Expression of p53, {\it * ras\/} and PCNA in human colonic neoplasms: Possible biomarkers of malignant potential

Colorectal cancer is a leading cause of cancer mortality and early detection can significantly improve the clinical outcome. Most colorectal cancers arise from benign neoplastic lesions recognized as adenomas. Only a small percentage of all adenomas will become malignant. Thus, there is a need to identify specific markers of malignant potential. Studies at the molecular level have demonstrated an accumulation of genetic alterations, some hereditary but for the most occurring in somatic cells. The most common are the activation of ras, an oncogene involved in signal transduction, and the inactivation of p53, a tumor suppressor gene implicated in cell cycle regulation. In this study, 38 carcinomas, 95 adenomas and 20 benign polyps were analyzed by immunohistochemistry for the abnormal expression of p53 and ras proteins. An index of cellular proliferation was also measured by labeling with PCNA. A general overexpression of p53 was immunodetected in 66% of the carcinomas, while 26% of adenomas displayed scattered individual positive cells or a focal high concentration of positive cells. This later was more associated with severe dysplasia. Ras protein was detected in 37% of carcinomas and 32% of adenomas mostly throughout the tissue. p53 immunodetection was more frequent in adenomas originating in colons with synchronous carcinomas, particularly in patients with familial adenomatous polyposis and it may be a useful marker in these cases. Difference in the frequency of p53 and ras alterationbs was related to the location of the neoplasm. Immunodetection of p53 protein was correlated to the presence of a mutation in p53 gene at exon 7 and 5 in 4/6 carcinomas studied and 2 villous adenomas. Thus, we characterized in adenomas the abnormal expression of two proteins encoded by the most commonly altered genes in colorectal cancer. p53 alteration appears to be more specifically associated with transition to malignancy than ras. By using immunohistochemistry, a technique that keeps the architecture of the tissue intact, it was possible to correlate these alterations to histopathological characteristics that were associated with higher risks for transformation: villous content, dysplasia and size of adenoma. ^

Mechanism of mRNA stability control mediated by AU -rich element: Characterization of cis-elements and trans-factors

Regulation of cytoplasmic deadenylation, the first step in mRNA turnover, has direct impact on the fate of gene expression. AU-rich elements (AREs) found in the 3′ untranslated regions of many labile mRNAs are the most common RNA-destabilizing elements known in mammalian cells. Based on their sequence features and functional properties, AREs can be divided into three classes. Class I or class III ARE directs synchronous deadenylation, whereas class II ARE directs asynchronous deadenylation with the formation of poly(A)-intermediates. Through systematic mutagenesis study, we found that a cluster of five or six copies of AUUUA motifs forming various degrees of reiteration is the key feature dictating the choice between asynchronous versus synchronous deadenylation. A 20–30 nt AU-rich sequence immediately 5 ′ to this cluster of AUUUA motifs can greatly enhance its destabilizing ability and is an integral part of the AREs. These two features are the defining characteristics of class II AREs. ^ To better understand the decay mechanism of AREs, current methods have several limitations. Taking the advantage of tetracycline-regulated promoter, we developed a new transcriptional pulse strategy, Tet-system. By controlling the time and the amount of Tet addition, a pulse of RNA could be generated. Using this new system, we showed that AREs function in both growth- and density-arrested cells. The new strategy offers for the first time an opportunity to investigate control of mRNA deadenylation and decay kinetics in mammalian cells that exhibit physiologically relevant conditions. ^ As a member of heterogeneous nuclear RNA-binding protein, hnRNP D 0/AUF1 displays specific affinities for ARE sequences in vitro . But its in vivo function in ARE-mediated mRNA decay is unclear. AUF1/hnRNP D0 is composed of at least four isoforms derived by alternative RNA splicing. Each isoform exhibits different affinity for ARE sequence in vitro. Here, we examined in vivo effect of AUF1s/hnRNP D0s on degradation of ARE-containing mRNA. Our results showed that all four isoforms exhibit various RNA stabilizing effects in NIH3T3 cells, which are positively correlated with their binding affinities for ARE sequences. Further experiments indicated that AUF1/hnRNP D0 has a general role in modulating the stability of cytoplasmic mRNAs in mammalian cells. ^

