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Background: For omics experiments, detailed characterisation of experimental material with respect to its genetic features, its cultivation history and its treatment history is a requirement for analyses by bioinformatics tools and for publication needs. Furthermore, meta-analysis of several experiments in systems biology based approaches make it necessary to store this information in a standardised manner, preferentially in relational databases. In the Golm Plant Database System, we devised a data management system based on a classical Laboratory Information Management System combined with web-based user interfaces for data entry and retrieval to collect this information in an academic environment.
Results: The database system contains modules representing the genetic features of the germplasm, the experimental conditions and the sampling details. In the germplasm module, genetically identical lines of biological material are generated by defined workflows, starting with the import workflow, followed by further workflows like genetic modification (transformation), vegetative or sexual reproduction. The latter workflows link lines and thus create pedigrees. For experiments, plant objects are generated from plant lines and united in so-called cultures, to which the cultivation conditions are linked. Materials and methods for each cultivation step are stored in a separate ACCESS database of the plant cultivation unit. For all cultures and thus every plant object, each cultivation site and the culture's arrival time at a site are logged by a barcode-scanner based system. Thus, for each plant object, all site-related parameters, e. g. automatically logged climate data, are available. These life history data and genetic information for the plant objects are linked to analytical results by the sampling module, which links sample components to plant object identifiers. This workflow uses controlled vocabulary for organs and treatments. Unique names generated by the system and barcode labels facilitate identification and management of the material. Web pages are provided as user interfaces to facilitate maintaining the system in an environment with many desktop computers and a rapidly changing user community. Web based search tools are the basis for joint use of the material by all researchers of the institute.
Conclusion: The Golm Plant Database system, which is based on a relational database, collects the genetic and environmental information on plant material during its production or experimental use at the Max-Planck-Institute of Molecular Plant Physiology. It thus provides information according to the MIAME standard for the component 'Sample' in a highly standardised format. The Plant Database system thus facilitates collaborative work and allows efficient queries in data analysis for systems biology research.
Bio-jETI
(2008)
Background: With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout.
Methods: Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution.
Conclusions: As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.
Background
Serotonin induces fluid secretion from Calliphora salivary glands by the parallel activation of the InsP3/Ca2+ and cAMP signaling pathways. We investigated whether cAMP affects 5-HT-induced Ca2+ signaling and InsP3-induced Ca2+ release from the endoplasmic reticulum (ER).
Results
Increasing intracellular cAMP level by bath application of forskolin, IBMX or cAMP in the continuous presence of threshold 5-HT concentrations converted oscillatory [Ca2+]i changes into a sustained increase. Intraluminal Ca2+ measurements in the ER of ß-escin-permeabilized glands with mag-fura-2 revealed that cAMP augmented InsP3-induced Ca2+ release in a concentration-dependent manner. This indicated that cAMP sensitized the InsP3 receptor Ca2+ channel for InsP3. By using cAMP analogs that activated either protein kinase A (PKA) or Epac and the application of PKA-inhibitors, we found that cAMP-induced augmentation of InsP3-induced Ca2+ release was mediated by PKA not by Epac. Recordings of the transepithelial potential of the glands suggested that cAMP sensitized the InsP3/Ca2+ signaling pathway for 5-HT, because IBMX potentiated Ca2+-dependent Cl- transport activated by a threshold 5-HT concentration.
Conclusion
This report shows, for the first time for an insect system, that cAMP can potentiate InsP3-induced Ca2+ release from the ER in a PKA-dependent manner, and that this crosstalk between cAMP and InsP3/Ca2+ signaling pathways enhances transepithelial electrolyte transport.
