In recent years it has become evident that functional RNAs in living organisms are not just curious remnants from a primoridal RNA world but an ubiquitous phenomenon complementing protein enzyme based activity. Functional RNAs, just like proteins, depend in many cases upon their well-defined and evolutionarily conserved three-dimensional structure. In contrast to protein folds, however, RNA molecules have a biophysically important coarse-grained representation: their secondary structure. At this level of resolution at least, RNA structures can be efficiently predicted given only the sequence information. As a consequence, computational studies of RNA routinely incorporate structural information explicitly. RNA secondary structure prediction has proven useful in diverse fields ranging from theoretical models of sequence evolution and biopolymer folding, to genome analysis and even the design biotechnologically or pharmaceutically useful molecules.

<p>Currently centered on molecular data, bacterial and archaeal relationships are often based on their relative branching in 16S rRNA based phylogenetic trees. The availability of numerous bacterial genome sequences over the past two decades has provided new information for insights previously inaccessible to the field of taxonomy. Through utilization of comparative genomics, numerous molecular markers in the form of insertions and deletions within conserved regions of proteins, also known as Conserved Signature Indels or CSIs, have been discovered for various prokaryotic taxa. Using these techniques, we have analyzed relationships among the bacterial phyla of Thermotogae and Synergistetes and the conglomeration of bacterial organisms known as the PVC super-phylum. Through identification of large numbers of CSIs we have described the phyla Thermotogae and Synergistetes, and their sub-groups, in molecular terms for the first time. The identified molecular markers support a reconstruction of the current taxonomic divisions of these phyla. Similarly, previously only observed to group in phylogenetic trees, we have identified molecular markers for the PVC clade of bacterial phyla which are indicative of their shared ancestry. Further, in response to recent suggestions of extensive lateral gene transfer masking evolutionary relationships, an argument in favour of Darwinian mode of evolution for prokaryotic organisms is made using the identified molecular markers identified here along with markers previously identified in similar studies. Due to their taxonomic specificity, the markers that we have discovered provide useful tools for biochemical tests aiming for an understanding of the unique characteristics of the bacterial groups to which they are specific.</p> / Master of Science (MSc)

During its intraerythrocytic stages (IE), Plasmodium falciparum, the causative agent of the deadliest human malaria, remodels the host red cell membrane with a poorly defined assortment of parasite-­encoded proteins that undergo antigenic variation. Despite the requirement for immunologic stealth, exported parasite proteins also mediate strain-independent functions such as endothelial sequestration that are critical for parasite survival and pathogenesis. This thesis explores the hypothesis that P. falciparum displays novel structurally conserved proteins on the IE surface and these proteins may serve as useful antigens for a broadly effective anti-­malarial vaccine. In order to test this hypothesis, we developed an in vitro selection technique that sequentially incorporates unique P. falciparum isolates as the targets for Systematic Evolution of Ligands by EXponential enrichment (Serial-SELEX) to generate nucleic acid molecular probes, aptamers, capable of recognizing conserved cell surface determinants. Ten of 11 enriched aptamers were -parasite selective and three of these aptamers demonstrated strain-independent binding to P. falciparum. Aptamer recognition extended beyond the parasites used in Serial-SELEX to other laboratory and recent field isolates. Surprisingly the same three broadly binding aptamer selected against P. falciparum also recognized all laboratory-adapted and clinical isolates of P. vivax and P. knowlesi tested, strongly supporting our hypothesis that structurally conserved molecules are present on the surface IEs. Competition studies showed that the aptamers bound a single target which was confirmed as an IE membrane protein. Aptamer­‐mediated affinity purification and tandem mass spectrometry enabled identification of the aptamer target as parasite-encoded protein. Discovery of a protein conserved between the major human malarias may have implications for vaccine development and validates the Serial‑SELEX technique as a powerful tool for antigen discovery.

