A complete proteome analysis of the chloroplast stroma, using 2D-PAGE, from spinach and Arabidopsis was performed. To improve the identification of proteins a computer program named SPECLUST was used. In SPECLUST, peak masses that are similar in many spots cluster together because they originate from the same protein with different locations on the gel. Within this program peaks in a cluster can be investigated in detail by peaks-in-common, and the unidentified masses that differ between spots in a cluster could be caused by protein modifications, which was analysed further by MS/MS. The thylakoid is an internal membrane system in the chloroplast where protein complexes involved in photosynthesis are housed. Enclosed in the thylakoid membrane is the chloroplast lumen, with a proteome estimated to contain 80-200 different proteins. Because the chloroplast lumen is close to the photosynthesis machinery in the plant, one can expect that the lumen proteome will change depending on if the plant is dark or light adapted. DIGE analysis of lumen proteins found that 15 lumen proteins show increased relative abundance in light-adapted plants. In addition co-expression analysis of lumen protein genes suggests that the lumen protein genes are uniformly transcriptionally regulated, not only by light but in a general manner. Plastocyanin is one of the proteins involved in the electron transfer in photosynthesis. Two homologous plastocyanin isoforms are encoded by the genes PETE1 and PETE2 in the nuclear genome of Arabidopsis, where PETE2 is the more abundant isoform. Knockout mutants of each of the plastocyanin isoforms shows that a 90% reduction of plastocyanin levels affects rates of photosynthesis and growth only slightly. A corresponding over-expression of plastocyanin in each of the two knockout mutants results in essentially wild-type photosynthetic performance. Reduced plastocyanin levels make the plant sensitive to Cu stress and therefore plastocyanin plays a major role as a Cu sink. A by-product of photosynthesis is hydrogen peroxide, which may be harmful for the plant. The discovery that an abundant protein found in the chloroplast lumen, TL29, shared sequence homology to Ascorbate Peroxidase (APX) was therefore of interest. We have evidence that TL29 is not an APX protein; it lacks the heme-binding active site and shows no activity. TL29 is located in the grana region and is electrostaticaly attached to the thylakoid membrane. It has four isoforms, with different pIs, both in the native and denatured form. It has no interaction with ascorbate, when compared to raAPX1. TL29 has two cysteine residues and one of them seems to have redox-regulated function, proposing that it may interact with other proteins close to PSII.

The minimum set cover problem is, without question, among the most ubiquitous and well-studied problems in computer science. Its theoretical hardness has been fully characterized--logarithmic approximability has been established, and no sublogarithmic approximation exists unless P=NP. However, the gap between real-world instances and the theoretical worst case is often immense--many covering problems of practical relevance admit much better approximations, or even solvability in polynomial time. Simple combinatorial or geometric structure can often be exploited to obtain improved algorithms on a problem-by-problem basis, but there is no general method of determining the extent to which this is possible. In this thesis, we aim to shed light on the relationship between the structure and the hardness of covering problems. We discuss several measures of structural complexity of set cover instances and prove new algorithmic and hardness results linking the approximability of a set cover problem to its underlying structure. In particular, we provide: - An APX-hardness proof for a wide family of problems that encode a simple covering problem known as Special-3SC. - A class of polynomial dynamic programming algorithms for a group of weighted geometric set cover problems having simple structure. - A simplified quasi-uniform sampling algorithm that yields improved approximations for weighted covering problems having low cell complexity or geometric union complexity. - Applications of the above to various capacitated covering problems via linear programming strengthening and rounding. In total, we obtain new results for dozens of covering problems exhibiting geometric or combinatorial structure. We tabulate these problems and classify them according to their approximability.

The minimum set cover problem is, without question, among the most ubiquitous and well-studied problems in computer science. Its theoretical hardness has been fully characterized--logarithmic approximability has been established, and no sublogarithmic approximation exists unless P=NP. However, the gap between real-world instances and the theoretical worst case is often immense--many covering problems of practical relevance admit much better approximations, or even solvability in polynomial time. Simple combinatorial or geometric structure can often be exploited to obtain improved algorithms on a problem-by-problem basis, but there is no general method of determining the extent to which this is possible. In this thesis, we aim to shed light on the relationship between the structure and the hardness of covering problems. We discuss several measures of structural complexity of set cover instances and prove new algorithmic and hardness results linking the approximability of a set cover problem to its underlying structure. In particular, we provide: - An APX-hardness proof for a wide family of problems that encode a simple covering problem known as Special-3SC. - A class of polynomial dynamic programming algorithms for a group of weighted geometric set cover problems having simple structure. - A simplified quasi-uniform sampling algorithm that yields improved approximations for weighted covering problems having low cell complexity or geometric union complexity. - Applications of the above to various capacitated covering problems via linear programming strengthening and rounding. In total, we obtain new results for dozens of covering problems exhibiting geometric or combinatorial structure. We tabulate these problems and classify them according to their approximability.

