Molecular and biochemical analyses of wounding in mesocarp of peach (Prunus persica L. Batsch) ripe fruits

The physiological and molecular responses of ripe fruit to wounding were evaluated in two peach (Prunus persica) varieties ('Glohaven', GH, melting and 'BigTop', BT, slow melting nectarine) by comparing mesocarp samples from wedges (as in minimal processing) and whole fruit as the control. Slight differences between the two varieties were detected in terms of ethylene production, whereas total phenol and flavonoid concentrations, and PPO and POD enzyme activities showed a general increase in wounded GH but not in BT. This was associated with the better appearance of the BT wedges at the end of the experimental period (72 h). Microarray (genome-wide ?PEACH3.0) analysis revealed that a total number of 2218 genes were differentially expressed (p < 0.01, log2 fold change expression ratio >1 or <-1) in GH 24 h after wounding compared to the control. This number was much lower (1208) in BT. According to the enrichment analysis, cell wall, plasma membrane, response to stress, secondary metabolic processes, oxygen binding were the GO categories over-represented among the GH up-regulated genes, whereas plasma membrane and response to endogenous stimulus were the categories over-represented among the down-regulated genes. Only 32 genes showed a common expression trend in the two varieties 24 h after wounding, whereas a total of 512 genes (with highly represented transcription factors), displayed opposite behavior. Quantitative RT-PCR analysis confirmed the microarray data for 18 out of a total of 20 genes selected. Specific WRKY, AP2/ERF and HSP20 genes were markedly up-regulated in wounded GH, indicating the activation of regulatory and signaling mechanisms probably related to different hormone categories. Compared to BT, the expression of specific genes involved in phenylpropanoid and triterpenoid biosynthetic pathways showed a more pronounced induction in GH, highlighting the difference between the two peach varieties in terms of molecular responses to wounding in the mesocarp tissue.

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.

(Table 1) Boron-isotope measurements of shallow-dwelling planktonic foraminifera of ODP Holes 144-817A, 144-872C and 143-865C

Knowledge of the evolution of atmospheric carbon dioxide concentrations throughout the Earth's history is important for a reconstruction of the links between climate and radiative forcing of the Earth's surface temperatures. Although atmospheric carbon dioxide concentrations in the early Cenozoic era (about 60 Myr ago) are widely believed to have been higher than at present, there is disagreement regarding the exact carbon dioxide levels, the timing of the decline and the mechanisms that are most important for the control of CO2 concentrations over geological timescales. Here we use the boron-isotope ratios of ancient planktonic foraminifer shells to estimate the pH of surface-layer sea water throughout the past 60 million years, which can be used to reconstruct atmospheric CO2 concentrations. We estimate CO2 concentrations of more than 2,000 p.p.m. for the late Palaeocene and earliest Eocene periods (from about 60 to 52 Myr ago), and find an erratic decline between 55 and 40 Myr ago that may have been caused by reduced CO2 outgassing from ocean ridges, volcanoes and metamorphic belts and increased carbon burial. Since the early Miocene (about 24 Myr ago), atmospheric CO2 concentrations appear to have remained below 500 p.p.m. and were more stable than before, although transient intervals of CO2 reduction may have occurred during periods of rapid cooling approximately 15 and 3 Myr ago.

Eocene sedimentary calcium carbonate contents and stable isotope composition of benthic foraminifera

