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In dieser Arbeit sollen zwei Themenkomplexe, jeder für sich außerordentlich interessant und vielschichtig, betrachtet und verknüpft werden. Das direkte Einbinden von lebenden Tieren in die Lehre des Lebendigen ist nicht nur sinnvoll, sondern wichtig und wird auch von den Rahmenplänen Biologie empfohlen. Mit dem Einsatz von Tieren im Unterricht wird sich an verschiedenen Stellen beschäftigt (z.B. OGILVIE & STINSON 1995). Der Klasse Reptilia kommt dabei aber vergleichsweise wenig Beachtung zu. Voraussetzung für die Haltung von Tieren in der Schule, die in der Öffentlichkeit steht und eine beachtliche Vorbildsfunktion inne hat, ist unter anderem, dass eine „artgerechte“ Unterbringung und Pflege möglich ist. Was unter der Bezeichnung einer „artgerechten Tierhaltung“ verstanden wird, ist alles andere als eindeutig. Deshalb soll die Thematik mit Bezug auf die Reptilienhaltung in der Schule beleuchtet werden.
The conditionally-lethal pso4-1 mutant allele of the spliceosomal-associated PRP19 gene allowed us to study this gene’s influence on pre-mRNA processing, DNA repair and sporulation. Phenotypes related to intron-containing genes were correlated to temperature. Splicing reporter systems and RT–PCR showed splicing efficiency in pso4-1 to be inversely correlated to growth temperature. A single amino acid substitution, replacing leucine with serine, was identified within the N-terminal region of the pso4-1 allele and was shown to affect the interacting properties of Pso4-1p. Amongst 24 interacting clones isolated in a two-hybrid screening, seven could be identified as parts of the RAD2, RLF2 and DBR1 genes. RAD2 encodes an endonuclease indispensable for nucleotide excision repair (NER), RLF2 encodes the major subunit of the chromatin assembly factor I, whose deletion results in sensitivity to UVC radiation, while DBR1 encodes the lariat RNA splicing debranching enzyme, which degrades intron lariat structures during splicing. Characterization of mutagen-sensitive phenotypes of rad2{Delta}, rlf2{Delta} and pso4-1 single and double mutant strains showed enhanced sensitivity for the rad2{Delta} pso4-1 and rlf2{Delta} pso4-1 double mutants, suggesting a functional interference of these proteins in DNA repair processes in Saccharomyces cerevisiae.
Chemically modified bases are frequently used to stabilize nucleic acids, to study the driving forces for nucleic acid structure formation and to tune DNA and RNA hybridization conditions. In particular, fluorobenzene and fluorobenzimidazole base analogues can act as universal bases able to pair with any natural base and to stabilize RNA duplex formation. Although these base analogues are compatible with an A-form RNA geometry, little is known about the influence on the fine structure and conformational dynamics of RNA. In the present study, nano-second molecular dynamics (MD) simulations have been performed to characterize the dynamics of RNA duplexes containing a central 1'-deoxy-1'-(2,4-difluorophenyl)-ß-D-ribofuranose base pair or opposite to an adenine base. For comparison, RNA with a central uridine:adenine pair and a 1'-deoxy-1'-(phenyl)-ß-D-ribofuranose opposite to an adenine was also investigated. The MD simulations indicate a stable overall A-form geometry for the RNAs with base analogues. However, the presence of the base analogues caused a locally enhanced mobility of the central bases inducing mainly base pair shear and opening motions. No stable ‘base-paired’ geometry was found for the base analogue pair or the base analogue:adenine pairs, which explains in part the universal base character of these analogues. Instead, the conformational fluctuations of the base analogues lead to an enhanced accessibility of the bases in the major and minor grooves of the helix compared with a regular base pair.
The radiation-sensitive mutant pso4-1 of Saccharomyces cerevisiae shows a pleiotropic phenotype, including sensitivity to DNA cross-linking agents, nearly blocked sporulation and reduced mutability. We have cloned the putative yeast DNA repair gene PSO4 from a genomic library by complementation of the blocked UV-induced mutagenesis and of sporulation in diploids homozygous for pso4-1. Sequence analysis revealed that gene PSO4 consists of 1512 bp located upstream of UBI4 on chromosome XII and encodes a putative protein of 56.7 kDa. PSO4 is allelic to PRP19, a gene encoding a spliceosome-associated protein, but shares no significant homology with other yeast genes. Gene disruption with a destroyed reading frame of our PSO4 clone resulted in death of haploid cells, confirming the finding that PSO4/PRP19 is an essential gene. Thus, PSO4 is the third essential DNA repair gene found in the yeast S.cerevisiae.
