Expression of prostate-specific antigen variant MRNA transcripts in prostate cancer and benign prostatic hyperplasia

Prostate-specific antigen (PSA) is important in tumour detection, monitoring disease progression and tumour recurrence. however, PSA is not a cancerspecific marker as levels can also be elevated in benign prostatic disease. A number of different mRNA transcripts of PSA have also been identified in prostatic tissue, but have not been fully characterized (PSA 424, PSA 525, Schulz transcript). Tissue specimens from transurethral resection of the prostate (TURP) or radical prostatectomy were obtained from 17 men with BPH and 15 men with prostate cancer. Total RNA was extracted, and reverse-transcriptionpolymerase chain reaction (RT-PCR) and Southern analysis carried out using transcript-specific primers and probes to determine which mRNA PSA transcripts were expressed. Real-time PCR was performed to determine transcript levels between the two groups using transcript-specific primers and SYBR green fluorescence. Values obtained were normalized to a standard housekeeping gene, B2-microglobulin. Transcripts amplified by RT-PCR and real-time PCR were confirmed by DNA sequencing. Our results show that the transcripts were present in some, but not all, BPH and cancer samples indicating that they are not specific to either BPH or cancer. Analysis of real-time PCR normalized values using a Student’s t -test, shows that there is a significant difference between the two groups for PSA 424, but not wild-type PSA, PSA 525 or the Schulz transcript. Although a larger cohort of samples is needed to further confirm these results, these findings suggest that mRNA levels of PSA 424 may have some utility as a diagnostic or prognostic marker in prostate cancer detection.

Spatial and temporal patterns of aboveground net primary productivity (ANPP) along two freshwater-estuarine transects in the Florida Coastal Everglades

We present here a 4-year dataset (2001–2004) on the spatial and temporal patterns of aboveground net primary production (ANPP) by dominant primary producers (sawgrass, periphyton, mangroves, and seagrasses) along two transects in the oligotrophic Florida Everglades coastal landscape. The 17 sites of the Florida Coastal Everglades Long Term Ecological Research (FCE LTER) program are located along fresh-estuarine gradients in Shark River Slough (SRS) and Taylor River/C-111/Florida Bay (TS/Ph) basins that drain the western and southern Everglades, respectively. Within the SRS basin, sawgrass and periphyton ANPP did not differ significantly among sites but mangrove ANPP was highest at the site nearest the Gulf of Mexico. In the southern Everglades transect, there was a productivity peak in sawgrass and periphyton at the upper estuarine ecotone within Taylor River but no trends were observed in the C-111 Basin for either primary producer. Over the 4 years, average sawgrass ANPP in both basins ranged from 255 to 606 g m−2 year−1. Average periphyton productivity at SRS and TS/Ph was 17–68 g C m−2 year−1 and 342–10371 g C m−2 year−1, respectively. Mangrove productivity ranged from 340 g m−2 year−1 at Taylor River to 2208 g m−2 year−1 at the lower estuarine Shark River site. Average Thalassia testudinum productivity ranged from 91 to 396 g m−2 year−1 and was 4-fold greater at the site nearest the Gulf of Mexico than in eastern Florida Bay. There were no differences in periphyton productivity at Florida Bay. Interannual comparisons revealed no significant differences within each primary producer at either SRS or TS/Ph with the exception of sawgrass at SRS and the C−111 Basin. Future research will address difficulties in assessing and comparing ANPP of different primary producers along gradients as well as the significance of belowground production to the total productivity of this ecosystem.

Ethnic identity, self-esteem and academic factors in second -generation post-1970 Jamaican immigrants

