Seawater carbonate chemistry and biological processes of bivalve shellfish Mercenaria mercenaria and Argopecten irradians during experiments, 2011

The combustion of fossil fuels has enriched levels of CO2 in the world's oceans and decreased ocean pH. Although the continuation of these processes may alter the growth, survival, and diversity of marine organisms that synthesize CaCO3shells, the effects of ocean acidification since the dawn of the industrial revolution are not clear. Here we present experiments that examined the effects of the ocean's past, present, and future (21st and 22nd centuries) CO2concentrations on the growth, survival, and condition of larvae of two species of commercially and ecologically valuable bivalve shellfish (Mercenaria mercenariaand Argopecten irradians). Larvae grown under near preindustrial CO2concentrations (250 ppm) displayed significantly faster growth and metamorphosis as well as higher survival and lipid accumulation rates compared with individuals reared under modern day CO2 levels. Bivalves grown under near preindustrial CO2 levels displayed thicker, more robust shells than individuals grown at present CO2 concentrations, whereas bivalves exposed to CO2 levels expected later this century had shells that were malformed and eroded. These results suggest that the ocean acidification that has occurred during the past two centuries may be inhibiting the development and survival of larval shellfish and contributing to global declines of some bivalve populations.

On the effects of circulation, sediment resuspension and biological incorporation by diatoms in an ocean model of aluminium, link to model data

The distribution of dissolved aluminium in the West Atlantic Ocean shows a mirror image with that of dissolved silicic acid, hinting at intricate interactions between the ocean cycling of Al and Si. The marine biogeochemistry of Al is of interest because of its potential impact on diatom opal remineralisation, hence Si availability. Furthermore, the dissolved Al concentration at the surface ocean has been used as a tracer for dust input, dust being the most important source of the bio-essential trace element iron to the ocean. Previously, the dissolved concentration of Al was simulated reasonably well with only a dust source, and scavenging by adsorption on settling biogenic debris as the only removal process. Here we explore the impacts of (i) a sediment source of Al in the Northern Hemisphere (especially north of ~ 40° N), (ii) the imposed velocity field, and (iii) biological incorporation of Al on the modelled Al distribution in the ocean. The sediment source clearly improves the model results, and using a different velocity field shows the importance of advection on the simulated Al distribution. Biological incorporation appears to be a potentially important removal process. However, conclusive independent data to constrain the Al / Si incorporation ratio by growing diatoms are missing. Therefore, this study does not provide a definitive answer to the question of the relative importance of Al removal by incorporation compared to removal by adsorptive scavenging.

Seawater carbonate chemistry and biological processes of Porites panamensis during experiments, 2011

Survival of coral planulae, and the successful settlement and healthy growth of primary polyps are critical for the dispersal of scleractinian corals and hence the recovery of degraded coral reefs. It is therefore important to explore how the warmer and more acidic oceanic conditions predicted for the future could affect these processes. This study used controlled culture to investigate the effects of a 1 °C increase in temperature and a 0.2-0.25 unit decrease in pH on the settlement and survival of planulae and the growth of primary polyps in the Tropical Eastern Pacific coral Porites panamensis. We found that primary polyp growth was reduced only marginally by more acidic seawater but the combined effect of high temperature and lowered pH caused a significant reduction in growth of primary polyps by almost a third. Elevated temperature was found to significantly reduce the amount of zooxanthellae in primary polyps, and when combined with lowered pH resulted in a significant reduction in biomass of primary polyps. However, survival and settlement of planula larvae were unaffected by increased temperature, lowered acidity or the combination of both. These results indicate that in future scenarios of increased temperature and oceanic acidity coral planulae will be able to disperse and settle successfully but primary polyp growth may be hampered. The recovery of reefs may therefore be impeded by global change even if local stressors are curbed and sufficient sources of planulae are available.