Questions: 1. Are there differences among species in their preference for coniferous vs. deciduous forest? 2. Are tree and shrub species better colonizers of recent forest stands than herbaceous species? 3. Do colonization patterns of plant species groups depend on tree species composition? Location: Three deciduous and one coniferous recent forest areas in Brandenburg, NE Germany. Methods: In 34 and 21 transects in coniferous and deciduous stands, respectively, we studied the occurrence and percentage cover of vascular plants in a total of 150 plots in ancient stands, 315 in recent stands and 55 at the ecotone. Habitat preference, diaspore weight, generative dispersal potential and clonal extension were used to explain mechanisms of local migration. Regression analysis was conducted to test whether migration distance was related to species’ life-history traits. Results: 25 species were significantly associated with ancient stands and ten species were significantly more frequent in recent stands. Tree and shrub species were good colonizers of recent coniferous and deciduous stands. In the coniferous stands, all herbaceous species showed a strong dispersal limitation during colonization, whereas in the deciduous stands generalist species may have survived in the grasslands which were present prior to afforestation. Conclusions: The fast colonization of recent stands by trees and shrubs can be explained by their effective dispersal via wind and animals. This, and the comparably efficient migration of herbaceous forest specialists into recent coniferous stands, implies that the conversion of coniferous into deciduous stands adjacent to ancient deciduous forests is promising even without planting of trees.
Background: An increasing number of studies demonstrate that genetic differentiation and speciation in the sea occur over much smaller spatial scales than previously appreciated given the wide distribution range of many morphologically defined coral reef invertebrate species and the presumed dispersal-enhancing qualities of ocean currents. However, knowledge about the processes that lead to population divergence and speciation is often lacking despite being essential for the understanding, conservation, and management of marine biodiversity. Sponges, a highly diverse, ecologically and economically important reef-invertebrate taxon, exhibit spatial trends in the Indo-West Pacific that are not universally reflected in other marine phyla. So far, however, processes generating those unexpected patterns are not understood.
Results: We unraveled the phylogeographic structure of the widespread Indo-Pacific coral reef sponge Leucetta chagosensis across its known geographic range using two nuclear markers: the rDNA internal transcribed spacers (ITS 1&2) and a fragment of the 28S gene, as well as the second intron of the ATP synthetase beta subunit-gene (ATPSb-iII). This enabled the detection of several deeply divergent clades congruent over both loci, one containing specimens from the Indian Ocean ( Red Sea and Maldives), another one from the Philippines, and two other large and substructured NW Pacific and SW Pacific clades with an area of overlap in the Great Barrier Reef/Coral Sea. Reciprocally monophyletic populations were observed from the Philippines, Red Sea, Maldives, Japan, Samoa, and Polynesia, demonstrating long-standing isolation. Populations along the South Equatorial Current in the south-western Pacific showed isolation-by-distance effects. Overall, the results pointed towards stepping-stone dispersal with some putative long-distance exchange, consistent with expectations from low dispersal capabilities.
Conclusion: We argue that both founder and vicariance events during the late Pliocene and Pleistocene were responsible to varying degrees for generating the deep phylogeographic structure. This structure was perpetuated largely as a result of the life history of L. chagosensis, resulting in high levels of regional isolation. Reciprocally monophyletic populations constitute putative sibling ( cryptic) species, while population para- and polyphyly may indicate incipient speciation processes. The genetic diversity and biodiversity of tropical Indo-Pacific sponges appears to be substantially underestimated since the high level of genetic divergence is not necessarily manifested at the morphological level.
Der Beitrag zeigt in einem ersten Schritt, dass die "Absurda comica" ein theologisches Gleichnis darstellt, in dem der König die Rolle Gottes, Pickelhäring die Rolle des Teufels und die Handwerker die Rolle des Menschen übernehmen. Schlüssel für dieses Gleichnis ist Lk 9.60 und Mt 8.22, wo Christus von seinen Jüngern fordert, "die Toten ihre Toten begraben zu lassen", d.h. sich vom Reich der Welt abzuwenden. Auf die "Absurda comica" übertragen, besagt dies, dass die Handwerker die Rollenhaftigkeit und die Narrheit ihrer Existenz erkennen müssen, wenn sie vor Gott gerechtfertigt werden wollen. In einem zweiten Schritt wird gezeigt, dass die "Absurda comica" als ein solches Gleichnis in der Tradition der Fastnachtspiele steht, deren Funktion eben dieser Aufweis der menschlichen Narrheit war. Das protestantische Schuldrama trat dabei bewusst in die Tradition dieser Fastnachtspiele, wie sich gerade an der "Absurda comica" zeigen lässt. In einem dritten Schritt wird diese These in einem Vergleich mit Jacob Masens "Rusticus imperans" und Christian Weises "Tobias und die Schwalbe" bestätigt.
