Rifaximin-mediated changes to the epithelial cell proteome: 2-D gel analysis

Diarrhea remains a significant cause of worldwide morbidity and mortality. Over 4 million children die of diarrhea annually. Although antibiotics can be used as prophylaxis or for treatment of diarrhea, concern remains over antibiotic resistance. Rifaximin is a semi-synthetic rifamycin derivative that can be used to treat symptoms of infectious diarrhea, inflammatory bowel syndrome, bacterial overgrowth of the small bowel, pouchitis, and fulminant ulcerative colitis. Rifaximin is of particular interest because it is poorly adsorbed in the intestines, shows no indication of inducing bacterial resistance, and has minimal effect on intestinal flora. In order to better understand how rifaximin functions, we sought to compare the protein expression profile of cells pretreated with rifaximin, as compared to cells treated with acetone, rifamycin (control antibiotic), or media (untreated). 2-D gel electrophoresis identified 38 protein spots that were up- or down-regulated by over 2-fold in rifaximin treated cells compared to controls. 16 of these spots were down-regulated, including keratin, annexin A5, intestinal-type alkaline phosphatase, histone h4, and histone-binding protein RbbP4. 22 spots were up-regulated, including heat shock protein HSP 90 alpha, alkaline phosphatase, and fascin. Many of the identified proteins are associated with cell structure and cytoskeleton, transcription and translation, and cellular metabolism. A better understanding of the functionality of rifaximin will identify additional potential uses for rifaximin and determine for whom the drug is best suited. ^

Analysis of VirB4, a membrane-associated ATPase subunit essential for T -complex transport in Agrobacterium tumefaciens

Agrobacterium tumefaciens is a plant pathogen with the unique ability to export oncogenic DNA-protein complexes (T-complexes) to susceptible plant cells and cause crown gall tumors. Delivery of the T-complexes across the bacterial membranes requires eleven VirB proteins and VirD4, which are postulated to form a transmembrane transporter. This thesis examines the subcellular localization and oligomeric structure of the 87-kDa VirB4 protein, which is one of three essential ATPases proposed to energize T-complex transport and/or assembly. Results of subcellular localization studies showed that VirB4 is tightly associated with the cytoplasmic membrane, suggesting that it is a membrane-spanning protein. The membrane topology of VirB4 was determined by using a nested deletion strategy to generate random fusions between virB4 and the periplasmically-active alkaline phosphatase, $\sp\prime phoA$. Analysis of PhoA and complementary $\beta$-galactosidase reporter fusions identified two putative periplasmically-exposed regions in VirB4. A periplasmic exposure of one of these regions was further confirmed by protease susceptibility assays using A. tumefaciens spheroplasts. To gain insight into the structure of the transporter, the topological configurations of other VirB proteins were also examined. Results from hydropathy analyses, subcellular localization, protease susceptibility, and PhoA reporter fusion studies support a model that all of the VirB proteins localize at one or both of the bacterial membranes. Immunoprecipitation and Co$\sp{2+}$ affinity chromatography studies demonstrated that native VirB4 (87-kDa) and a functional N-terminally tagged HIS-VirB4 derivative (89-kDa) interact and that the interaction is independent of other VirB proteins. A $\lambda$ cI repressor fusion assay supplied further evidence for VirB4 dimer formation. A VirB4 dimerization domain was localized to the N-terminal third of the protein, as judged by: (i) transdominance of an allele that codes for this region of VirB4; (ii) co-retention of a His-tagged N-terminal truncation derivative and native VirB4 on Co$\sp{2+}$ affinity columns; and (iii) dimer formation of the N-terminal third of VirB4 fused to the cI repressor protein. Taken together, these findings are consistent with a model that VirB4 is topologically configured as an integral cytoplasmic membrane protein with two periplasmic domains and that VirB4 assembles as homodimers via an N-terminal dimerization domain. Dimer formation is postulated to be essential for stabilization of VirB4 monomers during T-complex transporter assembly. ^

Protein and organic phosphorus in particulate matter and mesoplankton fraction in waters of the East Pacific

Vertical distribution of organic phosphorus and phosphatase activity was studied in the Southeast Pacific Ocean. The average rate of mineralization of organic phosphorus in the 0-200 m layer was shown to differ by a factor of 5-10 in oligotrophic and eutrophic areas, while residence time of phosphorus in production-destruction cycles differed by a factor of only 2-5, apparently because of both concentration of organic phosphorus and phosphorolysis rate increased simultaneously in the areas.

Investigations on volcanic rocks in sediment core CRP-3 from the Ross Sea, Antarctica

The petrography, mineralogy and geochemistry of volcanic and subvolcanic rocks in CRP-3 core have been examined in detail in order to characterise and to compare them with volcanic and subvolcanic rocks cropping out in the Victoria Land area, and to define the clast provenance or to establish possible volcanic activity coeval with deposition. Clasts with sizes ranging from granule to boulder show geochemical and mineralogical features comparable with those of Ferrar Supergroup rocks. They display a subalkaline affinity and compositions ranging from basalts to dacite. Three different petrographic groups with distinct textural and grain size features (subophitic, intergranular-intersertal, and glassy-hyalopilitic) are recognised and are related to the emplacement/cooling mechanism. In the sand to silt fraction, the few glass shards that have been recognised are strongly altered: however chemical analyses show they have subalkalic magmatic affinity. Mineral compositions of the abundant free clinopyroxene grains found in the core, are less affected by alteration processes, and indicate an origin from subalkaline magmas. This excludes the presence, during the deposition of CRP-3 rocks of alkaline volcanic activity comparable with the McMurdo Volcanic Group. Strong alteration of the magmatic body intruded the Beacon sandstones obliterates the original mineral assemblage. Geochemical investigations confirm that intrusion is part of the Ferar Large Igneous Province.