Evaluating trophic cascades as drivers of regime shifts in different ocean ecosystems

In ecosystems that are strongly structured by predation, reducing top predator abundance can alter several lower trophic levels—a process known as a trophic cascade. A persistent trophic cascade also fits the definition of a regime shift. Such ‘trophic cascade regime shifts'' have been reported in a few pelagic marine systems—notably the Black Sea, Baltic Sea and eastern Scotian Shelf—raising the question of how common this phenomenon is in the marine environment. We provide a general methodology for distinguishing top-down and bottom-up effects and apply this methodology to time series from these three ecosystems. We found evidence for top-down forcing in the Black Sea due primarily to gelatinous zooplankton. Changes in the Baltic Sea are primarily bottom-up, strongly structured by salinity, but top-down forcing related to changes in cod abundance also shapes the ecosystem. Changes in the eastern Scotian Shelf that were originally attributed to declines in groundfish are better explained by changes in stratification. Our review suggests that trophic cascade regime shifts are rare in open ocean ecosystems and that their likelihood increases as the residence time of water in the system increases. Our work challenges the assumption that negative correlation between consecutive trophic levels implies top-down forcing.     

Gene overexpression and biochemical characterization of the biotechnologically relevant chlorogenic acid hydrolase from Aspergillus niger

The full-length gene that encodes the chlorogenic acid hydrolase from Aspergillus niger CIRM BRFM 131 was cloned by PCR based on the genome of the strain A. niger CBS 513.88. The complete gene consists of 1,715 bp and codes for a deduced protein of 512 amino acids with a molecular mass of 55,264 Da and an acidic pI of 4.6. The gene was successfully cloned and overexpressed in A. niger to yield 1.25 g liter(-1), i.e., 330-fold higher than the production of wild-type strain A. niger CIRM BRFM131. The histidine-tagged recombinant ChlE protein was purified to homogeneity via a single chromatography step, and its main biochemical properties were characterized. The molecular size of the protein checked by mass spectroscopy was 74,553 Da, suggesting the presence of glycosylation. ChlE is assembled in a tetrameric form with several acidic isoforms with pIs of around 4.55 and 5.2. Other characteristics, such as optimal pH and temperature, were found to be similar to those determined for the previously characterized chlorogenic acid hydrolase of A. niger CIRM BRFM 131. However, there was a significant temperature stability difference in favor of the recombinant protein. ChlE exhibits a catalytic efficiency of 12.5 x 10(6) M(-1) s(-1) toward chlorogenic acid (CGA), and its ability to release caffeic acid from CGA present in agricultural by-products such as apple marc and coffee pulp was clearly demonstrated, confirming the high potential of this enzyme.     

Inhibition of phospholipase A1, lipase and galactolipase activities of pancreatic lipase-related protein 2 by methyl arachidonyl fluorophosphonate (MAFP)

Methyl arachidonyl fluorophosphonate (MAFP) is a known inhibitor of cytosolic phospholipase A2 and some other serine enzymes. MAFP was found here to be an irreversible inhibitor of human pancreatic lipase-related protein 2 (HPLRP2), an enzyme displaying lipase, phospholipase A1 and galactolipase activities. In the presence of MAFP, mass spectrometry analysis of HPLRP2 revealed a mass increase of 351Da, suggesting a covalent binding of MAFP to the active site serine residue. When HPLRP2 was pre-incubated with MAFP before measuring residual activity, a direct inhibition of HPLRP2 occurred, confirming that HPLRP2 has an active site freely accessible to solvent and differs from most lipases in solution. HPLRP2 activities on tributyrin (TC4), phosphatidylcholine (PC) and monogalactosyl dioctanoylglycerol (C8-MGDG) were equally inhibited under these conditions. Bile salts were not required to trigger the inhibition, but they significantly increased the rate of HPLRP2 inhibition, probably because of MAFP micellar solubilization. Since HPLRP2 is active on various substrates that self-organize differently in the presence of water, HPLRP2 inhibition by MAFP was tested in the presence of these substrates after adding MAFP in the course of the lipolysis reaction. In this case, the rates of inhibition of lipase, phospholipase A1 and galactolipase activities were not equivalent (triglycerides>PC>MGDG), suggesting different enzyme/inhibitor partitioning between the aqueous phase and lipid aggregates. The inhibition by MAFP of a well identified phospholipase A1 (HPLRP2), present in pancreatic juice and also in human monocytes, indicates that MAFP cannot be used for discriminating phospholipase A2 from A1 activities at the cellular level.     

