Comparative carbon cycle dynamics of the present and last interglacial

Changes in temperature and carbon dioxide during glacial cycles recorded in Antarctic ice cores are tightly coupled. However, this relationship does not hold for interglacials. While climate cooled towards the end of both the last (Eemian) and present (Holocene) interglacials, CO₂ remained stable during the Eemian while rising in the Holocene. We identify and review twelve biogeochemical mechanisms of terrestrial (vegetation dynamics and CO₂ fertilization, land use, wild fire, accumulation of peat, changes in permafrost carbon, subaerial volcanic outgassing) and marine origin (changes in sea surface temperature, carbonate compensation to deglaciation and terrestrial biosphere regrowth, shallow-water carbonate sedimentation, changes in the soft tissue pump, and methane hydrates), which potentially may have contributed to the CO₂ dynamics during interglacials but which remain not well quantified. We use three Earth System Models (ESMs) of intermediate complexity to compare effects of selected mechanisms on the interglacial CO₂ and δ¹³ CO₂ changes, focusing on those with substantial potential impacts: namely carbonate sedimentation in shallow waters, peat growth, and (in the case of the Holocene) human land use. A set of specified carbon cycle forcings could qualitatively explain atmospheric CO₂ dynamics from 8ka BP to the pre-industrial. However, when applied to Eemian boundary conditions from 126 to 115 ka BP, the same set of forcings led to disagreement with the observed direction of CO₂ changes after 122 ka BP. This failure to simulate late-Eemian CO₂ dynamics could be a result of the imposed forcings such as prescribed CaCO₃ accumulation and/or an incorrect response of simulated terrestrial carbon to the surface cooling at the end of the interglacial. These experiments also reveal that key natural processes of interglacial CO₂ dynamics eshallow water CaCO₃ accumulation, peat and permafrost carbon dynamics are not well represented in the current ESMs. Global-scale modeling of these long-term carbon cycle components started only in the last decade, and uncertainty in parameterization of these mechanisms is a main limitation in the successful modeling of interglacial CO₂ dynamics.

The unstable CO2 feedback cycle on ocean planets

Ocean planets are volatile-rich planets, not present in our Solar system, which are thought to be dominated by deep, global oceans. This results in the formation of high-pressure water ice, separating the planetary crust from the liquid ocean and, thus, also from the atmosphere. Therefore, instead of a carbonate-silicate cycle like on the Earth, the atmospheric carbon dioxide concentration is governed by the capability of the ocean to dissolve carbon dioxide (CO2). In our study, we focus on the CO2 cycle between the atmosphere and the ocean which determines the atmospheric CO2 content. The atmospheric amount of CO2 is a fundamental quantity for assessing the potential habitability of the planet's surface because of its strong greenhouse effect, which determines the planetary surface temperature to a large degree. In contrast to the stabilizing carbonate-silicate cycle regulating the long-term CO2 inventory of the Earth atmosphere, we find that the CO2 cycle feedback on ocean planets is negative and has strong destabilizing effects on the planetary climate. By using a chemistry model for oceanic CO2 dissolution and an atmospheric model for exoplanets, we show that the CO2 feedback cycle can severely limit the extension of the habitable zone for ocean planets.

Tp53-dependent repression of cell cycle target genes: Global and mechanistic analysis

