Application of stellar photometry to the analysis of microarray images

Improvements in the analysis of microarray images are critical for accurately quantifying gene expression levels. The acquisition of accurate spot intensities directly influences the results and interpretation of statistical analyses. This dissertation discusses the implementation of a novel approach to the analysis of cDNA microarray images. We use a stellar photometric model, the Moffat function, to quantify microarray spots from nylon microarray images. The inherent flexibility of the Moffat shape model makes it ideal for quantifying microarray spots. We apply our novel approach to a Wilms' tumor microarray study and compare our results with a fixed-circle segmentation approach for spot quantification. Our results suggest that different spot feature extraction methods can have an impact on the ability of statistical methods to identify differentially expressed genes. We also used the Moffat function to simulate a series of microarray images under various experimental conditions. These simulations were used to validate the performance of various statistical methods for identifying differentially expressed genes. Our simulation results indicate that tests taking into account the dependency between mean spot intensity and variance estimation, such as the smoothened t-test, can better identify differentially expressed genes, especially when the number of replicates and mean fold change are low. The analysis of the simulations also showed that overall, a rank sum test (Mann-Whitney) performed well at identifying differentially expressed genes. Previous work has suggested the strengths of nonparametric approaches for identifying differentially expressed genes. We also show that multivariate approaches, such as hierarchical and k-means cluster analysis along with principal components analysis, are only effective at classifying samples when replicate numbers and mean fold change are high. Finally, we show how our stellar shape model approach can be extended to the analysis of 2D-gel images by adapting the Moffat function to take into account the elliptical nature of spots in such images. Our results indicate that stellar shape models offer a previously unexplored approach for the quantification of 2D-gel spots. ^

Effects of salinity, temperature and cadmium stress on cadmium -binding protein in the grass shrimp, {\it Palaemonetes pugio}

The combined effects of salinity, temperature and cadmium stress on survival and adaptation through cadmium-binding protein (CdBP) accumulation were studied in the grass shrimp, Palaemonetes pugio. In 96-hour bioassays, shrimp were exposed to zero or one of three levels of cadmium, under one of six different salinity (15, 25, or 35$\perthous$) and temperature (20 or 30$\sp\circ$C) regimes. CdBP concentrations were quantified in survivors from the 24 exposure groups. Salinity and temperature did not affect survivorship unless the shrimp were also exposed to cadmium. Grass shrimp were most sensitive to cadmium at low salinity-high temperature, and least sensitive at high salinity-low temperature. The incidence of cadmium-associated black lesions in gill tissue was influenced by salinity and temperature stress. P. pugio produced a 10,000 dalton metallothionein-like CdBP when exposed to at least 0.1 mg Cd$\sp{2+}$/L for 96 hours. Accumulation of CdBP was increased with increases in the exposure cadmium level, increases in temperature and decreases in salinity, independently and in conjunction with one another. Maximum CdBP concentrations occurred in grass shrimp that survived the salinity-temperature-cadmium conditions creating maximum stress as measured by highest mortality, not necessarily in shrimp exposed to the highest cadmium levels. The potential utility of this method as a monitor of physiological stress in estuarine biota inhabiting metal-polluted environments is discussed. ^

Organic temperature proxies in the subpolat region around Iceland

Subpolar regions are key areas to study natural climate variability, due to their high sensitivity to rapid environmental changes, particularly through sea surface temperature (SST) variations. Here, we have tested three independent organic temperature proxies (UK'37, TEX86 and LDI) on their potential applicability for SST reconstruction in the subpolar region around Iceland. UK'37, TEX86 and TEXL86 temperature estimates from suspended particulate matter showed a substantial discrepancy with instrumental data, while long chain alkyl diols were below detection limit in most of the stations. In the northern Iceland Basin, sedimenting particles revealed a seasonality in lipid fluxes i.e. high fluxes of alkenones and GDGTs were measured during late spring-summer, and high fluxes of long chain alkyl diols during late summer. The flux-weighted average temperature estimates had a significant negative (ca. 2.3°C for UK'37) and positive (up to 5°C for TEX86) offset with satellite-derived SSTs and temperature estimates derived from the underlying surface sediment. UK'37 temperature estimates from surface sediments around Iceland correlate well with summer mean sea surface temperatures, while TEX86 derived temperatures correspond with both annual and winter mean 0-200 m temperatures, suggesting a subsurface temperature signal. Anomalous LDI-SST values in surface sediments, and low mass flux of 1,13- and 1,15-diols compared to 1,14-diols, suggest that Proboscia diatoms are the major sources of long chain alkyl diols in this area rather than eustigmatophyte algae, and therefore the LDI cannot be applied in this region.

