Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

The goal of this study was to determine the energetic requirements of juvenile scalloped hammerhead sharks (Sphyrna lewini) in Kaneohe Bay, Oahu, Hawaii using a multidisciplinary approach. A large flume/respirometer (635 1) was constructed to determine the critical swimming speeds (Ucrit )' swimming kinematics (tailbeat frequency, tailbeat amplitude, and stride length), and oxygen consumption rates (V02 ) of juvenile sharks over a range of swimming speeds (U). Swimming kinematics were also compared with unconstrained sharks in a seawater pond. These experiments indicated that tailbeat frequency (TBF) and water temperature could be used as a predictor of U and V02 for free-swimming sharks in the field; however, the flume affected the sharks' swimming kinematics at slow speeds. The flume and pond kinematic comparisons were used to correct for flume effects on sharks' V02. An acoustic tailbeat-sensing transmitter was designed and constructed to quantify activity and energy consumption of free-swimming hammerhead shark pups in Kaneohe Bay. Sharks with transmitters behaved similarly to uninstrumented sharks, but incurred a 28% increase in cost of transport due to increased drag from the transmitters. These data were used to correct for the effects of the transmitter on freeswimming sharks in the field. Sharks tracked in Kaneohe Bay with tailbeat transmitters exhibited increased U during dawn and dusk, while sharks tracked in the warmer summer months had higher activity rates and metabolic rates (MR) than a shark tracked during the winter. Sharks tracked in this study had higher MR than those measured for other species of tropical sharks and, as a result, require higher daily rations. Low and negative growth rates determined from sharks in the Bay and declining catch rates over the season suggest that a large percentage of the pups in Kaneohe Bay may starve as the result of their high metabolic requirements. Although prey do not appear to be li~itingi lack of foraging experience compounded by a high daily metabolic demand may explain why sharks lose weight during summer months. Those pups that survive the winter experience lower MR due to seasonal temperature decline and less competition as the result of high neonatal mortality. / x, 130 leaves, bound : ill. (some col.) ; 29 cm. / Missing page 74.

RNA catalysis is of fundamental importance in many biological functions, such as the peptidyl transferase activity of the ribosome and genetic control by riboswitches, among others. Small ribozymes are a convenient system to increase our understanding about the structure, folding and catalytic mechanism of ribozymes. This dissertation includes analysis of certain aspects of the catalytic mechanism in the hairpin and hammerhead ribozyme. In the hairpin ribozyme, we studied the functional consequences of molecular substitutions at two conserved positions, A9 and A10. These nucleotides are located close to the scissile phosphate but their exact function is unclear since they do not appear to be making any essential interactions with other nucleotides in the catalytic core. G, C, U, 2-aminopurine, 2, 6-diaminopurine, purine, and inosine were substituted at A9 and A10 and their effects on cleavage and ligation rates were analyzed. The effect of the variations on tertiary structure and docking was monitored by hydroxyl radical footprinting and native gel electrophoresis. It was observed that all the variants that exhibited poor docking and/or tertiary structure formation were also ligation challenged whereas they performed normally in the cleavage reaction. We found a unique variant, A10G that cleaved five times faster than A10 but did not exhibit any ligation. Results suggested that ligation required a more kinetically stable core than that needed to carry out cleavage. The hammerhead ribozyme field featured extensive disagreements between the crystal structure of the minimal hammerhead released in the mid 90s and the accumulating biochemical data. Much of the conflict was resolved with the new crystal structure of the extended hammerhead ribozyme. This structure confirmed many of the biochemical findings and brought out some new interactions, notably the G8·C3 base pair. We studied numerous base substitutions to establish the importance of the base pair for cleavage and ligation. Catalysis requires the formation of the base pair but even the fastest base paired variant was 10-fold slower than G8·C3 base pair. Docking and tertiary structure analysis by hydroxyl radical footprinting and native gel electrophoresis emphasized the importance of having a purine at position 8 and a pyrimidine at 3. Catalysis in the unmodified ribozyme was uniquely accompanied by hydrolysis of the 2′, 3′- cyclic phosphate ring present on one of the cleavage products, leading to the generation of non-ligatable products during a ligation assay. We determined the ligation rate-pH profile for unmodified ribozyme that differed from the cleavage rate-pH profile only at high pH.

