Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies, many similarity based algorithms, mainly dependent on calculating sequence alignment matrices, have been proposed to find them. In these kinds of approaches, a significantly high similarity score between two coding sequences extracted from a given annotation tool means that one has the same genes. In a previous work article, we presented a quality test approach (QTA) that improves the core genes quality by combining two annotation tools (namely NCBI, a partially human-curated database, and DOGMA, an efficient annotation algorithm for chloroplasts). This method takes the advantages from both sequence similarity and gene features to guarantee that the core genome contains correct and well-clustered coding sequences (\emph{i.e.}, genes). We then show in this article how useful are such well-defined core genes for biomolecular phylogenetic reconstructions, by investigating various subsets of core genes at various family or genus levels, leading to subtrees with strong bootstraps that are finally merged in a well-supported supertree.Comment: 12 pages, 7 figures, IWBBIO 2015 (3rd International Work-Conference on Bioinformatics and Biomedical Engineering

Effekte der Selensupplementierung auf den Selenstatus beim Damwild (Dama dama) in Gehegehaltung

Aktuell gibt es für Selen (Se) keine Bedarfsempfehlungen für das Damwild (Dama dama) in Gehegehaltung. Diese Studie soll die typische Se-Aufnahme bei Gehegehaltung von Damwild ermitteln und klären, welche Parameter sich eignen, um die Se-Versorgung des Damwildes zu reflektieren. Dazu wurden 19 Damhirsche in zwei Gruppen unter identischen Bedingungen gehalten. Die Tiere ernährten sich von dem natürlichen Grasaufwuchs und Mischfutter (0,15 mg/kg TS bzw. 1,07 - 1,91 mg/kg TS). In Blut, Plasma und die Organen wurden der Se-Gehalt, die Aktivität der Se-abhängigen Glutathionperoxidase (GPx) sowie teilweise die Gesamt-GPx-Aktivität (gesGPx), die Aktivität der Glutathion-S-Transferase (GST) und die Expression verschiedener GPx analysiert. Durch die Se-Supplementierung wurden ein signifikanter Anstieg des Plasma-Se in der Versuchsgruppe und ein moderater Unterschied der Vollblut-Se-Konzentration sowie der Vollblut-GPx-Aktivität zwischen der Kontroll- und der Versuchsgruppe beobachtet (p = 0,08). Außerdem wurde in allen Organen der Versuchsgruppe ein höherer Se-Gehalt als in der Kontrollgruppe festgestellt. In der Hierarchie der untersuchten Organe ist die Niere am höchsten angeordnet, absteigend folgen der Herz- und Skelettmuskel, die Milz und die Leber. Eine Se-Aufnahme von 0,05 - 0,08 mg/kg TS führt beim Damwild nicht zur Ausprägung von Se-Mangelsymptomen und stellt daher eine ausreichende Se-Versorgung dar. Die Empfehlungen zur Se-Versorgung für Damwild sind somit nicht von Hauswiederkäuern zu übernehmen. Im Plasma und im Vollblut scheinen Se-Konzentrationen von 28 - 64 µg/l und 81 - 200 µg/l für eine ausreichende Se-Versorgung zu sprechen, in der Leber Se-Konzentrationen von 270 - 663 µg/kg TS.:Inhaltsverzeichnis Inhaltsverzeichnis I Abbildungsverzeichnis V Tabellenverzeichnis VI Verzeichnis der Anhangstabellen VIII Abkürzungsverzeichnis IX 1. Einleitung 1 