Evolution de la biocénose rotatorienne au cours des variations de l'état trophique du Léman et comparaison avec le lac de Constance

L'évolution comparée des biocénoses rotatoriennes du Léman et du Lac de Constance montre un parallélisme remarquable lors des changements continus de l'état trophique, tant avant qu'après le niveau maximal d'eutrophisation atteint par ces deux lacs. La comparaison avec un certain nombre d'autres milieux soumis également à un changement de leur niveau trophique met en évidence une variation très nette des effectifs des espèces méso-eutrophes et eutrophes en fonction de la progression ou de la régression de l'eutrophisation; ces changements sont beaucoup moins marqués en ce qui concerne l'association des espèces oligo-mésotrophes.Eutrophication of a lake must be expected to cause both abiotic and biotic responses. The changes in the trophic state of a lake certainly occur at all trophic levels, but to different extents depending on the character of the ecosystem; the subsequent evolution of the rotifer biocenosis is one of the most pronounced features occurring as an indirect consequence of eutrophication.In the last three decades, the rotifer community in Lake Geneva has presented important changes in structure, as a result of continuous changes in the trophism of the lake. This study covered a period of time sufficient to show possible true modifications of the community structure.Lake Geneva has undergone anthropogenic eutrophication since the 1950's. The lake reached its highest nutrient level during 1979-1980, which has decreased though since 1981 with the improvement of phosphorus removal in sewage treatment plants. A similar trend was observed in Lake Constance, with more important quantitative changes connected with previous results dating from the oligotrophic stage of this lake.Table 1 gives the variations in abundance of rotifer species observed during the eutrophication increase and during the decrease of the eutrophication level in some lakes of different trophic status.Figure 1 indicates the quantitative changes of the main rotifer species in Lake Geneva and Lake Constance. Compared to the maximal trophic level (indicated by arrow), data from Lake Geneva for 1959-1987 are similar to those obtained in Lake Constance between 1963 and 1978, if the previous data obtained for this lake during its oligotrophic stage are excluded.Figure 2 presents the general trend observed for the different trophic indicator groups during the increase or decrease of eutrophication. Throughout the eutrophication process, these groups exhibited a general increase for most of the different species, with the ratio "number of increasing species/number of decreasing species" growing from the oligo-mesotrophic group to the eutrophic one. During the decrease of eutrophication, the strength of meso-eutrophic and eutrophic indicator groups diminished more than that of the oligomesotrophic group.Many species have appeared during the eutrophication increase, mainly belonging to meso-eutrophic and eutrophic indicator groups, together with the settlement of some oligo-mesotrophicspecies (Ascomorpha saltans, Synchaeta oblonga, Notholca caudata). The proportion of meso-eutrophic and eutrophic species increased in the two lakes, but there is a trend in populations of the oligo-mesotrophic species to decrease, leading to a precocious disappearance of Ploesoma hudsoni and later of Ascomorpha ovalis, Gastropus stylifer, Ploesoma truncatum in Lake Constance, and of Synchaeta tremula and Notholca foliacea in both lakes.Decreasing eutrophication reduces the number of some mesoeutrophic (Trichocerca longiseta and T. pusilla in Lake Geneva, T. rousseleti in Lake Constance) and eutrophic species (Anuraeopsis fissa and Trichocera cylindrica in Lake Geneva, Pompholyx complanta in Lake Constance). However, the water quality has mot improved enough to allow a further increase in oligo-mesotrophic species, except for Conochilus unicornis in both lakes, and for Ascomorpha ecaudis, Kellicottia longispina and Synchaeta oblonga in Lake Geneva.Since 1981, the oligo-mesotrophic indicator group is numerically dominant in Lake Geneva (BALVAY and LAURENT, 1989c), preceding the euryecious one (Asplanchna priodonta + Keratella cochlearis), white the strength of the meso-eutrophic group decreases and the eutrophic one remains almost steady

Relargage du phosphore à l'interface eau-sédiment dans des étangs de pisciculture de la station Deroua (Béni Mellal, Maroc)

