STUDIES OF THE MOLECULAR MECHANISMS OF CHROMOSOME ABERRATION FORMATION (DNA REPAIR, CROSSLINKS, MITOMYCIN C)

The objective of this research has been to study the molecular basis for chromosome aberration formation. Predicated on a variety of data, Mitomycin C (MMC)-induced DNA damage has been postulated to cause the formation of chromatid breaks (and gaps) by preventing the replication of regions of the genome prior to mitosis. The basic protocol for these experiments involved treating synchronized Hela cells in G(,1)-phase with a 1 (mu)g/ml dose of MMC for one hour. After removing the drug, cells were then allowed to progress to mitosis and were harvested for analysis by selective detachment. Utilizing the alkaline elution assay for DNA damage, evidence was obtained to support the conclusion that Hela cells can progress through S-phase into mitosis with intact DNA-DNA interstrand crosslinks. A higher level of crosslinking was observed in those cells remaining in interphase compared to those able to reach mitosis at the time of analysis. Dual radioisotope labeling experiments revealed that, at this dose, these crosslinks were associated to the same extent with both parental and newly replicated DNA. This finding was shown not to be the result of a two-step crosslink formation mechanism in which crosslink levels increase with time after drug treatment. It was also shown not to be an artefact of the double-labeling protocol. Using neutral CsCl density gradient ultracentrifugation of mitotic cells containing BrdU-labeled newly replicated DNA, control cells exhibited one major peak at a heavy/light density. However, MMC-treated cells had this same major peak at the heavy/light density, in addition to another minor peak at a density characteristic for light/light DNA. This was interpreted as indicating either: (1) that some parental DNA had not been replicated in the MMC treated sample or; (2) that a recombination repair mechanism was operational. To distinguish between these two possibilities, flow cytometric DNA fluorescence (i.e., DNA content) measurements of MMC-treated and control cells were made. These studies revealed that the mitotic cells that had been treated with MMC while in G(,1)-phase displayed a 10-20% lower DNA content than untreated control cells when measured under conditions that neutralize chromosome condensation effects (i.e., hypotonic treatment). These measurements were made under conditions in which the binding of the drug, MMC, was shown not to interfere with the stoichiometry of the ethidium bromide-mithramycin stain. At the chromosome level, differential staining techniques were used in an attempt to visualize unreplicated regions of the genome, but staining indicative of large unreplicated regions was not observed. These results are best explained by a recombinogenic mechanism. A model consistent with these results has been proposed.^

The in vivo and in vitro formation of sticky DNA and the GAA.TTC trinucleotide repeat associated with Friedreich's ataxia

Friedreich's ataxia is caused by the expansion of the GAA•TTC trinucleotide repeat sequence located in intron 1 of the frataxin gene. The long GAA•TTC repeats are known to form several non-B DNA structures including hairpins, triplexes, parallel DNA and sticky DNA. Therefore it is believed that alternative DNA structures play a role in the loss of mRNA transcript and functional frataxin protein in FRDA patients. We wanted to further elucidate the characteristics for formation and stability of sticky DNA by evaluating the structure in a plasmid based system in vitro and in vivo in Escherichia coli. The negative supercoil density of plasmids harboring different lengths of GAA•TTC repeats, as well as either one or two repeat tracts were studied in E. coli to determine if plasmids containing two long tracts (≥60 repeats) in a direct repeat orientation would have a different topological effect in vivo compared to plasmids that harbored only one GAA•TTC tract or two tracts of < 60 repeats. The experiments revealed that, in fact, sticky DNA forming plasmids had a lower average negative supercoil density (-σ) compared to all other control plasmids used that had the potential to form other non-B DNA structures such as triplexes or Z-DNA. Also, the requirements for in vitro dissociation and reconstitution of the DNA•DNA associated region of sticky DNA were evaluated. Results conclude that the two repeat tracts associate in the presence of negative supercoiling and MgCl 2 or MnCl2 in a time and concentration-dependent manner. Interaction of the repeat sequences was not observed in the absence of negative supercoiling and/or MgCl2 or in the presence of other monovalent or divalent cations, indicating that supercoiling and quite specific cations are needed for the association of sticky DNA. These are the first experiments studying a more specific role of supercoiling and cation influence on this DNA conformation. To support our model of the topological effects of sticky DNA in plasmids, changes in sticky DNA band migration was measured with reference to the linear DNA after treatment with increasing concentrations of ethidium bromide (EtBr). The presence of independent negative supercoil domains was confirmed by this method and found to be segregated by the DNA-DNA associated region. Sequence-specific polyamide molecules were used to test the effect of binding of the ligands to the GAA•TTC repeats on the inhibition of sticky DNA. The destabilization of the sticky DNA conformation in vitro through this binding of the polyamides demonstrated the first conceptual therapeutic approach for the treatment of FRDA at the DNA molecular level. ^ Thus, examining the properties of sticky DNA formed by these long repeat tracts is important in the elucidation of the possible role of sticky DNA in Friedreich's ataxia. ^