Natürliche Standorte der Waldkiefer gibt es in Deutschland nur kleinflächig. Während Kiefernforste anstelle natürlicher Laubwälder heute oft landschaftsprägend sind, bildet die konkurrenzschwache und lichtbedürftige Kiefer ausschließlich auf extrem trockenen oder nassen, nährstoffarmen Standorten naturnahe Schlusswaldgesellschaften. Regionale Schwerpunkte liegen in subkontinentalen Regionen wie dem nordostdeutschen Tiefland und Bayern, ein „natürliches Kiefernareal" lässt sich aber kaum abgrenzen. An der Trockengrenze des Waldes finden sich auf Kalk- und Dolomitgesteinen artenreiche Karbonat-Trockenkiefernwälder mit Elementen der alpinen Rasen und Kalkmagerrasen in der Bodenvegetation. Diese Wälder besiedeln steile, südexponierte Felsen und morphodynamisch aktive Bereiche wie Rutschhänge und FlussSchotterböden im Umkreis der Alpen, kommen aber auch in den Mittelgebirgen vor. Ihr Gegenstück auf sauren Standorten sind die Sand- und Silikat-Kiefernwälder der Quarzsande und Sandstein-Verwitterungsböden, deren Bodenvegetation durch Zwergsträucher, Moose und Strauchflechten geprägt ist. Hier siedelt die Kiefer in den Tieflagen besonders auf Binnendünen und Sandern, aber auch auf Küstendünen der Ostsee, in den Mittelgebirgen z. B. auf den Sandsteinriffen der Sächsischen Schweiz. Der dritte Wuchsbereich natürlicher Kiefernwälder sind saure, nährstoffarme Moore, die ganz überwiegend von Regenwasser gespeist werden. Auch die Kiefern-Moorwälder sind in Nordostdeutschland und Bayern am häufigsten. Von diesen Standorten ausgehend, wo ihr Platz kaum von anderen Baumarten streitig gemacht wird, tritt die Waldkiefer immer wieder als Pionier auf weniger extremen Standorten auf. In der Naturlandschaft kam dies etwa nach Waldbränden oder Stürmen vor, doch der Mensch förderte die Kiefer durch Auflichtung der Wälder, Waldweide und Streunutzung stark. Auch die damit verbundene Nährstoffverarmung macht eine exakte Abgrenzung natürlicher Kiefernstandorte unmöglich. Die schlechtwüchsigen und forstwirtschaftlich nicht interessanten, ästhetisch aber sehr ansprechenden natürlichen Kiefernbestände sind heute vor allem durch Stickstoff-Immissionen gefährdet. Trotz ihrer oft kargen Erscheinung besitzen sie einen hohen Wert für die Biodiversität und den Artenschutz. Neben bodenbewohnenden Flechten und regionalen Relikt-Endemiten ist vor allem die in den letzten Jahrzehnten zunehmend gefährdete Vielfalt an Mykorrhiza-Pilzen hervorzuheben, die der Kiefer das Leben auf extrem nährstoffarmen Standorten überhaupt ermöglichen. Abschließend werden mögliche Schutz- bzw. Regenerationsmaßnahmen wie das Abplaggen flechtenreicher Kiefernstandorte vorgestellt.
Inositol phosphates (IPs) and their turnover products have been implicated to play important roles in stress signaling in eukaryotic cells. In higher plants genes encoding inositol polyphosphate kinases have been identified previously, but their physiological functions have not been fully resolved. Here we expressed Arabidopsis inositol polyphosphate 6-/3-kinase (AtIpk2 beta) in two heterologous systems, i.e. the yeast Saccharomyces cerevisiae and in tobacco (Nicotiana tabacum), and tested the effect on abiotic stress tolerance. Expression of AtIpk2 beta rescued the salt-, osmotic- and temperature-sensitive growth defects of a yeast mutant strain (arg82 Delta) that lacks inositol polyphosphate multikinase activity encoded by the ARG82/IPK2 gene. Transgenic tobacco plants constitutively expressing AtIpk2 beta under the control of the Cauliflower Mosaic Virus 35S promoter were generated and found to exhibit improved tolerance to diverse abiotic stresses when compared to wild type plants. Expression patterns of various stress responsive genes were enhanced, and the activities of anti-oxidative enzymes were elevated in transgenic plants, suggesting a possible involvement of AtIpk2 beta in plant stress responses.