'Hyperthermals' are intervals of rapid, pronounced global warming known from six episodes within the Palaeocene and Eocene epochs (~65-34 million years (Myr) ago) (Zachos et al., 2005, doi:10.1126/science.1109004; 2008, doi:10.1038/nature06588; Roehl et al., 2007, doi:10.1029/2007GC001784; Thomas et al., 2000; Cramer et al., 2003, doi:10.1029/2003PA000909; Lourens et al., 2005, doi:10.1038/nature03814; Petrizzo, 2005, doi:10.2973/odp.proc.sr.198.102.2005; Sexton et al., 2006, doi:10.1029/2005PA001253; Westerhold et al., 2007, doi:10.1029/2006PA001322; Edgar et al., 2007, doi:10.1038/nature06053; Nicolo et al., 2007, doi:10.1130/G23648A.1; Quillévéré et al., 2008, doi:10.1016/j.epsl.2007.10.040; Stap et al., 2010, doi:10.1130/G30777.1). The most extreme hyperthermal was the 170 thousand year (kyr) interval (Roehl et al., 2007) of 5-7 °C global warming (Zachos et al., 2008) during the Palaeocene-Eocene Thermal Maximum (PETM, 56 Myr ago). The PETM is widely attributed to massive release of greenhouse gases from buried sedimentary carbon reservoirs (Zachos et al., 2005; 2008; Lourenbs et al., 2005; Nicolo et al., 2007; Dickens et al., 1995, doi:10.1029/95PA02087; Dickens, 2000; 2003, doi:10.1016/S0012-821X(03)00325-X; Panchuk et al., 2008, doi:10.1130/G24474A.1) and other, comparatively modest, hyperthermals have also been linked to the release of sedimentary carbon (Zachos et al., 2008, Lourens et al., 2005; Nicolo et al., 2007; Dickens, 2003; Panchuk et al., 2003). Here we show, using new 2.4-Myr-long Eocene deep ocean records, that the comparatively modest hyperthermals are much more numerous than previously documented, paced by the eccentricity of Earth's orbit and have shorter durations (~40 kyr) and more rapid recovery phases than the PETM. These findings point to the operation of fundamentally different forcing and feedback mechanisms than for the PETM, involving redistribution of carbon among Earth's readily exchangeable surface reservoirs rather than carbon exhumation from, and subsequent burial back into, the sedimentary reservoir. Specifically, we interpret our records to indicate repeated, large-scale releases of dissolved organic carbon (at least 1,600 gigatonnes) from the ocean by ventilation (strengthened oxidation) of the ocean interior. The rapid recovery of the carbon cycle following each Eocene hyperthermal strongly suggests that carbon was resequestered by the ocean, rather than the much slower process of silicate rock weathering proposed for the PETM (Zachos et al., 2005; 2003). Our findings suggest that these pronounced climate warming events were driven not by repeated releases of carbon from buried sedimentary sources (Zachos et al., 2008, Lourens et al., 2005; Nicolo et al., 2007; Dickens, 2003; Panchuk et al., 2003) but, rather, by patterns of surficial carbon redistribution familiar from younger intervals of Earth history.

Faunal analysis and Mg/Ca records of planktic foraminifera in sediment core SO189/2_039KL

Climate phenomena like the monsoon system, El Niño Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) are interconnected via various feedback mechanisms and control the climate of the Indian Ocean and its surrounding continents on various timescales. The eastern tropical Indian Ocean is a key area for the interplay of these phenomena and for reconstructing their past changes and forcing mechanisms. Here we present records of upper ocean thermal gradient, thermocline temperatures (TT) and relative abundances of planktic foraminifera in core SO 189-39KL taken off western Sumatra (0°47.400' S, 99°54.510' E) for the last 8 ka that we use as proxies for changes in upper ocean structure. The records suggest a deeper thermocline between 8 ka and ca 3 ka compared to the late Holocene. We find a shoaling of the thermocline after 3 ka, most likely indicating an increased occurrence of upwelling during the late Holocene compared to the mid-Holocene which might represent changes in the IOD-like mean state of the Indian Ocean with a more negative IOD-like mean state during the mid-Holocene and a more positive IOD-like mean state during the past 3 ka. This interpretation is supported by a transient Holocene climate model simulation in which an IOD-like mode is identified that involves an insolation-forced long-term trend of increasing anomalous surface easterlies over the equatorial eastern Indian Ocean.

Concentrations of PCBs, DDT and thyroid hormones in gray (Halichoerus grypus) and ringed (Phoca hispida) seals

The high levels of polychlorinated biphenyls (PCBs) and DDT in gray seal (Halichoerus grypus) and ringed seal (Phoca hispida botnica) in the Baltic Sea have been associated with pathological disruptions, including bone lesions and reproductive failures. The underlying environmental and toxicological mechanisms leading to these pathological changes are not yet fully understood. The present study investigated the relationship between the individual contaminant load and bone- and thyroid-related effects in adult gray seals (n = 30) and ringed seals (n = 46) in the highly contaminated Baltic Sea and in reference areas (Sable Island, Canada, and Svalbard, Norway). In the gray seals, multivariate and correlation analyses revealed a clear relationship between circulating 1,25-dihydroxyvitamin D3 (1,25(OH)2D), calcium, phosphate, and thyroid hormone (TH) levels and hepatic PCB and DDT load, which suggests contaminant-mediated disruption of the bone and thyroid homeostasis. Contaminants may depress 1,25(OH)2D levels or lead to hyperthyroidism, which may cause bone resorption. In the ringed seals, associations between circulating 1,25(OH)2D, THs, and hepatic contaminants were less prominent. These results suggest that bone lesions observed in the Baltic gray seals may be associated with contaminant-mediated vitamin D and thyroid disruption.