ABSTRACT EFFECT OF SALT STRESS ON ANTIOXIDANT DEFENSE SYSTEMS OF SENSITIVE AND RESISTANT CULTIVARS OF LENTIL Cicerali, Iin Nur M.Sc., Department of Biotechnology Supervisor: Prof. Dr. Meral Y&uuml / cel Co-supervisor: Asst. Prof. Dr. F&uuml / sun (nci) Eyidoan June 2004, 90 pages In this study, two lentil cultivars (Lens culinaris, Medik.) (ILL5582-salt tolerant and ILL590) were characterized and compared due to their NaCl susceptibility and antioxidant mechanism was examined under laboratory conditions. Physiological parameters such as wet-dry weight, root-shoot lengths, cell membrane stability, lipid peroxidation in terms of malondialdehyde (MDA), H2O2, proline contents were determined. The activities of antioxidant enzymes such as superoxide dismutase (SOD: EC 1.15.1.1), catalase (CAT: EC 1.11.1.6), ascorbate peroxidase (APX: EC 1.11.1.11) and glutathione reductase (GR: EC 1.6.4.2) were examined and analyzed in 14 days old plant seedlings after 9 days of normal growth and 5 days of 100mM and 200mM NaCl stress conditions. Shoot-root length and wet-dry weight percent decrease were more in ILL590. Especially shoot tissues were affected more from the stress conditions when compared to root tissues. ii According to malondialdehyde (MDA) content and membrane stability results, lipid peoxidation was higher in ILL590 and significant increases were observed in shoot tissues. Proline concentration showed a remarkable increase in salt concentration dependent manner. Higher concentrations of proline in ILL5582 might be the reason of higher salt tolerance when compared to ILL590. Among the antioxidant enzymes SOD was the one which showed highest activity increase. At organ level roots showed highest activity when compared to leaves. In the organelle higher activity percent contribution was achieved by cytosolic Cu/ZnSOD isozyme. Higher percent increase of this isozyme was observed in ILL5582. This might be one of the tolerance mechanisms that get activated against NaCl stress. APX activity showed similar alterations in both cultivars. In leaf tissues significant increase was observed but in root tissues ascorbate peroxidase activity did not change significantly. Glutathione Reductase activity increase was significant in both cultivars leaf tissues but although ILL5582 showed a stress concentration dependent increase, ILL590 did not. The activity of CAT enzyme in leaf and root tissues of both cultivars did not significantly change under increasing salt stress conditions. The results suggested that the leaves were more susceptible to salt stress. Also when two cultivars were compared ILL5582 was found to be more tolerant against salt stress than ILL590 under laboratory conditions and SOD enzyme seemed to be the most active component of the salt tolerant mechanism.

Orientador: Fernando Braz Tangerino Hernandez / Resumo: A ocorrência de geadas nas pastagens causa perdas de alimento para os animais, reduzindo a produção de leite e carne. Existe uma diversidade de espécies forrageiras com grande potencial produtivo e ampla adaptação térmica, que podem ser cultivadas em áreas de risco desse fenômeno. No entanto é necessário caracterizar a tolerância dessas espécies a baixas temperaturas e as regiões com condições climáticas adequadas. Os métodos de avaliação de danos por baixas temperaturas são predominantemente qualitativos, baseados em critérios visuais que têm o viés da subjetividade. Esta tese teve como objetivos determinar as temperaturas mínimas de início de danos para sete espécies forrageiras e efetuar o zoneamento de risco de geadas para o estado do Paraná. Foram incluídas no estudo as forrageiras: Alfafa (Medicago sativa), Sorgo (Sorghum bicolor), Aveia Preta (Avena strigosa), Brachiaria brizantha cv. Marandu, Milheto (Pennisetum glaucum), capim Mombaça (Panicum maximum) e Tifton 85 (Cynodon spp). As plantas foram conduzidas em vasos em casa de vegetação até 60 dias e submetidas a baixas temperaturas no interior de uma câmara de crescimento com condições de luminosidade e temperatura controladas, atingindo valores mínimos de 0,2 -0,9, -1,8, -2,7, -4,1, -4,6 e -6,2oC, durante uma hora. Foram realizadas avaliações quantitativas pós testes de fluorescência da clorofila, condutividade elétrica de solução embebida com discos de folhas e atividade das enzimas ascorbato peroxidase (APX), cata... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