Most studies of p53 function have focused on genes transactivated by p53. It is less widely appreciated that p53 can repress target genes to affect a particular cellular response. There is evidence that repression is important for p53-induced apoptosis and cell cycle arrest. It is less clear if repression is important for other p53 functions. A comprehensive knowledge of the genes repressed by p53 and the cellular processes they affect is currently lacking. We used an expression profiling strategy to identify p53-responsive genes following adenoviral p53 gene transfer (Ad-p53) in PC3 prostate cancer cells. A total of 111 genes represented on the Affymetrix U133A microarray were repressed more than two fold (p ≤ 0.05) by p53. An objective assessment of array data quality was carried out using RT-PCR of 20 randomly selected genes. We estimate a confirmation rate of >95.5% for the complete data set. Functional over-representation analysis was used to identify cellular processes potentially affected by p53-mediated repression. Cell cycle regulatory genes exhibited significant enrichment (p ≤ 5E-28) within the repressed targets. Several of these genes are repressed in a p53-dependent manner following DNA damage, but preceding cell cycle arrest. These findings identify novel p53-repressed targets and indicate that p53-induced cell cycle arrest is a function of not only the transactivation of cell cycle inhibitors (e.g., p21), but also the repression of targets that act at each phase of the cell cycle. The mechanism of repression of this set of p53 targets was investigated. Most of the repressed genes identified here do not harbor consensus p53 DNA binding sites but do contain binding sites for E2F transcription factors. We demonstrate a role for E2F/RB repressor complexes in our system. Importantly, p53 is found at the promoter of CDC25A. CDC25A protein is rapidly degraded in response to DNA damage. Our group has demonstrated for the first time that CDC25A is also repressed at the transcript level by p53. This work has important implications for understanding the DNA damage cell cycle checkpoint response and the link between E2F/RB complexes and p53 in the repression of target genes. ^

The low molecular weight (LMW) isoforms of cyclin E provide a novel mechanism of cell cycle deregulation

Cyclin E, in complex with cyclin dependent kinase 2 (CDK2), is a positive regulator of G1 to S phase progression of the cell cycle. Deregulation of G1/S phase transition occurs in the majority of tumors. Cyclin E is overexpressed and post-translationally generates low molecular weight (LMW) isoforms in breast cancer, but not normal cells. Such alteration of cyclin E is linked to poor prognosis. Therefore, we hypothesized that the LMW isoforms of cyclin E provide a novel mechanism of cell cycle de-regulation in cancer cells. Insect cell expression system was used to explore the biochemical properties of the cyclin E isoforms. Non-tumorigenic (76NE6) and tumorigenic (T47D) mammary epithelial cells transfected with the cyclin E isoforms and breast tumor tissue endogenously expressing the LMW isoforms were used to study the biologic consequences of the LMW isoforms of cyclin E. All model systems studied show that the LMW forms (compared to full-length cyclin E) have increased kinase activity when partnered with CDK2. Increases in the percentage of cells in S phase and colony formation were also observed after overexpression of LMW compared to full-length cyclin E. The LMW isoforms of cyclin E utilize several mechanisms to attain their hyper-activity. They bind CDK2 more efficiently, and are resistant to inhibition by cyclin dependent kinase inhibitors (CKIs) as compared to full-length cyclin E. In addition, the LMW isoforms sequester the CKIs from full-length cyclin E abrogating the overall negative regulation of cyclin E. Despite their correlation with adverse biological consequences, the direct role of the LMW isoforms of cyclin E in mediating tumorigenesis remained unanswered. Subsequent to LMW cyclin E expression in 76NE6 cells, they lose their ability to enter quiescence and exhibit genomic instability, both characteristic of a tumor cell phenotype. Furthermore, injection of 76NE6 cells overexpressing each of the cyclin E isoforms into the mammary fat pad of nude mice revealed that the LMW isoforms of cyclin E yield tumors, whereas the full-length cyclin E does not. In conclusion, the LMW isoforms of cyclin E utilize several mechanisms to acquire a hyperactive phenotype that results in deregulation of the cell cycle and initiates the tumorigenic process in otherwise non-transformed mammary epithelial cells. ^