Magnetic properties and chemical composition at DSDP Hole 77-538A

Magnetic properties of doleritic and some metamorphic basement rocks underlying Catoche Knoll are studied. Doleritic rocks show a high saturation magnetic moment (2-5 emu/g) compared to metamorphic rocks (0.1-1 emu/g). Magnetic minerals of rocks from this hole show a high stability when heated in vacuo up to 600°C at a fixed rate of heating. Curie temperatures are distributed close to 550°C. These properties differ markedly from those of common submarine basalts observed before. X-ray microprobe analysis techniques were used to determine internal structures of ferromagnetic minerals; in most of ferromagnetic minerals there exist two different types of magnetic phases (i.e., products of high-temperature and low-temperature oxidations). Interpretations on the coexisting, seemingly contradictory, phases can be made based upon present analyses.

Effects of increased CO2 concentration on nutrient limited coastal summer plankton depend on temperature

Increasing seawater temperature and CO2 concentrations both are expected to increase coastal phytoplankton biomass and carbon to nutrient ratios in nutrient limited seasonally stratified summer conditions. This is because temperature enhances phytoplankton growth while grazing is suggested to be reduced during such bottom-up controlled situations. In addition, enhanced CO2 concentrations potentially favor phytoplankton species, that otherwise depend on costly carbon concentrating mechanisms (CCM). The trophic consequences for consumers under such conditions, however, remain little understood. We set out to experimentally explore the combined effects of increasing temperature and CO2 concentration for phytoplankton biomass and stoichiometry and the consequences for trophic transfer (here for copepods) on a natural nutrient limited Baltic Sea summer plankton community. The results show, that warming effects were translated to the next trophic level by switching the system from a bottom-up controlled to a mainly top-down controlled one. This was reflected in significantly down-grazed phytoplankton and increased zooplankton abundance in the warm temperature treatment (22.5°C). Additionally, at low temperature (16.5°C) rising CO2 concentrations significantly increased phytoplankton biomass. The latter effect however, was due to direct negative impact of CO2 on copepod nauplii which released phytoplankton from grazing in the cold but not in the warm treatments. Our results suggest that future seawater warming has the potential to switch trophic relations between phytoplankton and their grazers under nutrient limited conditions with the consequence of potentially disguising CO2 effects on coastal phytoplankton biomass.

