Thesis (Ph. D.)--University of Chicago, Dept. of Neurobiology, Pharmacology and Physiology, December 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (M.S.)--Miami University, Dept. of Microbiology, 2005. / Title from first page of PDF document. Document formatted into pages; contains [1], iv, 44 p. : ill. Includes bibliographical references (p. 40-44).

Thesis (Ph. D.)-- Göteborg University, 2006. / Includes bibliographical references.

Diss. (sammanfattning) Göteborg : Göteborgs universitet, 2010. / Härtill 4 uppsatser.

Thesis (M.S.)--Oregon State University, 2006. / Printout. Includes bibliographical references. Also available on the World Wide Web.

Thesis (Ph.D. (Biochemistry)) - Rhodes University, 2007.

Alcanivorax species are gram negative bacteria that usually require aliphatic hydrocarbon as the sole carbon source for growth. The ability to use petroleum in polluted environments as energy source makes Alcanivorax species biotechnologically relevant in bioremediation. Universal stress proteins confer ability to respond to unfavourable environments, thus the present study was done to analyse the genomic context of genes for universal stress proteins in Alcanivorax genomes. A combination of bioinformatics and visual analytics approaches were used to analyze genome-enabled data including sequences and gene expression datasets. On the basis of transcription unit and adjacent genes, two types of Alcanivorax USP genes observed were (i) adjacent to cyclic nucleotide-binding and oxygen sensing functions; and (ii) adjacent to sulfate transporter function. Both types of genes encode two universal stress protein domains (pfam00582) also referred to as tandem-type universal stress proteins. The sequence and structural characteristics of each of the four USP domains in Alcanivorax needs to be further investigated. This dissertation research evaluated data from Alcanivorax borkumensis cells (grown on either pyruvate or hexadecane as carbon source) that were stressed with 1-octanol and data collected at 15 min, 30 min, 60 min and 90 min after 1-octanol addition. The two genes for Alcanivorax borkumensis SK2 universal stress proteins, ABO_1340 and ABO_1511, had the same direction of expression for adjacent genes. A limitation of this research was that findings based on bioinformatics and visual analytics methods may need confirmation by molecular methods. The differences observed may also reflect the quality of the annotations provided for genes. The sequence and structural characteristics of each of the four USP domains in Alcanivorax needs to be further investigated. Further research is needed on the relationship between number, length and order of genes in operons that include genes for universal stress proteins. Additionally, in vitro studies to confirm the functional prediction made from the genomic context of the universal stress protein in Alcanivorax genome. The knowledge discovered from this genome context analytics research could contribute to improving the performance of Alcanivorax species in bioremediation of environments polluted with petroleum / College of Agriculture and Environmental Sciences / M. Sc. (Environmental Science)

xi, 52 p. ; ill. (some col.) A print copy of this title is available through the UO Libraries under the call number: SCIENCE QH445.2 .B35 2008 / Activation of Heat shock proteins (Hsps) is critical to adaptation to low oxygen levels (hypoxia) and enduring the oxidative stress of reoxygenation. Hsps are known to be regulated by Heat shock factor (Hsf), but my results demonstrate an unexpected regulatory link between the oxygen sensing and heat shock pathways. Hsf transcription is upregulated during hypoxia due to direct binding by Hypoxia-inducible Factor-1 (HIF-1) to HIF-1 response elements in an Hsf intron. This increase in Hsf transcripts is necessary for full Hsp induction during hypoxia and reoxygenation. The HIF-1-dependent increase in Hsps has a functional impact, as reduced production of Hsps decreases viability of adult flies exposed to hypoxia and reoxygenation. Thus, HIF-1 control of Hsf transcriptional levels is a regulatory mechanism for sensitizing heat shock pathway activity in order to maximize production of protective Hsps. This cross-regulation represents a mechanism by which the low oxygen response pathway has assimilated complex new functions by regulating the heat shock pathway's key transcriptional activator. Beyond studying the regulation of specific genes. I have also developed a method to identify small, yet important, changes within entire genomes. Genetic variation is the foundation of phenotypic traits, as well as many disease states. Variation can be caused by inversions, insertions, deletions, duplications, or single nucleotide polymorphisms (SNPs) within a genome. However, identifying a genetic change that is the cause of a specific phenotype or disease has been a difficult and laborious task for researchers. I developed a technique to quickly and accurately map genetic changes due to natural phenotypic variation or produced by genetic screens. I utilized massively parallel, high-throughput sequencing and restriction site associated DNA (RAD) markers, which are short tags of DNA adjacent to the restriction sites. These RAD markers generate a genome-wide signature of fragments for any restriction enzyme. Taken together with the fact that the vast majority of organisms have SNPs that disrupt restriction site sequences, the differences in the restriction fragment profiles between individuals can be compared. In addition, by using bulk segregant analysis, RAD tags can be used as high-density genetic markers to identify a genetic region that corresponds to a trait of interest. This dissertation includes both previously published and unpublished co-authored materials. / Adviser: Eric Johnson

