Structural determinants of subunit -subunit interactions and subcellular localization of the calcium /calmodulin -dependent protein kinase II

The multifunctional Ca$\sp{2+}$/calmodulin-dependent protein kinase II (CaM kinase) is a Ser/Thr directed protein kinase that participates in diverse Ca$\sp{2+}$ signaling pathways in neurons. The function of CaM kinase depends upon the ability of subunits to form oligomers and to interact with other proteins. Oligomerization is required for autophosphorylation which produces significant functional changes that include Ca$\sp{2+}$/calmodulin-independent activity and calmodulin trapping. Associations with other proteins localize CaM kinase to specific substrates and effectors which serves to optimize the efficiency and speed of signal transduction. In this thesis, we investigate the interactions that underlie the appropriate positioning of CaM kinase activity in cells. We demonstrate that the subcellular distribution of CaM kinase is dynamic in hippocampal slices exposed to anoxic/aglycemic insults and to high K$\sp{+}$-induced depolarization. We determine the localization of CaM kinase domains expressed in neurons and PC-12 cells and find that the C-terminal domain of the $\alpha$ subunit is necessary for localization to dendrites. Moreover, monomeric forms of the enzyme gain access to the nucleus. Attempts made to identify novel CaM kinase binding proteins using the yeast two-hybrid system resulted in the isolation of hundreds of positive clones. Those that have been sequenced are identical to CaM kinase isoforms. Finally, we report the discovery of specific regions within the C-terminal domain that are necessary and sufficient for subunit-subunit interactions. Differences between the $\alpha$ and $\beta$ isoforms were discovered that indicate unique structural requirements for oligomerization. A model for how CaM kinase subunits interact to form holoenzymes and how structural heterogeneity might influence CaM kinase function is presented. ^

The yeast STM1 protein binds G*G multiplex nucleic acids in vitro and associates with ribosomes in vivo

The formation of triple helical, or triplex DNA has been suggested to occur in several cellular processes such as transcription, replication, and recombination. Our laboratory previously found proteins in HeLa nuclear extracts and in S. cerevisiae whole cell extracts that avidly bound a Purine-motif (Pu) triplex probe in gel shift assays, or EMSA. In order to identify a triplex DNA-binding protein, we used conventional and affinity chromatography to purify the major Pu triplex-binding protein in yeast. Peptide microsequencing and data base searches identified this protein as the product of the STM1 gene. Confirmation that Stm1p is a Pu triplex-binding protein was obtained by EMSA using both recombinant Stm1p and whole cell extracts from stm1Δ yeast. Stm1p had previously been identified as G4p2, a G-quartet DNA- and RNA-binding protein. To study the cellular role and identify the nucleic acid ligand of Stm1p in vivo, we introduced an HA epitope at either the N- or C-terminus of Stm1p and performed immunoprecipitations with the HA.11 mAb. Using peptide microsequencing and Northern analysis, we positively identified a subset of both large and small subunit ribosomal proteins and all four rRNAs as associating with Stm1p. DNase I treatment did not affect the association of Stm1p with ribosomal components, but RNase A treatment abolished the association with all ribosomal proteins and RNA, suggesting this association is RNA-dependent. Sucrose gradient fractionation followed by Western and EMSA analysis confirmed that Stm1p associates with intact 80S monosomes, but not polysomes. The presence of additional, unidentified RNA in the Stm1p-immunoprecipitate, and the absence of tRNAs and elongation factors suggests that Stm1p binds RNA and could be involved in the regulation of translation. Immunofluorescence microscopy data showed Stm1p to be located throughout the cytoplasm, with a specific movement to the bud during the G2 phase of the cell cycle. A dramatically flocculent, large cell phenotype is observed when Stm1p has a C-terminal HA tag in a protease-deficient strain background. When STM1 is deleted in this background, the same phenotype is not observed and the deletion yeast grow very slowly compared to the wild-type. These data suggest that STM1 is not essential, but plays a role in cell growth by interacting with an RNP complex that may contain G*G multiplex RNA. ^

