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. ^

Heterotrimeric G protein -mediated signal transduction in Neurospora crassa

Heterotrimeric G protein-mediated signal transduction is one of numerous means that cells utilize to respond to external stimuli. G proteins consist of α, β andγ subunits. Extracellular ligands bind to seven-transmembrane helix receptors, triggering conformational changes. This is followed by activation of coupled G proteins through the exchange of GDP for GTP on the Gα subunit. Once activated, Gα-GTP dissociates from the βγ dimer. Both of these two moieties can interact with downstream effectors, such as adenylyl cyclase, phospholipase C, phosphodiesterases, or ion channels, leading to a series of changes in cellular metabolism and physiology. ^ Neurospora crassa is a eukaryotic multicellular filamentous fungus, with asexual/vegetative and sexual phases to its life cycle. Three Gα (GNA-1, GNA-2, GNA-3) and one Gβ (GNB-1) proteins have been identified in this organism. This dissertation investigates GNA-1 and GNB-1 mediated signaling pathways in N. crassa. ^ GNA-1 was the first identified microbial Gα that belongs to a mammalian superfamily (Gαi). Deletion of GNA-1 leads to multiple defects in N. crassa. During the asexual cycle, Δgna-1 strains display a slower growth rate and delayed conidiation on solid medium. In the sexual cycle, the Δgna-1 mutant is male-fertile but female-sterile. Biochemical studies have shown that Δ gna-1 strains have lower adenosine 3′–5 ′ cyclic monophosphate (cAMP) levels than wild type under conditions where phenotypic defects are observed. In this thesis work, strains containing one of two GTPase-deficient gna-1 alleles (gna-1 R178C, gna-1Q204L) leading to constitutive activation of GNA-1 have been constructed and characterized. Activation of GNA-1 causes uncontrolled aerial hyphae proliferation, elevated sensitivity to heat and oxidative stresses, and lower carotenoid synthesis. To further study the function of GNA-1, constructs to enable expression of mammalian Gαi superfamily members were transformed into a Δ gna-1 strain, and complementation of Δgna-1 defects investigated. Gαs, which is not a member of Gα i superfamily was used as a control. These mammalian Gα genes were able to rescue the vegetative growth rate defect of the Δ gna-1 strain in the following order: Gαz > Gα o > Gαs > Gαt > Gαi. In contrast, only Gαo was able to complement the sexual defect of a Δgna-1 strain. With regard to the thermotolerance phenotype, none of the mammalian Gα genes restored the sensitivity to a wild type level. These results suggest that GNA-1 regulates two independent pathways during the vegetative and sexual cycles in N. crassa. ^ GNB-1, a G protein β subunit from N. crassa, was identified and its functions investigated in this thesis work. The sequence of the gnb-1 gene predicts a polypeptide of 358 residues with a molecular mass of 39.7 kDa. GNB-1 exhibits 91% identity to Cryphonectria parasitica CPGB-1, and also displays significant homology with human and Dictyostelium Gβ genes (∼66%). A Δ gnb-1 strain was constructed and shown to exhibit defects in asexual spore germination, vacuole number and size, mass accumulation and female fertility. A novel role for GNB-1 in regulation of GNA-1 and GNA-2 protein levels was also demonstrated. ^

Pathways leading to apoptosis resistance in a murine B -cell lymphoma cell system