Chemistry and biological processes during experiments with spider crab Hyas araneus

The combined effects of ocean warming and acidification were compared in larvae from two popula- tions of the cold-eurythermal spider crab Hyas araneus, from one of its southernmost populations (around Helgo- land, southern North Sea, 54°N, habitat temperature 3-18°C; collection: January 2008, hatch: January-February 2008) and from one of its northernmost populations (Svalbard, North Atlantic, 79°N, habitat temperature 0-6°C; collection: July 2008, hatch: February-April 2009). Larvae were exposed to temperatures of 3, 9 and 15°C combined with present-day normocapnic (380 ppm CO2) and projected future CO2 concentrations (710 and 3,000 ppm CO2). Calcium content of whole larvae was measured in freshly hatched Zoea I and after 3, 7 and 14 days during the Megalopa stage. Significant differences between Helgoland and Svalbard Megalopae were observed at all investigated temperatures and CO2 condi- tions. Under 380 ppm CO2, the calcium content increased with rising temperature and age of the larvae. At 3 and 9°C, Helgoland Megalopae accumulated more calcium than Svalbard Megalopae. Elevated CO2 levels, especially 3,000 ppm, caused a reduction in larval calcium contents at 3 and 9°C in both populations. This effect set in early, at 710 ppm CO2 only in Svalbard Megalopae at 9°C. Fur- thermore, at 3 and 9°C Megalopae from Helgoland replenished their calcium content to normocapnic levels and more rapidly than Svalbard Megalopae. However, Svalbard Megalopae displayed higher calcium contents under 3,000 ppm CO2 at 15°C. The findings of a lower capacity for calcium incorporation in crab larvae living at the cold end of their distribution range suggests that they might be more sensitive to ocean acidification than those in temperate regions.

Two-dimensional IR correlation spectroscopy: Sequential events in the unfolding process of the λ Cro-V55C repressor protein

A question often posed in protein folding/unfolding studies is whether the process is fully cooperative or whether it contains sequential elements. To address this question, one needs tools capable of resolving different events. It seems that, at least in certain cases, two-dimensional (2D) IR correlation spectroscopy can provide answers to this question. To illustrate this point, we have turned to the Cro-V55C dimer of the λ Cro repressor, a protein known to undergo thermal unfolding in two discrete steps through a stable equilibrium intermediate. The secondary structure of this intermediate is compatible with that of a partially unfolded protein and involves a reorganization of the N terminus, whereas the antiparallel β-ribbon formed by the C-terminal part of each subunit remains largely intact. To establish whether the unfolding process involves sequential events, we have performed a 2D correlation analysis of IR spectra recorded over the temperature range of 20–95°C. The 2D IR correlation analysis indeed provides evidence for a sequential formation of the stable intermediate, which is created in three (closely related) steps. A first step entails the unfolding of the short N-terminal β-strand, followed by the unfolding of the α-helices in a second step, and the third step comprises the reorganization of the remaining β-sheet and of some unordered segments in the protein. The complete unfolding of the stable intermediate at higher temperatures also undergoes sequential events that ultimately end with the breaking of the H bonds between the two β-strands at the dimer interface.

Yersinia enterocolitica induces apoptosis in macrophages by a process requiring functional type III secretion and translocation mechanisms and involving YopP, presumably acting as an effector protein

Yersiniae, causative agents of plague and gastrointestinal diseases, secrete and translocate Yop effector proteins into the cytosol of macrophages, leading to disruption of host defense mechanisms. It is shown in this report that Yersinia enterocolitica induces apoptosis in macrophages and that this effect depends on YopP. Functional secretion and translocation mechanisms are required for YopP to act, strongly suggesting that this protein exerts its effect intracellularly, after translocation into the macrophages. YopP shows a high level of sequence similarity with AvrRxv, an avirulence protein from Xanthomonas campestris, a plant pathogen that induces programmed cell death in plant cells. This indicates possible similarities between the strategies used by pathogenic bacteria to elicit programmed cell death in both plant and animal hosts.

Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria

A negative feedback control of kaiC expression by KaiC protein has been proposed to generate a basic oscillation of the circadian clock in the cyanobacterium Synechococcus sp. PCC 7942. KaiC has two P loops or Walker's motif As, that are potential ATP-/GTP-binding motifs and DXXG motifs conserved in various GTP-binding proteins. Herein, we demonstrate that in vitro KaiC binds ATP and, with lower affinity, GTP. Point mutation by site-directed mutagenesis of P loop 1 completely nullified the circadian rhythm of kaiBC expression and markedly reduced ATP-binding activity. Moreover, KaiC can be autophosphorylated in vitro. These results suggest that the nucleotide-binding activity of KaiC plays important roles in the generation of circadian oscillation in cyanobacteria.