Das Thema der vorliegenden Arbeit war die molekulargenetische Charakterisierung der Funktion der Glukosesensoren Snf3 und Rgt2 in der Hefe S. cerevisiae. Snf3 und Rgt2 gehören zur Familie der Hexosetransporter. Sie unterscheiden sich von ihnen jedoch in ihrer Funktion als Glukosesensoren wie auch durch ihre ungewöhnlich langen Cterminalen Domänen. Snf3 und Rgt2 sind integrale Membranproteine, die als Reaktion auf extrazelluläre Glukose Signale auslösen, die zur Expression bestimmter Hexosetransporter führt. Einige Komponenten, die an der Signaltranduktion beteiligt sind, wurden bereits identifiziert. Jedoch ist der genaue Mechanismus, der zur Expression der Hexostransporter führt, noch nicht vollständig aufgeklärt. Im ersten Teil dieser Arbeit wurden die Proteine Snf3, Rgt2, Mth1, Std1 und Rgt1 auf direkte Interaktionen untereinander getestet, um Einblicke in den molekularen Mechanismus der Signaltransduktion zu erhalten. Desweiteren sollte festgestellt werden, ob die Protein-Wechselwirkungen von der C-Quelle abhängig sind. Es konnte gezeigt werden, dass zwischen den Membranproteinen Rgt2 bzw. Snf3 und den löslichen Proteinen Mth1 bzw. Std1 Interaktionen in Abhängigkeit von Glukose stattfanden. Diese Ergebnisse unterstützen das von Moriya und Johnston aufgestellte, gegenwärtige Modell für eine glukoseinduzierte HXT Genexpression. Im zweiten Teil dieser Arbeit wurde geprüft, ob sich aus dem Glukosesensor Snf3 durch eine Aminosäuresubstitution ein bifunktionaler Sensor für Glukose und Galaktose erzeugen läßt. Dazu wurden die für den Galaktosetransport verantwortlichen Aminosäuren in den homologen Positionen von Snf3 ausgetauscht. Die Bestimmungen der Regulation des Snf3-kontrollierten HXT7 Promotors ergaben, dass das mutierte Snf3 Protein, wie das Wildtyp-Snf3 Protein, eine normale Glukosesensorfunktion ausübt aber keine Galaktosesensorfunktion vorzeigt.
Background: The flavin in its FMN and FAD forms is a versatile cofactor that is involved in catalysis of most disparate types of biological reactions. These include redox reactions such as dehydrogenations, activation of dioxygen, electron transfer, bioluminescence, blue light reception, photobiochemistry (as in photolyases), redox signaling etc. Recently, hitherto unrecognized types of biological reactions have been uncovered that do not involve redox shuffles, and might involve the reduced form of the flavin as a catalyst. The present work addresses properties of reduced flavin relevant in this context. Results: N(5)-H exchange reactions of the flavin reduced form and its pH dependence were studied using the 15N-NMR-signals of 15N-enriched, reduced flavin in the pH range from 5 to 12. The chemical shifts of the N(3) and N(5) resonances are not affected to a relevant extent in this pH range. This contrasts with the multiplicity of the N(5)-resonance, which strongly depends on pH. It is a doublet between pH 8.45 and 10.25 that coalesces into a singlet at lower and higher pH values. From the line width of the 15N(5) signal the pH-dependent rate of hydrogen exchange was deduced. The multiplicity of the 15N(5) signal and the proton exchange rates are little dependent on the buffer system used. Conclusion: The exchange rates allow an estimation of the pKa value of N(5)-H deprotonation in reduced flavin to be ≥ 20. This value imposes specific constraints for mechanisms of flavoprotein catalysis based on this process. On the other hand the pK ≈ 4 for N(5)-H protonation (to form N(5)+-H2) would be consistent with a role of N(5)-H as a base.
Pflanzliche Biomasse bietet sich hervorragend als billiges und in großen Mengen verfügbares Ausgangssubstrat für industrielle Fermentationsprozesse an. Dabei könnte z.B. die Hefe Saccharomyces cerevisiae zur Herstellung von Bioalkohol eingesetzt werden. S. cerevisiae kann jedoch die in großen Mengen in der Biomasse enthaltenen Pentosen D-Xylose und L-Arabinose nicht vergären. Deshalb wäre ein Hefestamm mit entsprechend erweitertem Substratspektrum von großem wirtschaftlichen Interesse. In dieser Arbeit sollte rekombinante Hefestämme konstruiert bzw. optimiert werden, die in der Lage sind D-Xylose und/oder L-Arabinose zu Ethanol zu vergären. Zunächst wurde ein bereits vorhandener L-Arabinose vergärender Hefestamm unter Einsatz der Methoden der „gerichteten Evolution“ optimiert, L-Arabinose effektiver zu verstoffwechseln. Dies geschah durch repetitive Selektion auf Wachstum mit L-Arabinose als einziger Kohlenstoffquelle unter Sauerstoff-limitierten Bedingungen. Eine genetische und physiologische Charakterisierung des Stammes ergab, dass dieser sowohl Mutationen im Hefegenom als auch auf den L-Arabinose Stoffwechselweg exprimierenden Plasmiden erworben hatte. Dieser Stamm exprimierte die für den L-Arabinose Katabolismus notwendigen Enzyme und Transporter von vier verschiedenen Plasmiden. Für den industriellen Einsatz eines rekombinanten Hefestammes ist es jedoch unerlässlich, die Gene des L-Arabinose Katabolismus stabil in das Genom zu integrieren. In dieser Arbeit ist es gelungen, zwei der insgesamt drei essentiellen Gene des Stoffwechselweges in funktioneller Form in den rDNA-Locus von S. cerevisiae zu integrieren. Im letzten Teil der Arbeit konnte erstmals ein Hefestamm konstruiert werden, der sowohl die Gene des Stoffwechselweges für den L-Arabinose- als auch die des Stoffwechselweges für den D-Xylose-Katabolismus exprimiert. Der Stamm war in der Lage auf Nähragarplatten zu wachsen, bei denen L-Arabinose oder/und D-Xylose die einzigen Kohlenstoffquellen darstellten. Wachstumstests mit Flüssigkulturen sowie HPLC-Analysen des Zuckerverbrauchs ergaben jedoch, dass der Hefestamm überraschenderweise nicht in der Lage war, D-Xylose in Flüssigmedien zu verstoffwechseln. Mögliche Erklärungen hierfür werden diskutiert.
