The structural and functional relationship of the p53 tumor suppressor protein

The tumor-suppressing function of p53 can be affected in a variety of manners. Here, we describe a novel mechanism of transformation by mutant p53. Previously, it had been believed that mutant p53 molecules transform cells by oligomerizing with wild-type p53 and inactivating it. However, we demonstrated that there exists an additional mechanism of inactivation of p53 available to p53 mutants. It involves sequestration of cofactors necessary to p53, and subsequent interruption of its transactivation and tumor suppression functions. The p53 amino or carboxyl termini, known to interact with a large number of cellular factors, can affect wild-type p53 in this manner. Although they are unable to oligomerize with wild-type p53, they transform cells containing p53, and inhibit its transactivation ability. In addition, they interrupt growth suppression by p53, but not RB, confirming that they specifically affect p53 function, rather than having a general growth-stimulatory phenomenon. Also, we have cloned a p53 tumor mutation which results in expression of the amino terminus of p53. This provides a means to study the factor-sequestration transforming mechanism in vivo. Additionally, we found that the published sequence of the mdm2 gene is in error. mdm2 is a gene intimately involved with p53, blocking its ability to transform cells. Finally, previous data had established the influence of cell-cycle status on p53 function. In growth-arrested cells, wild-type p53 expressed by a transgene cannot activate transcription, but if these cells are forced to cycle by addition of cyclin E, p53 once again becomes functional. In this study, we extend these findings by examining only those cells successfully transfected, using fluorescence-activated cell sorting. Our results support the previous data, that cyclin E pushes growth-arrested cells back into the cell cycle. In summary, we have demonstrated the potential importance of cofactor association and protein modification to the abilities of p53 to cause transcription activation and repression, inhibition of DNA replication and induction of DNA repair, and initiation of cell-cycle arrest and apoptosis. Further elucidation of these processes and their roles in tumor suppression will prove fascinating indeed. ^

Searching for the ideal DNA recognition code of covalent ligands

The combitiatorial approach restriction endonuclease protection selection and amplification REPSA was successfully used to determine ideal DNA interactions sites of covalent ligands. Unlike most other combinatorial methods, REPSA is based on inhibition of enzymatic cleavage by specific ligand-DNA complexes, which enables identification of binding sites of various ligands. However, the inherent nature of this technique posses a problem during selection of binding sites of covalent ligands. By modifying the technique according to the nature of the ligand, we demonstrate the flexibility of REPSA in identifying the preferred binding sites for monocovalent ligands, topoisomerase I and tallimustine, and the bicovalent ligand topoisomerase II. From among the preferred binding sites, we identified the consensus binding sequence of camptothecin induced topoisomerase I cleavage as ‘aGWT/Gc’, and tallimustine consensus sequences as ‘GTTCTA’ and ‘TTTTTTC’. We have shown for the first time that preferential binding of tallimustine occurs at sequences not previously reported. Furthermore, our data indicate that tallimustine is a novel DNA minor groove, guanine-specific alkylating agent. ^ Additionally, we have demonstrated in vivo that sequence-specific covalent DNA-binding small molecules have the ability to regulate transcription by inhibiting RNA polymerase II. Tallimustine, binding to its preferred sequences located in the 5′ untranslated region were an effective impediment for transcribing polymerase II. The ability of covalent binding small molecules to target predetermined DNA sequences located downstream of the promoter suggests a general approach for regulation of gene expression. ^

Description and chemical composition of ferromanganese deposits from Trout Lake, northern Wisconsin

