Les travaux présentés dans cette thèse s'inscrivent dans le cadre bio-informatique de l'analyse des génomes. Plus particulièrement, ces travaux concernent l'expression des gènes et les éléments régulateurs, présents dans l'ADN, qui participent à la modulation de cette expression.<br />Le problème de la recherche de ces éléments régulateurs peut être envisagé sous l'angle informatique de la recherche de motifs approchés particuliers.<br /><br />La recherche de motifs régulateurs est une question difficile du fait de la faible spécificité des motifs recherchés. Pour pouvoir y répondre, il faut prendre en compte différentes formes d'information. En particulier, il est pertinent de prendre en compte la conservation entre espèces (génomique comparative), la conservation entre séquences génomiques partageant des éléments de régulation (gènes co-régulés) ou encore, dans certains cas, la conservation spatiale des sites de fixation.<br /><br />Dans ce cadre, nous proposons une méthode permettant de tirer parti, à la fois de la conservation spatiale, et de la conservation entre espèces. Cette approche se compose d'un algorithme de recherche locale et d'évaluateurs statistiques adaptés au problème de la recherche de motifs sur-représentés localement lorsque l'environnement de recherche est hétérogène, c'est-à-dire pour des séquences pouvant provenir d'organismes différents ou de régions différentes du génome. Ces travaux ont été mis en oeuvre dans un logiciel appelé TFM-Explorer, que nous avons évalué avec succès sur des données issues du génome humain, de la souris et du rat.

Thesis (Ph.D.)--Mississippi State University. Department of Biological Sciences. / Title from title screen. Includes bibliographical references.

Det finns en allmän uppfattning och en starkt förankrad föreställning om att kön är någonting statiskt som inte kan ifrågasättas eller ändras. Språk kan förmedla och upprätthålla diskriminerande åsikter och vara privilegierande för människor som är bekväma med, och följer rådande normer. I denna studie fokuseras prefixet cis-, som beskriver människor som lever som, och identifierar sig själva i enlighet med de normativa föreställningar som råder i samhället. Studiens teoretiska ramverk och metodologiskt tillvägagångssätt bygger på den kritiska diskursanalysen (CDA). Utvalda blogginlägg samt tidningstexter som berör prefixet cis- har analyserats för att få förståelse för vad prefixet cis- betyder för personerna som använder det. Som analysverktyg används innehållsanalys samt korpusanalys. Resultatet av undersökningen visar att ord med prefixet cis- främst används av två aktörer i samhället: transpersoner och feminister. Innehållsanalysen visar att dessa aktörer använder prefixet cis- med olika innebörd och att ord med prefixet cis- är politiskt laddade. Korpusanalysen visar att prefixet cis- är ett produktivt förled som förekommer i olika sammansättningar och används i olika kontext. Ord med cis- som förled fyller en funktion för att kunna belysa normen i samhället och på så vis kan debatten nyanseras kring det som ses som självklara rättesnören. Det vill säga det binära könssystemet och patriarkala maktstrukturer. Vidare visar korpusanalysen att sammansättningar med prefixet cis- har blivit mer etablerade i tryckt press och att ordet cisperson är det mest frekvent förekommande av de undersökta orden i studien.