A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy Johannesburg, 2002 / Hepatitis B virus (HBV) infection is endemic to several populous regions and is often complicated by cirrhosis and hepatocellular carcinoma (HCC). Present treatment of chronic HBV infection is usually ineffective and novel therapeutic approaches are an important medical objective. The X open reading frame (ORF) of HBV, HBx, is a conserved sequence that overlaps with the polymerase ORF and viral c/'s-elements, and is present within all viral transcripts. In addition, the HBx ORF encodes a 17 kDa transactivator protein, HBx, which is required for the establishment of viral infection and has been implicated in HBV-associated hepatocarcinogenesis. The HBx sequence thus represents a compelling target for applying nucleic acid hybridisation-based therapeutic agents for the inhibition of HBV gene expression and replication. / IT2018

No description available.

O tubarão-martelo, Sphyrna lewini é um dos mais valiosos recursos marinhos, e o preço pago por suas barbatanas no mercado Asiático pode atingir acima dos U$ 100,00/kg. A análise da composição de tamanhos e idades nas capturas, o estudo do crescimento desta espécie de grande porte e a evolução temporal dos desembarques, indicaram que este recurso se encontra sobreexplotado no sudeste e sul do Brasil, como reflexo de diferentes modalidades pesqueiras atuando ao longo de todo o seu ciclo de vida e à baixa resiliência desta espécie à pesca, por apresentar um crescimento lento (L&#8734 = 329,12 cm; K = 0,071 ano-1; to = -2,37 ano; sexos combinados), longevidade acima dos 40 anos e mortalidade natural baixa (M = 0,1 ano-1 na fase adulta), padrões estes típicos de uma espécie K-estrategista . A sobrepesca de recrutamento, ocorre nas áreas costeiras, principalmente pela pesca de arrasto e emalhe costeiro, não havendo a proteção das áreas de parto na primavera-verão. Neste caso há grandes capturas de neonatos e juvenis até 8 anos de idade. A tração adulta por sua vez é reduzida pela pesca de espinheI e de emalhe de superfície principalmente na zona de talude. Modelos de análise de covariância indicaram maiores capturas desta espécie na pesca de espinheI de monofilamento de superfície durante os meses de primavera-verão, na zona de talude (200 e 3000 m) e a existência de uma relação linear positiva entre a captura em peso e o esforço em número de anzóis. Medidas de manejo e conservação para esta espécie são sugeridas. / The scalloped hammerhead shark Sphyrna lewini is one of the most valuable marine resources, due to its high-priced fins in the Asian market, which can reach U$ 100,00/kg. The analysis of the length and age composition in the catches, growth studies, and the annual development of its landings in southern Brazil, showed signs of overexploitation for the species. This effect was mainly caused by different fishing gears exploiting all the phases of its life-cycle and its low resilience to fishing pressure due to its slow-growing strategy (L&#8734 = 329,12 cm; K = 0,071 yr-1; to = -2,37 ano; both sexes), longevity (> 40 yrs.) and low natural mortality (M = 0,1 yr-1, during adult phase), which means a K\'strategic typical pattern. Recruitment overfishing use to happen in coastal areas by trawls and anchored gillnets activities which destroy the nurseries and juvenile grounds for the species, mainly in spring-summer months when the parturition occurs. On the other hand, the adult fraction of the stock is reduced by surface longline and driftnets activities along the continental slope. For the surface monofilament longline fisheries, covariance models detected the highest catches of scalloped hammerhead sharks along the slope (between 200 - 3000 m depth), during spring-summer months. There was also a positive linear relationship between catch (in weight) and effort (hook number). Management and conservation measures are recommended for this species.

