Biogenic-to-lithogenic handoff of particulate Zn affects the Zn cycle in the Southern Ocean.

Zinc (Zn) is vital to marine organisms. Its active uptake by phytoplankton results in a substantial depletion of dissolved Zn, and Zn bound to particulate organic matter replenishes dissolved Zn in the ocean through remineralization. However, we found that particulate Zn changes from Zn bound to phosphoryls in cells to recalcitrant inorganic pools that include biogenic silica, clays, and iron, manganese, and aluminum oxides in the Southern Ocean water column. The abundances of inorganic pools increase with depth and are the only phases preserved in sediments. Changes in the particulate-Zn speciation influence Zn bioavailability and explain the decoupling of Zn and phosphorus and the correlation of Zn and silicon in the water column. These findings reveal a new dimension to the ocean Zn cycle, implicating an underappreciated role of inorganic Zn particles and their impact on biological productivity.

Distinct nitrogen isotopic compositions of healthy and cancerous tissue in mice brain and head&neck micro-biopsies.

BACKGROUND: Cancerous cells can recycle metabolic ammonium for their growth. As this ammonium has a low nitrogen isotope ratio (15N/14N), its recycling may cause cancer tissue to have lower 15N/14N than surrounding healthy tissue. We investigated whether, within a given tissue type in individual mice, tumoral and healthy tissues could be distinguished based on their 15N/14N. METHODS: Micro-biopsies of murine tumors and adjacent tissues were analyzed for 15N/14N using novel high-sensitivity methods. Isotopic analysis was pursued in Nude and C57BL/6 mice models with mature orthotopic brain and head&neck tumors generated by implantation of H454 and MEERL95 murine cells, respectively. RESULTS: In the 7 mice analyzed, the brain tumors had distinctly lower 15N/14N than healthy neural tissue. In the 5 mice with head&neck tumors, the difference was smaller and more variable. This was at least partly due to infiltration of healthy head&neck tissue by tumor cells. However, it may also indicate that the 15N/14N difference between tumoral and healthy tissue depends on the nitrogen metabolism of the healthy organ in question. CONCLUSIONS: The findings, coupled with the high sensitivity of the 15N/14N measurement method used here, suggest a new approach for micro-biopsy-based diagnosis of malignancy as well as an avenue for investigation of cancer metabolism.

No iron fertilization in the equatorial Pacific Ocean during the last ice age.

The equatorial Pacific Ocean is one of the major high-nutrient, low-chlorophyll regions in the global ocean. In such regions, the consumption of the available macro-nutrients such as nitrate and phosphate is thought to be limited in part by the low abundance of the critical micro-nutrient iron. Greater atmospheric dust deposition could have fertilized the equatorial Pacific with iron during the last ice age--the Last Glacial Period (LGP)--but the effect of increased ice-age dust fluxes on primary productivity in the equatorial Pacific remains uncertain. Here we present meridional transects of dust (derived from the (232)Th proxy), phytoplankton productivity (using opal, (231)Pa/(230)Th and excess Ba), and the degree of nitrate consumption (using foraminifera-bound δ(15)N) from six cores in the central equatorial Pacific for the Holocene (0-10,000 years ago) and the LGP (17,000-27,000 years ago). We find that, although dust deposition in the central equatorial Pacific was two to three times greater in the LGP than in the Holocene, productivity was the same or lower, and the degree of nitrate consumption was the same. These biogeochemical findings suggest that the relatively greater ice-age dust fluxes were not large enough to provide substantial iron fertilization to the central equatorial Pacific. This may have been because the absolute rate of dust deposition in the LGP (although greater than the Holocene rate) was very low. The lower productivity coupled with unchanged nitrate consumption suggests that the subsurface major nutrient concentrations were lower in the central equatorial Pacific during the LGP. As these nutrients are today dominantly sourced from the Subantarctic Zone of the Southern Ocean, we propose that the central equatorial Pacific data are consistent with more nutrient consumption in the Subantarctic Zone, possibly owing to iron fertilization as a result of higher absolute dust fluxes in this region. Thus, ice-age iron fertilization in the Subantarctic Zone would have ultimately worked to lower, not raise, equatorial Pacific productivity.

Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia.

Ninety per cent of marine organic matter burial occurs in continental margin sediments, where a substantial fraction of organic carbon escapes oxidation and enters long-term geologic storage within sedimentary rocks. In such environments, microbial metabolism is limited by the diffusive supply of electron acceptors. One strategy to optimize energy yields in a resource-limited habitat is symbiotic metabolite exchange among microbial associations. Thermodynamic and geochemical considerations indicate that microbial co-metabolisms are likely to play a critical part in sedimentary organic carbon cycling. Yet only one association, between methanotrophic archaea and sulphate-reducing bacteria, has been demonstrated in marine sediments in situ, and little is known of the role of microbial symbiotic interactions in other sedimentary biogeochemical cycles. Here we report in situ molecular and incubation-based evidence for a novel symbiotic consortium between two chemolithotrophic bacteria--anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species--in anoxic sediments of the Soledad basin at the Mexican Pacific margin. A mass balance of benthic solute fluxes and the corresponding nitrogen isotope composition of nitrate and ammonium fluxes indicate that anammox bacteria rely on Thioploca species for the supply of metabolic substrates and account for about 57 ± 21 per cent of the total benthic N2 production. We show that Thioploca-anammox symbiosis intensifies benthic fixed nitrogen losses in anoxic sediments, bypassing diffusion-imposed limitations by efficiently coupling the carbon, nitrogen and sulphur cycles.

Two modes of change in Southern Ocean productivity over the past million years.

Export of organic carbon from surface waters of the Antarctic Zone of the Southern Ocean decreased during the last ice age, coinciding with declining atmospheric carbon dioxide (CO(2)) concentrations, signaling reduced exchange of CO(2) between the ocean interior and the atmosphere. In contrast, in the Subantarctic Zone, export production increased into ice ages coinciding with rising dust fluxes, thus suggesting iron fertilization of subantarctic phytoplankton. Here, a new high-resolution productivity record from the Antarctic Zone is compiled with parallel subantarctic data over the past million years. Together, they fit the view that the combination of these two modes of Southern Ocean change determines the temporal structure of the glacial-interglacial atmospheric CO(2) record, including during the interval of "lukewarm" interglacials between 450 and 800 thousand years ago.

Deglacial pulses of deep-ocean silicate into the subtropical North Atlantic Ocean.

Growing evidence suggests that the low atmospheric CO2 concentration of the ice ages resulted from enhanced storage of CO2 in the ocean interior, largely as a result of changes in the Southern Ocean. Early in the most recent deglaciation, a reduction in North Atlantic overturning circulation seems to have driven CO2 release from the Southern Ocean, but the mechanism connecting the North Atlantic and the Southern Ocean remains unclear. Biogenic opal export in the low-latitude ocean relies on silicate from the underlying thermocline, the concentration of which is affected by the circulation of the ocean interior. Here we report a record of biogenic opal export from a coastal upwelling system off the coast of northwest Africa that shows pronounced opal maxima during each glacial termination over the past 550,000 years. These opal peaks are consistent with a strong deglacial reduction in the formation of silicate-poor glacial North Atlantic intermediate water (GNAIW). The loss of GNAIW allowed mixing with underlying silicate-rich deep water to increase the silicate supply to the surface ocean. An increase in westerly-wind-driven upwelling in the Southern Ocean in response to the North Atlantic change has been proposed to drive the deglacial rise in atmospheric CO2 (refs 3, 4). However, such a circulation change would have accelerated the formation of Antarctic intermediate water and sub-Antarctic mode water, which today have as little silicate as North Atlantic Deep Water and would have thus maintained low silicate concentrations in the Atlantic thermocline. The deglacial opal maxima reported here suggest an alternative mechanism for the deglacial CO2 release. Just as the reduction in GNAIW led to upward silicate transport, it should also have allowed the downward mixing of warm, low-density surface water to reach into the deep ocean. The resulting decrease in the density of the deep Atlantic relative to the Southern Ocean surface promoted Antarctic overturning, which released CO2 to the atmosphere.

