Investigations of stress responses in Saccharomyces cerevisiae: Transcriptional control and heat shock protein function

The baker's yeast, Saccharomyces cerevisiae responds to the cytotoxic effects of elevated temperature (37-42°C) by activating transcription of ∼150 genes, termed heat shock genes, collectively required to compensate for the abundance of misfolded and aggregated proteins and various physiological modifications necessary for the cell to survive and grow at heat shock temperatures. An intriguing facet of the yeast heat shock response is the remarkable similarity it shares with the global remodeling that occurs in mammalian cells in response to numerous pathophysiological conditions including cancer and cardiovascular disease and thus provides an ideal model system. I have therefore investigated several novel features of stress signaling, transcriptional regulation, and physiology. Initial work focused on the characterization of SYM1, a novel heat shock gene in yeast which was demonstrated to be required for growth on the nonfermentable carbon source ethanol at elevated temperature, and to be the functional ortholog of the mammalian kidney disease gene, Mpv17. Additional work addressed the role of two proteins, the Akt-related kinase, Sch9, and Sse1, the yeast Hsp110 protein chaperone homolog, in signaling by protein kinase A, establishing Sse1 as a critical negative regulator of this pathway. Furthermore, I have demonstrated a role for Sse1 in biogenesis and stability of the stress-response transcription factor, Msn2; a finding that has been extended to include a select subset of additional high molecular weight proteins, suggesting a more global role for this chaperone in stabilizing the cellular proteome. The final emphasis of my doctoral work has included the finding that celastrol, a compound isolated from the plant family Celasfraceae, a component of traditional Chinese herbal medicine, can activate heat shock transcription factor (Hsf1) in yeast and mammalian cells through an oxidative stress mechanism. Celastrol treatment simultaneously activates both heat shock and oxidative stress response pathways, resulting in increased cytoprotection. ^

Spectroscopic and functional investigations of the AMPA subtype of ionotropic glutamate receptors

Ion channels play a crucial role in the functioning of different systems of the body because of their ability to bridge the cell membrane and allow ions to pass in and out of the cell. Ionotropic glutamate receptors are one class of these important proteins and have been shown to be critical in propagating synaptic transmission in the central nervous system and in other diverse functions throughout the body. Because of their wide-ranging effects, this family of receptors is an important target for structure-function investigations to understand their mechanism of action. ^ α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are one subtype of glutamate receptors and have been shown to be the primary receptors involved in rapid excitatory signaling in the central nervous system. Agonist binding to the extracellular ligand binding domain of these receptors causes various conformational changes that culminate in formation of the ion channel. Previous structural investigations have provided important information about their mechanism of action, including uncovering a relationship between the degree of cleft closure in the binding domain and activation of the receptor. However, what question remains unanswered is how specific interactions between the agonist and the protein interplay with cleft closure to mediate receptor activation. ^ To investigate this question, I applied a multiscale approach to investigate the effects of agonist binding on various levels. Vibrational spectroscopy was utilized to investigate molecular-level interactions in the binding pocket, and fluorescence resonance energy transfer (FRET) was employed to measure cleft closure in the isolated ligand binding domain. The results of these studies in the isolated binding domain were then correlated to activation of the full receptor. These investigations showed a relationship between the strength of the interaction at the α-amine group of the agonist and extent of receptor activation, where a stronger interaction correlated to a larger activation, which was upheld even when the extent of cleft closure did not correlate to activation. These results show that this interaction at the α-amine group is critical in mediating the allosteric mechanism of activation and provide a bit more insight into how agonist binding is coupled to channel gating in AMPA receptors. ^

Geochemical investigations of elements in sediment core CRP-1 from the Ross Sea, Antarctica

Geochemical data are presented for samples from strata, mainly of Miocene age, in the Cape Roberts-1 core (western McMurdo Sound, Antarctica) to assess the sediment provenance. Bulk (major and trace element) chemistry together with bulk mineralogy of fine-grained sandstones, siltstones, mudstones, and diamictites indicate that chemical alteration of source materials, fractionation due to sedimentary sorting, and diagenetic effects were not significant in the Cape Roberts sediment history. Relevant geochemical parameters are consistent with the Cape Roberts sediments being derived mainly from the crystalline basement and the Beacon Supergroup. On the basis of element distributions, an additional contribution from the Ferrar Dolerite and, mainly above about 60 m, influxes of detritus derived from basanitic to intermediate members of the McMurdo Volcanic Group are recognised.