De l'urée et du super phosphate triple ont été appliqués aux étangs d'alevinage de carpes chinoises de la station Deroua pour stimuler la croissance des algues. Toutefois, une forte proportion de ce phosphore est fixée par les sédiments et sera libérée en grande quantité dans les étangs lorsque les sédiments sont en conditions anaérobies.Nous avons étudié le relargage des orthophosphates par les sédiments provenant de deux étangs différents. L'un (A1) en terre ce qui permet la percolation des éléments nutritifs vers les couches profondes, l'autre (C1) dont le fond recouvert d'une fine membrane en polyéthylène, est parfaitement imperméable et empêche toute perte. Par ailleurs, nous avons étudié les effets de l'oxygène dissous, du pH, des nitrates et du glucose sur le relargage des orthophosphates par les sédiments.Les résultats obtenus montrent qu'en anaérobiose, la solubilité du phosphore augmente dans l'eau interstitielle. Les orthophosphates libérés, dont la concentration peut atteindre 873 µg/l, proviennent de la fraction minérale en particulier du Fe(OOH)=P. Le sédiment C1 qui accumule de grandes quantités de matière organique libère plus de phosphore que le sédiment A1.L'addition des nitrates limite la mobilisation du phosphore à partir des sédiments. Le pH acide provoque la dissolution du phosphore lié au calcium alors qu'un pH alcalin provoque celle du phosphore lié aux hydroxydes de fer et sa précipitation partielle sur les carbonates présents dans les sédiments.In the Deroua fish farm (Béni-Mellal, Morocco), a series of ponds was lined with polyethylene to prevent water seepage (lined ponds, C). Another series of ponds was not lined (unlined ponds, A). The lined ponds do not need much fertiliser to enhance phytoplankton growth. They receive a small quantity of urea and triple super phosphate and accumulate high levels of organic matter in their sediments. The unlined ponds receive a large quantity of fertilisers. In the ponds, an important increase in phytoplankton growth occurred particularly after fertilisation with triple super phosphate. The phosphate (P) released from the sediment is the essential source of P for phytoplankton when the ponds are not fertilised.Sediment samples used in this study were collected in June 1999 from the A1 and C1 ponds of the Deroua fish farm. The bottom sediments were collected with a core sampler to provide samples from the 0-5 cm layer. The samples were mixed and analysed for pH, total Kjeldahl nitrogen (NTK), nitrates (N-NO3-), ammonium (N-NH4+), total iron (tot-Fe) and P-fractionation in eight replicates, using the Golterman method (1996).In this work, experiments were conducted to evaluate the P released from sediments of lined and unlined ponds under controlled conditions. The samples included: untreated sediments, sediments treated with hydrogen peroxide (H2O2), and sediments treated with chloroform (CHCl3). H2O2 was used to destroy the organic matter of sediment. To inactivate bacteria, CHCl3 was added to the sediments. CHCl3 does not modify the mineral and organic structures of sediments but does reduce the bacterial biomass. Urea and triple super phosphate were added to Chinese carp rearing ponds at Deroua fisheries farm to stimulate algal growth. However, phosphate bound to the sediments was released into the water column during anaerobic conditions. The released phosphate from lined pond (C1) enhanced the algal production.We have tested the fertilisation capacity of A1 and C1 ponds as well as the effects of different factors such as dissolved oxygen, pH, nitrate, and organic matter (glucose) on the phosphate released from the sediments. The results show that under anoxic conditions, phosphate solubility increased in the interstitial water. The released phosphate (873 µg/l) comes from the mineral fraction, particularly from Fe(OOH)=P. The P released from the A1 untreated sediment under oxic and anoxic conditions was low in comparison to the P released from the C1 untreated sediment and did not exceed 9.1 µg.g-1 d.w. (Figure 1). The removal of organic matter with H2O2 had a positive effect on the P released from the C1 sediments only after the second day of incubation. The inactivation of bacteria with CHCl3 had an inhibitory effect on the P released from the C1 sediments under oxic and anoxic conditions; however for the A1 sediments, this inactivation of bacteria had no effect on the kinetics of P release. Phosphorus release from the C1 sediments was important under anoxic conditions; the P came from Fe(OOH)=P after the reduction of Fe(OOH).The addition of nitrates decreased the mobilisation of phosphate from the sediments. Acid conditions increased the dissolution of calcium-bound phosphate, while alkaline conditions increased the dissolution of iron-bound phosphate and its re-precipitation onto carbonate present in sediments. High concentrations of organic matter (glucose) increased oxygen demand and favoured the development of reducing conditions. The phosphate was released from Fe(OOH)=P.The conceptual model of P released in fish ponds shows that, in semiarid climates and in calcareous areas, the polyethylene lining of ponds prevents not only the seepage of water but also the percolation of nutrients. Consequently, the P was more available for algal uptake in the lined ponds. More phosphate will be released concomitant with the process of the ponds becoming anoxic, as nitrate concentrations and the pH of sediments decrease

Polymer-Based Reconstruction of the Inferior Vena Cava in Rat: Stem Cells or RGD Peptide?

