Canopy-forming macroalgae create a specific surrounding habitat (the matrix) with their own ecological properties. Previous studies have shown a wide range of responses to canopy removal. Magnitude and strength of the effects of harvesting are thought to be context-dependent, with the macroalgal matrix that can either soften or exacerbate the impact of harvesting. We experimentally examined in situ the effect of harvesting on targeted commercial species, and how these potential impacts might vary in relation to its associated matrix. We found that patterns of recovery following the harvesting disturbance were variable and matrix specific, suggesting that local factors and surrounding habitat characteristics mediated the influence of harvesting. The greatest and longest effects of harvesting were observed for the targeted species that created a dominant and monospecific canopy on their site prior to the disturbance. Another relevant finding was the important natural spatiotemporal variability of macrobenthic assemblages associated with canopy-forming species, which raises concern about the ability to discriminate the natural variability from the disturbance impact. Finally, our results support the need to implement ecosystem-based management, assessing both the habitat conditions and ecological roles of targeted commercial species, in order to insure the sustainability of the resource.

Through experimental harvesting, followed by a 12-month monitoring of demographic attributes, we tested the influence of harvesting on the population dynamics of Himanthalia elongata. We further explore the data to test the hypothesis that the canopy would exert a negative effect on the other developmental stages (intraspecific competition) throughout the recovery cycle of the population. This showed that the H. elongata canopy plays a marked seasonal role not by precluding the presence of other developmental stages but by delaying or preventing their growth and development. The removal of the canopy facilitates the transition from one developmental stage to another, eventually permitting a fast recovery of size structure in the population. This study allows us to integrate population dynamics and intraspecific relationships in our understanding of macroalgal recovery patterns. (C) 2016 Elsevier Ltd. All rights reserved.

In 2009, the European Union has defined an organic label for macroalgae, which implies that the commercial harvest of algae shall not cause a significant impact on ecosystems. The aim of this work was to study the effects of hand harvesting of three algae: Fucus serratus, Palmaria palmata, and Porphyra linearis on the associated biodiversity and metabolism of the ecosystem. We used the BACI (Before-After Control-Impact) design to assess the impact of the disturbance (i) on the recovery of the harvested species, (ii) on the specific and functional diversity of the associated algal and animal communities, and (iii) for F. serratus and P. linearis, on the metabolism of the area, using benthic chambers. Our work is based on a mix of fundamental and applied research to identify the effects of commercial harvesting regarding long-term changes, biological and functional interactions, and system responses (including socio-economic interactions). Results of the 12-month monitoring on F. serratus showed that canopy loss seemed to have a negative impact mainly on the diversity of the animal community and the metabolism of the studied area. No significant effects were observed on the algal community. The harvesting impact on the animal community was amplified by the settlement of an ephemeral canopy of Ulva spp., a seasonal opportunistic green alga. Results of the 12-month monitoring of P. palmata after harvesting did not show any significant impact. This alga was epiphytic on the dominant canopy of F. serratus, which was thus maintained, minimizing the impact of the harvest. Finally, results of the 12-month monitoring of P. linearis were difficult to interpret because of an unexpected but continuous sand burial of the study site, one month after the beginning of the study and still covering the population after eight months. Hence, effects of P. linearis harvesting were overshadowed by the natural variability. So far, our results have shown that commercial harvesting has different effects according to the target species, which emphasizes the necessity to continue long-term monitoring. Finally, this study also points out the valuable use of a “fundamental research” approach to deal with a practical management issue.

Cell engineering technology using recombinant microorganisms has created new opportunities in the development of innovative drugs. This article presents the use of living genetically engineered microorganisms, such as bacteria or yeasts, as a new delivery vehicle to the gastrointestinal tract. This 'biodrug' concept was demonstrated using recombinant Saccharomyces cerevisiae expressing the plant cytochrome P450 73A1. This enzyme provides a relevant model for potential therapeutic applications, such as 'biodetoxication' in the digestive environment. An artificial gastrointestinal tract simulating human digestion was chosen as a powerful tool to validate the biodrug concept. This approach offers a novel strategy for drug discovery and testing.