Facies investigations on sediment core CRP-3 from the Ross Sea, Antarctica

The Cenozoic Victoria Land Basin (VLB) stratigraphic section penetrated by CRP-3 is mostly of Early Oligocene age. It contains an array of lithofacies comprising fine-grained mudrocks, interlaminated and interbedded mudrocks/sandstones, mud-rich and mud-poor sandstones, conglomerates and diamctites that are together interpreted as the products of shallow marine to possibly non-marine environments of deposition, affected by the periodic advance and retreat of tidewater glaciers. This lithofacies assemblage can be readily rationalised using the facies scheme designed originally for CRP-2/2A, and published previously. The uppermost 330 metres below sea floor (mbsf) shows a cyclical arrangement of lithofacies also similar to that recognised throughout CRP-2/2A, and interpreted to reflect cyclical variations in relative sea-level driven by ice volume fluctuations ('Motif A'). Between 330 and 480 mbsf, a series of less clearly cyclical units, generally fining-upward but nonetheless incorporating a significant subset of the facies assemblage, has been identified and noted in the Initial Report as 'Motif B' Below 480 mbsf, the section is arranged into a repetitive succession of fining-upward units, each of which comprises dolerite clast conglomerate at the base passing upward into relatively thick intervals of sandstones. The cycles present down 480 mbsf are defined as sequences, each interpreted to record cyclical variation of relative sea-level. The thickness distribution of sequences in CRP-3 provides some insights into the geological variables controlling sediment accumulation in the Early Oligocene section. The uppermost part of the section in CRP-3 comprises two or three thick, complete sequences that show a broadly symmetrical arrangement of lithofacies (similar to Sequences 9-11 in CRP-2/2A). This suggests a period of relatively rapid tectonic subsidence, which allowed preservation of the complete facies cycle. Below Sequence 3, however, is a considerable interval of thin, incomplete and erosionally truncated sequences (4-23), which incorporates both the remainder of Motif A sequences and all Motif B sequences recognised. The thinner and more truncated sequences suggest sediment accumulation under conditions of reduced accommodation, and given the lack of evidence for glacial conditions (see Powell et al., this volume) tends to argue for a period of reduced tectonic subsidence. The section below 480 mbsf consists of a series of fining-upward, conglomerate to sandstone intervals which cannot be readily interpreted in terms of relative sea-level change. A relatively mudrock-rich interval above the basal conglomerate/breccia (782-762 mbsf) may record initial flooding of the basin during early rift subsidence. The lithostratigraphy summarised above has been linked to seismic reflection data using depth conversion techniques (Henrys et al., this volume). The three uppermost reflectors ('o', 'p' and 'q') correlate to the package of thick sequences 1-3, and several deeper reflectors can also be correlated to sequence boundaries. The package of thick Sequences 1-3 shows a sheet-like cross-sectional geometry on seismic reflection lines, unlike the similar package recognised in CRP-2/2A.

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.

Geological investigations on sediment core MD07-3128

Glacial millennial-scale paleoceanographic changes in the Southeast Pacific and the adjacent Southern Ocean are poorly known due to the scarcity of well-dated and high resolution sediment records. Here we present new surface water records from sediment core MD07-3128 recovered at 53°S off the Pacific entrance of the Strait of Magellan. The alkenone-derived sea surface temperature (SST) record reveals a very strong warming of ca. 8°C over the last Termination and substantial millennial-scale variability in the glacial section largely consistent with our planktonic foraminifera oxygen isotope (d18O) record of Neogloboquadrina pachyderma (sin.). The timing and structure of the Termination and some of the millennial-scale SST fluctuations are very similar to those observed in the well-dated SST record from ODP Site 1233 (41°S) and the temperature record from Drowning Maud Land Antarctic ice core supporting the hemispheric-wide Antarctic timing of SST changes. However, differences in our new SST record are also found including a long-term warming trend over Marine Isotope Stage (MIS) 3 followed by a cooling toward the Last Glacial Maximum (LGM). We suggest that these differences reflect regional cooling related to the proximal location of the southern Patagonian Ice Sheet and related meltwater supply at least during the LGM consistent with the fact that no longer SST cooling trend is observed in ODP Site 1233 or any SST Chilean record. This proximal ice sheet location is documented by generally higher contents of ice rafted debris (IRD) and tetra-unsaturated alkenones, and a slight trend toward lighter planktonic d18O during late MIS 3 and MIS 2.

