DNA Sequence Representation methods

DNA sequence representation methods are used to denote a gene structure effectively and help in similarities/dissimilarities analysis of coding sequences. Many different kinds of representations have been proposed in the literature. They can be broadly classified into Numerical, Graphical, Geometrical and Hybrid representation methods. DNA structure and function analysis are made easy with graphical and geometrical representation methods since it gives visual representation of a DNA structure. In numerical method, numerical values are assigned to a sequence and digital signal processing methods are used to analyze the sequence. Hybrid approaches are also reported in the literature to analyze DNA sequences. This paper reviews the latest developments in DNA Sequence representation methods. We also present a taxonomy of various methods. A comparison of these methods where ever possible is also done

Genetic algorithm based indicator sequence method for exon prediction

Considerable research effort has been devoted in predicting the exon regions of genes. The binary indicator (BI), Electron ion interaction pseudo potential (EIIP), Filter method are some of the methods. All these methods make use of the period three behavior of the exon region. Even though the method suggested in this paper is similar to above mentioned methods , it introduces a set of sequences for mapping the nucleotides selected by applying genetic algorithm and found to be more promising

Church-Rosser groups and growing context-sensitive groups

A finitely generated group is called a Church-Rosser group (growing context-sensitive group) if it admits a finitely generated presentation for which the word problem is a Church-Rosser (growing context-sensitive) language. Although the Church-Rosser languages are incomparable to the context-free languages under set inclusion, they strictly contain the class of deterministic context-free languages. As each context-free group language is actually deterministic context-free, it follows that all context-free groups are Church-Rosser groups. As the free abelian group of rank 2 is a non-context-free Church-Rosser group, this inclusion is proper. On the other hand, we show that there are co-context-free groups that are not growing context-sensitive. Also some closure and non-closure properties are established for the classes of Church-Rosser and growing context-sensitive groups. More generally, we also establish some new characterizations and closure properties for the classes of Church-Rosser and growing context-sensitive languages.

Ground state correlation energy of the Be-sequence for Z = 4-20 in MCDF approximation

The ground state (J = 0) electronic correlation energy of the 4-electron Be-sequence is calculated in the Multi-Configuration Dirac-Fock approximation for Z = 4-20. The 4 electrons were distributed over the configurations arising from the 1s, 2s, 2p, 3s, 3p and 3d orbitals. Theoretical values obtained here are in good agreement with experimental correlation energies.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Konzeption von Entwicklungspfaden für Zulieferparks in der Automobilindustrie

Die Automobilindustrie reagiert mit Modularisierungsstrategien auf die zunehmende Produktkomplexität, getrieben durch die wachsenden Individualisierungsanforde-rungen auf der Kundenseite und der Modellpolitik mit neuen Fahrzeuganläufen. Die Hersteller verlagern die Materialbereitstellungskomplexität durch Outsourcing an die nächste Zulieferebene, den First Tier Suppliern, die seit Beginn der 90er Jahre zunehmend in Zulieferparks in unmittelbarer Werknähe integriert werden. Typische Merkmale eines klassischen Zulieferparks sind: Bereitstellung einer Halleninfrastruktur mit Infrastrukturdienstleistungen, Anlieferung der Teileumfänge im JIS-Verfahren (Just-in-Sequence = reihenfolgegenaue Synchronisation), lokale Wertschöpfung (Vormontagen, Sequenzierung) des Zulieferers, Vertragsbindung der First Tier Zulieferer für die Dauer eines Produktlebenszyklus und Einbindung eines Logistikdienstleisters. Teilweise werden zur Finanzierung Förderprojekte des öffent-lichen Sektors initiiert. Bisher fehlte eine wissenschaftliche Bearbeitung dieses Themas "Zulieferpark". In der Arbeit werden die in Europa entstandenen Zulieferparks näher untersucht, um Vor- und Nachteile dieses Logistikkonzeptes zu dokumentieren und Entwicklungs-trends aufzuzeigen. Abgeleitet aus diesen Erkenntnissen werden Optimierungs-ansätze aufgezeigt und konkrete Entwicklungspfade zur Verbesserung der Chancen-Risikoposition der Hauptakteure Automobilhersteller, Zulieferer und Logistikdienst-leister beschrieben. Die Arbeit gliedert sich in vier Haupteile, einer differenzierten Beschreibung der Ausgangssituation und den Entwicklungstrends in der Automobilindustrie, dem Vorgehensmodell, der Dokumentation der Analyseergebnisse und der Bewertung von Zulieferparkmodellen. Im Rahmen der Ergebnisdokumentation des Analyseteils werden vier Zulieferparkmodelle in detaillierten Fallstudien anschaulich dargestellt. Zur Erarbeitung der Analyseergebnisse wurde eine Befragung der Hauptakteure mittels strukturierten Fragebögen durchgeführt. Zur Erhebung von Branchentrends und zur relativen Bewertung der Parkmodelle wurden zusätzlich Experten befragt. Zur Segmentierung der Zulieferparklandschaft wurde die Methode der Netzwerk-analyse eingesetzt. Die relative Bewertung der Nutzenposition basiert auf der Nutzwertanalyse. Als Ergebnisse der Arbeit liegen vor: · Umfassende Analyse der Zulieferparklandschaft in Europa, · Segmentierung der Parks in Zulieferparkmodelle, Optimierungsansätze zur Verbesserung einer Win-Win-Situation der beteiligten Hauptakteure, · Relative Nutzenbewertung der Zulieferparkmodelle, · Entwicklungspfade für klassische Zulieferparks.

Cassava root peel as a replacement for maize in diets for growing pigs: effects on energy and nutrient digestibility, performance and carcass characteristics

Two experiments were conducted to evaluate cassava root peel (CRP) as diet component for fattening pigs. In the first experiment, ten male pigs were used to investigate the nutrient digestibility and the nutritive value of CRP as replacement for maize in the diet at 0 %, 30 %, 40 %, 50 % and 60 %, while supplementing free amino acids (fAA). During two experimental periods, faeces were quantitatively collected and analysed for chemical composition. In the second experiment, 40 pigs received the same diets as in Experiment 1, and daily feed intake and weekly weight changes were recorded. Four pigs per diet were slaughtered at 70 kg body weight to evaluate carcass traits. Digestibility of dry and organic matter, crude protein, acid detergent fibre and gross energy were depressed (p<0.05) at 60 % CRP; digestible energy content (MJ kg^(−1) DM) was 15.4 at 0 % CRP and 12.7 at 60 % CRP. In the second experiment, CRP inclusion had only a small impact on feed intake, weight gain and feed conversion ratio (p>0.05) as well as on the length of the small intestine and the Longissimus dorsi muscle area. The missing correlation of daily weight gain and feed-to-gain ratio up to a CRP inclusion of 40 % indicates that negative effects of CRP on pig growth can be avoided by respecting upper feeding limits. Hence, a combined use of CRP and fAA can reduce feeding costs for small-scale pig farmers in countries where this crop-by product is available in large amounts.