Foraminiferal isotope evidence of reduced nitrogen fixation in the ice age Atlantic Ocean.

Fixed nitrogen (N) is a limiting nutrient for algae in the low-latitude ocean, and its oceanic inventory may have been higher during ice ages, thus helping to lower atmospheric CO2 during those intervals. In organic matter within planktonic foraminifera shells in Caribbean Sea sediments, we found that the 15N/14N ratio from the last ice age is higher than that from the current interglacial, indicating a higher nitrate 15N/14N ratio in the Caribbean thermocline. This change and other species-specific differences are best explained by less N fixation in the Atlantic during the last ice age. The fixation decrease was most likely a response to a known ice age reduction in ocean N loss, and it would have worked to balance the ocean N budget and to curb ice age-interglacial change in the N inventory.

Glacial/interglacial changes in subarctic north pacific stratification.

Since the first evidence of low algal productivity during ice ages in the Antarctic Zone of the Southern Ocean was discovered, there has been debate as to whether it was associated with increased polar ocean stratification or with sea-ice cover, shortening the productive season. The sediment concentration of biogenic barium at Ocean Drilling Program site 882 indicates low algal productivity during ice ages in the Subarctic North Pacific as well. Site 882 is located southeast of the summer sea-ice extent even during glacial maxima, ruling out sea-ice-driven light limitation and supporting stratification as the explanation, with implications for the glacial cycles of atmospheric carbon dioxide concentration.

Measurement of the oxygen isotopic composition of nitrate in seawater and freshwater using the denitrifier method.

We report a novel method for measurement of the oxygen isotopic composition (18O/16O) of nitrate (NO3-) from both seawater and freshwater. The denitrifier method, based on the isotope ratio analysis of nitrous oxide generated from sample nitrate by cultured denitrifying bacteria, has been described elsewhere for its use in nitrogen isotope ratio (15N/14N) analysis of nitrate. (1) Here, we address the additional issues associated with 18O/16O analysis of nitrate by this approach, which include (1) the oxygen isotopic difference between the nitrate sample and the N20 analyte due to isotopic fractionation associated with the loss of oxygen atoms from nitrate and (2) the exchange of oxygen atoms with water during the conversion of nitrate to N2O. Experiments with 18O-labeled water indicate that water exchange contributes less than 10%, and frequently less than 3%, of the oxygen atoms in the N20 product for Pseudomonas aureofaciens. In addition, both oxygen isotope fractionation and oxygen atom exchange are consistent within a given batch of analyses. The analysis of appropriate isotopic reference materials can thus be used to correct the measured 18O/16O ratios of samples for both effects. This is the first method tested for 18O/16O analysis of nitrate in seawater. Benefits of this method, relative to published freshwater methods, include higher sensitivity (tested down to 10 nmol and 1 microM NO3-), lack of interference by other solutes, and ease of sample preparation.

A bacterial method for the nitrogen isotopic analysis of nitrate in seawater and freshwater.

We report a new method for measurement of the isotopic composition of nitrate (NO3-) at the natural-abundance level in both seawater and freshwater. The method is based on the isotopic analysis of nitrous oxide (N20) generated from nitrate by denitrifying bacteria that lack N2O-reductase activity. The isotopic composition of both nitrogen and oxygen from nitrate are accessible in this way. In this first of two companion manuscripts, we describe the basic protocol and results for the nitrogen isotopes. The precision of the method is better than 0.2/1000 (1 SD) at concentrations of nitrate down to 1 microM, and the nitrogen isotopic differences among various standards and samples are accurately reproduced. For samples with 1 microM nitrate or more, the blank of the method is less than 10% of the signal size, and various approaches may reduce it further.

Southward migration of the intertropical convergence zone through the Holocene.