Major and trace element concentrations of sediments from the IODP Exp302 sites

We analyzed a suite of sediment samples recovered in the central Arctic Ocean for major, trace, and rare earth elements in order to assess changes in terrigenous source material throughout the Cenozoic. The terrigenous component consists of two end-members. Input from a shale-like composition dominates bulk sediments, especially those deposited during the Paleocene and since the Miocene, and may represent sediment supply from the eastern Laptev Sea. Therefore, even though the environment and transport mechanisms may have varied from ice free to ice dominated, sequences of the early Paleogene and later Neogene appear to have been influenced by a single major terrigenous source. This suggests similar transport capabilities and trajectories for both ocean and drift currents through significant parts of the Cenozoic. Influence from a more mafic source appears to be more important through the early Eocene to the middle Miocene and most likely represents material from the western Laptev Sea or Kara Sea. Thus, Eocene major changes in surface water productivity appear broadly synchronous with those in terrigenous provenance. A combination of regional sea level variations, local shelf processes, and transport mechanisms are among the more probable causes for the observed source changes. Although the assignment of sources using chemistry presently is constrained by a lack of data from certain regions (e.g., eastern Siberian Sea) our results generally agree with inferences based on mineralogy or radiogenic isotopes and shed further light on long-term reconstructions of the central Arctic Ocean.

Sedimentological and clay mineralogical analysis of ODP sites in the central Fram Strait

This study presents the results of high-resolution sedimentological and clay mineralogical investigations on sediments from ODP Sites 908A and 909AlC located in the central Fram Strait. The objective was to reconstruct the paleoclimate and paleoceanography of the high northern latitudes since the middle Miocene. The sediments are characterised in particular by a distinctive input of ice-rafted material, which most probably occurs since 6 Ma and very likely since 15 Ma. A change in the source area at 1 1.2 Ma is clearly marked by variations within clay mineral composition and increasing accumulation rates. This is interpreted as a result of an increase in water mass exchange through the Fram Strait. A further period of increasing exchange between 4-3 Ma is identified by granulometric investigations and points to a synchronous intensification of deep water production in the North Atlantic during this time interval. A comparison of the components of coarse and clay fraction clearly shows that both are not delivered by the Same transport process. The input of the clay fraction can be related to transport mechanisms through sea ice and glaciers and very likely also through oceanic currents. A reconstruction of source areas for clay minerals is possible only with some restrictions. High smectite contents in middle and late Miocene sediments indicate a background signal produced by soil formation together with sediment input, possibly originating from the Greenland- Scotland Ridge. The applicability of clay mineral distribution as a climate proxy for the high northern latitudes can be confirmed. Based on a comparison of sediments from Site 909C, characterised by the smectite/illite and chlorite ratio, with regional and global climatic records (oxygen isotopes), a middle Miocene cooling phase between 14.8-14.6 Ma can be proposed. A further cooling phase between 10-9 Ma clearly shows similarities in its Progress toward drastic decrease in carbonate sedimentation and preservation in the eastern equatorial Pacific. The modification in sea water and atmosphere chemistry may represent a possible link due to the built-up of equatorial carbonate platforms. Between 4.8-4.6 Ma clay mineral distribution indicates a distinct cooling trend in the Fram Strait region. This is not accompanied by relevant glaciation, which would otherwise be indicated by the coarse fraction. The intensification of glaciation in the northern hemisphere is distinctly documented by a rapid increase of illite and chlorite starting from 3.3 Ma, which corresponds to oxygen isotope data trends from North Atlantic.

