zwenke (Brachypodium rupestre) in Hessen
Karl Peter Buttler
- Aus Hessen war Brachypodium rupestre bisher nur von einem
Fundort veröffentlicht. Durch gezielte Suche und einen Zufallsfund kamen in den letzten
Jahren fünf weitere hinzu. Die Wuchsorte sind anthropogene Böschungen von Straßen
und Hochwasserrückhaltebecken, nur in einem Fall wachsen die Pflanzen auf einem
naturnahen Standort in einer extensiv bewirtschafteten Stromtalwiese. Die Vorkommen
gehen wahrscheinlich alle auf Ansaat zurück, entweder auf direkte Ansaat am Wuchsort
oder ausgehend von den Primärpopulationen auf Verdriftung der Diasporen mit Hochwässern.
Die Art ist in Hessen als eingebürgerter Neophyt einzustufen.
Autochthone Weißtannenvorkommen in den Schluchten Fränkischer Keupergebiete : Diskussionsbeitrag zu deren genetischer Struktur, Artenausstattung, waldbaulicher Behandlung und Kartierung in Natura 2000
- Im Fränkischen Keuper gibt es in 2 etwa 100 km voneinander entfernt gelegenen Gebieten, dem Spalter Hügelland und dem Obermain-Hügelland, reizvolle Bachschluchten, in denen man reiche Tannenvorkommen vorfindet, die im Falle der obermainischen Rhätschluchten viele montane Arten aufweisen, und im Falle der mittelfränkischen Bachklingen buchenwaldähnliche Mischwälder bilden. Die von WALENTOWSKI et al. (2004) beschriebene hohe Artendiversität und der damit verbundene Wert von Tannenwaldgesell-schaften zeichnet auch die untersuchten Bestände aus. Es werden die Ergebnisse von Isoenzymanalysen präsentiert, aufgrund derer die Tannenvorkommen als autochthon eingestuft werden können. Die genetische Struktur der Tannenpopulationen wird im Vergleich der beiden Gebiete dargestellt. Vegetationskundlich sind die Bestände schwer einzu-ordnen, da Arten aus den Nadelwäldern, den Buchenwäldern sowie den Erlen-Ulmen-Auwäldern miteinander vergesellschaftet sind. Als potentiell natürliche Vegetation ist ein tannenreiches Galio-Fagetum oder Luzulo-Fagetum (Spalt) bzw. ein Vaccinio-Abietetum (Obermain) anzunehmen. Im Untersuchungsgebiet sind eine Reihe von Keuperschluchten als Natura 2000 Gebiete ausgewiesen. Es wird auf die Schwierigkeiten hingewiesen, die der aktuell hohe Fichtenreichtum für die Natura 2000-Lebensraumtypenkartierung der Bestände bedeutet, sowie für einen Schutz und Erhalt der Bestände plädiert.
Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea : research article
Stephan C. Schuster
- Background Differential expression of genes can be regulated on many different levels. Most global studies of gene regulation concentrate on transcript level regulation, and very few global analyses of differential translational efficiencies exist. The studies have revealed that in Saccharomyces cerevisiae, Arabidopsis thaliana, and human cell lines translational regulation plays a significant role. Additional species have not been investigated yet. Particularly, until now no global study of translational control with any prokaryotic species was available. Results A global analysis of translational control was performed with two haloarchaeal model species, Halobacterium salinarum and Haloferax volcanii. To identify differentially regulated genes, exponentially growing and stationary phase cells were compared. More than 20% of H. salinarum transcripts are translated with non-average efficiencies. By far the largest group is comprised of genes that are translated with above-average efficiency specifically in exponential phase, including genes for many ribosomal proteins, RNA polymerase subunits, enzymes, and chemotaxis proteins. Translation of 1% of all genes is specifically repressed in either of the two growth phases. For comparison, DNA microarrays were also used to identify differential transcriptional regulation in H. salinarum, and 17% of all genes were found to have non-average transcript levels in exponential versus stationary phase. In H. volcanii, 12% of all genes are translated with non-average efficiencies. The overlap with H. salinarum is negligible. In contrast to H. salinarum, 4.6% of genes have non-average translational efficiency in both growth phases, and thus they might be regulated by other stimuli than growth phase. Conclusions For the first time in any prokaryotic species it was shown that a significant fraction of genes is under differential translational control. Groups of genes with different regulatory patterns were discovered. However, neither the fractions nor the identity of regulated genes are conserved between H. salinarum and H. volcanii, indicating that prokaryotes as well as eukaryotes use differential translational control for the regulation of gene expression, but that the identity of regulated genes is not conserved For 70 H. salinarum genes potentiation of regulation was observed, but for the majority of regulated genes either transcriptional or translational regulation is employed.