The aberrant activation of signal transduction pathways has long been linked to uncontrolled cell proliferation and the development of cancer. The activity of one such signaling module, the Mitogen-Activated Protein Kinase (MAPK) pathway, has been implicated in several cancer types including pancreatic, breast, colon, and lymphoid malignancies. Interestingly, the activation of MAP-Kinase-Kinase-Kinase proteins often leads to the additional activation of NF-κB, a transcription factor that acts as a cell survival signal through its control of antiapoptotic genes. We have investigated the role of a specific dimer form of the NF-κB transcription factor family, NF-κB1 (p50) homodimers, in its control of the proto-oncogene, Bcl-2, and we have identified the MEK/ERK (MAPK) signaling cascade as a mediator of NF-κB1 activity. ^ Two murine B cell lymphoma cell lines were used for these studies: LY-as, an apoptosis proficient line with low Bcl-2 protein expression and no nuclear NF-κB activity, and LY-ar, a nonapoptotic line with constitutive p50 homodimer activity and 30 times more Bcl-2 protein expression than LY-as. Experiments modulating p50 activity correlated the activation of p50 homodimers with Bcl-2 expression and additional gel shift experiments demonstrated that the Bcl-2 P1 promoter had NF-κB sites with which recombinant p50 was able to interact. In vitro transcription revealed that p50 enhanced the production of transcripts derived from the Bcl-2 P1 promoter. These data strongly suggest that Bcl-2 is a target gene for p50-mediated transcription and suggest that the activation of p50 homodimers contributes to the expression of Bcl-2 observed in LY-ar cells. ^ Studies of upstream MAPK pathways that could influence NF-κB activity demonstrated that LY-ar cells had phosphorylated ERK proteins while LY-as cells did not. Treatment of LY-ar cells with the MEK inhibitors PD 98059, U0126, and PD 184352 led to a loss of phosphorylated ERK, a reversal of nuclear p50 homodimer DNA binding, and a decrease in the amount of Bcl-2 protein expression. Similarly, the activation of the MEK/ERK pathway in LY-as cells by phorbol ester led to Bcl-2 expression that could be blocked by PD 98059. Furthermore, treatment of LY-ar cells with TNFα, an IKK activator, did not change the suppressive effect of PD 98059 on p50 homodimer activity, suggesting an IKK-independent pathway for p50 homodimer activation. Lastly, all three MEK inhibitors sensitized LY-ar cells to radiation-induced apoptosis. ^ These data indicate that the activation of the MEK/ERK MAP-Kinase signaling pathway acts upstream of p50 homodimer activation and Bcl-2 expression in this B cell lymphoma cell system and suggest that the activation of MEK/ERK may be a key step in the progression of lymphoma to advanced-staged disease. Other researchers have used MEK inhibitors to inhibit cell growth and sensitize a number of tumors to chemotherapies. In light of our data, MEK inhibitors may additionally be useful clinically to radiosensitize cancers of lymphoid origin. ^

Noble metal abundances in ODP Leg 115 basalts (Table 1)

A comparison of 50 basalts recovered at Sites 706, 707, 713, and 715 along the Reunion hotspot trace during Ocean Drilling Program Leg 115 in the Indian Ocean shows that seafloor alteration had little effect on noble metal concentrations (Au, Pd, Pt, Rh, Ru, and Ir), determined by inductively coupled plasma-mass spectrometry (ICP-MS), which generally tend to decrease with magma evolution. Their compatible-element behavior may be related to the precipitation of Ir-Os-based alloys, chromite, sulfides, and/or olivine and clinopyroxene in some combination. The simplest explanation indicates silicate control of concentrations during differentiation. Basalts from the different sites show varying degrees of alkalinity. Noble metal abundances tend to increase with decreasing basalt alkalinity (i.e., with increasing percentages of mantle melting), indicating that the metals behave as compatible elements during mantle melting. The retention of low-melting-point Au, Pd, and Rh in mantle sulfides, which mostly dissolve before significant proportions of Ir-Os-based alloys melt, explains increasing Pd/Ir ratios with decreasing alkalinity (increasing melting percentages) in oceanic basalts. High noble metal concentrations in Indian Ocean basalts (weighted averages of Au, Pd, Rh, Pt, Ru, and Ir in Leg 115 basalts are 3.2, 8.1, 0.31, 7.3, 0.22, and 0.11 ppb, respectively), compared with basalts from some other ocean basins, may reflect fundamental primary variations in upper- mantle noble metal abundances

X-ray fluorescence (XRF) scannings and grain size analysis at sites in the Gulf of Cádiz