Bei N = 101 Arbeitnehmern verschiedener Berufe wurden mit der Experience Sampling Method (ESM) eine Woche lang Daten zum Flow-Erleben, zu Glück/Zufriedenheit und zur Zielausrichtung laufender Aktivitäten erhoben (N = 4603 Messungen). Die Daten wurden mit GLMM-Analysen ausgewertet. Auch bei der jetzt vollständigen Erfassung aller Flow-Komponenten mit der FKS bestätigte sich das „Paradoxon der Arbeit“, wonach während der Arbeit höhere Flow-Werte, aber niedrigere Werte für Glück/Zufriedenheit auftreten als jeweils in der Freizeit. Während der Arbeit waren Aktivitäten häufiger auf die Erreichung von Zielen ausgerichtet als während der Freizeit. Die Zielausrichtung wirkte auf Flow vs. Glück/Zufriedenheit signifikant verschieden. Während der Arbeit hat die Zielausrichtung auf Flow einen stark positiven Effekt, auf Glück/Zufriedenheit jedoch nicht. Im Freizeitbereich war der Effekt von Zielausrichtung auf Glück/Zufriedenheit sogar negativ. Das „Paradoxon der Arbeit“ lässt sich partiell als Effekt der Zielausrichtung verstehen.
A production study is presented that investigates the effects of word order and information structural context on the prosodic realization of declarative sentences in Hindi. Previous work on Hindi intonation has shown that: (i) non-final content words bear rising pitch accents (Moore 1965, Dyrud 2001, Nair 1999); (ii) focused constituents show greater pitch excursion and longer duration and that post-focal material undergoes pitch range reduction (Moore 1965, Harnsberger 1994, Harnsberger and Judge 1996); and (iii) focused constituents may be followed by a phrase break (Moore 1965). By means of a controlled experiment, we investigated the effect of focus in relation to word order variation using 1200 utterances produced by 20 speakers. Fundamental frequency (F0) and duration of constituents were measured in Subject-Object-Verb (SOV) and Object-Subject-Verb (OSV) sentences in different information structural conditions (wide focus, subject focus and object focus). The analyses indicate that (i) regardless of word order and focus, the constituents are in a strict downstep relationship; (ii) focus is mainly characterized by post-focal pitch range reduction rather than pitch raising of the element in focus; (iii) given expressions that occur pre-focally appear to undergo no reduction; (iv) pitch excursion and duration of the constituents is higher in OSV compared to SOV sentences. A phonological analysis suggests that focus affects pitch scaling and that word order influences prosodic phrasing of the constituents.
Background
Many animals live in environments where different types of predators pose a permanent threat and call for predator specific strategies. When foraging, animals have to balance the competing needs of food and safety in order to survive. While animals sometimes can choose between microhabitats that differ in their risk of predation, many habitats are uniform in their risk distribution. So far, little is known about adaptive antipredator behavior under uniform risk. We simulated two predator types, avian and mammalian, each representing a spatially uniform risk in the artificial resource landscapes. Voles served as experimental foragers.
Results
Animals were exposed to factorial combinations of weasel odour and ground cover to simulate avian and/or mammalian predation. We measured short and long term responses with video analysis and giving-up densities. The results show that previously experienced conditions cause delayed effects. After these effects ceased, the risks of both types of predation caused a reduction in food intake. Avian predation induced a concentration on a smaller number of feeding patches. While higher avian risk caused a delay in activity, the weasel odour shortened the latency until the voles started to be active.
Conclusion
We show that the voles differed in risk types and adjusted their feeding strategies accordingly. Responses to avian and mammalian risk differed both in strength and time scales. Uniformity of risk resulted in a concentration of foraging investment and lower foraging efficiency.
The Warm-Hot Intergalactic Medium (WHIM) arises from shock-heated gas collapsing in large-scale filaments and probably harbours a substantial fraction of the baryons in the local Universe. Absorption-line measurements in the ultraviolet (UV) and in the X-ray band currently represent the best method to study the WHIM at low redshifts. We here describe the physical properties of the WHIM and the concepts behind WHIM absorption line measurements of Hi and high ions such as Ovi, Ovii, and Oviii in the far-ultraviolet and X-ray band. We review results of recent WHIM absorption line studies carried out with UV and X-ray satellites such as FUSE, HST, Chandra, and XMM-Newton and discuss their implications for our knowledge of the WHIM.