An early Eocene carbon cycle perturbation at in the Southern Alps

At least two transient events of extreme global warming occurred superimposed on the long-term latest Paleocene and early Eocene warming trend in the Paleocene-Eocene thermal maximum (PETM) (or ETM1 ~55.5 Ma) and the Elmo (or ETM2 ?53.6 Ma). Other than warmth, the best known PETM is characterized by (1) significant injection of 13C-depleted carbon into the ocean-atmosphere system, (2) deep-sea carbonate dissolution, (3) strong biotic responses, and (4) perturbations of the hydrological cycle. Documentation of the other documented and suspected "hyperthermals" is, as yet, insufficient to assess whether they are similar in nature to the PETM. Here we present and discuss biomagnetostratigraphic data and geochemical records across two lower Eocene successions deposited on a continental margin of the western Tethys: the Farra and Possagno sections in the Venetian pre-Alps. We recognize four negative carbon isotope excursions within chron C24. Three of these shifts correlate to known or suspected hyperthermals: the PETM, the Eocene thermal maximum 2 (~53.6 Ma), and the informally named "X event" (~52.5 Ma). The fourth excursion lies within a reverse subchron and occurred between the latter two. In the Farra section, the X event is marked by a ~0.6 per mil negative carbon isotope excursion and carbonate dissolution. Furthermore, the event exhibits responses among calcareous nannofossils, planktic foraminifera, and dinoflagellates that are similar to, though less intense than, those observed across the PETM. Sedimentological and quantitative micropaleontological data from the Farra section also suggest increased weathering and runoff as well as sea surface eutrophication during this event.

Carbonate system of surface sediments from the South Pacific

B/Ca ratios in Cibicides mundulus and Cibicides wuellerstorfi have been shown to correlate with the degree of calcite saturation in seawater (D[CO32-]). In the South Pacific, a region of high importance in the global carbon cycle, these species are not continuously present in down-core records. Small numbers of epibenthic foraminifera in samples present an additional challenge, which can be overcome by using laser ablation-inductively coupled-mass spectrometry (LA-ICP-MS). We present a laser ablation based core-top calibration for Cibicides cf. wuellerstorfi, a C. wuellerstorfi morphotype that is abundant in the South Pacific and extend the existing global core top calibration for C. mundulus and C. wuellerstorfi to this region. B/Ca in C. cf. wuellerstorfi are linearly correlated with D[CO32-] and possibly display a higher sensitivity to calcite saturation changes than C. wuellerstorfi. Trace element profiles through C. wuellerstorfi and C. mundulus reveal an intra-shell B/Ca variation of ±36% around the mean shell value. Mg/Ca and B/Ca display opposite trends along the shell. Both phenomena likely result from ontogenetic effects. Intra-shell variability equals intra-sample variability, mean sample B/Ca values can thus be reliably calculated from averaged spot results of single specimen. In the global B/Ca-D[CO32-] range, we observe an inverse relationship between water mass age and D[CO32-].

Gametogenic cycle of Mesodesma donacium

Large-scale environmental patterns in the Humboldt Current System (HCS) show major changes during strong El Niño episodes, leading to the mass mortality of dominant species in coastal ecosystems. Here we explore how these changes affect the life-history traits of the surf clam Mesodesma donacium. Growth and mortality rates under normal temperature and salinity were compared to those under anomalous (El Niño) higher temperature and reduced salinity. Moreover, the reproductive spatial-temporal patterns along the distribution range were studied, and their relationship to large-scale environmental variability was assessed. M. donacium is highly sensitive to temperature changes, supporting the hypothesis of temperature as the key factor leading to mass mortality events of this clam in northern populations. In contrast, this species, particularly juveniles, was remarkably tolerant to low salinity, which may be related to submarine groundwater discharge in Hornitos, northern Chile. The enhanced osmotic tolerance by juveniles may represent an adaptation of early life stages allowing settlement in vacant areas at outlets of estuarine areas. The strong seasonality in freshwater input and in upwelling strength seems to be linked to the spatial and temporal patterns in the reproductive cycle. Owing to its origin and thermal sensitivity, the expansion and dominance of M. donacium from the Pliocene/Pleistocene transition until the present seem closely linked to the establishment and development of the cold HCS. Therefore, the recurrence of warming events (particularly El Niño since at least the Holocene) has submitted this cold-water species to a continuous local extinction-recolonization process.