PREPARATION AND CHARACTERIZATION OF FAD DEPENDENT NADPH CYTOCHROME P-450 REDUCTASE (FLAVOPROTEINS, APOFLAVOPROTEIN)

NADPH cytochrome P-450 reductase releases FMN and FAD upon dilution into slightly acidic potassium bromide. The flavins are released with positive cooperativity. Dithiothreitol protects the FAD dependent cytochrome c reductase activity against inactivation by free radicals. Behavior in potassium bromide is sensitive to changes in the pH. High performance hydroxylapatite resolved the FAD dependent reductase from holoreductase. For 96% FAD dependent reductase, the overall yield was 12%.^ High FAD dependence was matched by a low FAD content, with FAD/FMN as low as 0.015. There were three molecules of FMN for every four molecules of reductase. The aporeductase had negligible activity towards cytochrome c, ferricyanide, menadione, dichlorophenolindophenol, nitro blue tetrazolium, oxygen and acetyl pyridine adenine dinucleotide phosphate. A four minute incubation in FAD reconstituted one half to all of the specific activity, per milligram protein, of untreated reductase, depending upon the substrate. After a two hour reconstitution, the reductase eluted from hydroxylapatite at the location of holoreductase. It had little flavin dependence, was equimolar in FMN and FAD, and had nearly the specific activity (per mole flavin) of untreated reductase.^ The lack of activity and the ability of FMN to also reconstitute suggest that the redox center of FAD is essential for catalysis, rather than for structure. Dependence upon FAD is consistent with existing hypotheses for the catalytic cycle of the reductase. ^

Hydrogeological investigations in the upper Ouémé catchment in Benin, West Africa

The scope of this PhD thesis was the hydrogeological conceptualisation of the Upper Ouémé river catchment in Benin. The study area exceeds 14,500 km**2 and is underlain by a crystalline basement. At this setting the typical sequence of aquifers - a regolith aquifer at the top and a fractured bedrock aquifer at the bottom - is encountered, which is found in basement areas all over Africa and elsewhere in the world. The chosen regional approach revealed important information about the hydrochemistry and hydrogeology of this catchment. Based on the regional conceptual model a numerical groundwater flow model was designed. The numerical model was used to estimate the impact of climate change on the regional groundwater resources. This study was realised within the framework of the German interdisciplinary research project IMPETUS (English translation: "Integrated approach to the efficient management of scarce water resources in West Africa"), which is jointly managed by the German universities of Bonn and Cologne. Since the year 2000 the Upper Ouémé catchment was the principal target for investigations into the relevant processes of the regional water cycle. A first study from 2000 to 2003 (Fass, 2004, http://nbn-resolving.de/urn:nbn:de:hbz:5n-03849) focused on the hydrogeology of a small local catchment (~30 km**2). In the course of this thesis five field campaigns were underdone from the year 2004 to 2006. In the beginning of 2004 a groundwater monitoring net was installed based on 12 automatic data loggers. Manual piezometric measurements and the sampling of groundwater and surface water were realised for each campaign throughout the whole study area. Water samples were analysed for major ions, for a choice of heavy metals and for their composition by deuterium, oxygen-18 and tritium. The numerical model was performed with FEFLOW. The hydraulic and hydrochemical characteristics were described for the regolith aquifer and the bedrock aquifer. The regolith aquifer plays the role of the groundwater stock with low conductivity while the fractures of the bedrock may conduct water relatively fast towards extraction points. Flow in fractures of the bedrock depends on the connectivity of the fracture network which might be of local to subregional importance. Stable isotopes in combination with hydrochemistry proved that recharge occurs on catchment scale and exclusively by precipitation. Influx of groundwater from distant areas along dominant structures like the Kandi fault or from the Atacora mountain chain is excluded. The analysis of tritium in groundwater from different depths revealed the interesting fact of the strongly rising groundwater ages. Bedrock groundwater may possibly be much older than 50 years. Equilibrium phases of the silicate weathering products kaolinite and montmorillonite showed that the deeper part of the regolith aquifer and the bedrock aquifer feature either stagnant or less mobile groundwater while the shallow aquifer level is influenced by seasonal groundwater table fluctuations. The hydrochemical data characterised this zone by the progressive change of the hydrochemical facies of recently infiltrated rainwater on its flow path into deeper parts of the aquifers. Surprisingly it was found out that seasonal influences on groundwater hydrochemistry are minor, mainly because they affect only the groundwater levels close to the surface. The transfer of the hydrogeological features of the Upper Ouémé catchment into a regional numerical model demanded a strong simplification. Groundwater tables are a reprint of the general surface morphology. Pumping or other types of groundwater extraction would have only very local impact on the available groundwater resources. It was possible to integrate IMPETUS scenario data into the groundwater model. As a result it was shown that the impact of climate change on the groundwater resources until the year 2025 under the given conditions will be negligible due to the little share of precipitation needed for recharge and the low water needs for domestic use. Reason for concern is the groundwater quality on water points in the vicinity of settlements because of contamination by human activities as shown for the village of Dogué. Nitrate concentrations achieved in many places already alerting levels. Health risks from fluoride or heavy metals were excluded for the Upper Ouémé area.