GeneFisher-P
(2008)
Background: PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a service-oriented approach to model and implement GeneFisher-P, a process-based version of the GeneFisher web application, as a part of the Bio-jETI platform for service modeling and execution. We show how to introduce a flexible process layer to meet the growing demand for improved user-friendliness and flexibility.
Results: Within Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology.
The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI).
Conclusions: The resulting service-and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks.
Background: Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (Solanum tuberosum). Potato species are tetraploid and highly heterozygous.
Results: Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlo-typer uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes.
Conclusion: Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at http://www.gabipd.org/projects/satlotyper/. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.
The vacuolar H+-ATPase (V-ATPase) in the apical membrane of blowfly (Calliphora vicina) salivary gland cells energizes the secretion of a KCl-rich saliva in response to the neurohormone serotonin (5-HT). We have shown previously that exposure to 5-HT induces a cAMP-mediated reversible assembly of V-0 and V-1 subcomplexes to V-ATPase holoenzymes and increases V-ATPase-driven proton transport. Here, we analyze whether the effect of cAMP on V-ATPase is mediated by protein kinase A (PKA) or exchange protein directly activated by cAMP (Epac), the cAMP target proteins that are present within the salivary glands. Immunofluorescence microscopy shows that PKA activators, but not Epac activators, induce the translocation of V1 components from the cytoplasm to the apical membrane, indicative of an assembly of V-ATPase holoenzymes. Measurements of transepithelial voltage changes and microfluorometric pH measurements at the luminal surface of cells in isolated glands demonstrate further that PKA-activating cAMP analogs increase cation transport to the gland lumen and induce a V-ATPase-dependent luminal acidification, whereas activators of Epac do not. Inhibitors of PKA block the 5-HT-induced V-1 translocation to the apical membrane and the increase in proton transport. We conclude that cAMP exerts its effects on V-ATPase via PKA.
Interdisziplinarität und die damit verknüpften Fragen hat das Forschungsprojekt "Lernender Forschungszusammenhang" untersucht. Diese Publikation beschreibt ein Forschungskonzept, mit dem betriebliche Modernisierungsprojekte in fünf Großunternehmen interdisziplinär untersucht wurden. Die Forschungsergebnisse aus zwei dieser Unternehmen werden detailliert dargestellt. Der Leser kann entlang dokumentierter Forschungsergebnisse selbst nachvollziehen, in welcher Weise sich die Wissenschaftler aus unterschiedlichen Disziplinen lernend aufeinander bezogen haben.
Die Autoren bieten Arbeitsmaterialien an, mit deren Hilfe Schülerinnen und Schüler ihren privaten Energieverbrauch und den damit verbundenen Kohlendioxidausstoß ermitteln können. Neben einem kostenlos herunterzuladenden Computerprogramm, welches die Erstellung einer Energiebilanz ermöglicht und die entsprechenden Daten für die Berechnung von CO2-Emissionen bietet, werden Hilfestellungen geboten, um folgenden Fragen nachzugehen: Wieviel CO2-Ausstoß ist mit der Nutzung einzelner Geräte, Fahrzeuge oder allgemein mit verschiedenen Lebensstilen verbunden? und Wie kann der Kohlendioxid-Ausstoß verringert werden?
Speziell zur Sicherung der Versorgung mit Elektroenergie wird in diesem Einhefter eine Expertendiskussion des 28. ZEIT FORUM DER WISSENSCHAFT vom 18.12.2007 aufgegriffen. Die Experten vertreten dabei unterschiedliche Interessen. Ziel der Materialien ist es, Schülerinnen und Schüler ab Klasse 9 anzuregen, sich mit einem politischen Konflikt auseinanderzusetzen und begründet Stellung zu beziehen. Des weiteren finden sich in der Zusammenstellung die Lösungsansätze der effizienten Produktion und Nutzung elektrischer Energie, der Nutzung regenerativer Energiequellen sowie der Nutzung eines Energiemix. Dabei werden die verschiedenen Unterrichtsmethoden der Pro- und Contra-Diskussion, des Gruppenpuzzles, der Zukunftskonferenz und der Szenariotechnik angesprochen.
