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Polyploidy is common in higher eukaryotes, especially in plants, but it is generally assumed that most prokaryotes contain a single copy of a circular chromosome and are therefore monoploid. We have used two independent methods to determine the genome copy number in halophilic archaea, 1) cell lysis in agarose blocks and Southern blot analysis, and 2) Real-Time quantitative PCR. Fast growing H. salinarum cells contain on average about 25 copies of the chromosome in exponential phase, and their ploidy is downregulated to 15 copies in early stationary phase. The chromosome copy number is identical in cultures with a twofold lower growth rate, in contrast to the results reported for several other prokaryotic species. Of three additional replicons of H. salinarum, two have a low copy number that is not growth-phase regulated, while one replicon even shows a higher degree of growth phase-dependent regulation than the main replicon. The genome copy number of H. volcanii is similarly high during exponential phase (on average 18 copies/cell), and it is also downregulated (to 10 copies) as the cells enter stationary phase. The variation of genome copy numbers in the population was addressed by fluorescence microscopy and by FACS analysis. These methods allowed us to verify the growth phase-dependent regulation of ploidy in H. salinarum, and they revealed that there is a wide variation in genome copy numbers in individual cells that is much larger in exponential than in stationary phase. Our results indicate that polyploidy might be more widespread in archaea (or even prokaryotes in general) than previously assumed. Moreover, the presence of so many genome copies in a prokaryote raises questions about the evolutionary significance of this strategy.
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.
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.
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.
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.
Oral presentations Background: We selected peptide ligands for the HIV-1 packaging signal PSI by screening phage displayed peptide libraries. Peptide ligands were optimized by screening spot synthesis peptide membranes. The aim of this study is the functional characterization of these peptide ligands with respect to inhibition of HIV-1 replication. Methods: Phage displayed peptide libraries were screened with PSI-RNA structures. The Trp-rich peptide motifs were optimized for specific binding on spot synthesis peptide membranes. The best binding peptide was expressed intracellularly in fusion with RFP or linked to a protein transduction domain (PTD) for intracellular delivery. The effects on virion production were analyzed using pseudotyped lentiviral particles. Results: After positive and negative selection rounds, phages binding specifically to PSI-RNA were identified by ELISA. Peptide inserts contained conserved motifs of aromatic amino acids known to be implicated in binding of PSI-RNA by the natural Gag ligand. The filter assay identified HKWPWW as the best binding ligand for PSI-RNA, which is delivered into several cell lines by addition of a PTD. Compared to a control peptide, the HKWPWW peptide inhibited HIV-1 replication as deduced from reduced titers of culture supernatants. As HKWPWW also binds to the TAR-RNA like the natural nucleocapsid PSI-RNA ligand, the effect on Tat-TAR inhibition will also be analyzed. Currently T-cell lines are established which stably express HKWPWW as well as a control peptide, which will be infected with HIV-1 to monitor the ability of HKWPWW to inhibit wild type HIV-1 replication. Conclusion: The selection of a peptide ligand for PSI-RNA able to inhibit HIV-1 replication proves the suitability of the phage display technology for the selection of peptides binding to RNA-structures. This enables the indentification of peptides serving as leads to interfere with additional targets in the HIV-1 replication cycle.
In an effort to link quantitative morphometric information with molecular data on the population level, we have analysed 19 populations of the conchologically variable land snail Candidula unifasciata from across the species range for variation in quantitative shell traits and at the mitochondrial 16S ribosomal (r)DNA locus. In genetic analysis, including 21 additional populations, we observed two fundamental haplotype clades with an average pairwise sequence divergence of 0.209 ± 0.009 between clades compared to 0.017 ± 0.012 within clades, suggesting the presence of two different evolutionary lineages. Integrating additional shell material from the Senckenberg Malacological Collection, a highly significant discriminant analysis on the morphological shell traits with fundamental haplotype clades as grouping variable suggested that the less frequent haplotype corresponds to the described subspecies C. u. rugosiuscula, which we propose to regard as a distinct species. Both taxa were highly subdivided genetically (FST = 0.648 and 0.777 P < 0.001). This was contrasted by the partition of morphological variance, where only 29.6% and 21.9% of the variance were distributed among populations, respectively. In C. unifasciata, no significant association between population pairwise FST estimates and corresponding morphological fixation indices could be detected, indicating independent evolution of the two character sets. Partial least square analysis of environmental factors against shell trait variables in C. u. unifasciata revealed significant correlations between environmental factors and certain quantitative shell traits, whose potential adaptational values are discussed.
Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11ctd). In addition, the N-terminal domain of L11 (L11ntd) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11ntd, placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11–RNA–thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11ntd in elongation factor binding.
In the inundation area - the basin of the former larger Lake Chad - a special type of sorghum is grown on the clay soils (firgi). This dry-season guinea corn is also called dwarf sorghum or masakwa. In Kanuri, the dominant language in the region, sorghum is called ngawuli. The dry-season types are called ngawuli firgibe (lit. translated: sorghum of the firgi). During the dry season when the natural vegetation becomes dry and yellow, masakwa fields appear in prominent green covering large areas of the clay plains. The most important natural factor for this specialized dry season cropping is the presence of soils with a high clay content. For a better understanding of masakwa and its related issues, a multidisciplinary sub-project (G1) has been established within the SFB 268 (Joint Research Project: History of Culture and Language in the Natural Environment of the West-African Savannah). This project in which all disciplines participate is entitled: "Natural basis for masakwa cultivation and its meaning for the settlement history of the clay plains (firgi) in the Chad basin".
Während über Flora und Vegetation der Wälder, Savannen und Äcker Westafrikas zahlreiche Veröffentlichungen vorliegen, hat man sich mit der ruderalen Flora und Vegetation der Siedlungen bisher nur wenig beschäftigt. Im Rahmen der Forschungen des SFB 268 wurde daher in zwei Ortschaften von Burkina Faso eine Bestandsaufnahme der spontan im Siedlungsbereich und in seiner engeren Umgebung an Ruderalstandorten auftretenden Pflanzenarten durchgeführt, wobei, gemäß den Zielen des SFB 268, auf eine interdisziplinäre Relevanz der Ergebnisse Wert gelegt wurde. Daher standen die Fragen nach der Nutzung der Spontanflora durch die Bevölkerung im Vordergrund des Interesses. In der vorliegenden Arbeit wird über die für die menschliche Ernährung genutzten krautigen Wildpflanzen des Siedlungsbereiches berichtet.
The investigations carried out within the project in NE-Nigeria since 1989 have been focussing on the late Pleistocene and Holocene landscape development of the south eastern Chad basin. Areas of interest include palaeodune fields, clay plains and former beach ridge systems of Lake Chad. Transgressions and regressions of Lake Chad played an important role in the younger landscape history of NE-Nigeria and have also caused great environmental changes. The term „Megachad“ is well known and describes an enormous lake with an extension comparable with the Caspian Sea of today. The term „Microchad“ stands for the other recent extreme in terms of the lake dimensions varying during the times. Environmental changes in the surroundings of Lake Chad are closely connected with transgressions and regressions of the lake. These lake level changes can be climatically induced as well as non-climatically, due to human impact. Nearly all land units have more or less been influenced by the lake, spatially as well as temporally. It is important, though, to notice the scales of the changes. Some changes took place in a millennial scale, some in the scales of centuries or decades, and at least – as can be observed every year – in a seasonal scale.
Numerous ecologists postulate that West African savannas are mostly the result of degradation of formerly closed forests. This hypothesis can only be tested by palaeoecological investigations. The palynological results summarised in this paper document the history of the Sudanian and Sahelian savanna of NE-Nigeria during the last 11.500 years (uncal. BP). Both sites investigated provide evidence for the persistence of savanna throughout the entire Holocene. Patches of closed dry forest may have occurred, but never completely displaced the savanna vegetation. Humid conditions during the early and mid Holocene (from 10.000 BP onwards) caused a rapid spread of Guinean and Sudanian taxa into the northern vegetation zones. A slow return to drier climatic conditions between ca. 6800 BP and ca. 5500 BP can be recorded at both sites. Finally, between 3800 BP and 3300 BP a strong aridification resulted in the establishment of the modern vegetation zones. In both the Sahelian and Sudanian zone the vegetational changes appear to have been primarily controlled by climatic changes, whereas the effects of human activities remain palynologically silent even for the late Holocene.