Mineralogy and nannoplankton distribution in ODP Hole 194-1195A

Significant synchronous shifts in the chemistry, mineralogy, grain sizes and color of the sediments at 6 m below sea floor (mbsf) at ODP Site 1195 on the Marion Plateau (NE Australia) are interpreted to reflect a major regional paleoceanographic change: the initiation of the southern province of the Great Barrier Reef (GBR). The onset of this massive carbonate production centre nearby resulted primarily in increased deposition of carbonate-rich sediments of neritic origin. Both sedimentation rate and terrigenous input record a coincident decline attributed to inshore trapping of materials behind the reefs. Our best estimate places the development of reef framework in the southern part of the GBR between 560 and 670 kyr B.P., based on an age model combining magnetostratigraphic and biostratigraphic data. The proposed estimation agrees with previous studies reporting an age between 500 and 930 kyr B.P., constraining more tightly their results. However, it does not support research placing the birth of the GBR in Marine Isotope Stage (MIS) 11 (~400 kyr), nor the theory of a worldwide modern barrier reef development at that time.

Chemical composition and elemental oxide ratios to AI2O3 of bulk solids at DSDP Leg 64 Holes

Analyses of sediments from Leg 64 sites reveal a diverse and in one case unique geochemistry. Sites are characterized by high heat flow along an active, divergent plate boundary, or rapid accumulation of diatom muds, or both. The geochemical trends of Sites 474-476 at the tip of Baja California reflect changes4n the percentages of sedimentary components - particularly biogenous matter and mineralogy - that support interpretations of sedimentary environments inferred to be present since the commencement of subsidence along this young, passive continental margin. The sediments below dolerite sills in Holes 477, 477A, 478, and 481 show major mineralogic and chemical deviations from "average" hemipelagic sediments. The sills appear to have two functions: (1) they allow hydrothermal circulation and metamorphism in a partially closed system by trapping heat and fluids emanating from below, and (2) they expel heated interstitial fluids at the moment of intrusion and mobilize elements, most likely leading to the formation of metalliferous deposits along the surface traces of normal faults in the basin. The hydrothermal system as a whole appears to be localized and ephemeral, as is indicated by the lack of similar geochemical trends and high heat flow at Sites 478 and 481. Site 479 illustrates sedimentation in an oxygen-minimum zone with anoxic sediments and concomitant geochemical trends, especially for MnO. With few exceptions, geochemical trends are remarkably constant with depth, suggesting that Site 479 can serve as an "internal" standard or average sediment against which the magnitude of hydrothermal alteration at the basinal Sites 477, 478, and 481 can be measured.

AFLP data based on presence (1) and absence (0) of AFLP loci (A4-F171) in Gonyostomum semen

Many recent studies have found genetically differentiated populations in microorganisms despite potentially high dispersal. We designed a study to specifically examine the importance of physical dispersal barriers, i.e. geographic distance and lack of hydrological connectivity, in restricting gene flow and enhancing divergence in limnic microorganisms. We focused on the nuisance microalga Gonyostomum semen, which has recently expanded in northern Europe and differentiated into genetically distinct populations. Gonyostomum semen was sampled from six lakes distributed in two adjacent watersheds, which thereby comprised, both connected and non-connected lakes. The individual isolates were genotyped by Amplified Fragment Length Polymorphism. Several lake populations were differentiated from each other, but connectivity within watersheds could not explain the observed population genetic pattern. However, isolation by distance was moderate and might limit the gene flow among distant populations. In addition, we found low, but significant linkage disequilibrium, which indicates regular sexual recombination in this species, despite its high degree of asexual reproduction. Therefore, we conclude that the genetic properties of microalgae with occasional sexual reproduction essentially mirror regularly recombining species. Furthermore, the data indicated bottlenecks supporting the hypothesized recent range expansion of this species.