Titanium and iron concentration data from the anoxic Cariaco Basin, off the Venezuelan coast, can be used to infer variations in the hydrological cycle over northern South America during the past 14,000 years with subdecadal resolution. Following a dry Younger Dryas, a period of increased precipitation and riverine discharge occurred during the Holocene "thermal maximum." Since approximately 5400 years ago, a trend toward drier conditions is evident from the data, with high-amplitude fluctuations and precipitation minima during the time interval 3800 to 2800 years ago and during the "Little Ice Age." These regional changes in precipitation are best explained by shifts in the mean latitude of the Atlantic Intertropical Convergence Zone (ITCZ), potentially driven by Pacific-based climate variability. The Cariaco Basin record exhibits strong correlations with climate records from distant regions, including the high-latitude Northern Hemisphere, providing evidence for global teleconnections among regional climates.

Oligoribonucleotide-based gene-specific transcription inhibitors that target the open complex.

We have demonstrated that oligoribonucleotides that lack a 3'-OH group and cannot be extended by RNA polymerase can hybridize to the single-stranded DNA formed inside the transcription initiation bubble (or open complex) and inhibit transcription. Using the lacUV5/Escherichia coli RNA polymerase or trpEDCBA/E. coli RNA polymerase transcription system as a model, we have found that effective inhibitors are five nucleotides in length and must be complementary to the DNA template strand in the region from -5 to +2 about the transcription start site (designated +1). We have used the DNA cleavage activity of 1,10-phenanthroline-copper to confirm that the mechanism of inhibition is via oligoribonucleotide hybridization to the open complex and have used this cleavage chemistry to demonstrate that these oligonucleotide inhibitors hybridize in an antiparallel orientation to their DNA target. Systematic modification of the parent phosphodiester oligoribonucleotide pentamer revealed that the phosphorothioate backbone-containing analogs have increased open complex binding affinity and are more effective transcription inhibitors than their phosphodiester counterparts.

Artificial nucleases.

The oxidation of DNA and RNA provides a facile approach for investigating the interaction of nucleic acids with proteins and oligonucleotides. In this article, we have outlined our understanding of the mechanism of DNA scission by 1,10-phenanthroline-copper(I) in the presence of hydrogen peroxide. We also discuss results obtained by using 1,10-phenanthroline-oligonucleotide conjugates in probing the size of the transcriptionally active open complex. Finally, we outline an effective method for converting DNA-binding proteins into site-specific modification agents by using 1,10-phenanthroline-copper(I).

Glacial/interglacial variations in atmospheric carbon dioxide.

Twenty years ago, measurements on ice cores showed that the concentration of carbon dioxide in the atmosphere was lower during ice ages than it is today. As yet, there is no broadly accepted explanation for this difference. Current investigations focus on the ocean's 'biological pump', the sequestration of carbon in the ocean interior by the rain of organic carbon out of the surface ocean, and its effect on the burial of calcium carbonate in marine sediments. Some researchers surmise that the whole-ocean reservoir of algal nutrients was larger during glacial times, strengthening the biological pump at low latitudes, where these nutrients are currently limiting. Others propose that the biological pump was more efficient during glacial times because of more complete utilization of nutrients at high latitudes, where much of the nutrient supply currently goes unused. We present a version of the latter hypothesis that focuses on the open ocean surrounding Antarctica, involving both the biology and physics of that region.

PAN GU: a protein kinase that inhibits S phase and promotes mitosis in early Drosophila development.

Following completion of meiosis, DNA replication must be repressed until fertilization. In Drosophila, this replication block requires the products of the pan gu (png), plutonium (plu) and giant nuclei (gnu) genes. These genes also ensure that S phase oscillates with mitosis in the early division cycles of the embryo. We have identified the png gene and shown that it encodes a Ser/Thr protein kinase expressed only in ovaries and early embryos, and that the predicted extent of kinase activity in png mutants inversely correlates with the severity of the mutant phenotypes. The PLU and PNG proteins form a complex that has PNG-dependent kinase activity, and this activity is necessary for normal levels of mitotic cyclins. Our results reveal a novel protein kinase complex that controls S phase at the onset of development apparently by stabilizing mitotic cyclins.