Geochemistry of mafic clasts of ODP Holes 125-778A and 125-779A

Clasts of metamorphosed mafic igneous rock of diverse composition were recovered in two drill sites on a serpentine mud volcano in the outer Mariana forearc during Ocean Drilling Program Leg 125. These clasts are xenolithic fragments that have been entrained in the rising serpentine mud, and make up less that 9% of the total rock recovered at Sites 778 and 779. Most samples are metabasalt or metadiabase, although one clast of possible boninite and one cumulate gabbro were recovered. On the basis of trace element signatures, samples are interpreted to represent both arc-derived and mid-ocean ridge-derived compositions. Rocks with extremely low TiO2 (<0.3 wt%) and Zr (<30 ppm) are similar to boninite series rocks. Samples with low TiO2 (<0.9 wt%) and Zr (<50 ppm) and extreme potassium enrichment (K2O/Na2O >3.9) may represent island arc rocks similar to shoshonites. However, the K2O/Na2O ratios are much higher than those reported for shoshonites from modem or ancient arcs and may be the result of metamorphism. Samples with moderate TiO2 (1.4 to 1.5 wt%) and Zr (72 to 85 ppm) are similar to rocks from mid-ocean ridges. A few samples have TiO2 and Zr intermediate between island arc and mid-ocean ridge basalt-like rocks. Two samples have high iron (Fe2O3* = >12.8 to 18.5 wt%) (Fe2O3* = total iron calculated as Fe2O3) and TiO2 (>2.3 wt%) and resemble FeTi basalt recovered from mid-ocean ridges. Metamorphism in most samples ranges from low-temperature zeolite, typical of ocean floor weathering, to prehnite-pumpellyite facies and perhaps lower greenschist. Blue amphibole and lawsonite minerals are present in several samples. One diabase clast (Sample 9) exhibits Ca enrichment, similar to rodingite metamorphism, typical of mafic blocks in serpentinized masses. The presence of both low-grade (clays and zeolites) and higher grade (lawsonite) metamorphism indicates retrograde processes in these clasts. These clasts are fragments of the forearc crust and possibly of the subducting plate that have been entrained in the rising serpentine and may represent the deepest mafic rocks ever recovered from the Mariana forearc. The variable compositions and degree of metamorphism of these clasts requires at least two tectonic origins. The recovery of clasts with mid-ocean ridge and arc chemical affinities in a single drill hole requires these clasts to have been "mixed" on a small scale either (1) in the forearc crustal sequence, or (2) after inclusion in the rising serpentine mud. The source of the MORB-like samples and an explanation for the presence of both MORB-like and arc-like rocks in close proximity is critical to any model of the evolution of the Mariana forearc. The source of the MORB-like samples likely will be one (or more) of the following: (1) accretion of Pacific plate lithosphere, (2) remnants of original forearc crust (trapped plate), (3) volcanism in the supra-subduction zone (arc or forearc) environment, or (4) derivation from the subducting slab by faulting along the dÈcollement.

Curie temperatures and cell edges of ODP Leg 120 samples (Table 1)

Basalt samples recovered on Ocean Drilling Program Leg 120 from the Kerguelen Plateau were investigated by thermomagnetic analysis, X-ray diffraction, and ore microscopy. The basement samples could be divided into two groups based on Curie temperatures, cell-edge parameters, and optical magnetic mineralogy. Samples from Sites 748 and 750 underwent only low-temperature oxidation and displayed Curie temperatures for the titanomaghemites that ranged from 340° to 395°C. The basalts from Sites 747 and 749 mainly experienced high-temperature oxidation. High-temperature oxidation produced titanium-poor titanomagnetites with ilmenite-exsolution lamellae. Curie temperatures of the deuterically oxidized titanomaghemites varied from 490° to 620°C.

Age and chemical composition of apatites from five DSDP and ODP Sites in the Pacific, Atlantic and Indian Oceans

Since studies on deep-sea cores were carried out in the early 1990s it has been known that ambient temperature may have a marked affect on apatite fission track annealing. Due to sluggish annealing kinetics, this effect cannot be quantified by laboratory annealing experiments. The unknown amount of low-temperature annealing remains one of the main uncertainties for extracting thermal histories from fission track data, particularly for samples which experienced slow cooling in shallow crustal levels. To further elucidate these uncertainties, we studied volcanogenic sediments from five deep-sea drill cores, that were exposed to maximum temperatures between ~10° and 70°C over geological time scales of ~15-120 Ma. Mean track lengths (MTL) and etch pit diameters (Dpar) of all samples were measured, and the chemical composition of each grain analyzed for age and track length measurements was determined by electron microprobe analysis. Thermal histories of the sampled sites were independently reconstructed, based on vitrinite reflectance measurements and/or 1D numerical modelling. These reconstructions were used to test the most widely used annealing models for their ability to predict low-temperature annealing. Our results show that long-term exposure to temperatures below the temperature range of the nominal apatite fission track partial annealing zone results in track shortening ranging between 4 and 11%. Both chlorine content and Dpar values explain the downhole annealing patterns equally well. Low chlorine apatite from one drill core revealed a systematic relation between Si-content and Dpar value. The question whether Si-substitution in apatite has direct and systematic effects on annealing properties however, cannot be addressed by our data. For samples, which remained at temperatures <30°C, and which are low in chlorine, the Laslett et al. [Laslett G., Green P., Duddy I. and Gleadow A. (1987) Thermal annealing of fission tracks in apatite. Chem. Geol. 65, 1-13] annealing model predicts MTL up to 0.6 µm longer than those actually measured, whereas for apatites with intermediate to high chlorine content, which experienced temperatures >30°C, the predictions of the Laslett et al. (1987) model agree with the measured MTL data within error levels. With few exceptions, predictions by the Ketcham et al. [Ketcham R., Donelick R. and Carlson W. (1999) Variability of apatite fission-track annealing kinetics. III: Extrapolation to geological time scales. Am. Mineral. 84/9, 1235-1255] annealing model are consistent with the measured data for samples which remained at temperatures below ~30°C. For samples which experienced maximum temperatures between ~30 and 70°C, and which are rich in chlorine, the Ketcham et al. (1999) model overestimates track annealing.