Immigrants from Jamaica represent the largest number of migrants to the United States from the English speaking Caribbean. Research indicates that of all Caribbean immigrants they are most likely to retain the ethnic identity of their home country for the longest period of time. This dissertation explored the nature of ethnic identity and sought to determine its impact upon the additional variables of self-esteem and academic factors. A secondary analysis was carried out using data collected in the Spring of 1992 by Portes and Rumbaut on the children of immigrants attending the eighth and ninth grades in local schools in San Diego and southern Florida. A sample of 151 second-generation Jamaican immigrants was selected from the data set. ^ Six hypotheses yielded mixed results. Both parents who have a Jamaican ethnic identity present in the household are the best predictor Jamaican youth who retain a Jamaican ethnic identity. It was expected that ethnic identity would be a predictor of positive academic factors. The study showed that ethnic identity was not associated with one of the academic factors which were examined: help given with homework. ^ Neither family economic status nor parents' level of education played a significant role in the retention of Jamaican identity. Other findings were that there was no mean difference in the self-esteem scores of respondents who had similar ethnic identities to their parents and those who did not. There was also no difference found in the academic factors of either group. The study also showed that there was a small correlation between parent-child conflict and self-esteem. Specifically, the study found that the higher the conflict between youth and their parents, the lower the self-esteem of the youth. Finally it found that time lived in the U.S. was the best predictor of a higher GPA and it was also related to lower self-esteem. ^ Surprisingly, the study found that the relationship between ethnic identity and SES was the opposite of what was expected in that it found that SES was higher when there was no Jamaican identity. ^

The Allelic Abundance of Afghanistan, a Pool for West and South Eurasian Genes and a Blockade against Eastern Admixture

In this study, I divided samples from individuals within Afghanistan based upon geography (i.e., north versus south). I determined allelic frequencies and other statistical parameters for 15 STR loci (i.e., D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, Dl3S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA). I conducted pairwise comparisons with 19 neighboring Eurasian populations to assign Gstatistics and p-values. Categorizing the populations into five groups (i.e., Central Asia, East Asia, South Asia, the Middle East, and the Caucasus/Anatolia), I derived values for intra-population, inter-population, and total variance. Admixture analyses determined the highest allelic contributions to be from the Caucasus/ Anatolia, while negligible contributions were made by Central Asia and East Asia. A Correspondence Analysis revealed clustering of both northern and southern Afghanistan with Georgia, Turkey, northern Iran, and southern Iran of the Caucasus/ Anatolia and the Middle East. A Neighbor-Joining phylogenetic tree was constructed to generate bootstrap values over 1, 000 reiterations.

Physical oceanography, nutrients, and d18O measured on water bottle samples during POLARSTERN cruise ARK-XXII/2

Extremely low summer sea-ice coverage in the Arctic Ocean in 2007 allowed extensive sampling and a wide quasi-synoptic hydrographic and d18O dataset could be collected in the Eurasian Basin and the Makarov Basin up to the Alpha Ridge and the East Siberian continental margin. With the aim of determining the origin of freshwater in the halocline, fractions of river water and sea-ice meltwater in the upper 150 m were quantified by a combination of salinity and d18O in the Eurasian Basin. Two methods, applying the preformed phosphate concentration (PO*) and the nitrate-to-phosphate ratio (N/P), were compared to further differentiate the marine fraction into Atlantic and Pacific-derived contributions. While PO*-based assessments systematically underestimate the contribution of Pacific-derived waters, N/P-based calculations overestimate Pacific-derived waters within the Transpolar Drift due to denitrification in bottom sediments at the Laptev Sea continental margin. Within the Eurasian Basin a west to east oriented front between net melting and production of sea-ice is observed. Outside the Atlantic regime dominated by net sea-ice melting, a pronounced layer influenced by brines released during sea-ice formation is present at about 30 to 50 m water depth with a maximum over the Lomonosov Ridge. The geographically distinct definition of this maximum demonstrates the rapid release and transport of signals from the shelf regions in discrete pulses within the Transpolar Drift. The ratio of sea-ice derived brine influence and river water is roughly constant within each layer of the Arctic Ocean halocline. The correlation between brine influence and river water reveals two clusters that can be assigned to the two main mechanisms of sea-ice formation within the Arctic Ocean. Over the open ocean or in polynyas at the continental slope where relatively small amounts of river water are found, sea-ice formation results in a linear correlation between brine influence and river water at salinities of about 32 to 34. In coastal polynyas in the shallow regions of the Laptev Sea and southern Kara Sea, sea-ice formation transports river water into the shelf's bottom layer due to the close proximity to the river mouths. This process therefore results in waters that form a second linear correlation between brine influence and river water at salinities of about 30 to 32. Our study indicates which layers of the Arctic Ocean halocline are primarily influenced by sea-ice formation in coastal polynyas and which layers are primarily influenced by sea-ice formation over the open ocean. Accordingly we use the ratio of sea-ice derived brine influence and river water to link the maximum in brine influence within the Transpolar Drift with a pulse of shelf waters from the Laptev Sea that was likely released in summer 2005.