Sediments were collected with Eckman and Petersen dredges from the bottom of Trout Lake, northern Wisconsin, at 221 stations. Sampling was done with a spud sampler at 32 stations, and core samples were obtained with a Jenkins and Mortimer and a Twenhofel sampler at 17 stations. The shore and offshore deposits of the shores of Trout Lake and the shores of the islands are described. Megascopic descriptions are given of the samples collected with the Eckman and Petersen dredges. Sediments on bottoms of about 10 meters or deeper are mainly gyttja, or crusts composed of mixtures of organic matter, ferric hydroxide, and some form of manganese oxide. The latter deposits are extensive. Detailed descriptions of some of the samples of sands are given, and generalizations respecting size and distribution are made. Tables showing quartiles, medians, and coefficients of sorting and skewness of the coarse sediments collected from the bottom are given in tables. Mechanical analyses of all fine sediments, mainly gyttja, were not made, as previous experience seems to have demonstrated that results have no sedimentational value. Organic matter of the gyttja was determined and also the percentages of lignin in the organic matter. Core samples are composed almost entirely of fine materials, mainly gyttja, and determinations were made on these samples in the same way as on the samples obtained with the Eckman and Petersen dredges. Studies of the core samples show that the fine sediments usually contain in excess of 90 per cent moisture and there is very little change in the moisture content from top to bottom of cores. A map shows the distribution of the iron and manganese deposits. These deposits were found to contain 10 to 20 per cent of organic matter, 11 to 16 per cent of metallic iron, and 12 to 30 per cent of metallic manganese. No stratification of any kind was found in any of the deep-water sediments of Trout Lake except in the iron and manganese crusts. Absence of stratification is considered to be due to the slow rate of deposition and the mixing of sediments by organisms which dwell in them. The data indicate that the rate of deposition in the deep waters of Trout Lake is of the order of 1 foot in 15,000 years.

Clay mineralogy and multi-element chemistry of surface sediments on the Aiberian-Arctic Shelf

Clay mineral and bulk chemical (Si, Al, K, Mg, Sr, La, Ce, Nd) analyses of terrigenous surface sediments on the Siberian-Arctic shelf indicate that there are five regions with distinct, or endmember, sedimentary compositions. The formation of these geochemical endmembers is controlled by sediment provenance and grain size sorting. (1) The shale endmember (Al, K and REE rich sediment) is eroded from fine-grained marine sedimentary rocks of the Verkhoyansk Mountains and Kolyma-Omolon superterrain, and discharged to the shelf by the Lena, Yana, Indigirka and Kolyma Rivers. (2) The basalt endmember (Mg rich) originates from NE Siberia's Okhotsk-Chukotsk volcanic belt and Bering Strait inflow, and is prevalent in Chukchi Sea Sediments. Concentrations of the volcanically derived clay mineral smectite are elevated in Chukchi fine-fraction sediments, corroborating the conclusion that Chukchi sediments are volcanic in origin. (3) The mature sandstone endmember (Si rich) is found proximal to Wrangel Island and sections of the Chukchi Sea's Siberian coast and is derived from the sedimentary Chukotka terrain that comprises these landmasses. (4) The immature sandstone endmember (Sr rich) is abundant in the New Siberian Island region and reflects inputs from sedimentary rocks that comprise the islands. (5) The immature sandstone endmember is also prevalent in the western Laptev Sea, where it is eroded from sedimentary deposits blanketing the Siberian platform that are compositionally similar to those on the New Siberian Islands. Western Laptev can be distinguished from New Siberian Island region sediments by their comparatively elevated smectite concentrations and the presence of the basalt endmember, which indicate Siberian platform flood basalts are also a source of western Laptev sediments. In certain locations grain size sorting noticeably affects shelf sediment chemistry. (1) Erosion of fines by currents and sediment ice rafting contributes to the formation of the coarse-grained sandstone endmembers. (2) Bathymetrically controlled grain size sorting, in which fines preferentially accumulate offshore in deeper, less energetic water, helps distribute the fine-grained shale and basalt endmembers. An important implication of these results is that the observed sedimentary geochemical endmembers provide new markers of sediment provenance, which can be used to track sediment transport, ice-rafted debris dispersal or the movement of particle-reactive contaminants.