Der Autor stellt die Dringlichkeit vor, mit der im Zuge des Klimawandels im Technikunterricht auch energiepolitische Fragestellungen behandelt werden sollen. Er gibt einen Überblick über die im Themenheft bereitgestellten Beiträge, die Grundfragen der Sicherung von Lebensqualität - insbesondere die sichere, ökologisch vertretbare und wirtschaftliche Bereitstellung und Nutzung von Energie - behandeln. Schüler ab Klasse 9 sollen bei der Auseinandersetzung z.B. mit der zukünftigen Stromversorgung die Befähigung zur Technikbewertung und Technikgestaltung als grundlegende Kompetenz technischer Bildung erhalten. Eine tabellarische Übersicht gibt Auskunft über bisherige Beiträge in Arbeit + Technik, die den Themenschwerpunkt behandeln.
We describe an approach to modeling biological networks by action languages via answer set programming. To this end, we propose an action language for modeling biological networks, building on previous work by Baral et al. We introduce its syntax and semantics along with a translation into answer set programming, an efficient Boolean Constraint Programming Paradigm. Finally, we describe one of its applications, namely, the sulfur starvation response-pathway of the model plant Arabidopsis thaliana and sketch the functionality of our system and its usage.
The influence of information structure on tonal scaling in German is examined experimentally. Eighteen speakers uttered a total of 2277 sentences of the same syntactic structure, but with a varying number of constituents, word order and focus-given structure. The quantified results for German support findings for other Germanic languages that the scaling of high tones, and thus the entire melodic pattern, is influenced by information structure. Narrow focus raised the high tones of pitch accents, while givenness lowered them in prenuclear position and canceled them out postnuclearly. The effects of focus and givenness are calculated against all-new sentences as a baseline, which we expected to be characterized by downstep, a significantly lower scaling of high tones as compared to declination. The results further show that information structure alone cannot account for all variations. We therefore assume that dissimilatory tonal effects play a crucial role in the tonal scaling of German. The effects consist of final f0 drop, a steep fall from a raised high tone to the bottom line of the speaker, H-raising before a low tone, and H-lowering before a raised high tone. No correlation between word order and tone scaling could be established. 2008 Elsevier Ltd. All rights reserved.
Background
Epidemiological data indicate elevated psychosocial health risks for physicians, e.g., burnout, depression, marital disturbances, alcohol and substance abuse, and suicide. The purpose of this study was to identify psychosocial health resources and risk factors in profession-related behaviour and experience patterns of medical students and physicians that may serve as a basis for appropriate health promoting interventions.
Methods
The questionnaire -Related Behaviour and Experience "Work administered in cross-sectional surveys to students in the first (n = 475) and in the fifth year of studies (n = 355) in required courses at three German universities and to physicians in early professional life in the vicinity of these universities (n = 381).
Results
Scores reflecting a healthy behaviour pattern were less likely in physicians (16.7%) compared to 5th year (26.0%) and 1st year students (35.1%) while scores representing unambitious and resigned patterns were more common among physicians (43.4% vs. 24.4% vs. 41.0% and 27.3% vs. 17.2% vs. 23.3 respectively). Female and male responders differed in the domains professional commitment, resistance to stress and emotional well-being. Female physicians on average scored higher in the dimensions resignation tendencies, satisfaction with life and experience of social support, and lower in career ambition.
Conclusion
The results show distinct psychosocial stress patterns among medical students and physicians. Health promotion and prevention of psychosocial symptoms and impairments should be integrated as a required part of the medical curriculum and be considered an important issue during the further training of physicians.
QuantPrime
(2008)
Background
Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays.
Results
Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%.
Conclusion
QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.
Thermal radiation processes
(2008)
We discuss the different physical processes that are important to understand the thermal X-ray emission and absorption spectra of the diffuse gas in clusters of galaxies and the warm-hot intergalactic medium. The ionisation balance, line and continuum emission and absorption properties are reviewed and several practical examples are given that illustrate the most important diagnostic features in the X-ray spectra.
We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature.
Using ESTs for phylogenomics
(2008)
Background
While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets.
Results
We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences.
Conclusion
These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.