As part of a program targeted at developing a resorbable valved tube for replacement of the right ventricular outflow tract, we compared three biopolymers (polyurethane [PU], polyhydroxyalkanoate (the poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxyvalerate) [PHBVV]), and polydioxanone [PDO]) and two biofunctionalization techniques (using adipose-derived stem cells [ADSCs] or the arginine-glycine-aspartate [RGD] peptide) in a rat model of partial inferior vena cava (IVC) replacement. Fifty-three Wistar rats first underwent partial replacement of the IVC with an acellular electrospun PDO, PU, or PHBVV patch, and 31 nude rats subsequently underwent the same procedure using a PDO patch biofunctionalized either by ADSC or RGD. Results were assessed both in vitro (proliferation and survival of ADSC seeded onto the different materials) and in vivo by magnetic resonance imaging (MRI), histology, immunohistochemistry [against markers of vascular cells (von Willebrand factor [vWF], smooth muscle actin [SMA]), and macrophages ([ED1 and ED2] immunostaining)], and enzyme-linked immunosorbent assay (ELISA; for the expression of various cytokines and inducible NO synthase). PDO showed the best in vitro properties. Six weeks after implantation, MRI did not detect significant luminal changes in any group. All biopolymers were evenly lined by vWF-positive cells, but only PDO and PHBVV showed a continuous layer of SMA-positive cells at 3 months. PU patches resulted in a marked granulomatous inflammatory reaction. The ADSC and RGD biofunctionalization yielded similar outcomes. These data confirm the good biocompatibility of PDO and support the concept that appropriately peptide-functionalized polymers may be successfully substituted for cell-loaded materials

MetWAMer: eukaryotic translation initiation site prediction

<p>Abstract</p> <p>Background</p> <p>Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations.</p> <p>Results</p> <p>MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the <it>k</it>-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage.</p> <p>Conclusion</p> <p>We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.</p

An integrated ontology resource to explore and study host-virus relationships.

Our growing knowledge of viruses reveals how these pathogens manage to evade innate host defenses. A global scheme emerges in which many viruses usurp key cellular defense mechanisms and often inhibit the same components of antiviral signaling. To accurately describe these processes, we have generated a comprehensive dictionary for eukaryotic host-virus interactions. This controlled vocabulary has been detailed in 57 ViralZone resource web pages which contain a global description of all molecular processes. In order to annotate viral gene products with this vocabulary, an ontology has been built in a hierarchy of UniProt Knowledgebase (UniProtKB) keyword terms and corresponding Gene Ontology (GO) terms have been developed in parallel. The results are 65 UniProtKB keywords related to 57 GO terms, which have been used in 14,390 manual annotations; 908,723 automatic annotations and propagated to an estimation of 922,941 GO annotations. ViralZone pages, UniProtKB keywords and GO terms provide complementary tools to users, and the three resources have been linked to each other through host-virus vocabulary

Hepatitis C Virus Controls Interferon Production through PKR Activation

Hepatitis C virus is a poor inducer of interferon (IFN), although its structured viral RNA can bind the RNA helicase RIG-I, and activate the IFN-induction pathway. Low IFN induction has been attributed to HCV NS3/4A protease-mediated cleavage of the mitochondria-adapter MAVS. Here, we have investigated the early events of IFN induction upon HCV infection, using the cell-cultured HCV JFH1 strain and the new HCV-permissive hepatoma-derived Huh7.25.CD81 cell subclone. These cells depend on ectopic expression of the RIG-I ubiquitinating enzyme TRIM25 to induce IFN through the RIG-I/MAVS pathway. We observed induction of IFN during the first 12 hrs of HCV infection, after which a decline occurred which was more abrupt at the protein than at the RNA level, revealing a novel HCV-mediated control of IFN induction at the level of translation. The cellular protein kinase PKR is an important regulator of translation, through the phosphorylation of its substrate the eIF2α initiation factor. A comparison of the expression of luciferase placed under the control of an eIF2α-dependent (IRESEMCV) or independent (IRESHCV) RNA showed a specific HCV-mediated inhibition of eIF2α-dependent translation. We demonstrated that HCV infection triggers the phosphorylation of both PKR and eIF2α at 12 and 15 hrs post-infection. PKR silencing, as well as treatment with PKR pharmacological inhibitors, restored IFN induction in JFH1-infected cells, at least until 18 hrs post-infection, at which time a decrease in IFN expression could be attributed to NS3/4A-mediated MAVS cleavage. Importantly, both PKR silencing and PKR inhibitors led to inhibition of HCV yields in cells that express functional RIG-I/MAVS. In conclusion, here we provide the first evidence that HCV uses PKR to restrain its ability to induce IFN through the RIG-I/MAVS pathway. This opens up new possibilities to assay PKR chemical inhibitors for their potential to boost innate immunity in HCV infection