Two sites situated in the Sahelian and Sudanian zones of NE-Nigeria were chosen for pollen analysis. A sediment core from an interdunal depression in the eastern Manga Grassland provides information on the Holocene vegetation history of the Sahel between c. 9600-3400 B.P. The 3 m pollen record indicates an open savanna during the mid-Holocene. The presence of Sudano-Guinean taxa, which were mainly restricted to the interdunal depressions, points to more humid conditions. Already before c. 4000 B.P., a slow change towards drier conditions and the establishment of the modern Sahelian vegetation is visible in the diagram. This development was accompanied by high fire frequencies. A 16 m core from a crater lake (Lake Tilla) in the Sudanian zone of NE-Nigeria provides a pollen record which can be dated back to approximately 11-12000 B.P. Preliminary pollen spectra show a relatively constant pattern with a dominance of grass pollen even during the middle Holocene.
Im SW Burkina Fasos (sechs Monate Regenzeit und durchschnittlich über 1000 mm Niederschlag) wurden mehrere Trockenwälder auf ihr Artenspektrum und die Bodenverhältnisse hin untersucht. Die Waldformationen fallen durch die Dichte der Gehölzbedeckung, ihren Lianenreichtum und das fast vollständige Fehlen von Gräsern auf. Typische Gehölzarten sind Anogeissus leiocarpus, Diospyros mespiliformis und die Liane Saba senegalensis. Der dichte Strauchunterwuchs und die fehlende Grasschicht verhindern das regelmäßige Eindringen von Buschfeuern. Wegen der Dichte und des Alters der Bäume belegen diese Waldformationen, daß an den Standorten, zumindest für einen sehr langen Zeitraum, kein Feldbau betrieben wurde. Daher konnten sich, auch auf eher als ungünstig zu bewertenden Böden, Trockenwälder ausbilden, die zumindest in ihrer Physiognomie der potentiellen natürlichen Vegetation entsprechen. Jedoch finden sich in den Wäldern oft Spuren menschlicher Aktivitäten aus der Vergangenheit, so z.B. Steinsetzungen, Siedlungshügel und Gruben. Außerdem lassen sich vielfach Anzeichen einer rezenten Nutzung beobachten, so z.B. für die Entnahme von Werkholz, das Schneiteln mancher Baumarten zur Viehfuttergewinnung, gelegentliche Beweidung und das Sammeln von Wildpflanzen.
Les ferrières sont par définition les amas des déchets de la réduction du fer. De par son origine elles constituent des lithosols qui ont beaucoup évolué dans l’espace et dans le temps. A notre connaissance très peu d’études se sont penchées sur cette végétation qui couvre actuellement les sites de réduction du fer. L’inventaire floristique de plusieurs sites en zone soudanienne montre la fréquence de certaines espèces sur les ferrières. L’étude de la chorologie de toutes les espèces confondues ligneuses et herbacées, montrent que la plupart sont constituées par des espèces zoochores et quelques espèces anémochores. Elles sont disséminées principalement par les animaux d’élevage, par les oiseaux. Cette communication synthétise les données des différentes prospections et les premiers résultats de nos observations et analyses. Elle a deux objectifs : de montrer l’importance des activités anthropiques dans la formation du paysage végétal d’une part, et d’autre part de mettre en évidence le processus de colonisation des sols nus et des ferrières en zone soudanienne.
Au Sahel du Burkina Faso, le diagramme pollinique d'Oursi fournit des évidences sur l'apparition de l'agriculture, il y a environ 3000 ans. A partir de ces faits, le but principal des recherches archéologiques dans le cadre du SFB 268 était de trouver et de fouiller des sites qui seraient à même d'apporter des informations sur cette période décisive autour de 3000 ans avant l'actuel. Pour cela, nous avons concentré notre travail sur les provinces du Séno et plus particulièrement de l'Oudalan. Le paysage de cette région est marqué par des dunes qui s'organisent grossièrement en cordons d'orientation nord-est/sud-ouest à travers notre terrain.