(Table 1) Egg laying and hatching dates and guarding duration of Adélie penguins (Pygoscelis adeliae) on Petrel Island, Antarctica

1. In Polar Regions, the extent and dynamics of sea-ice are changing. This affects the ocean productivity which consecutively impacts plankton communities and polar top predators like penguins. Yet, the underlying behavioural and physiological mechanisms remain poorly understood. 2. Here we monitored the ecophysiological responses of Adelie penguin (Pygoscelis adeliae) pairs during two seasons of contrasting timing of sea-ice retreat. Beside classical breeding parameters like foraging trip duration, body mass and reproductive success, we also investigated food-related stress (via plasma corticosterone concentration), nutritional state (via metabolite levels) and the use of penguins' habitat (via blood isotopic values). 3. Body mass and reproductive success remained unchanged but foraging trips were shorter when sea-ice retreated earlier. Constant plasma corticosterone concentrations indicated that none of the feeding conditions resulted in a food-related stress. However metabolite levels were lower when sea-ice retreated early, suggesting that the foraging performance and the quality/quantity of food differed. Indeed isotopic ratios indicated that coastal prey like fish contributed more to the penguins' diet when sea-ice retreated prematurely. 4. The early sea-ice retreat was related to higher chlorophyll concentrations, known to favour krill recruitment. Paradoxically, this was not associated to a higher krill contribution in the penguins' diet. We propose that a shift in the phytoplankton quality (rather than quantity), affecting krill recruitment, forced penguins to switch to more available prey like coastal fish. 5. In some Antarctic regions, sea-ice is retreating earlier and earlier. In the present study, even though the timing of sea-ice retreat and the consecutive ocean productivity differed drastically between the 2 years, Adelie penguins were not severely affected because they were able to adjust their at-sea behaviour and thus maintained their body condition and reproductive success unchanged. 6. This suggests that the timing of sea-ice retreat does not represent an important threat to populations of Adelie penguins at least as long as alternative resources are still available and other environmental parameters like winter sea-ice extent are not dramatically altered.

(Table 1) Metal contents in marine green algae (Chlorophyta) with background and enhanced element concentrations in the environment

Character of metal accumulation in fractions of thalli of four species of marine green benthos algae under background and enhanced (0.3 mg/l) element concentrations in the environment was studied in short-term 24-hour experiments. Algae were shown to hold polysaccharide and protein mechanisms of metal accumulation. Variance analysis was applied to evaluate taxonomic and ecological features of metal distribution in fractions of thalli.

Seawater chemistry, nutrients, chlorophyll a, and growth rate of Phaeocystis globosa during experiments

Phaeocystis globosa (Prymnesiophyceae) is an ecologically dominating phytoplankton species in many areas around the world. It plays an important role in both the global sulfur and carbon cycles, by the production of dimethylsulfide (DMS) and the drawdown of inorganic carbon. Phaeocystis globosa has a polymorphic life cycle and is considered to be a harmful algal bloom (HAB) forming species. All these aspects make this an interesting species to study the effects of increasing carbon dioxide (CO2) concentrations, due to anthropogenic carbon emissions. Here, the combined effects of three different dissolved carbon dioxide concentrations (CO2(aq)) (low: 4 µmol/kg, intermediate: 6-10 µmol/kg and high CO2(aq): 21-24 µmol/kg) and two different light intensities (low light, suboptimal: 80 µmol photons/m**2/s and high light, light saturated: 240 µmol photons/m**2/s) are reported. The experiments demonstrated that the specific growth rate of P. globosa in the high light cultures decreased with increasing CO2(aq) from 1.4 to 1.1 /d in the low and high CO2 cultures, respectively. Concurrently, the photosynthetic efficiency (Fv/Fm) increased with increasing CO2(aq) from 0.56 to 0.66. The different light conditions affected photosynthetic efficiency and cellular chlorophyll a concentrations, both of which were lower in the high light cultures as compared to the low light cultures. These results suggest that in future inorganic carbon enriched oceans, P. globosa will become less competitive and feedback mechanisms to global change may decrease in strength.

DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.

Grain-size distribution and frictional behaviour of sediment cores from the Nice Slope

The upper shelf of the landslide-prone Ligurian Margin (Western Mediterranean Sea) off Nice well-known for the 1979 Airport Landslide is a natural laboratory to study preconditioning factors and trigger mechanisms for submarine landslides. For this study low-stress ring shear experiments have been carried out on a variety of sediments from >50 gravity cores to characterise the velocity-dependent frictional behaviour. Mean values of the peak coefficient of friction vary from 0.46 for clay-dominated samples (53 % clay, 46 % silt, 1 %) sand up to 0.76 for coarse-grained sediments (26 % clay, 57 % silt, 17 % sand). The majority of the sediments tested show velocity strengthening regardless of the grain size distribution. For clayey sediments the peak and residual cohesive strength increases with increasing normal stress, with values from 1.3 to 10.6 kPa and up to 25 % of all strength supported by cohesive forces in the shallowmost samples. A pseudo-static slope stability analysis reveals that the different lithologies (even clay-rich material with clay content >=50 %) tested are stable up to slope angles <26° under quasi-drained conditions.