Age determination and grain size distribution of sediment core GeoB3375-1

The palaeoclimatic conditions during the Last Glacial Maximum (LGM) of southern South America and especially latitudinal shifts of the southern westerly wind belt are still discussed controversially. Longer palaeoclimatic records covering the Late Quaternary are rare. A particularly sensitive area to Late Quaternary climatic changes is the Norte Chico, northern Chile, because of its extreme climatic gradients. Small shifts of the present climatic zonation could cause significant variations of the terrestrial sedimentary environment which would be recorded in marine terrigenous sediments. To unveil the history of shifting climatic zones in northern Chile, we present a sedimentological study of a marine sediment core (GeoB 3375-1) from the continental slope off the Norte Chico (27.5°S). Sedimentological investigations include bulk- and silt grain-size determinations by sieving, Atterberg separation, and detailed SediGraph analyses. Additionally, clay mineralogical parameters were obtained by X-ray diffraction methods. The 14C-dated core, covering the time span from approximately 10,000 to 120,000 cal. yr B.P., consists of hemipelagic sediments. Terrigenous sedimentological parameters reveal a strong cyclicity, which is interpreted in terms of variations of sediment provenance, modifications of the terrestrial weathering regimes, and modes of sediment input to the ocean. These interpretations imply cyclic variations between comparatively arid climates and more humid conditions with seasonal precipitation for northern Chile (27.5°S) through the Late Quaternary. The cyclicity of the terrigenous sediment parameters is strongly dominated by precessional cycles. For the palaeoclimatic signal, this means that more humid conditions coincide with maxima of the precession index, as e.g. during the LGM. Higher seasonal precipitation for this part of Chile is most likely derived from frontal winter rain of the Southern Westerlies. Thus, the data presented here favour not only an equatorward shift of this atmospheric circulation system during the LGM, but also precession-controlled latitudinal movements throughout the Late Quaternary. Precessional forcing of latitudinal movements of the westerly atmospheric circulation system may be conceivable through teleconnections to the Northern Hemisphere monsoonal system in the Atlantic Ocean region.

Northwards and eastwards velocities extracted from a historical run (for the year 2000) of the UVic Earth System Climate Model of Weaver et al. (2001)

This study provides a theoretical assessment of the potential bias due to differential lateral transport on multi-proxy studies based on a range of marine microfossils. Microfossils preserved in marine sediments are at the centre of numerous proxies for paleoenvironmental reconstructions. The precision of proxies is based on the assumption that they accurately represent the overlying watercolumn properties and faunas. Here we assess the possibility of a syn-depositional bias in sediment assemblages caused by horizontal drift in the water column, due to differential settling velocities of sedimenting particles based on their shape, size and density, and due to differences in current velocities. Specifically we calculate the post-mortem lateral transport undergone by planktic foraminifera and a range of other biological proxy carriers (diatoms, radiolaria and fecal pellets transporting coccolithophores) in several regions with high current velocities. We find that lateral transport of different planktic foraminiferal species is minimal due to high settling velocities. No significant shape- or size-dependent sorting occurs before reaching the sediment, making planktic foraminiferal ideal proxy carriers. In contrast, diatoms, radiolaria and fecal pellets can be transported up to 500km in some areas. For example in the Agulhas current, transport can lead to differences of up to 2°C in temperature reconstructions between different proxies in response to settling velocities. Therefore, sediment samples are likely to contain different proportions of local and imported particles, decreasing the precision of proxies based on these groups and the accuracy of the temperature reconstruction.

Sedimentology and mineralogy of surface sediments from the Chilean continental margin

The regional patterns of texture and composition of modern continental slope and pelagic sediments off Chile between 25°S and 43°S reflect the latitudinal segmentation of geological, morphological, and climatic features of the continental hinterland. Grain-size characteristics are controlled by the grain-size of source rocks, the weathering regime, and mode of sediment input (eolian off northern Chile vs fluvial further south). Bulk-mineral assemblages reveal a low grade of maturity. Regional variations are governed by the source-rock composition of the different geological terranes and the relative source-rock contribution of the Coastal Range and Andes, as controlled by the continental hydrology. The relative abundance of clay minerals is also predominantly influenced by the source-rock composition and partly by continental smectite neoformation. Latitudinal variations of illite crystallinities along the Chilean continental slope (and west of the Peru-Chile trench) clearly reflect modifications of the weathering regime which correspond to the strong climatic zonation of Chile.

