Liver proteome profiling of juvenile Chinese sturgeon (Acipenser sinensis) using GeLC-MS/MS approach

Chinese sturgeon (Acipenser sinensis), mainly distributed in the Yangtze River, has been listed as a grade I protected animal in China because of a dramatic decline in population owing to loss of natural habitat for reproduction and interference by human activities. Understanding the proteome profile of Chinese sturgeon liver would provide an invaluable resource for protecting and increasing the stocks of this species. In this study, we have analyzed proteome profiles of juvenile Chinese sturgeon liver using a one-dimensional gel electrophoresis coupled to LC-MS/MS approach. A total of 1059 proteins and 2084 peptides were identified. The liver proteome was found to be associated with diverse biological processes, cellular components and molecular functions. The proteome profile identified a variety of significant pathways including carbohydrate metabolism, fatty acid metabolism and amino acid metabolism pathways. It also established a network for protein biosynthesis, folding and catabolic processes. The proteome profile established in this study can be used for understanding the development of Chinese sturgeon and studying the molecular mechanisms of action under environmental or chemical stress, providing very useful omics information that can be applied to preserve this species.

Age determination and stable isotope ratios of sediment core RC11-83

The Southern Ocean is perhaps the only region where fluctuations in the global influence of North Atlantic Deep Water (NADW) can be monitored unambiguously in single deep-sea cores. A carbon isotope record from benthic foraminifera in a Southern Ocean core reveals large and rapid changes in the flux of NADW during the last deglaciation, and an abrupt increase in the NADW production rate which immediately preceded large-scale melting of the Northern Hemisphere ice sheets. This sudden strengthening of the NADW thermoha-line cell provides strong evidence for the importance of NADW in glacial-interglacial climate change.

Experiment on marine fungus Microascus brevicaulis strain

The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularide A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing besides higher production levels faster growth and differences in pellet formation. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of this fungus and its mutant. For this purpose, an optimised protein extraction protocol was established. Here, we show the first proteome study of a marine fungus. In total, 4759 proteins were identified. The central metabolic pathway of LF580 could be mapped by using KEGG pathway analysis and GO annotation. Using iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to a limited nutrient availability in wild type strain due to a strong pellet formation. This information can be applied to optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.

Effects of increased CO2 on fish gill and plasma proteome

Ocean acidification and warming are both primarily caused by increased levels of atmospheric CO2, and marine organisms are exposed to these two stressors simultaneously. Although the effects of temperature on fish have been investigated over the last century, the long-term effects of moderate CO2 exposure and the combination of both stressors are almost entirely unknown. A proteomics approach was used to assess the adverse physiological and biochemical changes that may occur from the exposure to these two environmental stressors. We analysed gills and blood plasma of Atlantic halibut (Hippoglossus hippoglossus) exposed to temperatures of 12°C (control) and 18°C (impaired growth) in combination with control (400 µatm) or high-CO2 water (1000 µatm) for 14 weeks. The proteomic analysis was performed using two-dimensional gel electrophoresis (2DE) followed by Nanoflow LC-MS/MS using a LTQ-Orbitrap. The high-CO2 treatment induced the up-regulation of immune system-related proteins, as indicated by the up-regulation of the plasma proteins complement component C3 and fibrinogen beta chain precursor in both temperature treatments. Changes in gill proteome in the high-CO2 (18°C) group were mostly related to increased energy metabolism proteins (ATP synthase, malate dehydrogenase, malate dehydrogenase thermostable, and fructose-1,6-bisphosphate aldolase), possibly coupled to a higher energy demand. Gills from fish exposed to high-CO2 at both temperature treatments showed changes in proteins associated with increased cellular turnover and apoptosis signalling (annexin 5, eukaryotic translation elongation factor 1 gamma, receptor for protein kinase C, and putative ribosomal protein S27). This study indicates that moderate CO2-driven acidification, alone and combined with high temperature, can elicit biochemical changes that may affect fish health.

Nitrogen isotope variations along the northeast Pacific margin

Glacial-interglacial changes in sedimentary d15N over the last 120 kyr display a remarkably similar pattern in timing and amplitude in core records extending from the denitrification zone in the eastern tropical North Pacific (ETNP), where subsurface denitrification is active, to the Oregon margin, where no denitrification occurs today. Low d15N values (4-6 per mil) generally characterize glacial stages 2 and 4, and higher d15N values (7-10 per mil) are representative of the Holocene, millennial-scale periods within stage 3, and stage 5. The inferred synchroneity of d15N variations along the entire margin implies that the nitrate isotopic signal produced in the oxygen-poor subsurface waters in the ETNP is rapidly advected northward and recorded at sites far beyond the boundaries of the modern denitrification zone. Similar to d15N, primary production indicators (percent Corg, Ba/Al, and percent opal) show glacial-interglacial as well as millennial-scale variations along the NE Pacific margin, with higher primary production during warm periods. However, the relative phasing between d15N and paleoproduction tracers within individual records changes latitudinally. Whereas d15N and primary production vary approximately synchronously in the midlatitudes, production lags d15N in the ETNP by several kiloyears. This lag calls for a new understanding of the processes driving denitrification in the ETNP. We suggest that oxygen input by the Equatorial Undercurrent as well as local organic matter flux controls denitrification rates in the ETNP. Moreover, the differences in relative timing point to a time-transgressive development of upwelling-favorable winds along the NE Pacific margin after the last glaciation, with those in the north developing several kiloyears earlier.

Geochemistry of eolian dust from sediment core LL44-GPC-3

The large-diameter piston core LL44-GPC3 from the central North Pacific Ocean records continuous sedimentation of eolian dust since the Late Cretaceous. Two intervals resolved by Nd and Pb isotopic data relate to dust coming from America (prior to ~40 Ma) and dust coming from Asia (since ~40 Ma). The Intertropical Convergence Zone (ITCZ) separates these depositional regimes today and may have been at a paleolatitude of ~23°N prior to 40 Ma. Such a northerly location of the ITCZ is consistent with sluggish atmospheric circulation and warm climate for the Northern Hemisphere of the early to middle Eocene. Since ~40 Ma, correlations between Nd (~7.55 > epsilon-Nd(t) > ~10.81) and Pb (18.625 < 206/4Pb < 18.879; 15.624 < 207/4Pb < 15.666; 38.611 < 208/4Pb < 38.960; 0.8294 < 207/6Pb < 0.8389; 2.0539 < 208/6Pb < 2.0743) isotopes reflect the progressive drying of central Asia triggered by the westward retreat of the paleo-Tethys. Comparisons between the changes with time in the isotopically well-defined dust flux and Nd and Pb isotopic compositions of Pacific deep water allow one to draw two major conclusions: (1) dust-bound Nd became a resolvable contribution to Pacific seawater only after the one order of magnitude increase in dust flux starting at ~3.5 Ma. Therefore eolian Nd was unimportant for Pacific seawater Nd prior to 3.5 Ma. (2) The lack of a response of Pacific deep water Pb to this huge flux increase suggests that dust-bound Pb has never been important. Instead, mobile Pb associated with island arc volcanic exhalatives probably consists of a significant contribution to Pacific deep water Pb and possibly to seawater elsewhere far away from landmasses.