Chemical composition of hydrothermal sulfide minerals from the Rainbow, Logachev-1, and Logachev-2 hydrothermal fields

Composition of ore minerals in MAR sulflde occurrences related to ultramaflc rocks was studied using methods of mineragraphy, electron microscopy, microprobe analysis, and X-ray analysis. Objects are located at various levels of maturity of sulflde mounds owing to differences in age, duration and degree of activity of the following hydrothermal systems: generally inactive Logatchev-1 field (up to 66.5 ka old), inactive Logatchev-2 field (3.9 ka), and generally active Rainbow field (up to 23 ka). Relative to MAR submarine ore occurrences in the basalt substrate, mineralization in the hydrothermal fields mentioned above is characterized by high contents of Au, Cd, Co, and Ni, along with presence of accessory minerals of Co and Ni. The studied mounds differ in quantitative ratios of major minerals and structural-textural features of ores that suggest their transformation. Ores in the Logatchev-1 field are characterized by the highest Cu content and development of a wide range of multistage contrast exsolution structures of isocubanite and bornite. In the Logatchev-2 field, sphalerite-chalcopyrite and gold-arsenic exsolution structures are present, but isocubanite exsolution structures are less diverse and contrast. The Rainbow field is marked by presence of homogenous isocubanite and the subordinate development of exsolution structures. The authors have identified four new phases in the Cu-Fe-S system. Phases X and Y (close to chalcopyrite and isocubanite, respectively) make up lamellae among isocubanite exsolution products in the Logatchev-1 and Logatchev-2 fields. Phase Y includes homogenous zones in zonal chimneys of the Rainbow field. Phases A and B formed in the orange bornite domain at low-temperature alteration of chalcopyrite in the Logatchev-1 field. Mineral assemblages of the Cu-S system are most abundant and diverse in the Logatchev-1 field, but their development is minimal in the Logatchev-2 field where mainly Cu-poor sulfides of the geerite-covellite series have been identified. Specific features of mineral assemblages mentioned above reflect the maturity grade of sulfide mounds and can serve as indicators of maturity.

Petrology and geochemistry of oceanic intraplate sheet-flow basalts at DSDP Hole 89-462A

Reentry of Hole 462A during Leg 89 resulted in the penetration of a further 140 m of basalt sheet-flows similar to those found during Leg 61 at the same site. Twelve volcanic units (45 to 56) were recognized, comprising a series of rapidly extruded, interlayered aphyric and poorly clinopyroxene-plagioclase-olivine phyric, nonvesicular basalts. All exhibit variable, mild hydration and oxidation, relative to fresh oceanic basalts, produced under reducing, low-CO2-activity conditions within the zeolite facies. Secondary assemblages are dominated by smectites, zeolites, and pyrite, produced by low-temperature reaction with poorly oxygenated seawater. No systematic mineralogical or chemical changes are observed with depth, although thin quenched units and more massive hypocrystalline units exhibit slightly different alteration parageneses. Chemically, the basalts are olivine- and quartz-normative tholeiites, characterized by low incompatible-element abundances, similar to mildly enriched MORB (approaching T-type), with moderate, chrondite-normalized, large-ionlithophile- element depletion patterns and generally lower or near-chrondritic ratios for many low-distribution-coefficient (KD) element pairs. In general, relative to cyclic MORB chemical variation, they are uniform throughout, although 3 chemical megagroups and 22 subgroups are recognized. It is considered that the megagroups represent separate low-pressure-fractionated systems (olivine + Plagioclase ± clinopyroxene), whereas minor variations within them (subgroups) indicate magma mixing and generation of near-steady-state conditions. Overall, relatively minor fractionation coupled with magma mixing produced a series of compositionally uniform lavas. Parental melts were produced by similar degrees of partial melting, although the source may have varied slightly in LIL-element content.