Strike-slip faults mediate the rise of crustal-derived fluids and mud volcanism in the deep sea

We report on newly discovered mud volcanoes located at about 4500 m water depth 90 km west of the deformation front of the accretionary wedge of the Gulf of Cadiz, and thus outside of their typical geotectonic environment. Seismic data suggest that fluid flow is mediated by a >400-km-long strike-slip fault marking the transcurrent plate boundary between Africa and Eurasia. Geochemical data (Cl, B, Sr, 87Sr/86Sr, Delta18O, DeltaD) reveal that fluids originate in oceanic crust older than 140 Ma. On their rise to the surface, these fluids receive strong geochemical signals from recrystallization of Upper Jurassic carbonates and clay-mineral dehydration in younger terrigeneous units. At present, reports of mud volcanoes in similar deep-sea settings are rare, but given that the large area of transform-type plate boundaries has been barely investigated, such pathways of fluid discharge may provide an important, yet unappreciated link between the deeply buried oceanic crust and the deep ocean.

Chemical, and Sr and Li isotopic composition of pore fluids and sediments from ODP Leg 170 and Leg 205 sites

Pore fluid and sediment chemical and isotopic data were obtained for samples from Ocean Drilling Program (ODP) Leg 205 Sites 1253, 1254, and 1255 in the Costa Rica subduction zone. The chemical and isotopic data reported here were generated in our shore-based laboratories to complement shipboard inorganic geochemical data. Li isotopic analyses were carried out by L.-H. Chan at Louisiana State University (USA). The data reported herein include fluoride, bromide, rubidium, cesium, and barium concentrations; Li and Sr isotopic compositions in pore fluids; and Rb, Cs, and Ba concentrations in representative bulk sediments. The data also include new pore fluid fluoride and bromide concentrations from corresponding ODP Leg 170 Sites 1039, 1040, and 1043. O.M. Saether's Site 1039 and 1040 fluoride concentration data are shown for comparison. Basal sediment fluoride concentrations and Li and Sr isotope ratios at both Sites 1253 and 1039 show reversals that approach modern seawater values. Br/Cl ratios are, however, conservative throughout the sediment section at Sites 1039 and 1253. The observed sharp F and Br concentration maxima, Rb and K concentration minima, the most radiogenic 87Sr/86Sr ratios, and highest 7Li values along the décollement and fracture zone (Sites 1040, 1043, 1254, and 1255) strengthen the evidence obtained during Leg 170 that a deeply sourced fluid, originating from fluid-rock reactions at ~150°C and corresponding to between 10 and 15 km depth, is transporting solutes to the ocean.