Background Fermentation of lignocellulosic biomass is an attractive alternative for the production of bioethanol. Traditionally, the yeast Saccharomyces cerevisiae is used in industrial ethanol fermentations. However, S. cerevisiae is naturally not able to ferment the pentose sugars D-xylose and L-arabinose, which are present in high amounts in lignocellulosic raw materials. Results We describe the engineering of laboratory and industrial S. cerevisiae strains to co-ferment the pentose sugars D-xylose and L-arabinose. Introduction of a fungal xylose and a bacterial arabinose pathway resulted in strains able to grow on both pentose sugars. Introduction of a xylose pathway into an arabinose-fermenting laboratory strain resulted in nearly complete conversion of arabinose into arabitol due to the L-arabinose reductase activity of the xylose reductase. The industrial strain displayed lower arabitol yield and increased ethanol yield from xylose and arabinose. Conclusion Our work demonstrates simultaneous co-utilization of xylose and arabinose in recombinant strains of S. cerevisiae. In addition, the co-utilization of arabinose together with xylose significantly reduced formation of the by-product xylitol, which contributed to improved ethanol production.
Background: Particle Swarm Optimization (PSO) is an established method for parameter optimization. It represents a population-based adaptive optimization technique that is influenced by several "strategy parameters". Choosing reasonable parameter values for the PSO is crucial for its convergence behavior, and depends on the optimization task. We present a method for parameter meta-optimization based on PSO and its application to neural network training. The concept of the Optimized Particle Swarm Optimization (OPSO) is to optimize the free parameters of the PSO by having swarms within a swarm. We assessed the performance of the OPSO method on a set of five artificial fitness functions and compared it to the performance of two popular PSO implementations. Results: Our results indicate that PSO performance can be improved if meta-optimized parameter sets are applied. In addition, we could improve optimization speed and quality on the other PSO methods in the majority of our experiments. We applied the OPSO method to neural network training with the aim to build a quantitative model for predicting blood-brain barrier permeation of small organic molecules. On average, training time decreased by a factor of four and two in comparison to the other PSO methods, respectively. By applying the OPSO method, a prediction model showing good correlation with training-, test- and validation data was obtained. Conclusion: Optimizing the free parameters of the PSO method can result in performance gain. The OPSO approach yields parameter combinations improving overall optimization performance. Its conceptual simplicity makes implementing the method a straightforward task.
The European Strategy on Invasive Alien Species T-PWS(2002) 8 mandates intensified research by member nations on invasive species. This research will not be restricted solely to the biology and remediation of invasive species, but will also evaluate their adverse health effects and economic impact. Previous studies of these issues have only been carried out in the Unites States of America, or in a limited, regional manner. Consequently, 20 plant and animal species from various problem areas (species which pose a threat to public health; losses to agriculture, fisheries, and forestry; damage to public roads and waterways; costs associated with the protection of native species threatened by non-native species as mandated by Recommendation 77 of the Bern Convention were assessed in Germany nation-wide. The accruing costs were sorted into 3 categories: a) direct economic losses, such as those caused by destructive pest species; b) ecological costs, in the form of extra care and protection of native taxa, biotopes, or ecosystems threatened by invasive species; c) costs of measures to combat invasive species. Because of the nature of available data, as well as the different biology and ecology of the invasive species, each had to be treated individually, and the associated costs vary greatly from species to species. Moreover, not all of the species investigated cause economic losses. Accordingly, a nuanced approach to alien species is essential. Cost assessment of losses deriving from ecological damage was only possible in a few cases. Ongoing, multi-year studies incorporating cost/benefit analysis will be necessary to resolve remaining issues.