Respiration and ingestion rates of calanoid copepod in the northern Benguela Current System measured ex situ during the RSS Discovery D356 cruise in 2010

Respiration rates of 16 calanoid copepod species from the northern Benguela upwelling system were measured on board RRS Discovery in September/October 2010 to determine their energy requirements and assess their significance in the carbon cycle. Copepod species were sampled by different net types. Immediately after the hauls, samples were sorted to species and stages (16 species; females, males and C5 copepodids) according to Bradford-Grieve et al. (1999). Specimens were kept in temperature-controlled refrigerators for at least 12 h before they were used in experiments. Respiration rates of different copepod species were measured onboard by optode respirometry (for details see Köster et al., 2008) with a 10-channel optode respirometer (PreSens Precision Sensing Oxy-10 Mini, Regensburg, Germany) under simulated in situ conditions in temperature-controlled refrigerators. Experiments were run in gas-tight glass bottles (12-13 ml). For each set of experiments, two controls without animals were measured under exactly the same conditions to compensate for potential bias. The number of animals per bottle depended on the copepods size, stage and metabolic activity. Animals were not fed during the experiments but they showed natural species-specific movements. Immediately after the experiments, all specimens were deep-frozen at - 80 °C for later dry mass determination (after lyophilisation for 48 h) in the home lab. The carbon content (% of dry mass) of each species was measured by mass-spectrometry in association with stable isotope analysis and body dry mass was converted to units of carbon. For species without available carbon data, the mean value of all copepod species (44% dry mass) was applied. For the estimation of carbon requirements of copepod species, individual oxygen consumption rates were converted to carbon units, assuming that the expiration of 1 ml oxygen mobilises 0.44 mg of organic carbon by using a respiratory quotient (RQ) of 0.82 for a mixed diet consisting of proteins (RQ = 0.8-1.0), lipids (RQ = 0.7) and carbohydrates (RQ = 1.0) (Auel and Werner, 2003). The carbon ingestion rates were calculated using the energy budget and the potential maximum ingestion rate approach. To allow for physiological comparisons of respiration rates of deep- and shallow-living copepod species without the effects of ambient temperature and different individual body mass, individual respiration rates were temperature- (15°C, Q10=2) and size-adjusted. The scaling coefficient of 0.76 (R2=0.556) is used for the standardisation of body dry mass to 0.3 mg (mean dry mass of all analysed copepods), applying the allometric equation R= (R15°C/M0.76)×0.30.76, where R is respiration and M is individual dry mass in mg.

Coral-algae metabolism and diurnal changes in the CO2-carbonate system of bulk sea water

Precise measurements were conducted in continuous flow seawater mesocosms located in full sunlight that compared metabolic response of coral, coral-macroalgae and macroalgae systems over a diurnal cycle. Irradiance controlled net photosynthesis (Pnet), which in turn drove net calcification (Gnet), and altered pH. Pnet exerted the dominant control on [CO3]2- and aragonite saturation state (Omega arag) over the diel cycle. Dark calcification rate decreased after sunset, reaching zero near midnight followed by an increasing rate that peaked at 03:00 h. Changes in Omega arag and pH lagged behind Gnet throughout the daily cycle by two or more hours. The flux rate Pnet was the primary driver of calcification. Daytime coral metabolism rapidly removes dissolved inorganic carbon (DIC) from the bulk seawater and photosynthesis provides the energy that drives Gnet while increasing the bulk water pH. These relationships result in a correlation between Gnet and Omega arag, with Omega arag as the dependent variable. High rates of H+ efflux continued for several hours following mid-day peak Gnet suggesting that corals have difficulty in shedding waste protons as described by the Proton Flux Hypothesis. DIC flux (uptake) followed Pnet and Gnet and dropped off rapidly following peak Pnet and peak Gnet indicating that corals can cope more effectively with the problem of limited DIC supply compared to the problem of eliminating H+. Over a 24 h period the plot of total alkalinity (AT) versus DIC as well as the plot of Gnet versus Omega arag revealed a circular hysteresis pattern over the diel cycle in the coral and coral-algae mesocosms, but not the macroalgae mesocosm. Presence of macroalgae did not change Gnet of the corals, but altered the relationship between Omega arag and Gnet. Predictive models of how future global changes will effect coral growth that are based on oceanic Omega arag must include the influence of future localized Pnet on Gnet and changes in rate of reef carbonate dissolution. The correlation between Omega arag and Gnet over the diel cycle is simply the response of the CO2-carbonate system to increased pH as photosynthesis shifts the equilibria and increases the [CO3]2- relative to the other DIC components of [HCO3]- and [CO2]. Therefore Omega arag closely tracked pH as an effect of changes in Pnet, which also drove changes in Gnet. Measurements of DIC flux and H+ flux are far more useful than concentrations in describing coral metabolism dynamics. Coral reefs are systems that exist in constant disequilibrium with the water column.