Aerosols over the Arabian Sea

This paper provides an overview of dust transport pathways and concentrations over the Arabian Sea during 1995. Results indicate that the transport and input of dust to the region is complex, being affected by both temporally and spatially important processes. Highest values of dust were found off the Omani coast and in the entrance to the Gulf of Oman. Dust levels were generally lower in summer than the other seasons, although still relatively high compared to other oceanic regions. The Findlater jet, rather than acting as a source of dust from Africa, appears to block the direct transport of dust to the open Arabian Sea from desert dust source regions in the Middle East and Iran/Pakistan. Dust transport aloft, above the jet, rather than at the surface, may be more important during summer. In an opposite pattern to dust, sea salt levels were exceedingly high during the summer monsoon, presumably due to the sustained strong surface winds. The high sea salt aerosols during the summer months may be impacting on the strong aerosol reflectance and absorbance signals over the Arabian Sea that are detected by satellite each year.

Chemical and isotope compositions of interstitial water in sediments from Mediterranean basin at DSDP Sites 42-372 and 42-374

The Br/Cl, Li/Cl and B/Cl ratios and boron isotope compositions of hypersaline pore fluids from DSDP Sites 372 and 374 were measured in an attempt to evaluate the origin of the brines. In Site 374 the relationships between the Cl concentrations (up to 5000 mM) and Br/Cl (~0.012), Na/Cl (as low as 0.1), B/Cl (0.0025), and d11B values (43-55?) of the deep pore water between 380 and 405 mbsf, located within the Messinian sediments, reflect remnants of ~65-fold evaporated sea water. The original evaporated sea water was modified by: (1) dilution with overlying or less saline water by about 30%; and (2) slight dissolution of NaCl evaporites. The variations in d11B show a continuous increase in d11B values with depth in Site 374, up to 66.7? at a depth of 300 mbsf (Upper Pliocene marl sediments). The conspicuous 11B enrichment trend is consistent with elemental boron depletion, which was calculated from the expected boron concentrations of evaporated sea water with corresponding Br/Cl and Na/Cl ratios. Li/Cl variations also show a depletion of Li relative to evaporated sea water. The apparent depletions of B and Li, as well as the 11B enrichment, reflect uptake of these elements by clay minerals at low water/sediment ratios.

Interstitial water chemistry of ODP Leg 103 sites

Interstitial waters were squeezed from strata recovered at Sites 637-641 of ODP Leg 103 on the Galicia margin, along the northwestern Iberian continental margin in the northeast Atlantic. Chemical profiles of Site 638 show the most complexity, which appears to be related to an unconformity in the strata between Cretaceous and Neogene sediments and to rapid deposition of Cretaceous syn-rift sediments upon pre-rift strata. Analyses of waters from all of the Leg 103 sites show generally antithetical trends for calcium and magnesium; calcium increases with depth as magnesium decreases. No calcium-magnesium 'crossover' profiles are observed in these data. Data from Site 637 show an unusual pattern; calcium increases with increasing depth, but magnesium remains relatively constant. Sulfate is either stable or shows an overall decrease with depth, and boron profiles show some structure. At all but one site (Site 638), strontium profiles do not show marked depth structure. The structure of alkalinity and silica profiles is highly site dependent. Bromide profiles are, in general, constant. In nearly every case, observed bromide concentrations are near average seawater values. Relatively low concentrations of iron and manganese are common within the upper 10 m of the sediment sequence and typically are near detection limits at deeper depths

Major ion concentrations and chlorine isotope composition of water-soluble chloride and structurally bound chloride in DSDP/ODP serpentinized ultramafic rocks