(Table 3) Barium barite and excess comparison, accumulation rates and productivity from surface sediments

Since Dymond et al. (1992, doi:10.1029/92PA00181) proposed the paleoproductivity algorithm based on "Bio-Ba", which relies on a strong correlation between Ba and organic carbon fluxes in sediment traps, this proxy has been applied in many paleoproductivity studies. Barite, the main carrier of particulate barium in the water column and the phase associated with carbon export, has also been suggested as a reliable paleoproductivity proxy in some locations. We demonstrate that Ba(excess) (total barium minus the fraction associated with terrigenous material) frequently overestimates Ba(barite) (barium associated with the mineral barite), most likely due to the inclusion of barium from phases other than barite and terrigenous silicates (e.g., carbonate, organic matter, opal, Fe-Mn oxides, and hydroxides). A comparison between overlying oceanic carbon export and carbon export derived from Ba(excess) shows that the Dymond et al. (1992) algorithm frequently underestimates carbon export but is still a useful carbon export indicator if all caveats are considered before the algorithm is applied. Ba(barite) accumulation rates from a wide range of core top sediments from different oceanic settings are highly correlated to surface ocean 14C and Chlorophyll a measurements of primary production. This relationship varies by ocean basin, but with the application of the appropriate f ratio to 14C and Chlorophyll a primary production estimates, the plot of Ba(barite) accumulation and carbon export for the equatorial Pacific, Atlantic, and Southern Ocean converges to a global relationship that can be used to reconstruct paleo carbon export.

Planktonic foraminiferal d18O and d13C values, derived sea-surface temperatures from d18O and selected planktonic foraminiferal species for core P69 of Hawke Bay off eastern North Island

Recent evidence suggests that the Subtropical Convergence (STC) zone east of New Zealand shifted little from its modern position along Chatham Rise during the last glaciation, and that offshore surface waters north of the STC zone cooled only slightly. However, at nearshore core site P69 (2195 m depth), 115 km off the east coast of North Island and ca 300 km north of the modern STC zone, planktonic foraminiferal species, transfer function data and stable oxygen and carbon isotope records suggest that surface waters were colder by up to 6°C during the late last glacial period compared to the Holocene, and included a strong upwelling signature. Presently site P69 is bathed by south-flowing subtropical waters in the East Cape Current. The nearshore western end of Chatham Rise supports a major bathymetric depression, the Mernoo Saddle, through which some exchange between northern subtropical and southern subantarctic water presently occurs. It is proposed that as a result of much intensified current flows south of the Rise during the last glaciation, a consequence of more compressed subantarctic water masses, lowered sea level, and an expanded and stronger Westerly Wind system, there was accelerated leakage northwards of both Australasian Subantarctic Water and upwelled Antarctic Intermediate Water over Mernoo Saddle in a modified and intensified Southland Current. The expanded cold water masses displaced the south-flowing warm East Cape Current off southeastern North Island, and offshore divergence was accompanied by wind-assisted upwelling of nutrient-rich waters in the vicinity of P69. A comparable kind of inshore cold water jetting possibly characterised most glacial periods since the latest Miocene, and may account for the occasional occurrence of subantarctic marine fossils in onland late Cenozoic deposits north of the STC zone, rather than invoking wholesale major oscillations of the oceanic STC itself.