La variation dans l'utilisation des ressources végétales est liée aux changements de mode de vie. Le Burkina Faso fait parti des pays habituellement indiqués comme en voie de développement. Ce qualificatif est vrai si on ne regarde que la croissance technologique. Le pays accuse certes un retard sur ce plan, mais la population sait bel et bien développer son intelligence humaine pour faire face à telle ou telle situation. Ainsi, devant une mauvaise récolte, personne n'acceptera de mourir de faim tant que dans l'environnement naturel existeront tous les éléments nécessaires pour survivre: l'eau, les plantes et les animaux. A ce moment-là, le mode de vie change; il ne s'agit plus de récolter, mais il s'agit de prélever, de cueillir. La cueillette, c'était un mode de vie dans l'époque préhistorique. L'homme se rabat sur tout ce qui peut fournir un aliment substantiel: les gros tubercules, les feuilles les plus tendres, les fruits et les graines. Si les trois dernières catégories d'aliments ne posent pas trop de problèmes, la première et les autres organes souterrains sont en général toxiques. Et là encore, l'homme va développer son intelligence pour éliminer cette toxicité mais après une grande perte en vie humaine. Dans le but de savoir un peu plus sur ces différentes périodes de disette et de famine, nous avons mené une enquête à Ouahigouya (Yatenga) et à Toma (Sourou), deux zones qui appartenaient à un même cercle pendant l'époque coloniale, période de la suppression de la Haute-Volta. Par ailleurs nous voulons vérifier la marge d'erreur qu'on peut avoir lors d'une enquête ethnobotanique en se situant dans le temps et l'espace. Cette communication entre en plus dans le cadre de nos travaux de recherche sur l'histoire de la végétation et de l'utilisation des ressources végétales.
L'homme vivant de la cueillette existe toujours au Burkina Faso. Les espèces que nous allons exposer par la suite ne font pas l'objet d'une culture. La plupart certes sont des espèces protégées lors des défrichements. Elles caractérisent souvent les différents faciès de savane rencontrés à travers le pays. Certaines ont des usages généralisés en temps normal, d'autres le sont en temps de disette ou de soudure. Ces espèces ligneuses sont à usages culinaires par leurs feuilles, leurs graines et leurs exsudats. Leur composition chimique montre un certain équilibre énergétique à la consommation et permet de comprendre la santé de nos paysans malgré ce qu'on laisse entendre sur la pauvreté et la sous-alimentation. Dans le cadre de nos travaux pour une meilleure connaissance des espèces tant sur le plan taxonomique, biologique qu'ethnobotanique, nous avons mené depuis cinq ans une enquête sur les différentes utilisations des espèces ligneuses. Le présent travail concerne particulièrement les espèces ligneuses dont certains organes sont utilisés dans alimentation humaine. Nous nous sommes limités à ne parler que d'une vingtaine d'espèces.
La métallurgie du fer jouit d'un regain d'intérêt en Afrique depuis une décénnie. Alors que les diffusionistes et les antidiffusionistes se sont affrontés dans les années 1970, on assiste aujourd'hui à une nouvelle fièvre du "fer" où les chercheurs, mettant de côté l'idéologie, travaillent avec acharnement sur les fourneaux de réduction et sur toutes les traces de cette métallurgie. Les résultats obtenus sont déja impressionnants. L'environnement constituent aussi, désormais, une préoccupation majeure des chercheurs. Les recherches en paléométallurgie au Burkina Faso n'échappent pas totalemennt à cette critique. C'est pour attirer plus d'attention sur l'important complément sociologique des investigations archéologiques que nous proposons en ces lignes les quelques informations relatives aux conditions sociales des forgerons, potiers et potières, réunis dans plusieurs nationalités du Burkina Faso par une sorte de communauté de destin: les arts du feu.
Le Burkina Faso est situé dans la zone soudano-sahélienne où les cultures sont quelquefois aléatoires; dans ces conditions les plantes ligneuses occupent une place importante dans la vie socio-économique du pays. Pourtant, une sécheresses climatique persistante de ces dernières décennies a entraîné une mortalité massive de ces ligneux surtout dans la zone sahélienne. Cette forte dégradation des ressources naturelles est variable d’une zone géo-graphique à une autre pour des raisons diverses. Si les phénomènes généraux de cette dégradation de la végétation et leurs causes sont souvent décrits par de nombreux auteurs, il existe par contre très peu de connaissances détaillées et spécifiques en fonction des zones géographiques sur la menace qui pèse sur les différentes espèces. Dans l’absence de bases scientifiques fiables sur la végétation du passé pour chacune des régions qui permettrait ainsi d’établir avec précision la liste des espèces disparues, il est donc nécessaire de se baser sur la perception de la population rurale qui se trouve bien placée pour déceler tout changement dans la flore. Dans ce contexte, cette étude menée auprès des gourmantchés, vise surtout à identifier les espèces disparues ou celles en voie de disparition dans les différentes zones écologiques à l’est du Burkina Faso; en outre, elle aborde les raisons évoquées par ces populations pour expliquer cette menace qui pèse sur chacune des espèces. L’enquête a enfin contribué à connaître les solutions envisagées par ces dernières pour anéantir ou réduire la menace.