An Internal Ribosome Entry Site Directs Translation of the 39-Gene from Pelargonium Flower Break Virus Genomic RNA: Implications for Infectivity

[EN] Pelargonium flower break virus (PFBV, genus Carmovirus) has a single-stranded positive-sense genomic RNA (gRNA) which contains five ORFs. The two 59-proximal ORFs encode the replicases, two internal ORFs encode movement proteins, and the 39-proximal ORF encodes a polypeptide (p37) which plays a dual role as capsid protein and as suppressor of RNA silencing. Like other members of family Tombusviridae, carmoviruses express ORFs that are not 59-proximal from subgenomic RNAs. However, in one case, corresponding to Hisbiscus chlorotic ringspot virus, it has been reported that the 39-proximal gene can be translated from the gRNA through an internal ribosome entry site (IRES). Here we show that PFBV also holds an IRES that mediates production of p37 from the gRNA, raising the question of whether this translation strategy may be conserved in the genus. The PFBV IRES was functional both in vitro and in vivo and either in the viral context or when inserted into synthetic bicistronic constructs. Through deletion and mutagenesis studies we have found that the IRES is contained within a 80 nt segment and have identified some structural traits that influence IRES function. Interestingly, mutations that diminish IRES activity strongly reduced the infectivity of the virus while the progress of the infection was favoured by mutations potentiating such activity. These results support the biological significance of the IRES-driven p37 translation and suggest that production of the silencing suppressor from the gRNA might allow the virus to early counteract the defence response of the host, thus facilitating pathogen multiplication and spread.This research was supported by grants BFU2006-11230 and BFU2009-11699 from the Spanish Ministerio de Ciencia e Innovacion (MICINN) and by grants ACOM/2006/210 and ACOMP/2009/040 (to CH) and GVPRE/2008/121 (to OF-M) from the Generalitat Valenciana. The latter was the recipient of an I3P postdoctoral contract from the Spanish Consejo Superior de Investigaciones Cientificas and an additional contract from MICINN. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Fernandez Miragall, O.; Hernandez Fort, C. (2011). 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A Tobamovirus Genome That Contains an Internal Ribosome Entry Site Functionalin Vitro. Virology, 232(1), 32-43. doi:10.1006/viro.1997.8525Skulachev, M. V., Ivanov, P. A., Karpova, O. V., Korpela, T., Rodionova, N. P., Dorokhov, Y. L., & Atabekov, J. G. (1999). Internal Initiation of Translation Directed by the 5′-Untranslated Region of the Tobamovirus Subgenomic RNA I2. Virology, 263(1), 139-154. doi:10.1006/viro.1999.9928Jaag, H. M., Kawchuk, L., Rohde, W., Fischer, R., Emans, N., & Prufer, D. (2003). An unusual internal ribosomal entry site of inverted symmetry directs expression of a potato leafroll polerovirus replication-associated protein. Proceedings of the National Academy of Sciences, 100(15), 8939-8944. doi:10.1073/pnas.1332697100Balvay, L., Rifo, R. S., Ricci, E. P., Decimo, D., & Ohlmann, T. (2009). Structural and functional diversity of viral IRESes. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1789(9-10), 542-557. doi:10.1016/j.bbagrm.2009.07.005Kneller, E. L. P., Rakotondrafara, A. M., & Miller, W. A. (2006). Cap-independent translation of plant viral RNAs. Virus Research, 119(1), 63-75. doi:10.1016/j.virusres.2005.10.010Rico, P., & Hern�ndez, C. (2004). Complete nucleotide sequence and genome organization of Pelargonium flower break virus. Archives of Virology, 149(3), 641-651. doi:10.1007/s00705-003-0231-5Martinez-Turino, S., & Hernandez, C. (2010). Identification and characterization of RNA-binding activity in the ORF1-encoded replicase protein of Pelargonium flower break virus. Journal of General Virology, 91(12), 