Stable isotope and Cd/Ca ratios of Neogloboquadrina pachyderma in high-latitude sediments

Recent studies have stressed the role of high latitude nutrient levels and productivity in controlling the carbon isotopic composition of the deep sea and the CO2 content of the atmosphere. We undertook a study of the chemical composition of the polar planktonic foraminifer Neogloboquadrina pachyderma (s., sinistral coiling) from 30 late Holocene samples and 49 down core records from the high-latitude North and South Atlantic Oceans to evaluate the history of sea surface chemical change from glacial to interglacial time. Stable isotopic analysis of coretop samples from the Atlantic, Pacific and Southern Oceans shows no significant correlation between the delta13C of N. pachyderma and either delta13C or PO4 in seawater. Conversely, Cd/Ca ratios in planktonic foraminifera are consistent with the PO4 content of surface waters. The level of maximum glaciation (18,000 yr B.P.), identified by CLIMAP and delta18O, was chosen for mapping. Isopleths of delta18O on N. pachyderma (s.) in the North Atlantic reveal a pattern largely influenced by sea surface temperature (S.S.T.) and generally support the S.S.T. reconstruction of CLIMAP. Differences between the two suggest significantly lower salinity in North Atlantic surface waters at high latitudes than in lower latitudes. Down core delta13C records of N. pachyderma confirm that low delta13C values occurred in the northeast Atlantic during the latest glacial maximum (Labeyrie and Duplessy, 1985, doi:10.1016/0031-0182(85)90069-0). However, a map of delta13C for the 18,000 yr B.P. level for a much larger region in the North Atlantic shows that minimum N. pachyderma delta13C occurred in temperate waters. N. pachyderma delta13C decreased toward the southwest, reaching a minimum of -1 per mil at 37°N. Despite the variability seen in delta13C records of N. pachyderma, none of our cores show significant temporal variability in Cd/Ca. From the combined Cd/Ca and delta13C data we can see no evidence for an upwelling gyre in the eastern North Atlantic during the latest glacial maximum, nor evidence that the southern and northern oceans had significantly different levels of preformed nutrients than today.

(Table 2) Hydrogen sulphide and methane content, and loss on ignition in sediments obtained in the Gotland Deep, Baltic Sea

The distribution of methane and hydrogen sulfide concentrations in sediments of various basins of the Baltic Sea was investigated during 4 cruises in 1995 and 1996. Significant differences in the concentrations of both compounds were recorded between the basins and also between different areas within the Gotland Deep. High-methane sediments with distinctly increasing concentrations from the surface to deeper layers were distinguished from low-methane sediments without a clear gradient. Methane concentrations exhibited a fair correlation with the sediment accumulation rate, determined by measuring the total thickness of the post-Ancylus Holocene sequence on echosounding profiles in the Gotland Deep. Only weak correlations were observed with the content of organic matter in the surface layers of the sediments. Hydrogen sulfide concentrations in the sediments showed a positive correlation with methane concentrations, but, in contrast to methane concentrations, were strongly influenced by the transition from oxic to anoxic conditions in the water column between 1995 and 1996. Sediments in the deepest part of the Gotland Basin (>237 m water depth), covering an area of approximately 35 km**2, were characterized by especially high accumulation rates (>70 cm/ka) and high methane and hydrogen sulfide contents. Concentrations of these compounds decreased rapidly towards the slope of the basin.