Stable carbon and oxygen isotope compositions of Eocene benthic foraminifera from ODP Site 207-1258

'Hyperthermals' are intervals of rapid, pronounced global warming known from six episodes within the Palaeocene and Eocene epochs (~65-34 million years (Myr) ago) (Zachos et al., 2005, doi:10.1126/science.1109004; 2008, doi:10.1038/nature06588; Roehl et al., 2007, doi:10.1029/2007GC001784; Thomas et al., 2000; Cramer et al., 2003, doi:10.1029/2003PA000909; Lourens et al., 2005, doi:10.1038/nature03814; Petrizzo, 2005, doi:10.2973/odp.proc.sr.198.102.2005; Sexton et al., 2006, doi:10.1029/2005PA001253; Westerhold et al., 2007, doi:10.1029/2006PA001322; Edgar et al., 2007, doi:10.1038/nature06053; Nicolo et al., 2007, doi:10.1130/G23648A.1; Quillévéré et al., 2008, doi:10.1016/j.epsl.2007.10.040; Stap et al., 2010, doi:10.1130/G30777.1). The most extreme hyperthermal was the 170 thousand year (kyr) interval (Roehl et al., 2007) of 5-7 °C global warming (Zachos et al., 2008) during the Palaeocene-Eocene Thermal Maximum (PETM, 56 Myr ago). The PETM is widely attributed to massive release of greenhouse gases from buried sedimentary carbon reservoirs (Zachos et al., 2005; 2008; Lourenbs et al., 2005; Nicolo et al., 2007; Dickens et al., 1995, doi:10.1029/95PA02087; Dickens, 2000; 2003, doi:10.1016/S0012-821X(03)00325-X; Panchuk et al., 2008, doi:10.1130/G24474A.1) and other, comparatively modest, hyperthermals have also been linked to the release of sedimentary carbon (Zachos et al., 2008, Lourens et al., 2005; Nicolo et al., 2007; Dickens, 2003; Panchuk et al., 2003). Here we show, using new 2.4-Myr-long Eocene deep ocean records, that the comparatively modest hyperthermals are much more numerous than previously documented, paced by the eccentricity of Earth's orbit and have shorter durations (~40 kyr) and more rapid recovery phases than the PETM. These findings point to the operation of fundamentally different forcing and feedback mechanisms than for the PETM, involving redistribution of carbon among Earth's readily exchangeable surface reservoirs rather than carbon exhumation from, and subsequent burial back into, the sedimentary reservoir. Specifically, we interpret our records to indicate repeated, large-scale releases of dissolved organic carbon (at least 1,600 gigatonnes) from the ocean by ventilation (strengthened oxidation) of the ocean interior. The rapid recovery of the carbon cycle following each Eocene hyperthermal strongly suggests that carbon was resequestered by the ocean, rather than the much slower process of silicate rock weathering proposed for the PETM (Zachos et al., 2005; 2003). Our findings suggest that these pronounced climate warming events were driven not by repeated releases of carbon from buried sedimentary sources (Zachos et al., 2008, Lourens et al., 2005; Nicolo et al., 2007; Dickens, 2003; Panchuk et al., 2003) but, rather, by patterns of surficial carbon redistribution familiar from younger intervals of Earth history.

(Table 19, page 199) Minor constituents of one of the San Clemente iron concretions and its metallic core

The chemical and mineralogical composition of pelagic sediments from the East Pacific Ocean has been determined with the aim of defining the ultimate sources and the mechanisms of formation of the solid phases. The distribution of elements between sea-water, the pore solution and the various solid components of the sediments permits interpretations of the variations in time and space of the gross chemical composition of pelagic clays. For example, manganese, present in sea-water in a divalent form, is apparently oxidized at the sediment-water interface to tetravalent species which subsequently become a part of the group of ferromanganese oxide minerals which are found in the marine environment. It is suggested the rate of manganese accumulation in sediments is some function of the length of time the sediment surface is in contact with sea-water. The contribution of chemical species from the different geospheres is considered. The quantitative importance of pelagic clays in the major sedimentary cycle is studied on the basis of the distribution of the weathered igneous rock products between continental and pelagic deposits and sea-water. These analyses of a wide variety of pelagic clays allow a reformulation of the geochemical balance and it is concluded that pelagic clays account for approximately 13 per cent of the total mass of sediments produced over geologic time.