In dem Entwurf einer European Strategy on Invasive Alien Species T-PVS (2002) 8 werden verstärkte Forschungsaktivitäten der Mitgliedstaaten angeregt, die nicht nur auf den biologischen Bereich oder Bekämpfung invasiver Arten beschränkt bleiben, sondern auch die Bewertung der Auswirkungen auf Gesundheitswesen und Volkswirtschaft untersuchen sollen. Derartige Studien wurden bisher nur für die Vereinigten Staaten von Amerika oder mit eher regionalen Charakter durchgeführt. Aus diesem Grunde wurden 20 Tiere und Pflanzen aus verschiedenen Problemgebieten (Gesundheitsgefährdende Arten, Schäden in Forst-, Land-, und Fischereiwirtschaft, im kommunalen Bereich, an aquatischen und terrestrischen Verkehrswegen sowie Kosten von Arten, die einheimische Spezies gefährden oder in der Empfehlung 77 der Berner Konvention aufgeführt sind) ausgewählt und beispielhaft für das Gebiet Deutschlands bearbeitet. Die entstehenden Kosten wurden in drei Kategorien aufgeschlüsselt: a) direkte ökonomische Schäden, beispielsweise durch Vorratsschädlinge, b) ökologische Schäden, verursacht durch Pflege und Schutz gefährdeter heimischer Arten, Biozönosen oder Ökosysteme und c) Kosten für Maßnahmen zur Bekämpfung invasiver Arten. Es zeigte sich, dass auf Grund der Datenlage sowie der unterschiedlichen Biologie und Ökologie der invasiven Arten jeweils individuelle Ansätze notwendig waren. Die hier ermittelten Kosten unterscheiden sich stark von Art zu Art. Nicht alle untersuchten Arten verursachen ökonomische Schäden. Eine differenzierte Betrachtung von Neobiota ist nach dem Prinzip der Einzelfallbewertung erforderlich. Die Monetisierung von ökologischen Schäden gelang hierbei nur in wenigen Fällen. Weitergehende, mehrjährige Studien sollten willingness to pay-Analysen einbeziehen, um offen gebliebene Fragen zu beantworten.
Im Rahmen dieser Diplomarbeit konnte das Plasmid pB6 isoliert werden, das die MNNG-Hyperresistenz einer rng1-1-Mutante komplementierte. Das komplementierende Gen dieses Plasmids konnte jedoch weder über 17 Subklone noch über Komplementationsanalysen identifiziert werden. Die Sensibilität gegen „Congo red“ konnte als ein weiterer Phänotyp des Stammes Q2rng1 bestimmt werden. Es wurden im Zuge der Subklonierung des Plasmids pB6 pRS424-Derivate gefunden, die unabhängig vom genetischen Hintergrund des transformierten Stammes, heterogenes Wachstum verursachten. Zurückzuführen war dies auf die Überexpression des ORFs YLR112w alleine oder gemeinsam mit dem ORF YLR111w. Neben der bereits beschriebenen MNNG-Hyperresistenz durch die Überexpression von SNG1 in Wildtypen, GSH-Mutanten und Reparaturdefizienten Stämmen, konnte auch in dem bereits gegen MNNG hyperresistenten Stamm Q2rng1 eine Steigerung der Resistenz durch SNG1 gezeigt werden. Des weiteren wurden Anzeichen gefunden, dass die MethioninAuxotrophie des Stammes Q3 auf die Disruption des GSH1-Gens zurückzuführen war. Zudem konnte nachgewiesen werden, dass die funktionierende GSH-Synthese letal auf eine ero1-Delta-Mutante wirkte. Als Auslöser für die Cadmium-Sensibilität der Stämme Q3 und Q4 konnten die bekannten Mutationen dieser Stämme im GSH1- und im LWG1-Gen ausgeschlossen werden.
Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse strains. The major gene trapping groups worldwide have recently joined together to centralize access to all publicly available gene trap lines by developing a user-oriented Website for the International Gene Trap Consortium (IGTC). This collaboration provides an impressive public informatics resource comprising ~45 000 well-characterized ES cell lines which currently represent ~40% of known mouse genes, all freely available for the creation of knockout mice on a non-collaborative basis. To standardize annotation and provide high confidence data for gene trap lines, a rigorous identification and annotation pipeline has been developed combining genomic localization and transcript alignment of gene trap sequence tags to identify trapped loci. This information is stored in a new bioinformatics database accessible through the IGTC Website interface. The IGTC Website (www.genetrap.org) allows users to browse and search the database for trapped genes, BLAST sequences against gene trap sequence tags, and view trapped genes within biological pathways. In addition, IGTC data have been integrated into major genome browsers and bioinformatics sites to provide users with outside portals for viewing this data. The development of the IGTC Website marks a major advance by providing the research community with the data and tools necessary to effectively use public gene trap resources for the large-scale characterization of mammalian gene function.
Prostaglandin E2 (PGE2) plays an important role in bone development and metabolism. To interfere therapeutically in the PGE2 pathway, however, knowledge about the involved enzymes (cyclooxygenases) and receptors (PGE2 receptors) is essential. We therefore examined the production of PGE2 in cultured growth plate chondrocytes in vitro and the effects of exogenously added PGE2 on cell proliferation. Furthermore, we analysed the expression and spatial distribution of cyclooxygenase (COX)-1 and COX-2 and PGE2 receptor types EP1, EP2, EP3 and EP4 in the growth plate in situ and in vitro. PGE2 synthesis was determined by mass spectrometry, cell proliferation by DNA [3H]-thymidine incorporation, mRNA expression of cyclooxygenases and EP receptors by RT-PCR on cultured cells and in homogenized growth plates. To determine cellular expression, frozen sections of rat tibial growth plate and primary chondrocyte cultures were stained using immunohistochemistry with polyclonal antibodies directed towards COX-1, COX-2, EP1, EP2, EP3, and EP4. Cultured growth plate chondrocytes transiently secreted PGE2 into the culture medium. Although both enzymes were expressed in chondrocytes in vitro and in vivo, it appears that mainly COX-2 contributed to PGE2-dependent proliferation. Exogenously added PGE2 stimulated DNA synthesis in a dose-dependent fashion and gave a bell-shaped curve with a maximum at 10-8 M. The EP1/EP3 specific agonist sulprostone and the EP1-selective agonist ONO-D1-004 increased DNA synthesis. The effect of PGE2 was suppressed by ONO-8711. The expression of EP1, EP2, EP3, and EP4 receptors in situ and in vitro was observed; EP2 was homogenously expressed in all zones of the growth plate in situ, whereas EP1 expression was inhomogenous, with spared cells in the reserve zone. In cultured cells these four receptors were expressed in a subset of cells only. The most intense staining for the EP1 receptor was found in polygonal cells surrounded by matrix. Expression of receptor protein for EP3 and EP4 was observed also in rat growth plates. In cultured chrondrocytes, however, only weak expression of EP3 and EP4 receptor was detected. We suggest that in growth plate chondrocytes, COX-2 is responsible for PGE2 release, which stimulates cell proliferation via the EP1 receptor.