Hexachlorocyclohexanes concentration in air and ocean water

Hexachlorocyclohexanes (HCHs) are ubiquitous organic pollutants derived from pesticide application. They are subject to long-range transport, persistent in the environment, and capable of accumulation in biota. Shipboard measurements of HCH isomers (a-, b- and g-HCH) in surface seawater and boundary layer atmospheric samples were conducted in the Atlantic and the Southern Ocean in October to December of 2008. SumHCHs concentrations (the sum of a-, g- and b-HCH) in the lower atmosphere ranged from 12 to 37 pg/m**3 (mean: 27 ± 11 pg/m**3) in the Northern Hemisphere (NH), and from 1.5 to 4.0 pg/m**3 (mean: 2.8 ± 1.1 pg/m**3) in the Southern Hemisphere (SH), respectively. Water concentrations were: a-HCH 0.33-47 pg/l, g-HCH 0.02-33 pg/l and b-HCH 0.11-9.5 pg/l. Dissolved HCH concentrations decreased from the North Atlantic to the Southern Ocean, indicating historical use of HCHs in the NH. Spatial distribution showed increasing concentrations from the equator towards North and South latitudes illustrating the concept of cold trapping in high latitudes and less interhemispheric mixing process. In comparison to concentrations measured in 1987-1999/2000, gaseous HCHs were slightly lower, while dissolved HCHs decreased by factor of 2-3 orders of magnitude. Air-water exchange gradients suggested net deposition for a-HCH (mean: 3800 pg/m**2/day) and g-HCH (mean: 2000 pg/m**2/day), whereas b-HCH varied between equilibrium (volatilization: <0-12 pg/m**2/day) and net deposition (range: 6-690 pg/m**2/day). Climate change may significantly accelerate the release of "old" HCHs from continental storage (e.g. soil, vegetation and high mountains) and drive long-range transport from sources to deposition in the open oceans. Biological productivities may interfere with the air-water exchange process as well. Consequently, further investigation is necessary to elucidate the long term trends and the biogeochemical turnover of HCHs in the oceanic environment.

(Table T1) Fluid inclusions in siltstone and sandstone grains from ODP Hole 210-1276A

Twenty samples of siltstones and sandstones were taken from Ocean Drilling Program Site 1276 during Leg 210 for fluid inclusion studies. With the exception of one sample of vein calcite, all inclusions were in quartz grains. The results of fluid-inclusion petrology and microthermometry indicate the presence of three fluid inclusion types (Types 1, 2, and 3). Type 1 fluid inclusions are two-phase (liquid + vapor) aqueous inclusions, and Type 2 inclusions are monophase fluid inclusions (liquid or vapor). These are common in all samples and are formed either as primary isolated inclusions or as secondary inclusions as trails along annealed fractures in the grain. Type 3 fluid inclusions are three-phase (liquid + vapor + solid) inclusions. Type 3 inclusions are rare and are observed as isolated inclusions or in a cluster with other types (i.e., Types 1 and 2). The predominant population throughout the different units sampled is two-phase (liquid + vapor) aqueous fluid inclusions (i.e., Type 1). The temperature of homogenization (TH) bivariate plots for Type 1 inclusions shows dominance throughout the hole of low- to medium-salinity fluids with minimum trapping temperatures between 150° and 400°C.

Bromine and iodine concentrations in sediments and pore fluids of ODP Leg 112

At the Peruvian convergent margin, two distinct pore fluid regimes are recognized from differences in their Cl- concentrations. The slope pore fluids are characterized by low Cl- concentrations, but elevated Br- and I- concentrations due to biogenic production. The shelf pore fluids exhibit elevated Cl- and Br- concentrations due to diffusive mixing with an evaporitic brine. In the slope pore fluids, the Br-, I-, and NH4+ concentrations are elevated following bacterial decomposition of organic matter, but the I- concentrations are in excess of those expected based on mass balance calculations using NH4+ and Br- concentrations. The slope sediment organic matter, which is enriched in iodine from oxidationreduction processes at the oxygenated sediment-water interface, is responsible for this enrichment. The increases in dissolved I- and the I- enrichments relative to NH4+ and Br- correlate well with sedimentation rates because of differential trapping following regeneration. The pore-fluid I-/Br- ratios suggest that membrane ion fiitration is not a major cause of the decreases in Cl- concentrations. Other possible sources for low Cl- water, including meteoric water, clathrate dissociation, and/or mineral dehydration reactions, imply that the diluting component of the slope low-Cl- fluids has flowed at least 1 km through the sediment. The low bottom-water oxygenation in the shelf is responsible for the low (if any) enrichment of iodine in the shelf sediments. Fluctuations in bottom-water oxygen concentrations in the past, however, may be responsible for the observed variations in the sediment I/Br ratios. Comparison of Na+/Cl- and Br-/Cl- molar ratios in the pore fluids shows that the shelf high-Cl- fluid formed from mixing with a brine that formed from seawater concentrated by twelve to nineteen times and probably was modified by halite dissolution. This dense brine, located below the sediment sections drilled, appears to have flowed a distance >500 km through the sediment.