In-situ Iron isotope measurements and mineral compositions from ODP Hole 206-1256D and IODP Hole 335-U1256D

In-situ Fe isotope measurements have been carried out to estimate the impact of the hydrothermal metamorphic overprint on the Fe isotopic composition of Fe-Ti-oxides and Fe-sulfides of the different lithologies of the drilled rocks from IODP Hole 1256D (eastern equatorial Pacific; 15 Ma crust formed at the East Pacific Rise). Most igneous rocks normally have a very restricted range in their 56Fe/54Fe ratio. In contrast, Fe isotope compositions of hot fluids (> 300 °C) from mid-ocean-ridge spreading centers define a narrow range that is shifted to lower delta 56Fe values by 0.2 per mil - 0.5 per mil as compared to igneous rocks. Therefore, it is expected that mineral phases that contain large amounts of Fe are especially affected by the interaction with a fluid that fractionates Fe isotopes during exsolution/precipitation of those minerals. We have used a femtosecond UV-Laser ablation system to determine mineral 56Fe/54Fe ratios of selected samples with a precision of < 0.1 per mil (2 sigma level) at micrometer-scale. We have found significant variations of the delta 56Fe (IRMM-014) values in the minerals between different samples as well as within samples and mineral grains. The overall observed scale of delta 56Fe (magnetite) in 1256D rocks ranges from - 0.12 to + 0.64 per mil, and of delta 56Fe (ilmenite) from - 0.77 to + 0.01 per mil. Pyrite in the lowermost sheeted dike section is clearly distinguishable from the other investigated lithological units, having positive delta 56Fe values between + 0.29 and + 0.56 per mil, whereas pyrite in the other samples has generally negative delta 56Fe values from - 1.10 to - 0.59 permil. One key observation is that the temperature dependent inter-mineral fractionations of Fe isotopes between magnetite and ilmenite are systematically shifted towards higher values when compared to theoretically expected values, while synthesized, well equilibrated magnetite-ilmenite pairs are compatible with the theoretical predictions. Theoretical considerations including beta-factors of different aqueous Fe-chlorides and Rayleigh-type fractionations in the presence of a hydrous, chlorine-bearing fluid can explain this observation. The disagreement between observed and theoretical equilibrium fractionation, the fact that magnetite, in contrast to ilmenite shows a slight downhole trend in the delta 56Fe values, and the observation of small scale heterogeneities within single mineral grains imply that a general re-equilibration of the magnetite-ilmenite pairs is overprinted by kinetic fractionation effects, caused by the interaction of magnetite/ilmenite with hydrothermal fluids penetrating the upper oceanic crust during cooling, or incomplete re-equilibration at low temperatures. Furthermore, the observation of significant small-scale variations in the 56Fe/54Fe ratios of single minerals in this study highlights the importance of high spatial-resolution-analyses of stable isotope ratios for further investigations.

Investigations on a sediment core from the Indian Ocean

The Multi-Sensor Core Logger (MSCL) enables non-destructive, quasi-continuous measuroments of physical properties, reducing the time needed for discrete sample analysis. Density, compressional wave velocity (Vp), and magnetic susceptibility are measured on water-saturated sediment cores. Rapid variations in the lithology can thus be more easily recognized. The advantages of MSCL measurements over traditional sedimentological investigation methods are illustrated using several examples. Density-Vp relationships provide detailed lithological information prior to splitting the sediment cores. In terrigenous sediments, density increases with Vp, whereas in biogenic sediments it decreases. In biogenic sediments in the South Atlantic, low densities and high Vp are associated with high opal content. In biogenic sediments in the Peru Basin, density increases with carbonate content. Carbonate, which is very important for deep-sea environmental protection and for paleoclimatic studies, can be determined quantitatively from MSCL measurements in this area. In terrigenous sediments in the Bengal Fan, the acoustic impedance (the product of density and Vp) increases with grain size. There, the grain-size distribution can be rapidly derived from the acoustic impedance. Moreover, in hemipelagic sediments in the Bengal Fan, it is possible to correlate variations in magnetic susceptibility with cyclic changes in the earth's orbital parameters - an important prerequisite for detailed stratigraphic studies.