High-throughput gene trapping is a random approach for inducing insertional mutations across the mouse genome. This approach uses gene trap vectors that simultaneously inactivate and report the expression of the trapped gene at the insertion site, and provide a DNA tag for the rapid identification of the disrupted gene. Gene trapping has been used by both public and private institutions to produce libraries of embryonic stem (ES) cells harboring mutations in single genes. Presently,~ 66% of the protein coding genes in the mouse genome have been disrupted by gene trap insertions. Among these, however, genes encoding signal peptides or transmembrane domains (secretory genes) are underrepresented because they are not susceptible to conventional trapping methods. Here, we describe a high-throughput gene trapping strategy that effectively targets secretory genes. We used this strategy to assemble a library of ES cells harboring mutations in 716 unique secretory genes, of which 61% were not trapped by conventional trapping, indicating that the two strategies are complementary. The trapped ES cell lines, which can be ordered from the International Gene Trap Consortium (http://www.genetrap.org), are freely available to the scientific community.
Background: Cancer gene therapy will benefit from vectors that are able to replicate in tumor tissue and cause a bystander effect. Replication-competent murine leukemia virus (MLV) has been described to have potential as cancer therapeutics, however, MLV infection does not cause a cytopathic effect in the infected cell and viral replication can only be studied by immunostaining or measurement of reverse transcriptase activity. Results: We inserted the coding sequences for green fluorescent protein (GFP) into the proline-rich region (PRR) of the ecotropic envelope protein (Env) and were able to fluorescently label MLV. This allowed us to directly monitor viral replication and attachment to target cells by flow cytometry. We used this method to study viral replication of recombinant MLVs and split viral genomes, which were generated by replacement of the MLV env gene with the red fluorescent protein (RFP) and separately cloning GFP-Env into a retroviral vector. Co-transfection of both plasmids into target cells resulted in the generation of semi-replicative vectors, and the two color labeling allowed to determine the distribution of the individual genomes in the target cells and was indicative for the occurrence of recombination events. Conclusions: Fluorescently labeled MLVs are excellent tools for the study of factors that influence viral replication and can be used to optimize MLV-based replication-competent viruses or vectors for gene therapy.
We have isolated the human protein SNEV as downregulated in replicatively senescent cells. Sequence homology to the yeast splicing factor Prp19 suggested that SNEV might be the orthologue of Prp19 and therefore might also be involved in pre-mRNA splicing. We have used various approaches including gene complementation studies in yeast using a temperature sensitive mutant with a pleiotropic phenotype and SNEV immunodepletion from human HeLa nuclear extracts to determine its function. A human–yeast chimera was indeed capable of restoring the wild-type phenotype of the yeast mutant strain. In addition, immunodepletion of SNEV from human nuclear extracts resulted in a decrease of in vitro pre-mRNA splicing efficiency. Furthermore, as part of our analysis of protein–protein interactions within the CDC5L complex, we found that SNEV interacts with itself. The self-interaction domain was mapped to amino acids 56–74 in the protein's sequence and synthetic peptides derived from this region inhibit in vitro splicing by surprisingly interfering with spliceosome formation and stability. These results indicate that SNEV is the human orthologue of yeast PRP19, functions in splicing and that homo-oligomerization of SNEV in HeLa nuclear extract is essential for spliceosome assembly and that it might also be important for spliceosome stability.
In order to further understand how DNA polymerases discriminate against incorrect dNTPs, we synthesized two sets of dNTP analogues and tested them as substrates for DNA polymerase a (pol alpha) and Klenow fragment (exo-) of DNA polymerase I (Escherichia coli ). One set of analogues was designed to test the importance of the electronic nature of the base. The bases consisted of a benzimidazole ring with one or two exocyclic substituent(s) that are either electron-donating (methyl and methoxy) or electronwithdrawing (trifluoromethyl and dinitro). Both pol a and Klenow fragment exhibit a remarkable inability to discriminate against these analogues as compared to their ability to discriminate against incorrect natural dNTPs. Neither polymerase shows any distinct electronic or steric preferences for analogue incorporation. The other set of analogues, designed to examine the importance of hydrophobicity in dNTP incorporation, consists of a set of four regioisomers of trifluoromethyl benzimidazole. Whereas pol a and Klenow fragment exhibited minimal discrimination against the 5- and 6-regioisomers, they discriminated much more effectively against the 4- and 7-regioisomers. Since all four of these analogues will have similar hydrophobicity and stacking ability, these data indicate that hydrophobicity and stacking ability alone cannot account for the inability of pol a and Klenow fragment to discriminate against unnatural bases. After incorporation, however, both sets of analogues were not efficiently elongated. These results suggest that factors other than hydrophobicity, sterics and electronics govern the incorporation of dNTPs into DNA by pol {alpha} and Klenow fragment.