2. Literaturübersicht 2 2.1 Se als chemisches Element 2 2.2 Geschichte des Se und seiner Proteine 3 2.3 Se-Gehalte in Boden, Pflanzen, Nahrungs- und Futtermitteln 4 2.3.1 Se-Gehalte im Boden 4 2.3.2 Se-Gehalte in Pflanzen 5 2.3.3 Se-Gehalte in Nahrungsmitteln 7 2.3.4 Se-Gehalte in Futtermitteln 8 2.4 Se im Stoffwechsel 9 2.4.1 Resorption 9 2.4.2 Transport, Metabolismus und Speicherung 10 2.4.2.1 Transport 10 2.4.2.3 Speicherung 11 2.4.3 Versorgung über Plazenta und Milch 12 2.4.4 Exkretion 14 2.5 Biologische Funktionen des Se 16 2.5.1 SeP 16 2.5.2 Funktionen 18 2.5.2.1 Spezielle Funktionen der GPx 18 2.5.2.2 Weitere Funktionen der Selenoenzyme 20 2.6 Damwild (Dama dama) 21 2.6.1 Systematische und historische Einordnung des Damwildes 21 2.6.2 Physiologie und Ernährung des Damwildes 22 2.6.3 Se-Status bei Cerviden 23 2.7 Se-Bedarf 24 2.8 Se- und Enzymwerte im Organismus 25 2.8.1 Se-Gehalte im Blut 25 2.8.2 Se-Gehalte in verschiedenen Organen 28 2.9 Se und Erkrankungen 30 2.9.1 Se-Mangel assoziierte Erkrankungen 30 2.9.2 Se-Toxizität 31 2.9.2.1 Die akute Se-Intoxikation 32 2.9.2.2 Die subakute Se-Intoxikation 33 2.9.2.3 Die chronische Se-Intoxikation 33 3 Tiere, Material und Methoden 35 3.1 Versuchsziel 35 3.2 Tiere 35 3.3 Haltung 35 3.4 Fütterung und Supplementierung 35 3.5 Versuchsablauf 37 3.6 Probenentnahmen 38 3.6.1 Blutproben 38 3.6.2 Organ- und Gewebeproben 38 3.6.3 Wiegen 40 3.6.4 Futterproben 41 3.7 Versuchsparameter 43 3.8 Analytische Methoden 43 3.8.1 Futteranalyse 43 3.8.1.1 TS 43 3.8.1.2 Rohasche (Ra) 44 3.8.1.3 Organische Substanz (oS) 44 3.8.1.4 Rohprotein (Rp) 44 3.8.1.5 Rohfett (Rfe) 44 3.8.1.6 Rohfaser (Rfa) 44 3.8.1.7 N-freie Extraktstoffe (NfE) 45 3.8.1.8 Spurenelemente: Se, Cu, Zn 45 3.8.2 Vollblut-, Plasma-, Organ- und Gewebeanalyse 45 3.8.2.1 Histologie der Skelettmuskulatur 45 3.8.2.2 Se-Gehalt 46 3.8.2.3 TS-Gehalt 47 3.8.2.4 GPx-Aktivität 47 3.8.2.5 Proteingehalt 48 3.8.2.6 Hämoglobingehalt 49 3.8.2.7 GPx-mRNA-Expression 49 3.8.2.8 α -Glutathion-S-Transferase-Aktivität (GST) 53 3.9 Statistische Auswertung 54 4. Ergebnisse 55 4.1 KM der Tiere und Gewichte der Schlachtkörperhälften 55 4.1.1 KM der Tiere zu Versuchsbeginn 55 4.1.2 Gewichte der Schlachtkörperhälften zu Versuchende 55 4.2 Histologie der Skelettmuskulatur 56 4.3 Se-Gehalte in Plasma, Vollblut und Organen 58 4.3.1 Se-Gehalte in Plasma und Vollblut 58 4.3.2 Se-Gehalte in verschiedenen Organen 59 4.4 Se-abhängige und -unabhängige Enzyme 60 4.4.1 GPx-Aktivitäten in Plasma und Vollblut 60 4.4.2 GPx-Aktivität in verschiedenen Organen 62 4.4.3 GPx-mRNA-Expression 63 4.4.4 α-GST-Aktivität 64 5. Diskussion 67 5.1 Kritik der Methoden 67 5.1.1 Se-Supplementierung der Tiere 67 5.1.1.1 Futteraufnahme 67 5.1.1.2 Höhe der Se-Supplementierung 67 5.1.1.3 Dauer der Se-Supplementierung 68 5.1.1.4 Art der Se-Supplementierung 68 5.1.2 Probengewinnung 69 5.1.3 Untersuchungsparameter 69 5.1.4 Vitamin E 69 5.2 Diskussion der Versuchsergebnisse 70 5.2.1 Einschätzung der Se-Versorgung vor Se-Supplementierung 70 5.2.2 Einschätzung der Se-Versorgung nach unterschiedlicher Se-Supplementierung 72 6. Zusammenfassung 81 7. Summary 83 8. Literaturverzeichnis 85 9. Anhang……………………………………………………………………..110 Danksagung 11