The invariant phenylalanine of precursor proteins discloses the importance of Omp85 for protein translocation into cyanelles
Jürgen M. Steiner
- Background Today it is widely accepted that plastids are of cyanobacterial origin. During their evolutionary integration into the metabolic and regulatory networks of the host cell the engulfed cyanobacteria lost their independency. This process was paralleled by a massive gene transfer from symbiont to the host nucleus challenging the development of a retrograde protein translocation system to ensure plastid functionality. Such a system includes specific targeting signals of the proteins needed for the function of the plastid and membrane-bound machineries performing the transfer of these proteins across the envelope membranes. At present, most informations on protein translocation are obtained by the analysis of land plants. However, the analysis of protein import into the primitive plastids of glaucocystophyte algae, revealed distinct features placing this system as a tool to understand the evolutionary development of translocation systems. Here, bacterial outer membrane proteins of the Omp85 family have recently been discussed as evolutionary seeds for the development of translocation systems. Results To further explore the initial mode of protein translocation, the observed phenylalanine dependence for protein translocation into glaucophyte plastids was pursued in detail. We document that indeed the phenylalanine has an impact on both, lipid binding and binding to proteoliposomes hosting an Omp85 homologue. Comparison to established import experiments, however, unveiled a major importance of the phenylalanine for recognition by Omp85. This finding is placed into the context of the evolutionary development of the plastid translocon. Conclusion The phenylalanine in the N-terminal domain signs as a prerequisite for protein translocation across the outer membrane assisted by a primitive translocon. This amino acid appears to be optimized for specifically targeting the Omp85 protein without enforcing aggregation on the membrane surface. The phenylalanine has subsequently been lost in the transit sequence, but can be found at the C-terminal position of the translocating pore. Thereby, the current hypothesis of Omp85 being the prokaryotic contribution to the ancestral Toc translocon can be supported.
Predicting olfactory receptor neuron responses from odorant structure
Marien De Bruyne
- Background Olfactory receptors work at the interface between the chemical world of volatile molecules and the perception of scent in the brain. Their main purpose is to translate chemical space into information that can be processed by neural circuits. Assuming that these receptors have evolved to cope with this task, the analysis of their coding strategy promises to yield valuable insight in how to encode chemical information in an efficient way. Results We mimicked olfactory coding by modeling responses of primary olfactory neurons to small molecules using a large set of physicochemical molecular descriptors and artificial neural networks. We then tested these models by recording in vivo receptor neuron responses to a new set of odorants and successfully predicted the responses of five out of seven receptor neurons. Correlation coefficients ranged from 0.66 to 0.85, demonstrating the applicability of our approach for the analysis of olfactory receptor activation data. The molecular descriptors that are best-suited for response prediction vary for different receptor neurons, implying that each receptor neuron detects a different aspect of chemical space. Finally, we demonstrate that receptor responses themselves can be used as descriptors in a predictive model of neuron activation. Conclusions The chemical meaning of molecular descriptors helps understand structure-response relationships for olfactory receptors and their 'receptive fields'. Moreover, it is possible to predict receptor neuron activation from chemical structure using machine-learning techniques, although this is still complicated by a lack of training data.