Chemical composition and fluxes of deep sea suspended matter within and over the 9°50'N hydrothermal field, EPR

Results of geochemical studies of suspended matter from the water mass over the hydrothermal field at 9°50'N on the East Pacific Rise are reported. The suspended matter was sampled in background waters, in the buoyant plume, and in the near-bottom waters. Contents of Si, Al, P, Corg, Fe, Mn, Cu, Zn, Ni, Co, As, Cr, Cd, Pb, Ag, and Hg were determined. No definite correlations were found between the elements in the background waters. Many of the chemical elements correlated with Fe and associated with its oxyhydroxides in the buoyant plume. In the near-bottom waters trace elements are associated with Fe, Zn, and Cu (probably, with their sulfides formed during mixing of hydrothermal fluids with seawater). Chemical composition of sediment matter precipitated in a sediment trap was similar to the near-bottom suspended matter.

Permeability measurements on sheared and unsheared samples from different IODP Holes of Leg 316 and from IODP Hole 315-C0001E and ODP Hole 190-1174B

At subduction zones, the permeability of major fault zones influences pore pressure generation, controls fluid flow pathways and rates, and affects fault slip behavior and mechanical strength by mediating effective normal stress. Therefore, there is a need for detailed and systematic permeability measurements of natural materials from fault systems, particularly measurements that allow direct comparison between the permeability of sheared and unsheared samples from the same host rock or sediment. We conducted laboratory experiments to compare the permeability of sheared and uniaxially consolidated (unsheared) marine sediments sampled during IODP Expedition 316 and ODP Leg 190 to the Nankai Trough offshore Japan. These samples were retrieved from: (1) The décollement zone and incoming trench fill offshore Shikoku Island (the Muroto transect); (2) Slope sediments sampled offshore SW Honshu (the Kumano transect) ~ 25 km landward of the trench, including material overriden by a major out-of-sequence thrust fault, termed the "megasplay"; and (3) A region of diffuse thrust faulting near the toe of the accretionary prism along the Kumano transect. Our results show that shearing reduces fault-normal permeability by up to 1 order of magnitude, and this reduction is largest for shallow (< 500 mbsf) samples. Shearing-induced permeability reduction is smaller in samples from greater depth, where pre-existing fabric from compaction and lithification may be better developed. Our results indicate that localized shearing in fault zones should result in heterogeneous permeability in the uppermost few kilometers in accretionary prisms, which favors both the trapping of fluids beneath and within major faults, and the channeling of flow parallel to fault structure. These low permeabilities promote the development of elevated pore fluid pressures during accretion and underthrusting, and will also facilitate dynamic hydrologic processes within shear zones including dilatancy hardening and thermal pressurization.

Average compositions and analyses range for clinopyroxene, olivines, orthopyroxene, and spinel from the MARK area at DSDP Site 45-395A, and ODP Site 153-920

Mineral compositions of residual peridotites collected at various locations in the Mid-Atlantic Ridge south of the Kane transform (MARK area) are consistent with generally smaller degrees of melting in the mantle near the large offset Kane transform than near the other, small offset, axial discontinuities in the area. We propose that this transform fault effect is due to along-axis variations in the final depth of melting in the subaxial mantle, reflecting the colder thermal regime of the ridge near the Kane transform. Calculations made with a passive mantle flow regime suggest that these along-axis variations in the final depth of melting would not produce the full range of crustal thickness variations observed in the MARK area seismic record. It is therefore likely that the transform fault effect in the MARK area is combined with other mechanisms capable of producing crustal thickness variations, such as along-axis melt migration, the trapping of part of the magma in a cold mantle root beneath the ridge, or active mantle upwelling.