Granulometry of two sediment cores from Maxwell Bay, South Shetland Islands, West Antarctica

The climate evolution of the South Shetland Islands during the last c. 2000 years is inferred from the multiproxy analyses of a long (928 cm) sediment core retrieved from Maxwell Bay off King George Island. The vertical sediment flux at the core location is controlled by summer melting processes that cause sediment-laden meltwater plumes to form. These leave a characteristic signature in the sediments of NE Maxwell Bay. We use this signature to distinguish summer and winter-dominated periods. During the Medieval Warm Period, sediments are generally finer which indicates summer-type conditions. In contrast, during the Little Ice Age (LIA) sediments are generally coarser and are indicative of winter-dominated conditions. Comparison with Northern and Southern Hemisphere, Antarctic, and global temperature reconstructions reveals that the mean grain-size curve from Maxwell Bay closely resembles the curve of the global temperature reconstruction. We show that the medieval warming occurred earlier in the Southern than in the Northern Hemisphere, which might indicate that the warming was driven by processes occurring in the south. The beginning of the LIA appears to be almost synchronous in both hemispheres. The warming after the LIA closely resembles the Northern Hemisphere record which might indicate this phase of cooling was driven by processes occurring in the north. Although the recent rapid regional warming is clearly visible, the Maxwell Bay record does not show the dominance of summer-type sediments until the 1970s. Continued warming in this area will likely affect the marine ecosystem through meltwater induced turbidity of the surface waters as well as an extension of the vegetation period due to the predicted decrease of sea ice in this area.

Mineralogy and nannoplankton distribution in ODP Hole 194-1195A

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

Age model and Nd isotope ratios of DSDO Hole 43-386 and ODP Hole 210-1276A

Modern thermohaline circulation plays a role in latitudinal heat transport and in deep-ocean ventilation, yet ocean circulation may have functioned differently during past periods of extreme warmth, such as the Cretaceous. The Late Cretaceous (100-65 Ma) was an important period in the evolution of the North Atlantic Ocean, characterized by opening ocean gateways, long-term climatic cooling and the cessation of intermittent periods of anoxia (oceanic anoxic events, OAEs). However, how these phenomena relate to deep-water circulation is unclear. We use a proxy for deep-water mass composition (neodymium isotopes; e-Nd) to show that, at North Atlantic ODP Site 1276, deep waters shifted in the early Campanian (~78-83 Ma) from e-Nd values of ~-7 to values of ~-9, consistent with a change in the style of deep-ocean circulation but >10 Myr after a change in bottom water oxygenation conditions. A similar, but more poorly dated, trend exists in e-Nd data from DSDP Site 386. The Campanian e-Nd transition observed in the North Atlantic records is also seen in the South Atlantic and proto-Indian Ocean, implying a widespread and synchronous change in deep-ocean circulation. Although a unique explanation does not exist for the change at present, we favor an interpretation that invokes Late Cretaceous climatic cooling as a driver for the formation of Southern Component Water, which flowed northward from the Southern Ocean and into the North Atlantic and proto-Indian Oceans.

A refined Pliocene to early Pleistocene chronostratigraphic frame at ODP Hole 653A (West Mediterranean)

Two planktonic foraminiferal oxygen isotope records of ODP Hole 653A (Tyrrhenian Sea) are presented for the time period extending from approximately 0.8 to 3.0 Ma. Six, generally accepted, synchronous bioevents were used to precise the oxygen isotope chronology and to identify the oxygen isotope stages 22 down to 114. Subsequently, this oxygen isotope chronology was used to determine the synchronism or diachronism of various other biostratigraphic events with those recorded in the Singa and Ficarazzi land sections (Italy) and those in other DSDP/ODP sites. New results concern the diachronity of the FOD of the planktonic foraminiferal species N. atlantica, G.truncatulinoides truncatulinoides and G. inflata between ODP Hole 653A and the Italian landsections. Because many species entered the Mediterranean in short term fluxes, strongly related to the southward migration of cool North Atlantic surface waters, their time distribution through the Pliocene-Pleistocene generally corresponds to alternated intervals of presence and absence. This should explain most of the apparently diachronous appearances and disappearances. Alternating presence-absence patterns are of less importance for the various nannofossil events. The LOD of D. surculus occurs during the transition of stage 100 to 101 in both ODP Hole 653A and the Singa section, which is in perfect agreement with the disappearance of this species from the open ocean. The LOD of D. pentaradiatus in the Mediterranean occurs in stages 100-99, which seems to be consistent with the extinction of this species in the southern Hemisphere. G. oceanica, which corresponds to the 4 µm < Gephyrocapsa spp <5.5 µm is recorded in stages 65 to 64 at ODP Hole 653A. The Gephyrocapsa spp. >5.5 µm first occurred in stage 51 at Hole 653A, which fits within the uncertainty interval for this event stretching from stage 51 to 47 in the open ocean and seems therefore a useful tool for conventional biostratigraphy in the Mediterranean.