Contourites in the Gulf of Cádiz preserve a unique archive of Mediterranean Outflow Water (MOW) variability over the past 5.3 Ma. In our study we investigate the potential of geochemical data obtained by XRF scanning to decipher bottom current processes and paleoclimatic evolution at two different sites drilled through contourite deposits in the northern Gulf of Cadiz: Site U1387, which is bathed by the upper MOW core, and Site U1389, located more proximal to the Straits of Gibraltar. The lack of major downslope transport at both locations during the Pleistocene makes them ideal locations for the purpose of our study. The results indicate that the Zr/Al ratio, representing the relative enrichment of heavy minerals (zircon) over less dense alumosilicates under strong bottom current flow, is the most useful indicator for a semi-quantitative assessment of current strength. While most elements are biased by current-related processes, the bromine record, representing organic content, preserves the most pristine climate signal rather independent of grain size changes. Hence, Br can be used for chronostratigraphy and site-to-site correlation in addition to stable isotope stratigraphy. Based on these findings we reconstructed MOW variability for Marine Isotope Stages 1-5 using the Zr/Al ratio from Site U1387. The results reveal abrupt, millennial-scale variations of MOW strength during Greenland Stadials (GS) and Interstadials (GI) with strong MOW during GS and glacial Terminations and a complex behavior during Heinrich Stadials. Millennial-scale variability persisting during periods of poorly expressed GS/GI cyclicities implies a strong internal oscillation of the Mediterranean/North Atlantic climate system.

Analyses of lake La Thuile sediment core

Lake La Thuile, in the Northern French Prealps (874 m a.s.l.), provides an 18 m long sedimentary sequence spanning the entire Lateglacial/Holocene period. The high resolution multi-proxy (sedimentological, palynological, geochemical) analysis of the uppermost 6.2 meters reveals the Holocene dynamics of erosion in the catchment in response to landscape modifications. The mountain belt is at relevant altitude to study past human activities and the watershed is sufficiently disconnected from large valleys to capture a local sedimentary signal. From 12,000 to 10,000 cal. BP (10 to 8 ka cal. BC), the onset of hardwood species triggered a drop in erosion following the Lateglacial/Holocene transition. From 10,000 to 4500 cal. BP (8 to 2.5 ka cal. BC), the forest became denser and favored slope stabilization while erosion processes were very weak. A first erosive phase was initiated at ca . 4500 cal. BP without evidence of human presence in the catchment. Then, the forest declined at approximately 3000 cal. BP, suggesting the first human influence on the landscape. Two other erosive phases are related to anthropic activities: approximately 2500 cal. BP (550 cal. BC) during the Roman period and after 1600 cal. BP (350 cal. AD) with a substantial accentuation in the Middle Ages. In contrast, the lower erosion produced during the Little Ice Age, when climate deteriorations are generally considered to result in an increased erosion signal in this region, suggests that anthropic activities dominated the erosive processes and completely masked the natural effects of climate on erosion in the late Holocene.

Dissolved chemical elements in river waters of the Wrangel Island

Pioneer information about chemical composition of river waters in the Wrangel Island has been obtained. It is shown that water composition reflects the lithogeochemical specifics of primary rocks and ore mineralization. In contrast to many areas of the Russian Far North river waters of the island are characterized by elevated background value of total mineralization (i.e., total dissolved solids, TDS) (0.3-2 g/l) and specific chemical type (SO4-Ca-Mg). This is related to abundance of Late Carboniferous gypsiferous and dolomitic sequences in the mountainous area of the island. It has also been established that salt composition of some streams is appreciably governed by supergene alterations of sulfide mineralization associated with quartz-carbonate vein systems. They make up natural centers of surface water contamination. Waters in such streams are characterized by low pH values (2.4-5.5), high TDS (up to 6-23 g/l) and SO4-Mg composition. These waters are also marked by anomalously high concentrations of heavy and non-ferrous metals, as well as REE, U, and Th.