Monte Carlo Study of Order-Disorder Layering Transitions in the Blume-Capel Model

The order-disorder layering transitions, of the Blume-Capel model, are studied using the Monte Carlo (MC) simulations, in the presence of a variable crystal field. For a very low temperature, the results are in good agreement with the ground state study. The first order transition line, found for low temperatures, is connected to the second order transition line, seen for higher temperatures, by a tri-critical point, for each layer. The reentrant phenomena, caused by a competition of thermal fluctuations and an inductor magnetic field created by the deeper layers, is found for the first $k_0$ layers from the surface, where $k_0$ is exactly the number of layering transitions allowed by the ground state study. The layer magnetizations $m_k$, the magnetic susceptibilities $\chi_{m,k}$ and the quadrupolar magnetic susceptibilities $\chi_{q,k}$ and the corresponding critical exponent, for each layer $k$, are also investigated.Comment: 10 pages Latex, 9 figures Postscript forma

Hexatic-Herringbone Coupling at the Hexatic Transition in Smectic Liquid Crystals: 4-ϵ\epsilon Renormalization Group Calculations Revisited

Simple symmetry considerations would suggest that the transition from the smectic-A phase to the long-range bond orientationally ordered hexatic smectic-B phase should belong to the XY universality class. However, a number of experimental studies have constantly reported over the past twenty years "novel" critical behavior with non-XY critical exponents for this transition. Bruinsma and Aeppli argued in Physical Review Letters {\bf 48}, 1625 (1982), using a $4-\epsilon$ renormalization-group calculation, that short-range molecular herringbone correlations coupled to the hexatic ordering drive this transition first order via thermal fluctuations, and that the critical behavior observed in real systems is controlled by a `nearby' tricritical point. We have revisited the model of Bruinsma and Aeppli and present here the results of our study. We have found two nontrivial strongly-coupled herringbone-hexatic fixed points apparently missed by those authors. Yet, those two new nontrivial fixed-points are unstable, and we obtain the same final conclusion as the one reached by Bruinsma and Aeppli, namely that of a fluctuation-driven first order transition. We also discuss the effect of local two-fold distortion of the bond order as a possible missing order parameter in the Hamiltonian.Comment: 1 B/W eps figure included. Submitted to Physical Review E. Contact: [email protected]

Analysis of chronic aortic regurgitation by 2D and 3D echocardiography and cardiac MRI

Purpose: The study compares the feasibility of the quantitative volumetric and semi-quantitative approach for quantification of chronic aortic regurgitation (AR) using different imaging modalities. Methods: Left ventricular (LV) volumes, regurgitant volumes (RVol) and regurgitant fractions (RF) were assessed retrospectively by 2D, 3D echocardiography and cMRI in 55 chronic AR patients. Semi-quantitative parameters were assessed by 2D echocardiography. Results: 22 (40%) patients had mild, 25 (46%) moderate and 8 (14%) severe AR. The quantitative volumetric approach was feasible using 2D, 3D echocardiography and cMRI, whereas the feasibility of semi-quantitative parameters varied considerably. LV volume (LVEDV, LVESV, SVtot) analyses showed good correlations between the different imaging modalities, although significantly increased LV volumes were assessed by cMRI. RVol was significantly different between 2D/3D echocardiography and 2D echocardiography/cMRI but was not significantly different between 3D echocardiography/cMRI. RF was not statistically different between 2D echocardiography/cMRI and 3D echocardiography/cMRI showing poor correlations (r < 0.5) between the different imaging modalities. For AR grading by RF, moderate agreement was observed between 2D/3D echocardiography and 2D echocardiography/cMRI and good agreement was observed between 3D echocardiography/cMRI. Conclusion: Semi-quantitative parameters are difficult to determine by 2D echocardiography in clinical routine. The quantitative volumetric RF assessment seems to be feasible and can be discussed as an alternative approach in chronic AR. However, RVol and RF did not correlate well between the different imaging modalities. The best agreement for grading of AR severity by RF was observed between 3D echocardiography and cMRI. LV volumes can be verified by different approaches and different imaging modalities