(Table 1) Element analyses of DSDP Hole 15-149

An iridium anomaly has been found in coincidence with the known microtektite level in cores from Deep Sea Drilling Project site 149 in the Caribbean Sea. The iridium was probably not in the microtektites but deposited simultaneously with them; this could occur if the iridium was deposited from a dust cloud resulting from a bolide impact, as suggested for the anomaly associated with the Cretaceous-Tertiary boundary. Other workers have deduced that the microtektites are part of the North American strewn tektite field, which is dated at about 34 million years before present, and that the microtektite horizon in deep-sea cores is synchronous with the extinction of five radiolarian species. Mass extinctions also occur in terrestrial mammals within 4 million years of this time. The iridium anomaly and the tektites and microtektites are supportive of a major bolide impact about 34 million years ago.

(Table 1) Geochemistry of ash layers at DSDP Leg 57 Holes

The study of the main characteristics of ash layers in Leg 57 cores shows that they are suitable for an analysis of the effect on eruptive activity of their distribution. We found (1) sediment recovery good and ash layers numerous; (2) sedimentary environment generally free from terrigenous clastic material; (3) reworking limited; (4) volcanic glass very acidic, ranging from rhyolitic to rhyodacitic composition; and (5) alteration and diagenesis negligible above the lower Miocene. The curves of explosive volcanic activity in Holes 438, 439, and 440 display two stages of high activity: an early one around 16 m.y. and a late one starting 5 m.y. B.P., both stages being separated by an upper Miocene quiescence. Detail in these results is limited by the chemical composition of the glass and accounts only for trends in explosive acid volcanism. Nevertheless, results are roughly in agreement with other data from the Northwest Pacific, although some discrepancies in the correlation of intensity of the episodes occur. The data from Leg 57 support the hypothesis of synchronous pulses in explosive volcanism.

Dust flux records from the Subarctic North Pacific

We present a new record of eolian dust flux to the western Subarctic North Pacific (SNP) covering the past 27000 years based on a core from the Detroit Seamount. Comparing the SNP dust record to the NGRIP ice core record shows significant differences in the amplitude of dust changes to the two regions during the last deglaciation, while the timing of abrupt changes is synchronous. If dust deposition in the SNP faithfully records its mobilization in East Asian source regions, then the difference in the relative amplitude must reflect climate-related changes in atmospheric dust transport to Greenland. Based on the synchronicity in the timing of dust changes in the SNP and Greenland, we tie abrupt deglacial transitions in the 230Th-normalized 4He flux record to corresponding transitions in the well-dated NGRIP dust flux record to provide a new chronostratigraphic technique for marine sediments from the SNP. Results from this technique are complemented by radiocarbon dating, which allows us to independently constrain radiocarbon paleoreservoir ages. We find paleoreservoir ages of 745 ± 140 yr at 11653 yr BP, 680 ± 228 yr at 14630 yr BP and 790 ± 498 yr at 23290 yr BP. Our reconstructed paleoreservoir ages are consistent with modern surface water reservoir ages in the western SNP. Good temporal synchronicity between eolian dust records from the Subantarctic Atlantic and equatorial Pacific and the ice core record from Antarctica supports the reliability of the proposed dust tuning method to be used more widely in other global ocean regions.