ABSTRACT CONSERVED CHARGES IN ASYMPTOTICALLY (ANTI)-DE SITTER SPACETIME G&Uuml / LL&Uuml / , iBRAHiM M.S., Department of Physics Supervisor: Assoc. Prof. Dr. Bayram Tekin August 2005, 77 pages. In this master&rsquo / s thesis, the Killing vectors are introduced and the Killing equation is derived. Also, some information is given about the cosmological constant. Then, the Abbott-Deser (AD) energy is reformulated by linearizing the Einstein equation with cosmological constant. From the linearized Einstein equation, Killing charges are derived by using the properties of Killing vectors. Using this formulation, energy is calculated for some specific cases by using the Schwarzschild-de Sitter metric. Last, the Einstein-Gauss-Bonnet model is studied. The equations of motion are calculated by solving the generic action at quadratic order. Following this, all energy calculations are renewed for this model. Some useful relations and calculations are shown in Appendix (A-B) parts. &Ouml / Z ASiMPTOTiK (ANTi)-DE SITTER UZAYZAMANINDA KORUNAN Y&Uuml / KLER G&Uuml / LL&Uuml / , iBRAHiM Y&uuml / ksek Lisans, Fizik B&ouml / l&uuml / m&uuml / Tez Y&ouml / neticisi: Assoc. Prof. Dr. Bayram Tekin Agustos 2005, 77 sayfa. Bu master &ccedil / aliSmasinda, Killing vekt&ouml / rler tanimlandi ve Killing denklemi &ccedil / ikarildi. Ayrica evrenbilimsel sabit, de-Sitter ve Anti-de Sitter uzaylari hakkinda bilgi verildi. Sonra, Abbott-Deser (AD) enerjisi, evrenbilimsel sabitli Einstein denklemi dogrusallaStirilarak yeniden form&uuml / le edildi. DogrusallaStirilmiS Einstein denkleminden, Killing vekt&ouml / rlerin &ouml / zellikleri kullanilarak Killing y&uuml / kleri (Deser-Tekin denklemi) &ccedil / ikarildi. Schwarzschild-de Sitter metrigi kullanilarak &ouml / zel durumlar i&ccedil / in enerji hesaplandi. Son olarak Einstein-Gauss-Bonnet (GB) modeli &ccedil / aliSildi. ikinci dereceden genel eylem &ccedil / &ouml / z&uuml / lerek hareket denklemleri hesaplandi. Bundan sonra, t&uuml / m enerji hesaplamalari bu model i&ccedil / in tekrarlandi. Bazi faydali hesaplamalar ek (A-B) kisimlarinda g&ouml / sterilmiStir.

Submitted by Geandra Rodrigues (geandrar@gmail.com) on 2018-04-04T18:08:27Z No. of bitstreams: 1 anacarolinaribeirogomesmaia.pdf: 687971 bytes, checksum: 19edf64a9349768df07f14662c3d6df6 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2018-04-05T11:27:48Z (GMT) No. of bitstreams: 1 anacarolinaribeirogomesmaia.pdf: 687971 bytes, checksum: 19edf64a9349768df07f14662c3d6df6 (MD5) / Made available in DSpace on 2018-04-05T11:27:48Z (GMT). No. of bitstreams: 1 anacarolinaribeirogomesmaia.pdf: 687971 bytes, checksum: 19edf64a9349768df07f14662c3d6df6 (MD5) Previous issue date: 2015-05-04 / PROQUALI (UFJF) / A NTPDase 1 (50 kDa) de promastigotas de Leishmania infantum foi purificada por eletroforese em gel não-desnaturante. A identidade desta proteína ou de seu domínio B conservado (r83-122) foi confirmada por “Western blots” utilizando soros imunes produzidos contra a apirase de batata (SA), r-potDomínioB (SB), um polipeptídeo recombinante derivado do domínio B desta proteína vegetal, e LbB1LJ (SC; r82-103) e LbB2LJ (SD; r102-121), peptídeos sintéticos derivados do domínio B da NTPDase 1 de L. braziliensis. Sua antigenicidade foi evidenciada em “Western blots” pela reatividade com soros de cães com leishmaniose visceral. Os soros imunes SC ou SD inibiram sua atividade (87-99%) em preparação de promastigotas, sugerindo um efeito direto sobre o domínio B. Por ELISA, 45-50% de 38 cães infectados foram soropositivos para LbB1LJ e LbB2LJ confirmando a antigenicidade deste domínio. / The NTPDase 1 (50 kDa) of Leishmania infantum promastigotes was purified by nondenaturing gel electrophoresis. The identity of this protein or of its conserved domain B (r83-122) was confirmed by Western blots using immune sera raised against potato apyrase (SA); r-potDomainB (SB), a recombinant polypeptide derived from the B domain of this vegetable protein, and LbB1LJ (SC; r82-103) and LbB2LJ (SD; r102-121), synthetic peptides derived from the B domain of the L. braziliensis NTPDase 1. Its antigenicity was evidenced in Western blots by the reactivity with serum samples from dogs with visceral leishmaniasis. The immune sera SC and SD inhibited its activity (87- 99%) in promastigotes preparation, suggesting a direct effect on the B domain. By ELISA, 45-50% of 38 infected dogs were seropositive for LbB1LJ and LbB2LJ confirming the antigenicity of this domain.