Differential gene transfers and gene duplications in primary and secondary endosymbioses

BACKGROUND: Most genes introduced into phototrophic eukaryotes during the process of endosymbiosis are either lost or relocated into the host nuclear genome. In contrast, groEL homologues are found in different genome compartments among phototrophic eukaryotes. Comparative sequence analyses of recently available genome data, have allowed us to reconstruct the evolutionary history of these genes and propose a hypothesis that explains the unusual genome distribution of groEL homologues. RESULTS: Our analyses indicate that while two distinct groEL genes were introduced into eukaryotes by a progenitor of plastids, these particular homologues have not been maintained in all evolutionary lineages. This is of significant interest, because two chaperone proteins always co-occur in oxygenic photosynthetic organisms. We infer strikingly different lineage specific processes of evolution involving deletion, duplication and targeting of groEL proteins. CONCLUSION: The requirement of two groEL homologues for chaperon function in phototrophs has provided a constraint that has shaped convergent evolutionary scenarios in divergent evolutionary lineages. GroEL provides a general evolutionary model for studying gene transfers and convergent evolutionary processes among eukaryotic lineages

Order-disorder layering transitions of a spin-1 Ising model in a variable crystal field

The magnetic order-disorder layering transitions of a spin-1 Ising model are investigated, under the effect of a variable surface crystal field $\Delta_{s}$, using the mean field theory. Each layer $k$, of the film formed with $N$ layers, disorders at a finite surface crystal field distributed according to the law $\Delta_k=\Delta_s/k^\alpha$, $k=1,2,...,N$ and $\alpha$ being a positive constant. We have established the temperature-crystal field phase diagrams and found a constant tricritical point and a reentrant phenomenon for the first $k_0$ layers. This reentrant phenomenon is absent for the remaining $N-k_0$ layers, but the tricritical points subsist and depend not only on the film thickness but also on the exponent $\alpha$. On the other hand, the thermal behaviour of the surface magnetisation for a fixed value of the surface crystal field $\Delta_{s}$ and selected values of the parameter $\alpha$ are established.Comment: 10 Pages Latex, 9 Figures Postscript. To appear in JMMM (2002

Structures and orientational transitions in thin films of tilted hexatic smectics

We present detailed systematic studies of structural transformations in thin liquid crystal films with the smectic-C to hexatic phase transition. For the first time all possible structures reported in the literature are observed for one material (5 O.6) at the variation of temperature and thickness. In unusual modulated structures the equilibrium period of stripes is twice with respect to the domain size. We interpret these patterns in the frame work of phenomenological Landau type theory, as equilibrium phenomena produced by a natural geometric frustration in a system having spontaneous splay distortion.Comment: 7 pages, 6 figure

Dislocation loops in overheated free-standing smectic films

Static and dynamic phenomena in overheated free-standing smectic-A films are studied using a generalization of de Gennes' theory for a confined presmectic liquid. A static application is to determine the profile of the film meniscus and the meniscus contact angle, the results being compared with those of a recent study employing de Gennes' original theory. The dynamical generalization of the theory is based on on a time-dependent Ginzburg-Landau approach. This is used to compare two modes for layer-thinning transitions in overheated films, namely "uniform thinning" vs. nucleation of dislocation loops. Properties such as the line tension and velocity of a moving dislocation line are evaluated self-consistently by the theory.Comment: 16 pages, 8 figure