Members of the tautomerase superfamily are characterized by a [beta-alpha-beta] structural fold motif as well as a catalytic N-terminal proline (Pro-1). Three members of the superfamily are involved in the degradation of the nematocide 1,3-dichloropopene; trans-3-chloroacrylic acid dehalogenase (CaaD), cis-3-chloroacrylic acid dehalogenase (cis-CaaD) and malonate semialdehyde decarboxylase (MSAD). CaaD and cis-CaaD are involved in the hydration of their respective 3-chloroacrylic acid isomers to generate malonate semialdehyde. Subsequently, MSAD is responsible for catalyzing the decarboxylation of malonate semialdehyde to generate acetaldehyde. All three of these enzymes contain an N-terminal proline (Pro-1) that functions as a general acid, in contrast to other tautomerase superfamily members, such as 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), where Pro-1 acts as a catalytic base. Two new members of the tautomerase superfamily have been cloned and characterized; FG41 MSAD, a homologue of MSAD from Coryneform Bacterium strain FG41, and Cg10062, a homologue of cis-CaaD from Corynebacterium glutamicum, with low-level cis-CaaD and CaaD activities. As part of an effort to delineate the mechanisms of CaaD, cis-CaaD and Cg10062, secondary activities for all three enzymes were characterized. The three enzymes function as efficient phenylpyruvate tautomerases (PPT), converting phenylenolpyruvate to phenylpyruvate. The activity also indicates that the active site of these three enzymes can ketonize enol compounds, thereby providing evidence for the presence of an enediolate intermediate. The characterization of FG41 MSAD uncovered an activity it shares with MSAD. FG41 MSAD catalyzes the hydration of 2-oxo-3-pentynoate, but at a rate that is 50-fold less efficient than that of MSAD (as assessed by kcat/Km values). Mutagenesis studies of FG41 MSAD revealed that a single mutation resulted in a 8-fold increase in the activity. The characterization of Cg10062 and attempts to enhance the low-level cis-CaaD activity demonstrated the need for a bacterial screen that could screen a library of mutants. The resulting bacterial screen could be used to screen other members of the superfamily for dehalogenase activity. An in-depth exploration of the Cg10062 and FG41 MSAD activities may lead to a better understanding of the mechanism of cis-CaaD and MSAD and further delineate the evolutionary pathway for the tautomerase superfamily. / text

No description available.

This work focuses on a simple template assisted approach for fabricating I-III-VI semiconductor nanowire arrays. Vertically aligned nanowires of p-CIS of controllable diameter and thickness are electrodeposited, from an acidic electrolyte solution, inside porous aluminum templates using a three electrode set up with saturated calomel electrode as the reference. AAO template over ITO-glass was used as starting template for the device fabrication. The deposited CIS is annealed at different temperatures in a reducing environment (95% Ar+ 5% H2) for 30 minutes. X-ray diffraction of the nanowires showed nanocrystalline cubic phase structures with a strong orientation in the <112> direction. The effective bandgap of the deposited CIS nanowires determined using the Near Infrared (NIR) Spectrometer was found to be 1.07eV. The type of CIS electrodeposited inside the porous alumina template is determined to be p-type from the Schottky diode obtained with ITO-CIS-Au structure. Schottky diodes were characterized and analyzed at room temperature.

Nano structured solar cells provide an opportunity for increased open circuit voltages and and short circuit currents in solar cells due to quantum confinement of the window and absorber materials and an increase in the optical path length for the incident light. In this study, both bulk and nano heterojunctions of CIS/CdS and Cu2S/CdS devices have been fabricated and studied on plain glass substrates and inside porous alumina templates to compare their performance. The devices have also been characterized SEM, XRD and JV measurements. The J-V curves have also been analyzed for series resistance, diode ideality factor and reverse saturation current density.

<p>Part I: Extensive studies for treating hypercholesterolemia, one of the major causes of human morbidity throughout the world, have led to the development of statin drugs-the most prevalent drug prescribed today. In addition to statins, SCH 351448 has attracted considerable interest from many synthetic groups as it is the only selective activator of low-density lipoprotein receptor (LDL-R) containing structural features such as a C2-symmetry and 2,6-cis-tetrahydropyrans. Even though direct dimerization has been the most efficient method for the construction of C2-symmetric macrodiolides, total syntheses of SCH 351448 were only achived by stepwise dimerizations. In this chapter, attempts were made to exploit the inherent C2-symmetric macrodioloide via direct dimerization using various single monomeric units, but they did not prove to be viable. Therefore, formal synthesis of SCH 351448 was accomplished through two tandem sequences; cross-metathesis/conjugate addition and allylic oxidation/conjugate addition reactions, to stereoselectively construct 2,6-cis-tetrahydropyrans embedded in SCH 351448. The 1,4-syn aldol and the Suzuki coupling reactions were effective for the construction of the monomeric units. This convergent route should be broadly applicable to the synthesis of a diverse set of analogues of SCH 351448 for further biological studies.</p><p>Part II: Histone deacetylases (HDACs) play a significant role in tumorigenesis and have been recognized as one of the target enzymes for cancer therapy. Extensive studies in small molecules inhibiting HDAC enzymes have resulted in pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) and class I HDAC inhibitor FK228, approved by FDA in 2006 and 2009, respectively. Recently, largazole, a natural product was isolated from Symploca sp. presented HDAC inhibitory activity. Due to its unique differential cytotoxicity, potency, and class selectivity, structure-activity relationship (SAR) studies of largazole have been achieved to improve the potency and class selectivity. In addition to such biological activities, pharmacokinetic characteristics and isoform selectivity should be improved for the therapeutic potential of cancer therapy. In this chapter, two types of largazole analogues were synthesized by a convergent route that involved an efficient and high yielding multistep sequence. The synthesis of three disulfide analogues to improve pharmacokinetics and five linker analogues to enhance HDAC isoform selectivity is disclosed. The evaluation of biological studies is in progress.</p> / Dissertation