European mink (Mustela lutreola) and American mink (Neovison vison) detection histories in Northern Spain between 2000 and 2011

Understanding changes over time in the distribution of interacting native and invasive species that may be symptomatic of competitive exclusion is critical to identify the need for and effectiveness of management interventions. Occupancy models greatly increase the robustness of inference that can be made from presence/absence data when species are imperfectly detected, and recent novel developments allow for the quantification of the strength of interaction between pairs of species. We used a two-species multi-season occupancy model to quantify the impact of the invasive American mink on the native European mink in Spain through the analysis of their co-occurrence pattern over twelve years (2000 - 2011) in the entire Spanish range of European mink distribution, where both species were detected by live trapping but American mink were culled. We detected a negative temporal trend in the rate of occupancy of European mink and a simultaneous positive trend in the occupancy of American mink. The species co-occurred less often than expected and the native mink was more likely to become extinct from sites occupied by the invasive species. Removal of American mink resulted in a high probability of local extinction where it co-occurred with the endemic mink, but the overall increase in the probability of occupancy over the last decade indicates that the ongoing management is failing to halt its spread. More intensive culling effort where both species co-exist as well as in adjacent areas where the invasive American mink is found at high densities is required in order to stop thedecline of European mink.

Extensive boiling as a precipitation mechanism for precious and base metal ores, Bienaventurada Mine, Huancavelica, Perú

The Bienaventurada mine operates a polymetallic Ag-Pb-Zn (Cu, Au) vein system of the low sulphidation epithermal type. Fluid inclusions, FI, are abundant in quartz, sphalerite and adularia. FI petrography demonstrates typical primary growth zoning which occurs frequently in crystalline quartz, and defines the most common primary FI. These are usually very small, but several types of primary, P, and secondary, S, FI Assemblages (FIAs) comprising FI of measurable size (3 to > 100 μm) can also be identified through careful petrographic work. The fluids are aqueous and undersaturated, and no evidence of CO2 was found; the degree of fill is usually high (~70-80 %) in the L-rich inclusions, but extremely low in V-rich inclusions. The measured microthermometric values are very consistent in the FIAs selected; they are for the most part roughly similar in the P and S assemblages: the median is typically ~258ºC for total homogenization temperatures, Th, and -1.5 ºC for ice melting temperatures, Tm (corresponding to 2.57 wt% NaCl eq). The widespread occurrence of L-rich and V-rich FI in the same FIA and the consistent Th values point to an extensive boiling system along the vein. In these conditions, Th equals T of trapping, and the ores are assumed to have been precipitated from an aqueous low salinity boiling fluid, of likely meteoric origin, at some 250-280º C, under ~500 m hydrostatic head.

Comparison of experimental and numerical sloshing loads in partially filled tanks

Sloshing describes the movement of liquids inside partially filled tanks, generating dynamic loads on the tank structure. The resulting impact pressures are of great importance in assessing structural strength, and their correct evaluation still represents a challenge for the designer due to the high level of nonlinearities involved, with complex free surface deformations, violent impact phenomena and influence of air trapping. In the present paper, a set of two-dimensional cases, for which experimental results are available, is considered to assess the merits and shortcomings of different numerical methods for sloshing evaluation, namely two commercial RANS solvers (FLOW-3D and LS-DYNA), and two academic software (Smoothed Particle Hydrodynamics and RANS). Impact pressures at various critical locations and global moment induced by water motion in a partially filled rectangular tank, subject to a simple harmonic rolling motion, are evaluated and predictions are compared with experimental measurements. 2012 Copyright Taylor and Francis Group, LLC.

Effects of the 4N(v) chromosome from Aegilops ventricosa on agronomic and quality traits in bread wheat

Advanced wheat lines carrying the Hessian fly resistance gene H27 were obtained by backcrossing the wheat/Aegilops ventricosa introgression line, H-93-33, to commercial wheat cultivars as recurrent parents. The Acph-N v 1 marker linked to the gene H27 on the 4Nv chromosome of this line was used for marker assisted selection. Advanced lines were evaluated for Hessian fly resistance in field and growth chamber tests, and for other agronomic traits during several crop seasons at different localities of Spain. The hessian fly resistance levels of lines carrying the 4Nv chromosome introgression (4D/4Nv substitution and recombination lines that previously were classified by in situ hybridisation) were high, but always lower than that of their Ae. ventricosa progenitor. Introgression lines had higher grain yields in infested field trials than those without the 4Nv chromosome and their susceptible parents, but lower grain yields under high yield potential conditions. The 4Nv introgression was also associated with later heading, and lower tiller and grain numbers/m2 . In addition, it was associated with longer and more lax spikes, and higher values of grain weight and grain protein content. However, the glutenin and gliadin expression, as well as the bread-making performance, were similar to those of their recurrent parents