In this dissertation, we investigate a number of geometric problems in different settings. We present lower bounds and approximation algorithms for geometric problems in sequential and distributed settings. For the sequential setting, we prove the first hardness of approximation results for the following problems: \begin{itemize} \item Red-Blue Geometric Set Cover is APX-hard when the objects are axis-aligned rectangles. \item Red-Blue Geometric Set Cover cannot be approximated to within $2^{\log^{1-1/{(\log\log m)^c}}m}$ in polynomial time for any constant $c < 1/2$, unless $P=NP$, when the given objects are $m$ triangles or convex objects. This shows that Red-Blue Geometric Set Cover is a harder problem than Geometric Set Cover for some class of objects. \item Boxes Class Cover is APX-hard. \end{itemize} We also define MaxRM-3SAT, a restricted version of Max3SAT, and we prove that this problem is APX-hard. This problem might be interesting in its own right.\\ In the distributed setting, we define a new model, the fixed-link model, where each processor has a position on the plane and processors can communicate to each other if and only if there is an edge between them. We motivate the model and study a number of geometric problems in this model. We prove lower bounds on the communication complexity of the problems in the fixed-link model and present approximation algorithms for them. We prove lower bounds on the number of expected bits required for any randomized algorithm in the fixed-link model with $n$ nodes to solve the following problems, when the communication is in the asynchronous KT1 model: \begin{itemize} \item $\Omega(n^2/\log n)$ expected bits of communication are required for solving Diameter, Convex Hull, or Closest Pair, even if the graph has only a linear number of edges. \item $\Omega( min\{n^2,1/\epsilon\})$ expected bits of communications are required for approximating Diameter within a $1-\epsilon$ factor of optimal, even if the graph is planar. \item $\Omega(n^2)$ bits of communications is required for approximating Closest Pair in a graph on an $[n^c] \times [n^c]$ grid, for any constant $c>1+1/(2\lg n)$, within $\frac{n^{c-1/2}}{4}-\epsilon$ factor of optimal, even if the graph is planar. \end{itemize} We also present approximation algorithms in geometric communication networks with $n$ nodes, when the communication is in the asynchronous CONGEST KT1 model: \begin{itemize} \item An $\epsilon$-kernel, and consequently $(1-\epsilon)$-\diamapprox~ and \ep -Approximate Hull with $O(\frac{n}{\sqrt{\epsilon}})$ messages plus the costs of constructing a spanning tree. \item An $\frac{n^c}{\sqrt{\frac{k}{2}}}$-Approximate Closest Pair on an $[n^c] \times [n^c]$ grid , for a constant $c>1/2$, plus the cost of computing a spanning tree, for any $k\leq {n-1}$. \end{itemize} We also define a new version of the two-party communication problem, Path Computation, where two parties communicate through a path. We prove a lower bound on the communication complexity of this problem. / Graduate

La comparaison de réseaux biologiques est actuellement l'une des approches les plus prometteuses pour aider à la compréhension du fonctionnement des organismes vivants. Elle apparaît comme la suite attendue de la comparaison de séquences biologiques dont l'étude ne représente en réalité que l'aspect génomique des informations manipulées par les biologistes. Dans cette thèse, nous proposons une approche innovante permettant de comparer deux réseaux biologiques modélisés respectivement par un graphe orienté D et un graphe non-orienté G, et dotés d'une fonction f établissant la correspondance entre les sommets des deux graphes. L'approche consiste à extraire automatiquement une structure dans D, biologiquement significative, dont les sommets induisent dans G, par f, une structure qui soit aussi biologiquement significative. Nous réalisons une étude algorithmique du problème issu de notre approche en commençant par sa version dans laquelle D est acyclique (DAG). Nous proposons des algorithmes polynomiaux pour certains cas, et nous montrons que d'autres cas sont algorithmiquement difficiles (NP-complets). Pour résoudre les instances difficiles, nous proposons une bonne heuristique et un algorithme exact basé sur la méthode branch-and-bound. Pour traiter le cas où D est cyclique, nous introduisons une méthode motivée par des hypothèses biologiques et consistant à décomposer D en DAGs tels que les sommets de chaque DAG induisent dans G un sous-graphe connexe. Nous étudions également dans cette thèse, l'inférence des voies de signalisation en combinant les informations sur les causes et sur les effets des événements extra-cellulaires. Nous modélisons ce problème par un problème d'orientation de graphes mixtes et nous effectuons une étude de complexité permettant d'identifier les instances faciles et celles difficiles.