Mineralogy and geochemistry of sulfide minerals and bulk rocks from ODP Hole 176-735B

Ocean Drilling Program (ODP) Leg 176 built upon the work of ODP Leg 118 wherein the 500-m section that was sampled represented the most complete recovery of an intact portion of lower oceanic crust ever described. During Leg 176, we deepened Hole 735B to >1500 m below seafloor in an environment where gabbroic rocks have been tectonically exposed at the Southwest Indian Ridge. This new expedition extended the remarkable recovery (>85%) that allowed unprecedented investigations into the nature of the lower oceanic crust as a result of Leg 118. Sulfide mineral and bulk rock compositions were determined from samples in the 1000-m section of oceanic gabbros recovered during Leg 176. The sulfide assemblage of pyrrhotite, chalcopyrite, pentlandite, and troilite is present throughout this section, as it is throughout the 500-m gabbroic section above that was sampled during Leg 118. Troilite is commonly present as lamellae, and the only interval where troilite was not observed is from the uppermost 150 m of the section sampled during Leg 118, which is intensely metamorphosed. The common presence of troilite indicates that much of the sulfide assemblage from Hole 735B precipitated from a magmatic system and subsequently underwent low-temperature reequilibration. Evaluation of geochemical trends in bulk rock and sulfides indicates that the combined effects of olivine accumulation in troctolites and high pentlandite to pyrrhotite ratios account for the sporadic bulk rock compositions high in Ni. Bulk rock and sulfide mineral geochemical indicators that are spatially coincident with structural and physical properties anomalies indicate a heretofore unrecognized lithologic unit boundary in this section. Platinum-group element (PGE) compositions were also determined for 36 samples from throughout the section that were recovered during Leg 176. Whereas most samples had low (<0.4 ppb) PGE concentrations, rare samples had elevated PGE values, but no unique common trend between these samples is evident.

Geochemical provenance analysis of fine-grained sediment of sediment core AND1-1

Bulk chemical fine-grained sediment compositions from southern Victoria Land glacimarine sediments provide significant constraints on the reconstruction of sediment provenance models in the McMurdo Sound during Late Cenozoic time. High-resolution (~ 1 ka) geochemical data were obtained with a non-destructive AVAATECH XRF Core Scanner (XRF-CS) on the 1285 m long ANDRILL McMurdo Ice Shelf Project (MIS) sediment core AND-1B. This data set is complemented by high-precision chemical analyses (XRF and ICP-OES) on discrete samples. Statistical analyses reveal three geochemical facies which are interpreted to represent the following sources for the sediments recovered in the AND-1B core: 1) local McMurdo Volcanic Group (MVG) rocks, 2) Transantarctic Mountain rocks west of Ross Island (W TAM), and 3) Transantarctic Mountain rocks from more southerly areas (S TAM). Data indicate in combination with other sediment facies analyses (McKay et al., 2009, doi:10.1130/B26540.1) and provenance scenarios (Talarico and Sandroni, 2009, doi:10.1016/j.gloplacha.2009.04.007) that diamictites at the drill site are largely dominated by local sources (MVG) and are interpreted to indicate cold polar conditions with dry-based ice. MVG is interpreted to indicate cold polar condition with dry-based ice. A mixture of MVG and W TAM is interpreted to represent polar conditions and the S TAM facies is interpreted to represent open-marine conditions. Down-core variations in geochemical facies in the AND-1B core are interpreted to represent five major paleoclimate phases over the past 14 Ma. Cold polar conditions with major MVG influence occur below 1045 mbsf and above 120 mbsf. A section of warmer climate conditions with extensive peaks of S TAM influence characterizes the rest of the core, which is interrupted by a section from 525 to 855 mbsf of alternating influences of MVG and W TAM.