Mineralogy and petrology of Black Sea Basin sediments

The origin and modes of transportation and deposition of inorganic sedimentary material of the Black Sea were studied in approximately 60 piston, gravity, and Kasten cores. The investigation showed that the sediment derived from the north and northwest (especially from the Danube) has a low calcite-dolomite ratio and a high quartz-feldspar ratio. Rock fragments are generally not abundant; garnet is the principal heavy mineral and illite is the predominant clay mineral. This sedimentary material differs markedly from that carried by Anatolian rivers, which is characterized by a high calcite-dolomite ratio and a low quartz-feldspar ratio. Rock fragments are abundant; pyroxene is the principal heavy mineral and montmorillonite is the predominant clay mineral. In generel, the clay fraction is large in all sediments (27.6-86.9 percent), and the lateral distributian indicates an increase in clay consent from the coasts toward two centers in the western and eastern Black Sea basin. Illite is the most common clay mineral in the Black Sea sediments. The lateral changes in composition of the clay mineral can easily be traced to the petrologic character of northern (rich in illite) and southern (rich in montmorillonite) source areas. In almost all cores, a rhythmic change of the montmorillonite-illite ratio with depth was observed. These changes may be related to the changing influence of the two provinces during the Holocene and late Pleistocene. Higher montmorillonite content seems to indicate climctic changes, probably stages of glaciation end permafrost in the northern area, at which time the illite supply was diminished to a large extent. The composition of the sand fraction is relatad to the different petrologic and morphologic characteristics of two major source provimces: (1) a northern province (rich in quartz, feldspars, and garnet) characterized by a low elevation, comprising the Danube basin area and the rivers draining the Russian platform; and (2) a southern province (rich in pyroxene and volcanic and metamorphic rocks) in the mountainous region of Anatolia and the Caucasus, characterized by small but extremely erosive rivers. The textural properties (graded bedding) of the deep-sea send layers clearly suggest deposition from turbidity currents. The carbonate content of the contemporary sediments ranges from 5 to 65 percent. It increases from the coast to a maximum in two centers in the western and eastern basin. This pattern reflects the distribution of the <2-µm fraction. The contemporary mud sedimentation is governed by two important factors: (1) the deposition of terrigenous allochthonous material of low carbonate content originating from the surrounding hinterland (northern and southern source areas), and (2) the autochthonous production of large quantities of biogenic calcite by coccolithophores during the last period of about 3,000-4,000 years.

Stable isotope record of foraminifera from the Southern Ocean

Sediment cores from the southern continental margin of Australia are near the formation region of Antarctic Intermediate Water (AAIW) and Subantarctic Mode Water and record the changes in these water masses from the last glacial maximum through the present. Carbon and oxygen isotopes were measured on the benthic foraminiferal species Planulina wuellerstrorfi for both the Recent and last glacial maximum sections of the cores and were then used to reconstruct temperature and carbon isotopic water column profiles. The glacial oxygen isotope profile indicates a vertical temperature structure for this region similar to that in today's Subantarctic Zone. Although intermediate water delta13C cannot be used as a nutrient tracer in this region because of the large influence of air-sea carbon isotopic exchange on this water mass, delta13C can be used as a water mass tracer. Today, AAIW properties reflect contributions from cool, fresh Antarctic Surface Waters (2/3) and warm, salty waters from the Indian Ocean (1/3). When examined in conjuction with the glacial delta13C and delta18C data from the north Indian and Southern Oceans, our data suggest a much reduced contribution of North Indian Ocean intermediate water to glacial Antarctic Intermediate Water relative to the contribution of Antarctic Surface Water. This fresher, cooler glacial Antarctic Intermediate Water would be distributed to the intermediate-depth ocean, thus decreasing the transport of salt produced in the North Indian Ocean to the rest of the world's oceans. Combined with evidence for a reduced influence of North Atlantic Deep Water, these results suggest major changes in the pathways for the redistribution of heat and salt in the glacial ocean.

Substitutions in the glycogenin-1 gene are associated with the evolution of endothermy in sharks and tunas

We thank Sean Tracey and Jaime McAllister for supplying albacore and southern bluefin tuna samples, Eva Giacomello for collecting the skipjack tuna sample, Elena Sarropoulou for providing the Atlantic bonito assembly, Helen Hipperson for assistance in the lab, Barbara Block and Ziheng Yang for advice, the editors and reviewers for comments, and the Leverhulme Trust and BBSRC for funding

Projected responses of North American grassland songbirds to climate change and habitat availability at their northern range limits in Alberta, Canada