This thesis discusses the structure-function studies on triosephosphate isomerase (TIM) from Plasmodium falciparum (Pf), directed towards understanding the roles of highly conserved residues by site derected mutagenesis. Chapter 1 provides an introductory overview to the relevant literature on triosephosphate isomerase. In addition, this Chapter provides an analysis of conserved residues in TIM, and amino acid diversity at specific positions in the structure using a dataset of 503 TIM sequences. Chapter 2 reports the work on the completely conserved residue, C126 in TIM, which is proximal to the active site. Five mutants, C126S, C126A, C126V, C126M and C126T have been characterized. Crystal structures of 3-phosphoglycolate (PGA) bound C126S mutant and the unliganded forms of the C126S and C126A mutants have been determined at a resolution of 1.7 Å to 2.1 Å. Kinetic studies reveal a ~5 fold drop in kcat for the C126S and C126A mutants, while a ~ 10 fold drop is observed for the other three mutants. All the mutants show reduced stability at lower concentration and higher temperature. Chapter 3 presents the kinetic and structural characterization for the E97Q and E97D mutants of Pf TIM. A 4000 fold reduction in kcat is observed for E97Q, 100 fold reduction for the E97D mutant, while a ~ 9000 fold drop in activity for the control mutant, E165A. A large conformational change for the critical K12 side chain is observed in the crystal structure of the E97Q mutant, while it remains unchanged in the E97D structure. The results are interpreted to invoke a direct role for E97 in the catalytic proton transfer cycle, eliminating the need to invoke the formation of the energetically unfavorable imidazolate anion at H95. Chapter 4 reports investigations with position 96 by the biochemical and structural characterization of single mutants, F96Y, F96A and the double mutants, F96S/S73A and F96S/L167V. F96Y showed ~100 fold drop in activity, F96A revealed ~10 fold drop in activity, while F96S/S73A showed 100 fold lower activity than that of the wild type enzyme. Interestingly, the double mutant F96S/L167V proved to be a partial pseudorevertant, showing 10 fold higher activity than the single mutant, F96S. Chapter 5 describes the cloning, and preliminary kinetic and biophysical characterization of the enzyme, Dm TIM. A survey of disease causing mutations in TIM and the relationship of these sites of mutation to the active site and the dimer interface of TIM is presented in this Chapter.

This thesis investigates how seven communities in a subregion of the Sierra Norte of Oaxaca are conserving high forest cover in the absence of national protected areas. To conduct this study I relied on archival research and the review of community documents, focus group interviews and land use transects to explore historical and current land use. I found that communities have conserved 88.34% of the subregion as forest cover, or 58,596 hectares out of a total territory of 66,264 hectares. Analysis suggests that the communities have undergone a historical transition from more passive conservation to more active, conscious conservation particularly in the last decade. This thesis further contends that communities deserve additional financial compensation for this active conservation of globally important forests for biodiversity conservation and that exercises in systematic conservation planning ignore the reality that existing biodiversity conservation in the subregion is associated with community ownership.

Many partial differential equations (PDEs) admit conserved quantities like mass or energy. Those quantities are often essential to establish well-posed results. When approximating a PDE by a finite-difference scheme, it is natural to ask whether related discretized quantities remain conserved under the scheme. Such conservation may establish the stability of the numerical scheme. We present an algorithm for checking the preservation of a polynomial quantity under a polynomial finite-difference scheme. In our algorithm, schemes can be explicit or implicit, have higher-order time and space derivatives, and an arbitrary number of variables. Additionally, we present an algorithm for, given a scheme, finding conserved quantities. We illustrate our algorithm by studying several finite-difference schemes.

In partial differential equations (PDEs), conserved quantities like mass and momentum are fundamental to understanding the behavior of the described physical systems. The preservation of conserved quantities is essential when using numerical schemes to approximate solutions of corresponding PDEs. If the discrete solutions obtained through these schemes fail to preserve the conserved quantities, they may be physically meaningless and unreliable. Previous approaches focused on checking conservation in PDEs and numerical schemes, but they did not give adequate attention to systematically handling parameters. This is a crucial aspect because many PDEs and numerical schemes have parameters that need to be dealt with systematically. Here, we investigate if the discrete analog of a conserved quantity is preserved under the solution induced by a parametric finite difference method. In this thesis, we modify and enhance a pre-existing algorithm to effectively and reliably deduce conserved quantities in the context of parametric schemes, using the concept of comprehensive Groebner systems. The main contribution of this work is the development of a versatile algorithm capable of handling various parametric explicit and implicit schemes, higher-order derivatives, and multiple spatial dimensions. The algorithm’s effectiveness and efficiency are demonstrated through examples and applications. In particular, we illustrate the process of selecting an appropriate numerical scheme among a family of potential discretization for a given PDE.

No description available.