Eight DSDP/ODP cores were analyzed for major ion concentrations and d37Cl values of water-soluble chloride (d37Clwsc) and structurally bound chloride (d37Clsbc) in serpentinized ultramafic rocks. This diverse set of cores spans a wide range in age, temperature of serpentinization, tectonic setting, and geographic location of drilled serpentinized oceanic crust. Three of the cores were sampled at closely spaced intervals to investigate downhole variation in Cl concentration and chlorine isotope composition. The average total Cl content of all 86 samples is 0.26±0.16 wt.% (0.19±0.10 wt.% as water-soluble Cl (Xwsc) and 0.09±0.09 wt.% as structurally bound Cl (Xsbc)). Structurally bound Cl concentration nearly doubles with depth in all cores; there is no consistent trend in water-soluble Cl content among the cores. Chlorine isotope fractionation between the structurally bound Cl**- site and the water-soluble Cl**- site varies from -1.08? to +1.16?, averaging to +0.21?. Samples with negative fractionations may be related to reequilibration of the water-soluble chloride with seawater post-serpentinite formation. Six of the cores have positive bulk d37Cl values (+0.05? to +0.36?); the other two cores (173-1068A (Leg-Hole) and 84-570) have negative bulk d37Cl values (-1.26? and -0.54?). The cores with negative d37Cl values also have variable Cl**-/SO4**2- ratios, in contrast to all other cores. The isotopically positive cores (153-920D and 147-895E) show no isotopic variation with depth; the isotopically negative core (173-1068A) decreases by ~1? with depth for both the water-soluble and structurally bound Cl fractions. Non-zero bulk d37Cl values indicate Cl in serpentinites was incorporated during original hydration and is not an artifact of seawater infiltration during drilling. Cores with positive d37Cl values are most likely explained by open system fractionation during hydrothermal alteration, with preferential incorporation of 37Cl from seawater into the serpentinite and loss of residual light Cl back to the ocean. Fluid / rock ratios were probably low as evidenced by the presence of water-soluble salts. The two isotopically negative cores are characterized by a thick overlying sedimentary package that was in place prior to serpentinization. We believe the low d37Cl values of these cores are a result of hydration of ultramafic rock by infiltrating aqueous pore fluids from the overlying sediments. The resulting serpentinites inherit the characteristic negative d37Cl values of the pore waters. Chlorine stable isotopes can be used to identify the source of the serpentinizing fluid and ultimately discern chemical and tectonic processes involved in serpentinization.

Geochemistry and radionuclide content of sediment and water samples obtained from the Ob and Irtysh river, Russia

This paper reports the results of the investigations of 2006-2007 on the distribution and migration forms of artificial radionuclides and chemical elements in the Ob-Irtysh water system. Three regions were studied. One of them is a local segment of the Ob River upstream from the confluence with the Irtysh River; its investigation allowed us to estimate the general radioecological state of the aquatic environment affected by the activity of the Tomsk 7 plant. The second region is a local segment of the Irtysh River upstream from its confluence with the Ob River, where the influence of emissions from the NPO Mayak could be estimated. The third region is the water area of the Ob River after its confluence with the Irtysh River. It characterizes the real level of radioactive and chemical contamination of the middle reaches of the Ob River. In order to explain horizontal variations in the distribution of radionuclides in the upper layer of bottom sediments collected at various sites, the results of sorption-kinetic experiments with radioactive tracers in the precipitate-solution system were used. The investigation of the migration forms of trace elements and radionuclides occurring in river water was based on the method of tangential-flow membrane filtration. Chemical element contents were determined in 400-ml water samples. A set of Millipore polysulfone membranes with pore sizes of 8, 1.2, 0.45, 0.1, and 0.025 µm was employed. Taking into account the ultralow specific concentrations of radionuclides in the water, they were analyzed in 300-500 litre samples using Millipore polysulfone membranes with pore sizes of 0.45 µm and 15 kDa. This allowed us to estimate the percentages of cesium-137 and plutonium-239, 240 in the suspended particulate fraction, colloids, and dissolved species.

Physico-chemical parameters of sediment core PG1972-1 (09-Tik-03) from a Tundra Lake, Northeastern Siberia

Thermokarst lakes in the Siberian Arctic contain sediment archives that can be used for paleoenvironmental inference. Until now, however, there has been no study from the inner Lena River Delta with a focus on diatoms. The objective of this study was to investigate how the diatom community in a thermokarst lake responded to past limnogeological changes and what specific factors drove variations in the diatom assemblage. We analysed fossil diatom species, organic content, grain-size distribution and elemental composition in a sediment core retrieved in 2009 from a shallow thermokarst lake in the Arga Complex, western Lena River Delta. The core contains a 3,000-year record of sediment accumulation. Shifts in the predominantly benthic and epiphytic diatom species composition parallel changes in sediment characteristics. Paleoenvironmental and limnogeological development, inferred from multiple biological and sedimentological variables, are discussed in the context of four diatom zones, and indicate a strong relation between changes in the diatom assemblage and thermokarst processes. We conclude that limnogeological and thermokarst processes such as lake drainage, rather than direct climate forcing, were the main factors that altered the aquatic ecosystem by influencing, for example, habitat availability, hydrochemistry, and water level.

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.