Across North America, grassland songbirds have undergone steep population declines over recent decades, commonly attributed to agricultural intensification. Understanding the potential interactions between the impacts of climate change on the future distributions of these species and the availability of suitable vegetation for nesting can support improved risk assessments and conservation planning for this group of species. We used North American bioclimatic niche models to examine future changes in suitable breeding climate for 15 grassland songbird species at their current northern range limits along the boreal forest–prairie ecotone in Alberta, Canada. Our climate suitability projections, combined with the current distribution of native and tame pasture and cropland in Alberta, suggest that some climate-mediated range expansion of grassland songbirds in Alberta is possible. For six of the eight species projected to experience expansions of suitable climate area in Alberta, this suitable climate partly overlaps the current distribution of suitable land cover. Additionally, for more than half of the species examined, most of the area of currently suitable climate was projected to remain suitable to the end of the century, highlighting the importance of Alberta for the long-term persistence of these species. Some northern prairie-endemic species exhibited substantial projected northward shifts of both the northern and southern edges of the area of suitable climate. Baird’s Sparrow (Ammodramus bairdii) and Sprague’s Pipit (Anthus spragueii), both at-risk grassland specialists, are predicted to have limited climate stability within their current ranges, and their expansion into new areas of suitable climate may be limited by the availability of suitable land cover. Our results highlight the importance of the preservation and restoration of remaining suitable grassland habitat within areas of projected climate stability and beyond current northern range limits for the long-term persistence of many grassland songbird species in the face of climate change.

Degradation rates and productivity signals of organic-walled dinoflagellate cyst species in surface sediment samples

To understand the role of the ocean within the global carbon cycle, detailed information is required on key-processes within the marine carbon cycle; bio-production in the upper ocean, export of the produced material to the deep ocean and the storage of carbon in oceanic sediments. Quantification of these processes requires the separation of signals of net primary production and the rate of organic matter decay as reflected in fossil sediments. This study examines the large differences in degradation rates of organic-walled dinoflagellate cyst species to separate these degradation and productivity signals. For this, accumulation rates of cyst species known to be resistant (R-cysts) or sensitive (S-cysts) to aerobic degradation of 62 sites are compared to mean annual chlorophyll-a, sea-surface temperature, sea-surface salinity, nitrate and phosphate concentrations of the upper waters and deep-water oxygen concentrations. Furthermore, the degradation of sensitive cysts, as expressed by the degradation constant k and reaction time t, has been related to bottom water [O2]. The studied sediments were taken from the Arabian Sea, north-western African Margin (North Atlantic), western-equatorial Atlantic Ocean/Caraibic, south-western African margin (South Atlantic) and Southern Ocean (Atlantic sector). Significant relationships are observed between (a) accumulation rates of R-cysts and upper water chlorophyll-a concentrations, (b) accumulation rates of S-cysts and bottom water [O2] and (c) degradation rates of S-cysts (kt) and bottom water [O2]. Relationships that are extremely weak or are clearly insignificant on all confidence intervals are between (1) S-cyst accumulation rates and chlorophyll-a concentrations, sea-surface temperature (SST), sea-surface salinity (SSS), phosphate concentrations (P) and nitrate concentrations (N), (2) between R-cyst accumulation rates and bottom water [O2], SST, SSS, P and N, and between (3) kt and water depth. Co-variance is present between the parameters N and P, N, P and chlorophyll-a, oxygen and water depth. Correcting for this co-variance does not influence the significance of the relationship given above. The possible applicability of dinoflagellate cyst degradation to estimate past net primary production and deep ocean ventilation is discussed.

(Table 1) Comparison of diatom-bound and bulk sedimentary d15N values of ODP Holes 175-1082A and 175-1084A

The Matuyama Diatom Maximum (MDM) is a time of peak opal accumulation from 2.6 to ~2.0 Ma within the Benguela Current upwelling system that was initiated by increased influence of Southern Ocean water on the eastern South Atlantic. We measured opal, total organic carbon (TOC), and CaCO3 fluxes and C and N stable isotopes in sediments deposited from 2.4 to 1.95 Ma at Sites 1082 and 1084 to explore the biogeochemical dynamics within the Benguela region. The infusion of Southern Ocean water delivered dissolved nutrients and Southern Ocean flora and fauna, resulting in local opal accumulation increasing up to 8 g/cm**2/ky and the production of diatom mats. Some d15N measurements of diatom-bound organic matter indicate that the mats grew within the Benguela region. The bulk sediment d15N records are taken to reflect changes in the d15N of nitrate in the incoming water, where lower values at 2.4 Ma reflect less nitrate utilization in the Antarctic. A long-term increase in relative nitrate uptake in the Southern Ocean is evidenced by the gradual increase in d15N toward 1.9 Ma.