Petrographic description and geochemistry of basalts and altered volcanic rocks from ODP Leg 183 sites

The basalts recovered during Legs 183 and 120 from the southern, central, and northernmost parts of the Kerguelen Plateau (Holes 1136A, 1138A, 1140A, and 747C, respectively), as well as those recovered from the eastern part of the crest of Elan Bank (Hole 1137A), represent derivates from tholeiitic melts. In the northern part of the Kerguelen Plateau (Hole 1140A), basalts may have formed from two sources located at different depths. This is reflected in the presence of both low- and high-titanium basalts. The basalts are variably altered by low-temperature hydrothermal processes (at temperatures up to 120°C), and some are affected by subaerial weathering. The hydrothermal alteration led mainly to the formation of smectites, chlorite minerals, mixed-layer hydromica-smectite and smectite-chlorite minerals, hydromica, serpentine(?), clinoptilolite, heulandite, stilbite, analcime, mordenite, thomsonite, natrolite(?), calcite, quartz, and dickite(?). Alteration of extrusive basalts is mainly related to horizontal fluid flow within permeable contact zones between lava flows. Under a nonoxidizing environment of alteration, the tendency to lose most of elements, including rare earth elements, from basalts dominates. Under on oxidizing environment, basalts accumulate many elements.

Major, trace and rare earth elements and minerals at DSDP Legs 69-70 Holes

We obtained major and trace element data on 113 samples from basalts drilled during DSDP Legs 69 and 70 in the Costa Rica Rift area. The majority have major and trace element characteristics typical of ocean-ridge tholeiities. Most of the basalts are relatively MgO rich (MgO > 8 wt.%) and have Mg values (MgO/MgO + 0.85FeO x 100) of about 53, characteristics that clearly indicate that the various magmas underwent only a small amount of crystal fractionation before being erupted onto the seafloor. According to their normative mineralogies, the rocks are olivine tholeiites. A few samples plot close to the diopside-hypersthene join of the projected basalt tetrahedron. Except for basalts from two thin intervals in Hole 504B, which differ significantly from all the other basalts of the hole, practically no chemical downhole variation could be established. In the two exceptional intervals, both TiO2 and P2O5 contents are markedly enriched among the major oxides. The trace elements in these intervals are distinguished by relatively high contents of magmatophile elements and have flat to enriched chondrite-normalized distribution patterns of light rare earth elements (LREE). Most of the rocks outside these intervals are strongly depleted in large-ionlithophile (LIL) elements and LREE. We offer no satisfactory hypothesis for the origin of these basalts at this time. They might have originated within pockets of mantle materials that were more primitive than the LIL-element-depleted magmas that were the source of the other basalts. A significant change with depth in the type of alteration occurs in the 561 meters of basalt cored in Hole 504B. According to the behavior of such alteration-sensitive species as K2O, H2O-, CO2, S, Tl, and the iron oxidation ratio, the alteration is oxidative in the upper part and nonoxidative or even reducing in the lower part. The oxidative alteration may have resulted from low temperature basalt/seawater interaction, whereas hydrothermal solutions may be responsible for the nonoxidative alteration.

Magnetic properties of basalts from DSDP Hole 69-504B

The NRM intensity, AF demagnetization characteristics, hysteresis parameters, initial susceptibility, and thermomagnetic characteristics of 18 basalt specimens from Deep Sea Drilling Project Hole 504B were determined. In six samples, the grain size was large enough to allow microprobe analysis. We conclude (1) that the dominant magnetic mineral is titanomagnetite/titanomaghemite; (2) that, except for the upper few meters of the core where the grains are in the stable monodomain state, the grain size of the magnetic mineral lies in the pseudo-single-domain range (< 10 µm); (3) that maghemitization (i.e., low-temperature (< 350°C) oxidation) has taken place. We discuss possible geological histories.