Background: Costly structures need to represent an adaptive advantage in order to be maintained over evolutionary times. Contrary to many other conspicuous shell ornamentations of gastropods, the haired shells of several Stylommatophoran land snails still lack a convincing adaptive explanation. In the present study, we analysed the correlation between the presence/absence of hairs and habitat conditions in the genus Trochulus in a Bayesian framework of character evolution. Results: Haired shells appeared to be the ancestral character state, a feature most probably lost three times independently. These losses were correlated with a shift from humid to dry habitats, indicating an adaptive function of hairs in moist environments. It had been previously hypothesised that these costly protein structures of the outer shell layer facilitate the locomotion in moist habitats. Our experiments, on the contrary, showed an increased adherence of haired shells to wet surfaces. Conclusion: We propose the hypothesis that the possession of hairs facilitates the adherence of the snails to their herbaceous food plants during foraging when humidity levels are high. The absence of hairs in some Trochulus species could thus be explained as a loss of the potential adaptive function linked to habitat shifts.
Homing in with GPS
(2000)
Flight paths of homing pigeons were measured with a newly developed recorder based on GPS. The device consists of a GPS receiver board, a logging facility, an antenna, a power supply, a DCDC converter and a casing. It has a weight of 33g and works reliably with a sampling rate of 1/s with an operation time of about 3 h, providing timeindexed data on geographic positions, ground speed and altitude. The data are downloaded when the bird is recaptured. The devices are fixed to the birds with a harness. The measured complete flight paths show many details: e.g. initial loops flown immediately after release and large detours flown by some pigeons. We are here presenting 3 examples of flight paths from a release site 17.3 km Northeast of the home loft in Frankfurt. Mean speed in flight, duration of breaks and length of the flight path were calculated. The pigeons chose different routes and have different individual tendencies to fly loops over the village close to the release site.
This paper describes a first version of the GPS flight recorder for homing pigeons. The GPS recorder consists of a hybrid GPS board, a patch antenna 19*19 mm, a 3 V Lithium battery as power supply, a DCDC converter, a logging facility and an additional microprocessor. It has a weight of 33g. Prototypes were tested and worked reliably with a sampling rate of 1/sec and with an operation time of about 3 h. In first tests on homing pigeons 9 flight paths were recorded, showing details like loops flown immediately after the release, complete routes over 30 km including detours, rest periods and speed.
Die Datenbank BioLIS wird durch die Universitätsbibliothek Johann Christian Senckenberg (Frankfurt/M.) kostenfrei online zur Verfügung gestellt. Sie weist deutsche biologische Zeitschriftenliteratur aus dem Zeit¬raum 1970 bis 1996 nach – damit ist BioLIS eine wesentliche Ergänzung zu der Datenbank „Biological Abstracts“. Die bibliografischen Angaben zu den nachgewiesenen Aufsätzen werden durch umfassende Schlagwörter und Namen behandelter Organismen ergänzt, so dass Spezialrecherchen insbesondere nach Literatur über bestimmte Organismen möglich sind.
Die Bioinformatik dient der Lösung biologischer Probleme und Erkenntnisgewinnung mit Hilfe informatischer Methodik. und stellt das Bindeglied zwischen der Informationswissenschaft und der Lehre des Lebens dar. Eine festgeschriebene Definition des Begriffes „Bioinformatik" existiert nicht: Sie umfaßt ein weites Feld, beginnend bei der automatischen Sequenzierung ganzer Genome, über Funktionsanalysen durch Homologiesuchen in Datenbanken, Strukturvorhersagen und Modelling, bis hin zur chipgesteuerten Prothetik. Unterstützende Arbeit in der Molekularbiologie leistet die Bioinformatik bei der Aufnahme und Verwaltung von Nukleotid– und Aminosäuresequenzen in Datenbanken. Der rasante Fortschritt bei der Sequenzierung ganzer Genome führt zu explosionsartig ansteigender Datenfülle und damit zu stetig wachsenden bioinformatischen Anwendungsmöglichkeiten, die ihrerseits notwendig sind, um diese Datenfülle zu bewältigen. Die Genomprojekte erbrachten bislang die vollständige Sequenz der Genome von Species aus allen drei Überreichen: Eubakterien: Haemophilus influenza [17], Mycoplasma genitalium [18], Synechocystis sp [29]. u.a. Archaebakterien: Methanococcus jannaschii [16] u.a. Eukaryonten: Saccharomyces cerevisiae u.a. Ende 1998 soll auch die Sequenzierung des Nemathelminten (Rundwurm) Caenorhabditis elegans und den Menschen abgeschlossen sein................ Im Rahmen dieser Diplomarbeit sollte ein Programm entwickelt werden, das die intrinsischen Eigenschaften eines Proteins vorhersagt. Es soll die Ausgabe der Ergebnisse von drei Programmen (Coils2, TopPred2 und SignalP) analysieren und interpretieren, eine Prognose über die Präsenz von Coiled Coils, Transmembranregionen und Signalpeptiden erstellen und die betroffenen Bereiche der Aminosäuresequenz angeben. Die Nutzung dieses Hilfsmittels ist über das World-Wide-Web möglich. In einem weiteren Teil soll die Funktion von Proteinen, deren funktionelle Eigenschaften unbekannt sind, über Homologiesuchen und Deutung der Ähnlichkeiten zu Proteinen mit bekannter Funktion aufgeklärt und beschrieben werden. Es handelt sich hierbei um Proteine, die aufgrund von Sequenzähnlichkeit in 58 Familien, sogenannten UPFs (uncharacterized protein families), zusammengefaßt sind.