The purpose of this work was to analyse in vivo the influence of sudden oxygen depletion on Saccharomyces cerevisiae, grown in glucose-limited chemostat culture, using a recently developed cyclone reactor coupled with (31)P NMR spectroscopy. Before, during and after the transition, intracellular and extracellular phosphorylated metabolites as well as the pHs in the different cellular compartments were monitored with a time resolution of 2.5 min. The employed integrated NMR bioreactor system allowed the defined glucose-limited continuous cultivation of yeast at a density of 75 g DW/l and a p(O(2)) of 30% air saturation. A purely oxidative metabolism was maintained at all times. In vivo (31)P NMR spectra obtained were of excellent quality and even allowed the detection of phosphoenolpyruvate (PEP). During the switch from aerobic to anaerobic conditions, a rapid, significant decrease of intracellular ATP and PEP levels was observed and the cytoplasmic pH decreased from 7.5 to 6.8. This change, which was accompanied by a transient influx of extracellular inorganic phosphate (P(i)), appeared to correlate linearly with the decrease of the ATP concentration, suggesting that the cause of the partial collapse of the plasma membrane pH gradient was a reduced availability of ATP. The complete phosphorous balance established from our measurement data showed that polyphosphate was not the source of the increased intracellular P(i). The derived intracellular P(i), ATP and ADP concentration data confirmed that the glycolytic flux at the level of glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase and enolase enzymes is mainly controlled by thermodynamic constraints.

Summary— The changes in distribution and density of mitochondria and the level of mitochondrial RNA during Drosophila oogenesis were studied simultaneously in the 3 cell types ie follicle cells, nurse cells and oocyte, making up the egg chamber. Up to stage 6, mitochondrial density (mitochondrial and cellular areas ratio) was elevated and increased similarly in both follicle and nurse cells. Thereafter the mitochondrial density of follicle cells continued to increase and that of the nurse cells declined markedly while the nurse cell mitochondria assembled in dense groups and decreased in size. This can be related to a transfer of nurse cell cytoplasm, including mitochondria, to the oocyte. In the oocyte from stage 4 to stage 7 we observed a significant decrease of the mitochondrial density due to the absence of mitochondrial biogenesis. Then the cytoplasm transfer caused mitochondrial density to increase up to the level found in the nurse cells at the end of oogenesis. The mature oocyte contains enough mitochondria to supply 15 000 somatic cells. Our results strongly suggest that the variations in size, distribution and density of mitochondria relate to the particular energetic requirements of the different cell types during the first half of oogenesis. Later they relate to the developmental requirements of the nurse cells and the oocyte, in particular the storage of mitochondria in the oocyte. The level of mitochondrial RNA was studied through in situ hybridization. Throughout oogenesis the follicle and nurse cell RNA evolved similarly. Up to stage 9, there was no change in RNA densities in these cells, suggesting a correlation with the cell volume and/or the nuclear DNA content. Thereafter the cellular RNA concentration declined rapidly. In the oocyte the RNA concentration evolved differently especially from stage 10 to the end, the RNA density being stabilized. This can be related to the injection of nurse cell mitochondria, followed by their assignment to reserve status. Our results suggest that the mt RNA density is under extramitochondrial control mechanisms.