3075-3084. doi:10.1099/vir.0.023093-0Martínez-Turiño, S., & Hernández, C. (2011). A membrane-associated movement protein of Pelargonium flower break virus shows RNA-binding activity and contains a biologically relevant leucine zipper-like motif. Virology, 413(2), 310-319. doi:10.1016/j.virol.2011.03.001Martinez-Turino, S., & Hernandez, C. (2009). Inhibition of RNA silencing by the coat protein of Pelargonium flower break virus: distinctions from closely related suppressors. Journal of General Virology, 90(2), 519-525. doi:10.1099/vir.0.006098-0Rico, P., & Hernández, C. (2009). Characterization of the subgenomic RNAs produced by Pelargonium flower break virus: Identification of two novel RNAs species. Virus Research, 142(1-2), 100-107. doi:10.1016/j.virusres.2009.01.018Koh, D. C.-Y., Wong, S.-M., & Liu, D. X. (2003). Synergism of the 3′-Untranslated Region and an Internal Ribosome Entry Site Differentially Enhances the Translation of a Plant Virus Coat Protein. Journal of Biological Chemistry, 278(23), 20565-20573. doi:10.1074/jbc.m210212200Hellen, C. U. T. (2001). Internal ribosome entry sites in eukaryotic mRNA molecules. Genes & Development, 15(13), 1593-1612. doi:10.1101/gad.891101Martínez-Salas, E. (1999). Internal ribosome entry site biology and its use in expression vectors. Current Opinion in Biotechnology, 10(5), 458-464. doi:10.1016/s0958-1669(99)00010-5Dobrikova, E., Florez, P., Bradrick, S., & Gromeier, M. (2003). Activity of a type 1 picornavirus internal ribosomal entry site is determined by sequences within the 3’ nontranslated region. Proceedings of the National Academy of Sciences, 100(25), 15125-15130. doi:10.1073/pnas.2436464100Belsham, G. J. (2009). Divergent picornavirus IRES elements. Virus Research, 139(2), 183-192. doi:10.1016/j.virusres.2008.07.001Fernández-Miragall, O., Quinto, S. L. de, & Martínez-Salas, E. (2009). Relevance of RNA structure for the activity of picornavirus IRES elements. Virus Research, 139(2), 172-182. doi:10.1016/j.virusres.2008.07.009Pestova, T. V., Kolupaeva, V. G., Lomakin, I. B., Pilipenko, E. V., Shatsky, I. N., Agol, V. I., & Hellen, C. U. T. (2001). Molecular mechanisms of translation initiation in eukaryotes. Proceedings of the National Academy of Sciences, 98(13), 7029-7036. doi:10.1073/pnas.111145798FERNANDEZ-MIRAGALL, O. (2003). Structural organization of a viral IRES depends on the integrity of the GNRA motif. RNA, 9(11), 1333-1344. doi:10.1261/rna.5950603ROBERTSON, M. E. M., SEAMONS, R. A., & BELSHAM, G. J. (1999). A selection system for functional internal ribosome entry site (IRES) elements: Analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES. RNA, 5(9), 1167-1179. doi:10.1017/s1355838299990301Dorokhov, Y. L., Skulachev, M. V., Ivanov, P. A., Zvereva, S. D., Tjulkina, L. G., Merits, A., … Atabekov, J. G. (2002). Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry. Proceedings of the National Academy of Sciences, 99(8), 5301-5306. doi:10.1073/pnas.082107599Xia, X., & Holcik, M. (2009). Strong Eukaryotic IRESs Have Weak Secondary Structure. PLoS ONE, 4(1), e4136. doi:10.1371/journal.pone.0004136Lu, J., Zhang, J., Wang, X., Jiang, H., Liu, C., & Hu, Y. (2006). In vitro and in vivo identification of structural and sequence elements in the 5’ untranslated region of Ectropis obliqua picorna-like virus required for internal initiation. Journal of General Virology, 87(12), 3667-3677. doi:10.1099/vir.0.82090-0Yang, L. J., Hidaka, M., Sonoda, J., Masaki, H., & Uozumi, T. (1997). Mutational Analysis of the Potato Virus Y 5′ Untranslated Region for Alteration in Translational Enhancement in Tobacco Protoplasts. Bioscience, Biotechnology, and Biochemistry, 61(12), 2131-2133. doi:10.1271/bbb.61.2131BERGAMINI, G., PREISS, T., & HENTZE, M. W. (2000). Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system. RNA, 6(12), 1781-1790. doi:10.1017/s1355838200001679Bradrick, S. S. (2006). 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