The GPS recorder consists of a GPS receiver board, a logging facility, an antenna, a power supply, a DC-DC converter and a casing. Currently, it has a weight of 33 g. The recorder works reliably with a sampling rate of 1/s and with an operation time of about 3 h, providing time-indexed data on geographic positions and ground speed. The data are downloaded when the animal is recaptured. Prototypes were tested on homing pigeons. The records of complete flight paths with surprising details illustrate the potential of this new method that can be used on a variety of medium-sized and large vertebrates.
Wiederfang von zwei Sumpfmeisen (Parus palustris) nach einer Serie von Orientierungsversuchen
(1989)
We controlled two Marsh Tits in mist nets after they have been in orientation experiments for several weeks and released at the site of capture. One was controlled 1 1/2 years after the tests. There does not seem to be any impact of the experiments on the ability to survive well.
Die Schleiereule (Tyto alba) ist eine in fast allen Regionen der Erde vorkommende Eulenart. In Mitteleuropa erreicht sie die nördlichste Grenze ihres Verbreitungsgebiets. Man trifft sie hier in tiefergelegenen, waldarmen Gegenden an. Eine Arbeitsgruppe der Hessischen Gesellschaft für Ornithologie und Naturschutz (HGON) und des Deutschen Bund für Vogelschutz (DBV) führt im hessischen Main-Kinzig-Kreis seit 1976 Maßnahmen zum Schutz der Schleiereulen durch. Dazu gehören das Anbringen von Brutkisten an geeigneten Stellen und Winterfütterungsversuche. Die Brutkisten wurden jedes Jahr kontrolliert und die sich darin befindenden Jungvögel beringt. Ziel der vorliegenden Arbeit ist die Darstellung von Ergebnissen der Untersuchungen aus den zurückliegenden 12 Jahren. Dabei wird das Hauptaugenmerk einamal auf die Brutbiologie der Schleiereule und zum anderen auf die Disnigration der jungen Eulen gelegt.
DCD – a novel plant specific domain in proteins involved in development and programmed cell death
(2005)
Background: Recognition of microbial pathogens by plants triggers the hypersensitive reaction, a common form of programmed cell death in plants. These dying cells generate signals that activate the plant immune system and alarm the neighboring cells as well as the whole plant to activate defense responses to limit the spread of the pathogen. The molecular mechanisms behind the hypersensitive reaction are largely unknown except for the recognition process of pathogens. We delineate the NRP-gene in soybean, which is specifically induced during this programmed cell death and contains a novel protein domain, which is commonly found in different plant proteins.
Results: The sequence analysis of the protein, encoded by the NRP-gene from soybean, led to the identification of a novel domain, which we named DCD, because it is found in plant proteins involved in d evelopment and c ell d eath. The domain is shared by several proteins in the Arabidopsis and the rice genomes, which otherwise show a different protein architecture. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell by pathogens or ozone.
Conclusion: It is tempting to speculate, that the DCD domain mediates signaling in plant development and programmed cell death and could thus be used to identify interacting proteins to gain further molecular insights into these processes.
Background: The cosmopolitan moon jelly Aurelia is characterized by high degrees of morphological and ecological plasticity, and subsequently by an unclear taxonomic status. The latter has been revised repeatedly over the last century, dividing the genus Aurelia in as many as 12 or as little as two species. We used molecular data and phenotypic traits to unravel speciation processes and phylogeographic patterns in Aurelia.
Results: Mitochondrial and nuclear DNA data (16S and ITS-1/5.8S rDNA) from 66 world-wide sampled specimens reveal star-like tree topologies, unambiguously differentiating 7 (mtDNA) and 8 (ncDNA) genetic entities with sequence divergences ranging from 7.8 to 14% (mtDNA) and 5 to 32% (ncDNA), respectively. Phylogenetic patterns strongly suggest historic speciation events and the reconstruction of at least 7 different species within Aurelia. Both genetic divergences and life history traits showed associations to environmental factors, suggesting ecological differentiation forced by divergent selection. Hybridization and introgression between Aurelia lineages likely occurred due to secondary contacts, which, however, did not disrupt the unambiguousness of genetic separation.