Meiobenthos investigations in the Black Sea during Poseidon cruise POS317/3

Meiobenthos densities and higher taxon composition were studied in an active gas seepage area at depths from 182 to 252 m in the submarine Dnieper Canyon located in the northwestern part of the Black Sea. The meiobenthos was represented by Ciliata, Foraminifera, Nematoda, Polychaeta, Bivalvia, Gastropoda, Amphipoda, and Acarina. Also present in the sediment samples were juvenile stages of Copepoda and Cladocera which may be of planktonic origin. Nematoda and Foraminifera were the dominant groups. The abundance of the meiobenthos varied between 2397 and 52593 Ind./m**2. Maximum densities of Nematoda and Foraminifera were recorded in the upper sediment layer of a permanent H2S zone at depths from 220 to 250 m. This dense concentration of meiobenthos was found in an area where intense methane seeps were covered by methane-oxidizing microbial mats. Results suggest that methane and its microbial oxidation products are the factors responsible for the presence of a highly sulfidic and biologically productive zone characterized by specially adapted benthic groups. At the same time, an inverse correlation was found between meiofauna densities and methane concentrations in the uppermost sediment layers. The hypothesis is that the concentration of Nematoda and Foraminifera within the areas enriched with methane is an ecological compromise between the food requirements of these organisms and their adaptations to the toxic H2S.

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

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

Investigations on sediments from Lake Nam Co (Tibetan Plateau)

This study focuses on the analysis of lake sediments retrieved from the deepest part of Lake Nam Co (Tibetan Plateau). One gravity core of 115 cm length, covering the last ~ 4000 cal BP, was analyzed for geochemical and biological parameters. High organic content at ~ 4000 cal BP and the coinciding presence of pyrite framboids until ~ 2000 cal BP point to hampered decomposition of organic material due to anoxic conditions within the lake sediments. At the same time sedimentological and biological proxies suggest a rather high lake level, but still ~ 5 m below the recent one, with less saline lake water due to enhanced monsoonal activity. During this time a change in the source of organic matter to lowered input of terrestrial components is observed. A rather quick shift to a dry environment with less monsoonal influence and a lake level ~ 15 m lower than today at ~ 2000 cal BP lead to the oxygenation of sediment, the degradation of organic matter and the absence of pyrite. Oscillations of the lake level thereafter were of minor amplitude and not able to establish anoxia at the lake bottom again. A wet spell between ~ 1500 cal BP and ~ 1150 cal BP is visible in proxies referring to catchment hydrology and the ostracod-based water depth transfer function gives only a slightly elevated lake level. The last ~ 300 years are characterized by low TOC and rising TN values reflecting enhanced nutrient supply and hence an advancing influence of human activity in the catchment. Decreasing TOC/TN values point to a complete shift to almost solely aquatic biomass production. These results show that hydrological variations in terms of lake level change based on monsoonal strength can be linked to redox conditions at the lake bottom of Nam Co. Comparison with other archives over larger parts of the Tibetan Plateau and beyond exhibits a rather homogeneous climatic pattern throughout the late Holocene.

Seismic investigations of the Greenland ice sheet at EGIG points

The compressional and the shear wave velocities in the Greenland ice sheet are derived from seismic records of the EGIG 1959. Further the variation of velocities in the firn and the dependance of Poisson's ratio from depth are determined. At Station Centrale, two P-waves are recorded from underground layers. Their velocities show that the ice basement consists of crystalline rocks. The P-wave velocities derived from reflections agree well with those obtained by refraction shooting. From this agreement results that the ice is ± homogenous and ± isotropic for Pwaves. The elastic constants for isotropic ice are calculated. Finally the temperature dependence of the velocities is discussed.

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.