Geochemistry on rocks from Shackleton Range

During the GEISHA expedition (Geologische Expedition in die Shackleton Range 1987/88), the Pioneers Escarpment was visited and sampled extensively for the first time. Most of the rock types encountered represent amphibolite facies metamorphics, but evidence for granulite facies conditions was found in cores of garnet. These conditions must have been at least partly reached during the peak of metamorphism. For the Pioneers Escarpment a varicolored succession of sedimentary and bimodal volcanic origin is typical. It comprises: quartzites muscovite quartzite, sericite quartzite, fuchsite quartzite, garnet-quartz schists etc.; pelites: mica schists and plagioclase or plagioclase-microcline gneisses, aluminous schists; marls and carbonates: grey meta-limestones, carbonaceous quartzites, but also pure white, often fine-grained, saccharoidal marble, or a variety of tremolite marble, olivine (forsterite) marble, diopside-clinopyroxene-tremolite marble, etc.; basic volcanic rocks: amphibole fels, amphibolite schist, garnet amphibolite, and acidic to intermediate volcanic rocks: garnet-biotite schist, epidote-biotite-plagioclase gneiss, microcline gneiss. These rocks are considered to be a supracrustal unit, called the Pioneers Group. In the easternmost parts of the Pioneers Escarpment, e.g. at Vindberget, nonmetamorphic shales, sandstones and greywackes crop out, which are cover rocks of possibly Jurassic age. These metasediments, which represent a quartz-pelite-carbonate (QPC) association, indicate that deposition took place on a stable shelf, i.e. on the submerged rim of a craton. Marine shallow-water sedimentation including marls and aluminous clays form the protoliths. The volcanics may be part of a bimodal volcanics-arkose-conglomerate (BVAC) association. Geochemical analyses support the assumption of volcanic protoliths. This is demonstrated especially by the elevated amounts of the immobile, incompatible high-field-strength elements (HFSE) Nb, Ta, Ti, Y, and Zr encountered in some of the gneisses. Microscopic investigation suggests the existence of ortho-amphibolites. This is confirmed by the geochemistry. A bimodal volcanic association is evident. The amphibolites plot in both the tholeiite and calc-alkaline fields. The acidic volcanics are mainly rhyolitic. The sediments and volcanics were subjected to conditions of 10-11 kbar and 600°C during the peak of metamorphism, i.e. granulite facies metamorphism, which can be deduced from the Fe mole ratios of 0.71-0.73 in the garnet cores. Due to the relatively low temperatures, no anatectic melting took placc. The rims of the garnets show a Fe mole ratio of 0.84-0.86, and the coexisting mineral association garnet-biotite-staurolite-kyanite indicate amphibolite facies. The thermobarometry shows P-T conditions of 5-6 kbar and 570-580°C for this stage. The metamorphic history indicates deep burial at depths down to 35 km (subduction?) i.e. high pressure metamorphism, followed by pressure release due to uplift associated with retrograde metamorphism. This may have happened during a pre-Ross metamorphic event or orogeny. The Ross Orogeny at about 500 Ma probably just led to the weak greenschist facies overprint that is evident in the rocks of the Pioneers Group. Finally, sedimentation resumed in the area of the present Shackleton Range, or at least in the eastern part of the Pioneers Escarpment, probably when detritus from erosion of the basement (Read Group and Pioneers Group) was deposited, forming sandstones and greywackes of possibly Jurassic age. There is no indication that these sediments belong to the former Turnpike Bluff Group.

Precious metals and volatiles in rocks of the Mid-Atlantic Ridge near 15°20'N

Distribution patterns of gold, platinum group metals (PGE), and volatile components are studied in the main rock types of the Mid-Atlantic Ridge lithosphere (ultrabasites, gabbro, and basalts) from the transform fracture zone at 15°20'N. It is ascertained that PGE content depends on the reduction degree of fluids, on rock types, and on their formation conditions. It is noted that concentrations of refractory elements (Os, Ir, Rh) decrease, while those of fusible elements (Pt, Pd, Au) increase with depth. The chondrite type of distribution is only noted in the ultrabasite rocks. Increase in water and CO2 contents and in oxidation degree of fluids occurs with transition from basalts to ultrabasites, as well as from normal magmatic systems to fluid-enriched anomalous systems.