Submitted by (edna.saturno@ufrpe.br) on 2017-02-17T14:32:33Z No. of bitstreams: 1 Natalia Priscila Alves Bezerra.pdf: 2116155 bytes, checksum: 25ac05e8bfcb1edeee75fcfaf93d7ec7 (MD5) / Made available in DSpace on 2017-02-17T14:32:33Z (GMT). No. of bitstreams: 1 Natalia Priscila Alves Bezerra.pdf: 2116155 bytes, checksum: 25ac05e8bfcb1edeee75fcfaf93d7ec7 (MD5) Previous issue date: 2013-02-15 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The hammerhead shark (Sphyrna lewini) has a circuntropical distribution, ranging from coastal and semi-oceanic tropical and temperate regions to and island ecosystems. Located near the equator, the Saint Peter and Saint Paul Archipelago (SPSPA) is a group of small islands where hammerhead sharks are frequently observed. For that reason, the SPSPA was selected for the study of hammerhead shark movements, through satellite tagging, using PSAT (Pop up satellite archival transmitting tag).Three females were tagged, two in October 2010 (TM 1: 250 cm TL e TM 2: 260 cm TL), and one in March 2012 (TM 3: 200 cm TL). Although all tags were programmed to remain attached to the animals, collecting data, for 70 days, TM 1 and TM 2 tags were released prematurely, on the 7th and 5th day of monitoring, respectively. TM3 tag was released at the programmed date. According to the deploy and pop-up information (TM 1 e TM 2) and geolocation (TM 3), all sharks remained in SPSPA surroundings during the monitoring period, diving at great depths, mainly during the night, with the deepest dive of 728 m being recorded for TM 3. TM 1 and TM 2 had a depth preference between the surface and 150 m, while TM3 had a more restricted depth preference (surface to 75 m) during both periods, day and night. The temperature profile indicated that the three tagged hammerhead sharks preferred to be in temperatures between 24° C and above 26°C. Despite the great amount of time spent by all sharks in depths attributed to thermocline in SPSPA, the specimens moved from the mixing layer to the mesopelagic zone. In spite of the relevance of the obtained information for the understanding of the species movement patterns, complimentary studies are yet necessary to elucidate its migratory behavior. / O tubarão martelo (Sphyrna lewini) apresenta distribuição circuntropical, abrangendo desde as áreas costeiras e semi-oceânicas das regiões tropicais e temperadas até aos ecossistemas insulares. Localizado próximo à região equatorial, o arquipélago de São Pedro e São Paulo (ASPSP) é um conjunto de pequenas ilhas onde existe a ocorrência do tubarão martelo. Por essa razão, o ASPSP foi o local escolhido para o monitoramento via satélite da espécie através da utilização do transmissor eletrônico PSAT (Pop up satellite archival transmitting tag). Foram marcadas três fêmeas, duas em outubro de 2010 (TM 1 e TM 2) medindo 250 cm e 260 cm (CT), respectivamente, e uma última em março de 2012 (TM 3) com 200 cm de CT. Embora os três transmissores os três transmissores tenham sido programados para coletarem dados por 70 dias, ocorreu o desprendimento prematuro das marcas do TM 1 e TM 2, após um período de fixação aos tubarões de apenas 7 e 5 dias, respectivamente. De acordo com os dados de marcação e soltura dos transmissores (TM 1 e TM 2) e de geolocalização (TM 3), os três tubarões permaneceram no entorno do ASPSP durante o período em que foram monitorados. Os três espécimes foram capazes de realizar incursões frequentes a grandes profundidades principalmente durante a noite, com o mergulho mais profundo registrado a 728 m, atribuído ao TM 3. Os tubarões TM 1 e TM 2 frequentaram preferencialmente as profundidades entre a superfície e 150 m tanto de dia quanto à noite. Já o TM 3 passou a maior parte do tempo em uma faixa que variou entre a superfície e 75 m de profundidade em ambos os períodos. Os perfis de temperatura indicaram que os três espécimes permaneceram com maior frequência em águas aquecidas, entre 24 °C e acima de 26 °C, no período diurno e noturno. A despeito do elevado tempo de permanência dos três tubarões em profundidades atribuídas à termoclina nas proximidades do ASPSP, os espécimes se deslocaram desde a camada de mistura até a zona mesopelágica. Apesar da relevância das informações obtidas para a compreensão dos padrões de deslocamento da espécie, são necessários ainda estudos complementares para elucidar o seu comportamento migratório.