Respiration rates and abundances of dominant copepods of the northern Benguela Current System

Respiration rates of 16 calanoid copepod species from the northern Benguela upwelling system were measured on board RRS Discovery in September/October 2010 to determine their energy requirements and assess their significance in the carbon cycle. Individual respiration rates were standardised to a mean copepod body mass and a temperature regime typical of the northern Benguela Current. These adjusted respiration rates revealed two different activity levels (active and resting) in copepodids C5 of Calanoides carinatus and females of Rhincalanus nasutus, which reduced their metabolism during dormancy by 82% and 62%, respectively. An allometric function (Imax) and an energy budget approach were performed to calculate ingestion rates. Imax generally overestimated the ingestion rates derived from the energy budget approach by >75%. We suggest that the energy budget approach is the more reliable approximation with a total calanoid copepod (mainly females) consumption of 78 mg C m-2 d-1 in neritic regions and 21 mg C m-2 d-1 in oceanic regions. The two primarily herbivorous copepods C. carinatus (neritic) and Nannocalanus minor (oceanic) contributed 83% and 5%, respectively, to total consumption by calanoid copepods. Locally, C. carinatus can remove up to 90% of the diatom biomass daily. In contrast, the maximum daily removal of dinoflagellate biomass by N. minor was 9%. These estimates imply that C. carinatus is an important primary consumers in the neritic province of the northern Benguela system, while N. minor has little grazing impact on phytoplankton populations further offshore. Data on energy requirements and total consumption rates of dominant calanoid copepods of this study are essential for the development of realistic carbon budgets and food-web models for the northern Benguela upwelling system.

Properties of seawater (partial pressure of carbon dioxide (pCO2)) from a ProOceanus CO2-Pro sensor mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements of partial pressure of carbon dioxide (pCO2), using a ProOceanus CO2-Pro instrument mounted on the flowthrough system. This automatic sensor is fitted with an equilibrator made of gas permeable silicone membrane and an internal detection loop with a non-dispersive infrared detector of PPSystems SBA-4 CO2 analyzer. A zero-CO2 baseline is provided for the subsequent measurements circulating the internal gas through a CO2 absorption chamber containing soda lime or Ascarite. The frequency of this automatic zero point calibration was set to be 24 hours. All data recorded during zeroing processes were discarded with the 15-minute data after each calibration. The output of CO2-Pro is the mole fraction of CO2 in the measured water and the pCO2 is obtained using the measured total pressure of the internal wet gas. The fugacity of CO2 (fCO2) in the surface seawater, whose difference with the atmospheric CO2 fugacity is proportional to the air-sea CO2 fluxes, is obtained by correcting the pCO2 for non-ideal CO2 gas concentration according to Weiss (1974). The fCO2 computed using CO2-Pro measurements was corrected to the sea surface condition by considering the temperature effect on fCO2 (Takahashi et al., 1993). The surface seawater observations that were initially estimated with a 15 seconds frequency were averaged every 5-min cycle. The performance of CO2-Pro was adjusted by comparing the sensor outputs against the thermodynamic carbonate calculation of pCO2 using the carbonic system constants of Millero et al. (2006) from the determinations of total inorganic carbon (CT ) and total alkalinity (AT ) in discrete samples collected at sea surface. AT was determined using an automated open cell potentiometric titration (Haraldsson et al. 1997). CT was determined with an automated coulometric titration (Johnson et al. 1985; 1987), using the MIDSOMMA system (Mintrop, 2005). fCO2 data are flagged according to the WOCE guidelines following Pierrot et al. (2009) identifying recommended values and questionable measurements giving additional information about the reasons of the questionability.