An analysis of clinical outcomes using color doppler testicular ultrasound for testicular torsion.

OBJECTIVES: To delineate the clinical outcomes of color Doppler ultrasound (US) in the equivocal torsion patient. METHODS: From 1992 to 1997, 130 patients (<23 years old) from 2 institutions underwent US imaging using a 7.5-mHz linear transducer to evaluate an acute scrotum equivocal, or of low suspicion, for torsion. The US reports and hospital charts of these patients were retrospectively reviewed. RESULTS: After clinical and radiologic evaluation, torsion was excluded in 110 patients without surgical exploration. In 3 patients, intermittent testicular torsion was diagnosed and in 17 patients, emergent exploration was performed for US diagnosis of testicular torsion. Twenty-five patients (22.7%) were subsequently lost to follow-up. Follow-up of 85 patients with US negative for torsion (mean length of follow-up = 466.9 days) revealed no testicular atrophy in 83. Two patients underwent delayed orchiectomy/contralateral orchiopexy for missed testicular torsion. Of 17 patients with US positive for torsion, 9 underwent orchiectomy for a necrotic torsed testis, 7 viable torsed testes were found, and 1 torsed appendix testis was found. Therefore, color Doppler US for the equivocal acute scrotum yielded a 1% false-positive rate, sensitivity of 88.9%, and specificity of 98.8%. CONCLUSION: When faced with ruling out testicular torsion, it is necessary to integrate the multiple pieces of patient data, knowing that each piece of data may have inaccuracies. With this in mind, this analysis of outcomes verifies that color Doppler US is an excellent adjunctive study in the clinically real situation in which the clinical evaluation is equivocal or low suspicion.

An approach to gene-specific transcription inhibition using oligonucleotides complementary to the template strand of the open complex.

The single-stranded region of DNA within the open complex of transcriptionally active genes provides a unique target for the design of gene-specific transcription inhibitors. Using the Escherichia coli lac UV5 and trp EDCBA promoters as in vitro models of open complex formation, we have identified the sites inside these transcription bubbles that are accessible for hybridization by short, nuclease-resistant, non-extendable oligoribonucleotides (ORNs). Binding of ORNs inside the open complex was determined by linking the chemical nuclease bis(1,10-phenanthroline) cuprous chelate [(OP)(2)Cu(+)] to the ORN and demonstrating template-specific DNA scission. In addition, these experiments were supported by in vitro transcription inhibition. We find that the most effective inhibitors are 5 nt long and have sequences that are complementary to the DNA template strand in the region near the transcription start site. The ORNs bind to the DNA template strand, forming an antiparallel heteroduplex inside the open complex. In this system, RNA polymerase is essential not only to melt the duplex DNA but also to facilitate hybridization of the incoming ORN. This paradigm for gene-specific inactivation relies on the base complementarity of the ORN and the catalytic activity and sequence specificity of RNA polymerase for the site- and sequence-specific recognition and inhibition of transcriptionally active DNA.

Racial differences in prostate cancer growth: apoptosis and cell proliferation in Caucasian and African-American patients.