DNA methylation is a reversible biological signal

The pattern of DNA methylation plays an important role in regulating different genome functions. To test the hypothesis that DNA methylation is a reversible biochemical process, we purified a DNA demethylase from human cells that catalyzes the cleavage of a methyl residue from 5-methyl cytosine and its release as methanol. We show that similar to DNA methyltransferase, DNA demethylase shows CpG dinucleotide specificity, can demethylate mdCpdG sites in different sequence contexts, and demethylates both fully methylated and hemimethylated DNA. Thus, contrary to the commonly accepted model, DNA methylation is a reversible signal, similar to other physiological biochemical modifications.

Unbinding process of adsorbed proteins under external stress studied by atomic force microscopy spectroscopy

We report the study of the dynamics of the unbinding process under a force load f of adsorbed proteins (fibrinogen) on a solid surface (hydrophilic silica) by means of atomic force microscopy spectroscopy. By varying the loading rate rf, defined by f = rf t, t being the time, we find that, as for specific interactions, the mean rupture force increases with rf. This unbinding process is analyzed in the framework of the widely used Bell model. The typical dissociation rate at zero force entering in the model lies between 0.02 and 0.6 s−1. Each measured rupture is characterized by a force f0, which appears to be quantized in integer multiples of 180–200 pN.

Retinoic acid (RA) and As2O3 treatment in transgenic models of acute promyelocytic leukemia (APL) unravel the distinct nature of the leukemogenic process induced by the PML-RARα and PLZF-RARα oncoproteins

Acute promyelocytic leukemia (APL) is associated with chromosomal translocations always involving the RARα gene, which variably fuses to one of several distinct loci, including PML or PLZF (X genes) in t(15;17) or t(11;17), respectively. APL in patients harboring t(15;17) responds well to retinoic acid (RA) treatment and chemotherapy, whereas t(11;17) APL responds poorly to both treatments, thus defining a distinct syndrome. Here, we show that RA, As2O3, and RA + As2O3 prolonged survival in either leukemic PML-RARα transgenic mice or nude mice transplanted with PML-RARα leukemic cells. RA + As2O3 prolonged survival compared with treatment with either drug alone. In contrast, neither in PLZF-RARα transgenic mice nor in nude mice transplanted with PLZF-RARα cells did any of the three regimens induce complete disease remission. Unexpectedly, therapeutic doses of RA and RA + As2O3 can induce, both in vivo and in vitro, the degradation of either PML-RARα or PLZF-RARα proteins, suggesting that the maintenance of the leukemic phenotype depends on the continuous presence of the former, but not the latter. Our findings lead to three major conclusions with relevant therapeutic implications: (i) the X-RARα oncoprotein directly determines response to treatment and plays a distinct role in the maintenance of the malignant phenotype; (ii) As2O3 and/or As2O3 + RA combination may be beneficial for the treatment of t(15;17) APL but not for t(11;17) APL; and (iii) therapeutic strategies aimed solely at degrading the X-RARα oncoprotein may not be effective in t(11;17) APL.

Biological impact on mineral dissolution: Application of the lichen model to understanding mineral weathering in the rhizosphere

Microorganisms modify rates and mechanisms of chemical and physical weathering and clay growth, thus playing fundamental roles in soil and sediment formation. Because processes in soils are inherently complex and difficult to study, we employ a model based on the lichen–mineral system to identify the fundamental interactions. Fixed carbon released by the photosynthetic symbiont stimulates growth of fungi and other microorganisms. These microorganisms directly or indirectly induce mineral disaggregation, hydration, dissolution, and secondary mineral formation. Model polysaccharides were used to investigate direct mediation of mineral surface reactions by extracellular polymers. Polysaccharides can suppress or enhance rates of chemical weathering by up to three orders of magnitude, depending on the pH, mineral surface structure and composition, and organic functional groups. Mg, Mn, Fe, Al, and Si are redistributed into clays that strongly adsorb ions. Microbes contribute to dissolution of insoluble secondary phosphates, possibly via release of organic acids. These reactions significantly impact soil fertility. Below fungi–mineral interfaces, mineral surfaces are exposed to dissolved metabolic byproducts. Through this indirect process, microorganisms can accelerate mineral dissolution, leading to enhanced porosity and permeability and colonization by microbial communities.