Potential role of phospholipase D2 in increasing interleukin-2 production by T-lymphocytes through activation of mitogen-activated protein kinases ERK1/ERK2

Hydrolysis of phosphatidylcholine by phospholipase D (PLD) leads to the generation of phosphatidic acid (PA), which is itself a source of diacylglycerol (DAG). These two versatile lipid second messengers are at the centre of a phospholipid signalling network and as such are involved in several cellular functions. However, their role in T-cell activation and functions are still enigmatic. In order to elucidate this role, we generated a human and a murine T-cell line that stably overexpressed the PLD2 isoform. Analysis of the Ras-MAPK pathway upon phorbol myristate acetate (PMA) and ionomycin stimulation revealed that PLD2 promoted an early and sustained increase in ERK1/2 phosphorylation in both cell lines. This response was inhibited by 1-butanol, a well known distracter of PLD activity, or upon overexpression of a dominant negative PLD2, and it was concomitant with a boost of PA/DAG production. As a functional consequence of this PLD2-dependent MAPK activation, interleukin-2 production evoked by PMA/ionomycin stimulation or CD3/CD28 engagement was enhanced in the two T-cell lines overexpressing PLD2. Thus, PLD2 emerged as an early player upstream of the Ras-MAPK-IL-2 pathway in T-cells via PA and DAG production, raising new possibilities of pharmacological manipulation in immune disorders.     

Cloning and characterization of a tyrosinase gene from the white-rot fungus Pycnoporus sanguineus, and overproduction of the recombinant protein in Aspergillus niger

A new tyrosinase-encoding gene (2,204 bp) and the corresponding cDNA (1,857 nucleotides) from the white-rot fungus Pycnoporus sanguineus BRFM49 were cloned. This gene consisted of seven exons and six introns and encoded a predicted protein of 68 kDa, exceeding the mature tyrosinase by 23 kDa. P. sanguineus tyrosinase cDNA was over-expressed in Aspergillus niger, a particularly suitable fungus for heterologous expression of proteins of biotechnological interest, under the control of the glyceraldehyde-3-phosphate-dehydrogenase promoter as strong and constitutive promoter. The glucoamylase preprosequence of A. niger was used to target the secretion. This construction enabled the production of recombinant tyrosinase in the extracellular medium of A. niger. The identity of the purified recombinant protein was confirmed by N-terminal amino acid sequencing. The maturation process was shown to be effective in A. niger, and the recombinant enzyme was fully active, with a molecular mass of 45 kDa. The best transformant obtained, A. niger D15#26-e, produced extracellular tyrosinase activities of 534 and 1,668 U l⁻¹ for monophenolase and diphenolase, respectively, which corresponded to a protein yield of ca. 20 mg l⁻¹.     

Distinct Pathways for Tumor Necrosis Factor Alpha and Ceramides in Human Cytomegalovirus Infection

Human cytomegalovirus (HCMV) infection can be fatal to immunocompromised individuals. We have previously reported that gamma interferon and tumor necrosis factor alpha (TNF-α) synergistically inhibit HCMV replication in vitro. Ceramides have been described as second messengers induced by TNF-α. To investigate the mechanisms involved in the inhibition of HCMV by TNF-α, in the present study we have analyzed ceramide production by U373 MG astrocytoma cells and the effects of TNF-α versus ceramides on HCMV replication. Our results show that U373 MG cells did not produce ceramides upon incubation with TNF-α. Moreover, long-chain ceramides induced by treatment with exogenous bacterial sphingomyelinase inhibited HCMV replication in synergy with TNF-α. Surprisingly, short-chain permeant C6-ceramide increased viral replication. Our results show that the anti-HCMV activity of TNF-α is independent of ceramides. In addition, our results suggest that TNF-α and endogenous long-chain ceramides use separate pathways of cell signalling to inhibit HCMV replication, while permeant C6-ceramide appears to activate a third pathway leading to an opposite effect.Human cytomegalovirus (HCMV) infections are well controlled in the immunocompetent host. Cellular immune responses (CD4⁺ and CD8⁺ T cells and NK cells) which accompany both acute and latent infections (for a review, see reference 4) are thought to be the main components of this control. HCMV infection during immunosuppression such as in cancer, transplantations, or AIDS results in severe pathology (4). We have previously shown that tumor necrosis factor alpha (TNF-α), in synergy with gamma interferon (IFN-γ), inhibits the replication of HCMV (7). In mice, TNF-α is involved in the clearance of CMV infection (25). TNF-α is a cytokine with multiple effects which is produced by many cell types, including macrophages and CD8⁺ and CD4⁺ T lymphocytes (for a review, see reference 40), and is known to possess antiviral effects (20, 47). The molecular mechanisms involved in the signalling by TNF-α depend on the type of receptor, p55 (TNF-R1) or p75 (TNF-R2) (5), to which it binds. Some cells express only one type of TNF-α receptor; however, expression of these receptors is not always mutually exclusive (5). The cytotoxicity of TNF-α has been reported to be mediated by TNF-R1 (38), whose intracellular region carries a death domain which signals for programmed cell death (39). Signalling through TNF-R1 with specific antibodies can also protect Hep-G2 cells from vesicular stomatitis virus-mediated cytopathic effects (48). Ceramide production after TNF-α treatment has been widely reported (16, 19, 31) and has also been shown to depend on signalling through the TNF-R1 receptor (45). In these experiments concerning myeloid cells, TNF-α induced the activation of a sphingomyelinase, which cleaved sphingomyelin to release ceramide and phosphocholine. The production of ceramides can lead to cell apoptosis (11, 14, 23) or cell cycle arrest (13). Induction of apoptosis by TNF-α has been mimicked by exogenous sphingomyelinase and by synthetic, short-chain, permeant ceramides, which suggests that ceramides, as second messengers, are sufficient to induce the cytotoxic effects of TNF-α (11, 23). Acidic and neutral sphingomyelinases activated in different cell compartments may be responsible for the diverse effects of TNF-α (46), with the former being involved in signalling through NF-κB (34) and the latter being involved in signalling through a ceramide-activated protein kinase and phospholipase A₂ (46).One of the characteristics of HCMV infection is the increase in the content of intracellular DNA, reported to be of viral (3, 8, 18) or cellular (12, 37) origin. Since TNF-α has been known to display antiproliferative properties and to block cells in the G₁ phase (29), we initially tested its effects on the cell cycle of infected cells. Then, based on studies reporting that TNF-α induces ceramides in cells (16, 19, 31) and on a study showing the role of ceramide in cell cycle blockade (13), we originally postulated that ceramide was responsible for the antiviral effect of TNF-α. In the present study, we used astrocytoma cells (U373 MG) as a model for brain cells, which are important targets of HCMV in vivo (22). In contrast to fibroblasts, infected U373 MG cells release smaller quantities of virus particles even though all the cells were infected in our experiments. We believe that the U373 MG model is closer to HCMV infection in vivo. We show that ceramides are not produced by U373 MG cells upon incubation with even high concentrations of TNF-α. In addition, we demonstrate that exogenously added sphingomyelinase induces anti-HCMV effects whereas permeant C6-ceramide increases HCMV proliferation in U373 MG cells. This suggests that lipid second messengers can modulate HCMV infection and that TNF-α and ceramides use distinct signalling pathways in the control of HCMV infection. This is supported by our observation that the protein kinase JNK1 is activated exclusively by TNF-α in U373 MG cells and that TNF-α and exogenous sphingomyelinase act in synergy on HCMV infection.     

Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo

The water-accessible volumes, the amounts of all significant osmolytes, and the protein concentration in the cytoplasm of aerobically grown Escherichia coli K-12 have been determined as a function of the osmolarity of the minimal growth medium. The volume of cytoplasmic water (Vcyto) decreases linearly with increasing osmolarity from 2.23(+/- 0.12) microliters/mg dry weight in cells grown at 0.10 OSM to 1.18(+/- 0.06) microliters/mg dry weight at 1.02 OSM. Above 0.28 OSM, growth rate decreases linearly with increasing osmolarity. The growth rate extrapolates to zero at an osmolarity of approximately 1.8, corresponding to an estimated Vcyto of 0.5(+/- 0.2) microliters/mg dry weight. Measurements of Vcyto in titrations of non-growing cells with the plasmolyzing agent NaCl were used to obtain volumes of "bound" water (presumably water of macromolecular hydration) and cytoplasmic osmotic coefficients for cells grown in medium of low (0.10 OSM) and moderate (0.28 OSM) osmolarity. The volume of bound water Vb is similar in the two osmotic conditions (Vb = 0.40(+/- 0.04) microliters/mg dry wt), and corresponds to approximately 0.5 g H2O/g cytoplasmic macromolecule. Since Vcyto decreases with increasing osmolarity, whereas Vb appears to be independent of osmolarity, water of hydration becomes a larger fraction of Vcyto as the osmolarity of the growth medium increases. Growth appears to cease at the osmolarity where Vcyto is approximately equal to Vb. K+ and glutamate (Glu-) are the only significant cytoplasmic osmolytes in cells grown in medium of low osmolarity. The amount of K+ greatly exceeds that of Glu-. Analysis of cytoplasmic electroneutrality indicates that the cytoplasm behaves like a concentrated solution of the K+ salt of cytoplasmic polyanions, in which the amount of additional electrolyte (K+ Glu-) increases with increasing osmolarity. As the osmolarity of the growth medium becomes very low, the cytoplasm approaches an electrolyte-free K+-polyanion solution. In vivo osmotic coefficients were determined from the variation of Vcyto with external osmolarity in plasmolysis titrations of non-growing cells. The values obtained (phi = 0.54(+/- 0.06) for cells grown at 0.10 OSM and phi = 0.71(+/- 0.11) at 0.28 OSM) indicate a high degree of non-ideality of intracellular ions arising from coulombic interactions between K+ and cytoplasmic polyanions. Analysis of these osmotic coefficients using polyelectrolyte theory indicates that the thermodynamic activity of cytoplasmic K+ increases from approximately 0.14 M in cells grown at an external osmolarity of 0.10 OSM to approximately 0.76 M at 1.02 OSM.(ABSTRACT TRUNCATED AT 400 WORDS)