BACKGROUND: Epidemiologic evidence reveals striking racial differences in incidence and clinical behavior of prostate cancer among American men. In this study, we assessed the incidence of apoptosis and cell proliferation in prostate cancer specimens from African-American and Caucasian patients in an attempt to identify potential differences in tumor growth determinants between the two ethnic groups. METHODS: Apoptosis and cell proliferation were analyzed in archival paraffin-embedded prostatic tumors from 44 African-American and 35 Caucasian age-matched men who underwent radical prostatectomy for localized prostate cancer. Both groups had comparable preoperative prostate-specific antigen (PSA) levels, clinical stage, and Gleason scores, and neither group of patients received neoadjuvant therapy prior to surgery. Apoptotic status in prostate tumors was evaluated in situ, using the transferase deoxyuridine end labeling (TUNEL) assay, and the expression profile of two apoptotic proteins, bcl-2 and bax. The proliferative index was determined on the basis of Ki-67 antigen immunoreactivity. RESULTS: Apoptosis in malignant prostate cells was significantly higher in African American than Caucasian men (11.6% vs. 4.2%, P < 0. 001). Interestingly, the rate of cell proliferation of prostate tumor cells was similar in the two ethnic groups (4.5% and 4.2%). The antiapoptotic protein bcl-2 was detected at significantly higher levels in tumors from Caucasian than African-American patients (40. 8% vs. 31.6%, P < 0.05). Expression of bax, the apoptosis promoter, was consistently high among tumor epithelial cells in specimens from both racial groups (68%). CONCLUSIONS: These findings provide a novel insight into the molecular determinants of tumor growth that may underlie the ethnic differences in prostate cancer incidence and clinical behavior. Downregulation of bcl-2 expression may be potentially responsible for the loss of apoptotic control in prostate tumors from African-American men. This study may have significant clinical implications in the development of novel diagnostic approaches for biologically aggressive prostate cancer from diverse racial origin.

Endoscopic retrograde stenting for allograft hydronephrosis.

BACKGROUND AND OBJECTIVES: Ureteral obstruction occurs in 2% to 10% of all renal transplant recipients. Antegrade endourologic intervention has been the gold standard of therapy but carries significant morbidity. This study was designed to investigate the feasibility of retrograde stenting of these difficult ureters and to determine whether it can be performed with minimal morbidity without general or regional anesthesia. METHODS: Ninety-seven consecutive patients were found to have renal allograft hydronephrosis by ultrasonography, between August 1993 and March 1997. Of these, 61 (63%) had confirmation of obstruction by MAG-3 imaging, with equivocal results in 25 (26%). The remaining 11 patients had a rising creatinine concentration despite Foley catheter drainage. All patients had retrograde stenting attempted under local anesthesia followed by intravenous sedation if necessary. If stent placement was unsuccessful, the procedure was repeated under regional or general anesthesia. RESULTS: A total of 85 patients (88%) were managed successfully with retrograde stenting. Of these procedures, 24 (28%) were performed under local anesthesia alone, while 57 (67%) required both local anesthesia and intravenous sedation. Only 4 patients (5%) required general anesthesia. No patient suffered any morbidity associated with retrograde stenting. Of the 12 patients in whom retrograde stenting failed, 2 had renal allograft rupture and 10 had ureteral necrosis at surgical exploration. CONCLUSIONS: Retrograde stenting of the hydronephrotic renal allograft can be achieved with a high success rate and minimal morbidity, usually without general or regional anesthesia. If the ureter cannot be managed in a retrograde fashion, a high index of suspicion for a serious allograft complication should exist.

Real-time transesophageal echocardiography for intraoperative surveillance of patients with renal cell carcinoma and vena caval extension undergoing radical nephrectomy.

PURPOSE: Vena caval tumor thrombus associated with renal cell carcinoma occurs in 4 to 10% of all renal tumors. There is significant operative morbidity and mortality in removing these tumors. We investigate the use of real-time transesophageal echocardiography intraoperatively and to identify tumor thrombus migration and air embolus, which are 2 potentially fatal complications of this procedure. MATERIALS AND METHODS: A total of 13 consecutive patients with renal masses and vena caval extension underwent extirpative surgery monitored with real-time transesophageal echocardiography. RESULTS: In 11 cases the involved kidney and tumor thrombus were removed without morbidity and no evidence of tumor migration or air embolus. Transesophageal echocardiography revealed a 5 cm. tumor thrombus in the right atrium which was removed by immediate atriotomy in 1 of the remaining 2 cases, and a large volume of air in the right atrium that was percutaneously evacuated in the other. These intraoperative complications were unsuspected and only recognized due to the use of transesophageal echocardiography. CONCLUSIONS: Real-time transesophageal echocardiography is a useful adjunct to surgery in patients with renal cell carcinoma and vena caval extension. Transesophageal echocardiography facilitates identification of tumor thrombus migration and air embolization, which are potentially fatal complications, and allows for immediate intraoperative intervention.