We have done a comparative analysis of RNA from six mitochondrial genes (rDNA, ND2, COI, COIII, ND4-ND5, Cyt b) during Drosophila oogenesis, using in situ hybridization. This study showed the same variation for each of these transcripts, which is similar to that obtained with the total mitochondrial RNA (Tourmente et al. (1990) Biol. Cell 60, 119-127). A constant RNA density until stage 9, followed by a rapid decline, was observed in follicle and nurse cells. These results confirm those previously obtained (Tourmente et al., (1990) Biol. Cell 60, 119-127), in favor of the existence of a correlation between the mtRNA level and the cell volume and/or the nuclear DNA content, and suggest a global extra-mitochondrial, transcriptional control mechanism. We also show that the relative proportions of the different RNA are similar, whatever the stage and cell type examined, even though the total mtRNA quantity is different. They are comparable to those previously obtained by Northern analysis of Drosophila embryos (Berthier et al. (1986) Nucleic Acids Res. 14, 1400-1412, suggesting a posttranscriptional control independent of the cell type. Surprisingly, we have detected an extra-mitochondrial hybridization for COIII, both in light and electron microscopy. Northern analysis of poly(A)+RNA from ovaries or cultured cells revealed an 1.7 kb extra-mitochondrial RNA, which is probably of nuclear origin.

The activation of the catalytic center of aminoacyl-tRNA synthetases upon binding of the tRNA, previously reported in the case of yeast phenylalanyl-tRNA and valyl-tRNA synthetases [Renaud et al., (1981) Proc. Natl Acad. Sci. USA, 78, 1606-1608] has been investigated in other systems. It is shown that this property is encountered not only in cognate systems (phenylalanyl, valyl and arginyl) but also in the non-cognate systems which are particularly efficient in misaminoacylation reactions. The arginyl system, the peculiarity of which is to form the aminoacyladenylate only in the presence of the cognate tRNA, is shown to be a border-line case of this general process of catalytic center activation. In the case of the phenylalanyl system, the crucial role of the wybutine residue (adjacent to the anticodon) in the activation of phenylalanyl-tRNA synthetase by the tRNA core has been analysed by comparison with native or modified non-cognate tRNAs (tRNATyr, tRNAArg). It is proposed that upon complex formation between a tRNA and its cognate aminoacyl-tRNA synthetase, a multistep adaptation process takes place in order to promote the optimal rate for the aminoacylation reaction, thus contributing to the specificity of this reaction.

Yeast phenylalanyl‐tRNA synthetase was specifically labelled with a 3′‐oxidised tRNA Phe . Stoichiometric inactivation was achieved with the incorporation of 2 mol oxidised tRNA Phe /mol enzyme which corresponds exactly to the stoichiometry of tRNA binding. The labelled peptide has been isolated using a quick chromatographic procedure which can be applied to any covalent complex formed between a tRNA and an aminoacyl‐tRNA synthetase. The isolated peptide (18 amino acids) was found to encompass the unique cysteine sequence of the smaller β subunit of the enzyme.

The fluorescence properties of yeast tRNAPheCCF (tRNAPhe in which the 3'-terminal adenosine has been replaced by formycin) and tRNAPheCCFoxi-red (tRNAPheCCF after periodate oxidation followed by borohydride reduction) were studied in the complex with the cognate aminoacyl-tRNA synthetase. In both cases a conformational change affecting the 3' end was observed in a magnesium concentration range close to 1 mM. The modification of formycin fluorescence could be ascribed simultaneously to the existence of a tautomeric equilibrium of the fluorescent probe and to a pH effect raising from a prototropic effect at the active site of phenylalanyl-tRNA synthetase, and to a partial destacking of the 3'-formycin from the adjacent C residue. The observed transconformation, which can be related to the structure modification of the anticodon loop previously reported [Ehrlich, Lefèvre, and Remy (1980) Eur. J. Biochem. 103, 145-153], takes place in the magnesium concentration range allowing the transfer of the activated amino acid from the adenylate to the tRNA. The interconnection between the anticodon loop and the accepting end was further supported by the observation that wybutine excision hinders the specific structure modification of 3'-formycin upon binding to the synthetase. The tRNAPhe transconformations occurring in the complex with the cognate synthetase probably reflect a reciprocal adaptation of both macromolecules which might lead to the optimal aminoacylation velocity and thus contribute to the specificity of aminoacylation, since it was previously established that this specificity relies more strongly on the kinetics of the reaction than on a discrimination of tRNAs according to different affinities.