Conclusions: Our findings recommend Aurelia as a model system for using the combined power of organismic, ecological, and molecular data to unravel speciation processes in cosmopolitan marine organisms.
© 2002 Schroth et al; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any non-commercial purpose, provided this notice is preserved along with the article's original URL: http://www.biomedcentral.com/1471-2148/2/1
Background: In general shell-less slugs are considered to be slimy animals with a rather dull appearance and a pest to garden plants. But marine slugs usually are beautifully coloured animals belonging to the less-known Opisthobranchia. They are characterized by a large array of interesting biological phenomena, usually related to foraging and/or defence. In this paper our knowledge of shell reduction, correlated with the evolution of different defensive and foraging strategies is reviewed, and new results on histology of different glandular systems are included. Results: Based on a phylogeny obtained by morphological and histological data, the parallel reduction of the shell within the different groups is outlined. Major food sources are given and glandular structures are described as possible defensive structures in the external epithelia, and as internal glands. Conclusion: According to phylogenetic analyses, the reduction of the shell correlates with the evolution of defensive strategies. Many different kinds of defence structures, like cleptocnides, mantle dermal formations (MDFs), and acid glands, are only present in shell-less slugs. In several cases, it is not clear whether the defensive devices were a prerequisite for the reduction of the shell, or reduction occurred before. Reduction of the shell and acquisition of different defensive structures had an implication on exploration of new food sources and therefore likely enhanced adaptive radiation of several groups. © 2005 Wägele and Klussmann-Kolb; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited: http://www.frontiersinzoology.com/content/2/1/3/
Background: In rat, deafferentation of one labyrinth (unilateral labyrinthectomy) results in a characteristic syndrome of ocular and motor postural disorders (e.g., barrel rotation, circling behavior, and spontaneous nystagmus). Behavioral recovery (e.g., diminished symptoms), encompassing 1 week after unilateral labyrinthectomy, has been termed vestibular compensation. Evidence suggesting that the histamine H3 receptor plays a key role in vestibular compensation comes from studies indicating that betahistine, a histamine-like drug that acts as both a partial histamine H1 receptor agonist and an H3 receptor antagonist, can accelerate the process of vestibular compensation. Results: Expression levels for histamine H3 receptor (total) as well as three isoforms which display variable lengths of the third intracellular loop of the receptor were analyzed using in situ hybridization on brain sections containing the rat medial vestibular nucleus after unilateral labyrinthectomy. We compared these expression levels to H3 receptor binding densities. Total H3 receptor mRNA levels (detected by oligo probe H3X) as well as mRNA levels of the three receptor isoforms studied (detected by oligo probes H3A, H3B, and H3C) showed a pattern of increase, which was bilaterally significant at 24 h post-lesion for both H3X and H3C, followed by significant bilateral decreases in medial vestibular nuclei occurring 48 h (H3X and H3B) and 1 week post-lesion (H3A, H3B, and H3C). Expression levels of H3B was an exception to the forementioned pattern with significant decreases already detected at 24 h post-lesion. Coinciding with the decreasing trends in H3 receptor mRNA levels was an observed increase in H3 receptor binding densities occurring in the ipsilateral medial vestibular nuclei 48 h post-lesion. Conclusion: Progressive recovery of the resting discharge of the deafferentated medial vestibular nuclei neurons results in functional restoration of the static postural and occulomotor deficits, usually occurring within a time frame of 48 hours in rats. Our data suggests that the H3 receptor may be an essential part of pre-synaptic mechanisms required for reestablishing resting activities 48 h after unilateral labyrinthectomy.
The study of organisms with restricted dispersal abilities and presence in the fossil record is particularly adequate to understand the impact of climate changes on the distribution and genetic structure of species. Trochoidea geyeri (Soós 1926) is a land snail restricted to a patchy, insular distribution in Germany and France. Fossil evidence suggests that current populations of T. geyeri are relicts of a much more widespread distribution during more favourable climatic periods in the Pleistocene. Results: Phylogeographic analysis of the mitochondrial 16S rDNA and nuclear ITS-1 sequence variation was used to infer the history of the remnant populations of T. geyeri. Nested clade analysis for both loci suggested that the origin of the species is in the Provence from where it expanded its range first to Southwest France and subsequently from there to Germany. Estimated divergence times predating the last glacial maximum between 25–17 ka implied that the colonization of the northern part of the current species range occurred during the Pleistocene. Conclusion: We conclude that T. geyeri could quite successfully persist in cryptic refugia during major climatic changes in the past, despite of a restricted capacity of individuals to actively avoid unfavourable conditions.
Die Fundmeldungen in Band 24 von Botanik und Naturschutz in Hessen tragen die laufenden Nummern 1750 bis 1872 und stammen von Rolf Angersbach, Kurt Baumann, Ralph Baumgärtel, Dieter Bickler, Dirk Bönsel, Wolfgang Ehmke, Christian Feuring, Thomas Gregor, Volker Holzgreve, Karsten Horn, Heinz Kalheber, Gerwin Kasperek, Matthias Kellner, Detlef Mahn, Hans Reichert, Bernd Sauerwein, Hjalmar Thiel, Bärbel Wellmann und Jochen Wulfhorst.