Chemical composition of zoobenthos and bottom sediments from the gas-hydrate seep area near the Paramushir Island, Kuril Island arc

Bioaccumulation of metals by zoobenthos was investigated during cruise 11A of R/V Akademik Mstislav Keldysh in the vicinity of a gas-hydrate seep off Paramushir Island in the Sea of Okhotsk. Atomic absorption studies of concentrations of Al, Fe, Mn, Ni, Cu and Zn in zoobenthos (polychaetes, bivalves, ophiurans and echinoderms) collected from depths of 700-800 m indicated that their concentrations in individuals near the seep were not significantly different from those in individuals from other communities. Obtained results indicate that sea urchins and holothurians (non-sorting bottom-feeders) can separate mineral fraction of ingested bottom material.

Geochemistry, clay mineralogy and grain size distribution in various sediment cores drilled during ODP Leg 119 on the Antarctic continental shelf off Prydz Bay

Drilling was undertaken at five sites (739-743) on ODP Leg 119 on a transect across the continental shelf of Prydz Bay, East Antarctica, to elucidate the long-term glacial history of the area and to examine the importance of the area with respect to the development of the East Antarctic ice sheet as a whole. In addition to providing a record of glaciation spanning 36 m.y. or more, Leg 119 has provided information concerning the development of a continental margin under the prolonged influence of a major ice sheet. This has allowed the development of a sedimentary model that may be applicable not only to other parts of the Antarctic continental margin, but also to northern high-latitude continental shelves. The cored glacial sedimentary record in Prydz Bay consists of three major sequences, dominated by diamictite: 1. An upper flat-lying sequence that ranges in thickness from a few meters in inner and western Prydz Bay to nearly 250 m in the outer or eastern parts of the bay. The uppermost few meters consist of Holocene diatom ooze and diatomaceous mud with a minor ice-rafted component overlying diamicton and diamictite of late Miocene to Quaternary age. The diamictite is mainly massive, but stratified varieties and minor mudstone and diatomite also occur. 2. An upper prograding sequence cored at Sites 739 and 743, unconformly below the flat-lying sequence. This consists of a relatively steep (4° inclination) prograding wedge with a number of discrete sedimentary packages. At Sites 739 and 743 the sequence is dominated by massive and stratified diamictite, some of which shows evidence of slumping and minor debris flowage. 3. A lower, more gently inclined, prograding sequence lies unconformably below the flat-lying sequence at Site 742 and the upper prograding sequence at Site 739. This extends to the base of both sites, to 316 and 487 mbsf, respectively. It is dominated by massive, relatively clast-poor diamictite which is kaolinite-rich, light in color, and contains sporadic carbonate-cemented layers. The lower part of Site 742 includes well-stratified diamictites and very poorly sorted mudstones. The base of this site has indications of large-scale soft-sediment deformation and probably represents proximity to the base of the glacial sequence. Facies analysis of the Prydz Bay glacial sequence indicates a range of depositional environments. Massive diamictite is interpreted largely as waterlain till, deposited close to the grounding line of a floating glacier margin, although basal till and debris flow facies are also present. Weakly stratified diamictite is interpreted as having formed close to or under the floating ice margin and influenced by the input of marine diatomaceous sediment (proximal glaciomarine setting). Well-stratified diamictite has a stronger marine input, being more diatom-rich, and probably represents a proximal-distal glaciomarine sediment with the glaciogenic component being supplied by icebergs. Other facies include a variety of mudstones and diatom-rich sediments of marine origin, in which an ice-rafted component is still significant. None of the recovered sediments are devoid of a glacial influence. The overall depositional setting of the prograding sequence is one in which the grounded ice margin is situated close to the shelf edge. Progradation was achieved primarily by deposition of waterlain till. The flat-lying sequence illustrates a complex sequence of advances and retreats across the outer part of the shelf, with intermittent phases of ice loading and erosion. The glacial chronology is based largely on diatom stratigraphy, which has limited resolution. It appears that ice reached the paleoshelf break by earliest Oligocene, suggesting full-scale development of the East Antarctic ice sheet by that time. The ice sheet probably dominated the continental margin for much of Oligocene to middle Miocene time. Retreat, but not total withdrawal of the ice sheet, took place in late Miocene to mid-Pliocene time. The late Pliocene to Pleistocene was characterized by further advances across, and progradation of, the continental shelf. Holocene time has been characterized by reduced glacial conditions and a limited influence of glacial processes on sedimentation.