Calcareous nannofossils and planktic foraminiferal assemblages of ODP Hole 198-1210A

Calcareous nannofossil and planktic foraminiferal assemblages from ODP Hole 1210A in the northwestern Pacific Ocean were used to reconstruct surface-water conditions for the past 500 kyr. Stratigraphic control was provided by calcareous nannofossil events that are thought to be synchronous over a broad range of latitudes. Calcareous nannofossil and planktic foraminiferal assemblages and abundance patterns indicate the unlikelihood of long term (Milankovitch-scale) latitudinal shifts of the Kuroshio Extension over the last 500 kyr and illustrate two successive surface water-mass states, one that prevailed prior to 300 ka and one that existed after 300 ka. The relative abundance of very small placoliths and the absolute abundance of the upper photic zone (UPZ) coccolith species decrease abruptly at approximately 300 ka. The relative abundance of the lower photic zone (LPZ) species Florisphaera profunda greatly increases at the same time, although intervals during which the relative abundance of this taxon is very low or absent also occur prior to 300 ka. The absolute abundance of planktic foraminifera gradually increased after the 300-ka boundary, including peaks of Globoconella inflata. These assemblage and abundance changes suggest significant modifications to the surface water-mass structure. Surface water was weakly stratified prior to 300 ka, but alternated between intensely stratified and vertically mixed after 300 ka. Changes in the surface water-mass structure suggest an intensification of the East Asian summer and winter monsoon after 300 ka.

Benthic foraminifera of cores from ODP Leg 117

The relative abundances of benthic foraminifers from the Oman margin have been analyzed from ODP Sites 725 and 726 near the upper boundary of the oxygen-minimum zone (OMZ) and 728 near the lower boundary. The relative abundance pattern of the benthic foraminiferal species in the two shallow sites show synchronous changes, which, together with variations in the faunal composition, may be attributed to changes in the location of the upper boundary of the OMZ during the last 7 million years. At the deeper site, the relative abundance pattern shows considerable variation in the faunal composition during the last 8 million years. The strong dominance of the shallow-water species Ammonia beccarii during the early Pliocene at Site 728 suggests a water depth less than 400 m during the early Pliocene and subsequent subsidence during the middle and late Pliocene to the present > 1400 m water depth.

Dinoflagellate and other palynomorph abundance in sediments from ODP Leg 189 sites

At Ocean Drilling Program (ODP) Leg 189 Sites 1170-1172, the climatologically critical Eocene-Oligocene (E-O) transition is barren of any calcareous microfossils but contains rich marine organic walled dinoflagellate cyst (dinocyst) and diatom assemblages, suitable for detailed biostratigraphic and paleoenvironmental analysis. The resulting first-ever integrated dinocyst/diatom magnetostratigraphy allows confident correlation of the E-O interval between all Leg 189 sites, including Site 1168. Our correlations indicate that the (deep) opening of the Tasmanian Gateway occurred quasi-synchronously throughout the Tasmanian region, starting at ~35.5 Ma. At Sites 1170-1172, quantitatively, three distinct dinocyst assemblages may be distinguished that reflect the relatively rapid and pronounced stepwise environmental changes associated with the E-O transition in the Tasmanian region, from a pro-deltaic setting to a deep marine pelagic setting. Moreover, synchronous with the deepening of the gateway, at the southern and eastern Sites 1170-1172, typical endemic Antarctic assemblages were replaced by more cosmopolitan dinocyst communities. In marked contrast, at Site 1168 off western Tasmania, endemic Antarctic taxa are virtually absent during the E-O transition. At Sites 1170-1172, the endemic Antarctic dinocyst assemblage (Transantarctic Flora) drastically changes into a more cosmopolitan assemblage at ~35.5 Ma, with a more offshore character, reflecting the arrival of different oceanographic and environmental conditions associated with the deepening of the Tasmanian Gateway. In turn, this assemblage grades at ~34 Ma into one more typical for even more offshore and/or upwelling conditions at Site 1172. In slightly younger deposits at all sites, organic microfossils are virtually absent, reflecting winnowing and oxidation, indicative of a next step of oceanographic development. This phase may be dated as close to the Oceanic Anoxic (Oi)-1 18O (Antarctic glaciation) event (~33.3 Ma). In a single productive sample from the earliest Oligocene the northern Site 1172, a relatively warm-water cosmopolitan assemblage has been recovered. This aspect contrasts findings from coeval deposits from the Ross Sea, where endemic Antarctic species remain dominant. Somewhere between the paleogeographic positions of Site 1172 and the Ross Sea, a strong differentiation of surface waters occurred in the earliest Oligocene, possibly reflecting the onset of the Antarctic Circumpolar Current.