The interactions between yeast tRNAphe and phenylalanyl-tRNA synthetase were studied by analysis of the covalent adducts obtained upon monochromatic ultraviolet irradiation at different wavelengths (248, 282, 292, 302 and 313 nm). The high extent of inactivation of phenylalanyl-tRNA synthetase, together with the partial modification of tRNA, as well as the peculiar instability of most of the covalent bonds formed upon irradiation constitute severe limitations to the use of the technique and to the interpretation of the results. These disadvantages led us to select an irradiation wavelength of 248 nm and to use only mild isolation procedures allowing a good recovery of the covalent adducts formed. Seven major tryptic peptides of the enzyme were found to be cross-linked to tRNAPhe whereas six major T1-oligonucleotides were covalently linked to the protein, among these, the three cross-linked oligonucleotides previously described by Shoemaker and Schimmel (J. Biol. Chem. 250 (1975) 4440-4444) in the same system. The difference in the number of covalently linked oligonucleotides is discussed in the light of the instability of the covalent linkages. The localization of the six oligonucleotides at the inside of the two branches forming the L-shaped tRNA molecule is similar to that observed in the yeast valine system (Renaud et al., Eur. J. Biochem. 101 (1979) 475-483) and is consistent with the interaction model previously described (Rich and Schimmel, Nucl. Acids Res. 4 (1977) 1649-1665 and Ebel et al. in Transfer RNA: structure, properties and recognition, (1979) pp. 325-343 Cold Spring Harbor Laboratory, NY). The occurrence of covalent cross-linking upon irradiation in the tryptophan absorption band (302 nm) strongly suggests the participation of this residue in the stabilization of the tRNA enzyme complex.

Adenosine or CpCpA trinucleoside diphosphate can be aminoacylated by phenylalanyl-tRNA synthetase [L-phenylalanine:tRNAPhe ligase (AMP forming), EC 6.1.1.20] when the reaction takes place in the presence of tRNAPhe deprived of its 3' adenosine or pCpCpA terminus. This shows that, upon interaction with tRNA, a structural alteration of the enzyme's active site is achieved. This process may be a determining step in the specificity of the aminoacylation reaction.

These studies have been carried out in the yeast phenylalanyl- (α2β2 MW 260000) and valyl-(α-MW 130000)-tRNA synthetase systems. (1) In the yeast Phe system, the location of the stereospecific binding sites among the constitutive subunits was undertaken with several affinity and photoaffinity labelling techniques. ATP could be specifically cross-linked to the β subunit of PheRS, whereas Phe and Phe-AMP were cross-linked to both α and β subunits; but Phe-tRNAPhe and tRNAphe were exclusively linked to the β subunit. (2) The UV cross-linking technique was used to identify the areas of tRNAPhe and tRNAVal in contact with their cognate synthetase. Six different oligonucleotides, all located at the inside of L-shaped tRNA molecules, were found in close interaction with the enzymes. These results are in agreement with the regions of tRNA which, in the complex, are protected against the action of cobra venom RNase, which splits preferentially double stranded regions. (3) The adaptation of the tRNA and enzyme molecules one to another upon complex formation was studied by monitoring several fluorescence properties of Y base and tryptophan residues in the Phe system. A major Mg++ dependant conformational change was detected in the anticodon loop of tRNA. Tryptophan fluorescence quenching brings evidence for a completely asymmetric configuration of the enzyme in the complex with tRNA. In the Val system, using small angle neutron scattering, it was found that the RG of ValRS inside the 1:1 complex with tRNAVal in 50 mM phosphate is smaller than that of the free enzyme. The effect is attenuated by increasing ionic strength. The enzyme appears to surround the tRNA which is bound near its centre of mass.