AIDS is caused by a lentivirus, HIV-1. In addition to antiretroviral drugs that are currently in use for HIV/AIDS therapy, a number of gene therapy strategies have been designed as alternative therapies. Most of these therapies target HIV RNA/proteins, which are subject to high rate of mutation, resulting in escape mutants. Viral entry is mediated by CCR5 co-receptor in most routes of transmission. To downregulate CCR5 as a gene therapy approach, we targeted seven unique sites within the CCR5 mRNA by a multimeric hammerhead ribozyme, Rz1-7. Hammerhead ribozyme is a small RNA that cleaves a target RNA upon binding to it. Expressing the Rz1-7 from HIV-1- and MSCV-based vectors in otherwise susceptible cells inhibited replication of a CCR5-tropic strain of HIV-1 by 99-100%. The Rz1-7 will be tested for inhibition of HIV-1 replication in the CD4+ T-lymphoid and myeloid progeny of transduced human CD34+ hematopoietic progenitor stem cells. It may be preferable to interfere HIV-1 life cycle at the DNA level since a one-time inactivation might suffice to confer a complete and permanent inhibition of virus replication in the gene modified cells and their progeny. This is what other strategies that target the HIV-1 RNA/protein can hardly offer. For this purpose, group II introns, which are able to splice out and get incorporated into a specific DNA sequence, can be designed/modified to gain novel DNA targeting specificities. As a novel approach, we have examined whether insertion of a modified intron into an infectious HIV-1 clone at two sites within the integrase domain of HIV-1 pol gene could inhibit virus replication. Intron insertion into the HIV-1 clone was induced and mammalian cells were transfected with intron-inserted HIV-1 clones. Although similar amounts of HIV-1 RNA, protein, and progeny virus were produced from the clones as from wild-type HIV-1 provirus DNA, in the absence of a functional integrase, the HIV-1 reverse-transcribed DNA failed to integrate and virus replication was aborted. These results demonstrate that modified group II introns can confer complete inhibition of virus replication at the level of second round of infection. We are now developing vectors to assess whether intron insertion can take place in mammalian cells.

AIDS is caused by a lentivirus, HIV-1. In addition to antiretroviral drugs that are currently in use for HIV/AIDS therapy, a number of gene therapy strategies have been designed as alternative therapies. Most of these therapies target HIV RNA/proteins, which are subject to high rate of mutation, resulting in escape mutants. Viral entry is mediated by CCR5 co-receptor in most routes of transmission. To downregulate CCR5 as a gene therapy approach, we targeted seven unique sites within the CCR5 mRNA by a multimeric hammerhead ribozyme, Rz1-7. Hammerhead ribozyme is a small RNA that cleaves a target RNA upon binding to it. Expressing the Rz1-7 from HIV-1- and MSCV-based vectors in otherwise susceptible cells inhibited replication of a CCR5-tropic strain of HIV-1 by 99-100%. The Rz1-7 will be tested for inhibition of HIV-1 replication in the CD4+ T-lymphoid and myeloid progeny of transduced human CD34+ hematopoietic progenitor stem cells. It may be preferable to interfere HIV-1 life cycle at the DNA level since a one-time inactivation might suffice to confer a complete and permanent inhibition of virus replication in the gene modified cells and their progeny. This is what other strategies that target the HIV-1 RNA/protein can hardly offer. For this purpose, group II introns, which are able to splice out and get incorporated into a specific DNA sequence, can be designed/modified to gain novel DNA targeting specificities. As a novel approach, we have examined whether insertion of a modified intron into an infectious HIV-1 clone at two sites within the integrase domain of HIV-1 pol gene could inhibit virus replication. Intron insertion into the HIV-1 clone was induced and mammalian cells were transfected with intron-inserted HIV-1 clones. Although similar amounts of HIV-1 RNA, protein, and progeny virus were produced from the clones as from wild-type HIV-1 provirus DNA, in the absence of a functional integrase, the HIV-1 reverse-transcribed DNA failed to integrate and virus replication was aborted. These results demonstrate that modified group II introns can confer complete inhibition of virus replication at the level of second round of infection. We are now developing vectors to assess whether intron insertion can take place in mammalian cells.

Nucleic acids are important bio-macromolecules in living systems. They are involved in important functions like gene expression and regulation. Nucleoside triphosphates serve as precursors for biochemical synthesis of modified nucleic acids and nucleotide coenzymes. The modification of nucleic acids, particularly at nucleobases, can expand the function and chemical properties of nucleic acid. Herein, we report the chemical synthesis of a novel thiol-modified nucleoside S-(3-(acetylthio)propyl)-5-(mercaptomethyl)-uridine and the corresponding nucleotide via a “new synthetic methodology” developed in our laboratory. The synthesized triphosphate was used for RNA transcription. The activity and nuclease resistance of the transcribed RNA is studied. The results showed that the properties of the nucleotide with thiol functionality are as good as the native. The modified RNA can be used for RNA/protein complex structure studies and gold nanoparticles stabilizer. They can also serve as a probe in DNA/RNA microchip surface functionalization for detection of various diseases and pathogens.