Mineralogical and grain size analysis of ODP Hole 119-745B from the Southern Ocean

The upper Miocene to Pleistocene sediments recovered at ODP Sites 745 and 746 in the Australian-Antarctic Basin are characterized by cyclic facies changes. Sedimentological investigations of a detailed Quaternary section reveal that facies A is dominated by a high content of siliceous microfossils, a relatively low terrigenous sediment content, an ice-rafted component, low concentrations of fine sediment particles, and a relatively high smectite content. This facies corresponds to interglacial sedimentary conditions. Facies B, in contrast, is characteristic of glacial conditions and is dominated by a large amount of terrigenous material and a smaller opaline component. There is also a prominent ice-rafted component. The microfossils commonly are reworked and broken. The clay mineral assemblages show higher proportions of glacially derived illite and chlorite. A combination of four different processes, attributed to glacial-interglacial cycles, was responsible for the cyclic facies changes during Quaternary time: transport by gravity, ice, and current and changes in primary productivity. Of great importance was the movement of the grounding line of the ice shelves, which directly influenced the intensity of ice rafting and of gravitational sediment transport to the deep sea. The extension of the ice shelves was also responsible for the generation of cold and erosive Antarctic Bottom Water, which controlled the grain-size distribution, particularly of the fine fraction, in the investigated area.

Age determination, sedimentological, biogeochemical, and plant macrofossils analyses of outcrop PG2038-1

Thermokarst lakes are a widespread feature of the Arctic tundra, in which highly dynamic processes are closely connected with current and past climate changes. We investigated late Quaternary sediment dynamics, basin and shoreline evolution, and environmental interrelations of Lake El'gene-Kyuele in the NE Siberian Arctic (latitude 71°17'N, longitude 125°34'E). The water-body displays thaw-lake characteristics cutting into both Pleistocene Ice Complex and Holocene alas sediments. Our methods are based on grain size distribution, mineralogical composition, TOC/N ratio, stable carbon isotopes and the analysis of plant macrofossils from a 3.5-m sediment profile at the modern eastern lake shore. Our results show two main sources for sediments in the lake basin: terrigenous diamicton supplied from thermokarst slopes and the lake shore, and lacustrine detritus that has mainly settled in the deep lake basin. The lake and its adjacent thermokarst basin rapidly expanded during the early Holocene. This climatically warmer than today period was characterized by forest or forest tundra vegetation composed of larches, birch trees and shrubs. Woodlands of both the HTM and the Late Pleistocene were affected by fire, which potentially triggered the initiation of thermokarst processes resulting later in lake formation and expansion. The maximum lake depth at the study site and the lowest limnic bioproductivity occurred during the longest time interval of ~7 ka starting in the Holocene Thermal Maximum and lasting throughout the progressively cooler Neoglacial, whereas partial drainage and an extensive shift of the lake shoreline occurred ~0.9 cal. ka BP. Correspondingly, this study discusses different climatic and environmental drivers for the dynamics of a thermokarst basin.