Cyclophilin A (CypA) is the well-studied member of a group of ubiquitous and evolutionarily conserved families of enzymes called peptidyl–prolyl isomerases (PPIases). These enzymes catalyze the cis-trans isomerization of peptidyl-prolyl bond in many proteins. The distinctive functional path triggered by each isomeric state of peptidyl-prolyl bond renders PPIase-catalyzed isomerization a molecular switching mechanism to be used on physiological demand. PPIase activity has been implicated in protein folding, signal transduction, and ion channel gating as well as pathological condition such as cancer, Alzheimer’s, and microbial infections. The more than five order of magnitude speed-up in the rate of peptidyl–prolyl cis–trans isomerization by CypA has been the target of intense research. Normal and accelerated molecular dynamic simulations were carried out to understand the catalytic mechanism of CypA in atomistic details. The results reaffirm transition state stabilization as the main factor in the astonishing enhancement in isomerization rate by enzyme. The ensuing intramolecular polarization, as a result of the loss of pseudo double bond character of the peptide bond at the transition state, was shown to contribute only about −1.0 kcal/mol to stabilizing the transition state. This relatively small contribution demonstrates that routinely used fixed charge classical force fields can reasonably describe these types of biological systems. The computational studies also revealed that the undemanding exchange of the free substrate between β- and α-helical regions is lost in the active site of the enzyme, where it is mainly in the β-region. The resultant relative change in conformational entropy favorably contributes to the free energy of stabilizing the transition state by CypA. The isomerization kinetics is strongly coupled to the enzyme motions while the chemical step and enzyme–substrate dynamics are in turn buckled to solvent fluctuations. The chemical step in the active site of the enzyme is therefore not separated from the fluctuations in the solvent. Of special interest is the nature of catalysis in a more realistic crowded environment, for example, the cell. Enzyme motions in such complicated medium are subjected to different viscosities and hydrodynamic properties, which could have implications for allosteric regulation and function.

The expansion of gene-specific trinucleotide repeats is responsible for a growing list of human disorders, including myotonic dystrophy type 1 (DM1). Repeat instability for most of these disorders, including DM1, is characterized by complex patterns of inherited and ongoing tissue-specific instability and pathogenesis. While the mechanistic basis behind the unique locus-specific instability of trinucleotide repeats is currently unknown, DNA metabolic processes are likely to play a role. My thesis involves investigating the contribution of DNA replication to the trinucleotide instability of myotonic dystrophy type 1. Herein I have designed an in vivo primate model system, based on the SV40 replication system, to assess the contribution of DNA replication to DM1 repeat instability. This system allows the assessment, under controlled conditions, and manipulation of variables that may affect replication-associated repeat instability, under a primate cellular system. Using the SV40 model system, I not only confirmed previous observations that repeat length and replication direction affect repeat instability, but also for the first time determined that the location of the replication origin relative to the repeat tract plays an important role in repeat instability. This novel observation allowed for the development of a fork-shift model of repeat instability, in which cis-elements adjacent to the repeat tract affect replication, in turn altering the propensity for repeat instability. To further my study of DNA replication in DM1 repeat instability, I have mapped the origin of replication adjacent to the DM1 locus in human patient cells and the tissues of DM1 transgenic mice actively undergoing repeat instability. The position of the replication origins adjacent to the repeat tract at the DM1 locus places several known cis-elements, including CTCF binding sites, in a position to alter replication as predicted by the fork-shift model. My analysis of the CTCF sites showed them capable of altering replication and repeat instability at the DM1 locus. Taken together these results suggest that the placement of replication origins, repeat tracts and cis-elements, may mark trinucleotide repeat tracts, such as the DM1, for locus-, tissue- and development-specific replication-associated repeat instability.