PocketPicker: analysis of ligand binding-sites with shape descriptors
- Background Identification and evaluation of surface binding-pockets and occluded cavities are initial steps in protein structure-based drug design. Characterizing the active site's shape as well as the distribution of surrounding residues plays an important role for a variety of applications such as automated ligand docking or in situ modeling. Comparing the shape similarity of binding site geometries of related proteins provides further insights into the mechanisms of ligand binding. Results We present PocketPicker, an automated grid-based technique for the prediction of protein binding pockets that specifies the shape of a potential binding-site with regard to its buriedness. The method was applied to a representative set of protein-ligand complexes and their corresponding apo-protein structures to evaluate the quality of binding-site predictions. The performance of the pocket detection routine was compared to results achieved with the existing methods CAST, LIGSITE, LIGSITEcs, PASS and SURFNET. Success rates PocketPicker were comparable to those of LIGSITEcs and outperformed the other tools. We introduce a descriptor that translates the arrangement of grid points delineating a detected binding-site into a correlation vector. We show that this shape descriptor is suited for comparative analyses of similar binding-site geometry by examining induced-fit phenomena in aldose reductase. This new method uses information derived from calculations of the buriedness of potential binding-sites. Conclusions The pocket prediction routine of PocketPicker is a useful tool for identification of potential protein binding-pockets. It produces a convenient representation of binding-site shapes including an intuitive description of their accessibility. The shape-descriptor for automated classification of binding-site geometries can be used as an additional tool complementing elaborate manual inspections.
Single chain Fab (scFab) fragment
- Background The connection of the variable part of the heavy chain (VH) and and the variable part of the light chain (VL) by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv) was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv) fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab) with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. Results Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd) and the light chain (LC), resulting in the formation of a single chain Fab fragment (scFab), can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabdeltaC) connecting the constant part 1 of the heavy chain (CH1) and the constant part of the light chain (CL) were best suited for phage display and production of soluble antibody fragments. Beside the expression system E.coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies) as well as multimers were characterised. Conclusion A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of common standard sera for detection.
Light-dependent magnetoreception in birds : increasing intensity of monochromatic light changes the nature of the response
- Background The Radical Pair model proposes that magnetoreception is a light-dependent process. Under low monochromatic light from the short-wavelength part of the visual spectrum, migratory birds show orientation in their migratory direction. Under monochromatic light of higher intensity, however, they showed unusual preferences in other directions or axial preferences. To determine whether or not these responses are still controlled by the respective light regimes, European robins, Erithacus rubecula, were tested under UV, Blue, Turquoise and Green light at increasing intensities, with orientation in migratory direction serving as a criterion whether or not magnetoreception works in the normal way. Results Under low light with a quantal flux of 8 times 10 to 15 power quanta s-1 m-2, the birds were well oriented in their seasonally appropriate migratory direction under 424 nm Blue, 502 nm Turquoise and 565 nm Green light, indicating unimpaired magnetoreception. Under 373 nm UV of the same quantal flux, they were not oriented in migratory direction, showing a preference of the east-west axis instead, but they showed excellent orientation in migratory direction under UV of lower intensity. Intensities of above 36 times 10 to 15 power quanta s-1 m-2 of Blue, Turquoise and Green light elicited a variety of responses: disorientation, headings along the east-west axis, headings along the north-south axis or 'fixed' direction tendencies. These responses changed as the intensity was increased from 36 times 10 to the 15 power quanta s-1 m-2 to 54 and 72 times 10 to 15 power quanta s-1 m-2. Conclusion The specific manifestation of responses in directions other than migratory direction clearly depends on the ambient light regime. This implies that although mechanisms normally providing magnetic compass information seem disrupted, processes that are activated by light still control the behavior. It suggests complex interactions between different types of receptors, magnetic and visual. The nature of the receptors involved and details of their connections are not yet known; however, a role of the color cones in the processes mediating magnetic input is suggested.