Geochemistry of low-temperatuer altered basalts of ODP Hole 136-843B

The mineralogy and chemistry of altered basalts and the stable isotopic compositions of secondary vein carbonates were studied in cores from Ocean Drilling Program Hole 843B, located in 95-Ma crust of the Hawaiian Arch. Millimeter- to centimeter-sized dark alteration halos around veins are 5%-15% altered to celadonite and Fe-oxyhydroxides, plus minor saponite and calcite. Adjacent gray host rocks are about 15% altered to saponite and calcite. The dark halos are enriched in H2O+, CO2, FeT, K2O, MnO, and Fe3+/FeT and depleted in SiO2, Al2O3, MgO, and TiO2 relative to gray host rocks. Brown alteration halos occur around veins where veins are more abundant, and are similar to dark halos, but contain more Fe-oxyhydroxides and exhibit greater Fe2O3T contents and higher Fe3+/FeT. Stable isotopic compositions of vein carbonates are consistent with their precipitation from seawater at temperatures of 5°-40°C. Crosscutting relationships of veins and zoned vein and vesicle fillings reveal a sequence of secondary mineral formation and alteration conditions. Celadonite and Fe-oxyhydroxides formed and dark alteration halos developed relatively early, under oxidizing conditions at low temperatures (<50°C). Saponite formed later at lower seawater/rock ratios and under more reducing conditions. Calcite and pyrite formed last in veins and vesicles from more evolved, seawaterderived fluids at temperatures of 5°-40°C. A second stage of celadonite, with compositions distinct from the early celadonite, also occurred relatively late (within the "calcite stage"), and may be related to refracturing of the crust and introduction of less-evolved seawater solutions into the rocks. Trends to higher K2O contents are attributed to alteration, but high K/Ti, Ba, and Zr contents indicate the presence of enriched or transitional MORB. CO2 contents of Pacific ODP cores exhibit a general increase with age suggesting progressive fixation of CO2 as calcite in the crust, but this could be complicated by local heterogeneities in fracturing and calcite formation in the crust.

Paleomagnetic of igneous rocks of ODP Leg 114

A paleomagnetic study was made of 12 samples of trachytic basalt from the base of ODP Hole 698A on the Northeast Georgia Rise (southwest Atlantic) and four samples of andesitic basalt and nine samples of volcanic breccia from the base of ODP Hole 703A on the Meteor Rise (southeast Atlantic). The magnetic intensities of the Hole 703A samples are anomalously low, possibly reflecting alteration effects. The mean magnetic intensity of the Hole 698A samples is high, and compatible with the model of Bleil and Petersen (1983) for the variation of magnetic intensity with age in oceanic basalts, involving progressive low-temperature oxidation of titanomagnetite to titanomaghemite for some 20 m.y. followed by inversion to intergrowths of magnetite and other Fe-Ti oxides during the subsequent 100 m.y. These results support the interpretation of the Hole 698A basalts as true oceanic basement of Late Cretaceous age rather than a younger intrusion. Well-defined stable components of magnetization were identified from AF and thermal demagnetization of the Hole 698A basalts, and less well-defined components were identified for the Hole 703A samples. Studies of the magnetic homogeneity of the Hole 698A basalts, involving harmonic analysis of the spinner magnetometer output, indicate the presence of an unevenly distributed low-coercivity component superimposed on the more homogeneous high-coercivity characteristic magnetization. The former component is believed to reside in irregularly distributed multidomain magnetite grains formed along cracks within the basalt, whilst the latter resides in more uniformly distributed finer magnetic grains. The inclination values for the high-coercivity magnetization of five Hole 698A basalt samples form an internally consistent set with a mean value of 59° ± 5°. The corresponding Late Cretaceous paleolatitude of 40° ± 5° is shallower than expected for this site but is broadly compatible with models for the opening of the South Atlantic involving pivoting of South America away from Africa since the Early Cretaceous. The polarity of the stable characteristic magnetization of the Site 698 basalts is normal. This is consistent with their emplacement during the long Campanian to Maestrichtian normal polarity Chron C33N.