Made available in DSpace on 2014-10-09T12:35:32Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:04:01Z (GMT). No. of bitstreams: 0 / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Made available in DSpace on 2014-10-09T12:35:32Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:04:01Z (GMT). No. of bitstreams: 0 / Moluscos têm sido empregados como bioindicadores em estudos de contaminação ambiental. Nesse contexto, o caramujo de água doce Biomphalaria glabrata tem sido avaliado como um bom modelo laboratorial, e estudos prévios apontaram sua aplicação na pesquisa ambiental. A proteína HSP70 é uma molécula de 70 kDa, pertencente a uma família de proteínas com papel na manutenção da homeostase dos seres vivos: as proteínas de choque térmico (HSPs); e vem sendo estudada como potencial biomarcador de dano ambiental, indicando estresse e protegendo os organismos dos danos às proteínas. Neste trabalho, foi caracterizada a proteína HSP70 de B. glabrata pelo Western blot, com o objetivo de seu emprego em aplicações ambientais futuras. Para isso, caramujos de 5-6 meses de idade, com diâmetro de concha de 14,4 (±1,7) mm, foram expostos ao calor e ao cloreto de cádmio (CdCl2) a fim de se verificar a resposta desta proteína frente a esses estresses. Os animais foram dissecados para investigação da indução da HSP70. As proteínas foram extraídas dos tecidos com tampão RIPA, separadas em eletroforese desnaturante em gel de poliacrilamida, transferidas para uma membrana de nitrocelulose e detectadas com anticorpo específico para HSP70. A CL50/96h foi determinada como sendo 0,34 (0,30-0,37) ppm para o CdCl2 e serviu de referência para os experimentos de indução da proteína. Foi observado que a exposição a temperaturas subletais aumentou a resistência dos caramujos à temperatura letal de 42 °C. Exposições prévias ao calor de 33 °C e ao CdCl2 a 0,22 ppm aumentou a sobrevivência dos caramujos B. glabrata à concentração letal de CdCl2 (0,7 ppm) e à temperatura letal (42 °C), respectivamente. Os achados do Western blot apontaram para um possível papel da HSP70 nesse processo. Os resultados mostraram relação entre a proteína HSP70 e o aumento na sobrevivência aos estímulos letais após prévia exposição a estresses moderados. O Western blot mostrou uma indução da HSP70 nos grupos pré-expostos, se comparados aos grupos controles. A glândula digestiva foi o tecido mais responsivo, no que concerne à indução da proteína HSP70, comparando com tecidos de cabeça/pé e ovoteste. Foi encontrado o pico de indução da HSP70 nos caramujos B. glabrata após 48 horas de exposição ao calor de 33 °C, e após 96 horas de exposição ao CdCl2 a 0,22 ppm. Apesar do bem conhecido papel da HSP70 na termotolerância e tolerância a outros agentes estressores nos organismos vivos, esta foi a primeira vez que isto foi demonstrado no B. glabrata, oferecendo subsídios para a sua aplicação em estudos de monitoramento ambiental. Os resultados apresentados aqui abrem o caminho para estudos futuros dessa proteína no molusco, e fornecem mais bases para o conhecimento do B. glabrata. / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP