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Auguet, J. C., Borrego, C. M., Baneras, L., & Casamayor, E. O. (2008). Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark. Environ Microbiol, 10(10), 2527–2536.
Résumé: We designed and tested a set of specific primers for specific PCR amplification of the biotin carboxylase subunit gene (accC) of the Acetyl CoA carboxylase (ACCase) enzyme. The primer set yielded a PCR product of c. 460 bp that was suitable for denaturing gradient gel electrophoresis (DGGE) fingerprinting followed by direct sequencing of excised DGGE bands and sequence analysis. Optimization of PCR conditions for selective amplification was carried out with pure cultures of different bacteria and archaea, and laboratory enrichments. Next, fingerprinting comparisons were done in several aerobic and anaerobic freshwater planktonic samples. The DGGE fingerprints showed between 2 and 19 bands in the different samples, and the primer set provided specific amplification in both pure cultures and natural samples. Most of the samples had sequences grouped with bacterial accC, hypothetically related to the anaplerotic fixation of inorganic carbon. Some other samples, however, yielded accC gene sequences that clustered with Crenarchaeota and were related to the 3-hydroxypropionate/4-hydroxybutyrate cycle of autotrophic crenarchaeota. Such samples came from oligotrophic high mountain lakes and the hypolimnia of a sulfide-rich lake, where crenarchaeotal populations had been previously reported by 16S rRNA surveys. This study provided a fast tool to look for presence of accC genes in natural environments as potential marker for studies of carbon dioxide assimilation in the dark. After further refinement for better specificity against archaea, the new and novel primers could be very helpful to establish a target for crenarchaeota with implications for our understanding of archaeal carbon biogeochemistry.
Mots-Clés: Amino Acid Sequence Archaeal Proteins/genetics Bacterial Proteins/genetics Carbon Dioxide/*metabolism Carbon-Nitrogen Ligases/*genetics Cluster Analysis DNA Fingerprinting/*methods DNA Primers/genetics DNA; Archaeal/genetics DNA; Bacterial/genetics *Ecosystem Electrophoresis; DNA *Water Microbiology; Genetic Sequence Alignment Sequence Analysis; Polyacrylamide Gel Molecular Sequence Data Nucleic Acid Denaturation Phylogeny Polymerase Chain Reaction/methods *Polymorphism
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Bodin, N., Chassot, E., Sardenne, F., Zudaire, I., Grande, M., Dhurmeea, Z., et al. (2018). Ecological data for western Indian Ocean tuna. Ecology, 99(5), 1245.
Résumé: Tuna are marine apex predators that inhabit the tropical and sub-tropical waters of the Indian Ocean where they support socially and economically important fisheries. Key component of pelagic communities, tuna are bioindicator species of anthropogenic and climate-induced changes through modifications of the structure and related energy-flow of food webs and ecosystems. The IndianEcoTuna dataset provides a panel of ecological tracers measured in four soft tissues (white muscle, red muscle, liver, gonads) from 1,364 individuals of four species, i.e., the albacore (ALB, Thunnus alalunga), the bigeye (BET, T. obesus), the skipjack (SKJ, Katsuwomus pelamis), and the yellowfin (YFT, T. albacares), collected throughout the western Indian Ocean from 2009 to 2015. Sampling was carried out during routine monitoring programs, at sea by observers onboard professional vessels or at landing. For each record, the type of fishing gear, the conservation mode, as well as the fishing date and catch location are provided. Individuals were sampled to span a wide range of body sizes: 565 ALB with fork length from 58 to 118 cm, 155 BET from 29.5 to 173 cm, 304 SKJ from 30 to 74 cm, and 340 YFT from 29 to 171.5 cm. The IndianEcoTuna dataset combines: (1) 9,512 records of carbon and nitrogen stable isotopes (percent element weights, δ13C and δ15N values) in 1,185 fish, (2) 887 concentrations of total proteins in 242 fish, (3) 8,356 concentrations of total lipids and three lipid classes (triacylglycerols TAG; phospholipids PL; sterols ST) in 695 fish, and (4) 1,150 and 1,033 profiles of neutral and polar fatty acids in 397 and 342 fish, respectively. Information on sex and weights of the whole fish, gonads, liver and stomach is provided. Because of the essential trophic role and wide-ranging of tuna in marine systems, and the large panel of tropho-energetic tracers and derived-key quantitative parameters provided (e.g., niche width, trophic position, condition indices), the IndianEcoTuna dataset should be of high interest for global and regional research on marine trophic ecology and food web analysis, as well as on the impacts of anthropogenic changes on Indian Ocean marine ecosystems. There are no copyright restrictions for research and/or teaching purposes. Usage of the dataset must include citation of this Data Paper.
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Jean, N., Dumont, E., Herzi, F., Balliau, T., Laabir, M., Masseret, E., et al. (2017). Modifications of the soluble proteome of a mediterranean strain of the invasive neurotoxic dinoflagellate Alexandrium catenella under metal stress conditions. Aquat. Toxicol., 188, 80–91.
Résumé: The soluble proteome of the mediterranean strain ACT03 of the invasive neurotoxic dinoflagellate Alexandrium catenella exposed to lead or zinc at 6, 12 or 18 mu M (total concentrations), or under control conditions, was characterized by two-dimensional gel electrophoresis (2-DE). Zinc reduced (P < 0.05) the total number of protein spots (-41%, -52% and -60%, at 6, 12 or 18 M, respectively). Besides, most of the proteins constituting the soluble proteome were down-regulated in response to lead or zinc stresses. These proteins were involved mainly in photosynthesis (20-37% for lead; 36-50% for zinc) (ribulose-1,5-bisphosphate carboxylase/oxygenase: RUBISCO; ferredoxin-NADP(+) reductase: FNR; peridinin-chlorophyll a-protein: PCP), and in the oxidative stress response (29-34% for lead; 17-36% for zinc) (superoxide dismutase: SOD; proteasome alpha/beta subunits). These negative effects could be partly compensated by the up-regulation of specific proteins such as ATP-synthase beta subunit (+16.3 fold after exposure to lead at 12 M). Indeed, an increase in the abundance of ATP-synthase could enrich the ATP pool and provide more energy available for the cells to survive under metal stress, and make the ATP-synthase transport of metal cations out of the cells more efficient. Finally, this study shows that exposure to lead or zinc have a harmful effect on the soluble proteome of A. catenella ACT03, but also suggests the existence of an adaptative proteomic response to metal stresses, which could contribute to maintaining the development of this dinoflagellate in trace metal-contaminated ecosystems.
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Xiong, W., Gao, S., Lu, Y., Wei, L., Mao, J., Xie, J., et al. (2019). Latrophilin participates in insecticide susceptibility through positively regulating CSP10 and partially compensated by OBPC01 in Tribolium castaneum. Pest. Biochem. Physiol., 159, 107–117.
Résumé: Latrophilin (LPH) is an adhesion G protein-coupled receptor (aGPCR) that participates in multiple essential physiological processes. Our previous studies have shown that lph is not only indispensable for the development and reproduction of red flour beetles (Tribolium castaneum), but also for their resistance against dichlorvos or carbofuran insecticides. However, the regulatory mechanism of lph-mediated insecticide susceptibility remains unclear. Here, we revealed that knockdown of lph in beetles resulted in opposing changes in two chemoreception genes, chemosensory protein 10 (CSP10) and odorant-binding protein C01 (OBPC01), in which the expression of TcCSP10 was downregulated, whereas the expression of TcOBPC01 was upregulated. TcCSP10 and TcOBPC01 were expressed at the highest levels in early pupal and late larval stages, respectively. High levels of expression of both these genes were observed in the heads (without antennae) of adults. TcCSP10 and TcOBPC01 were significantly induced by dichlorvos or carbofuran between 12 and 72 h (hrs) after exposure, suggesting that they are likely associated with increasing the binding affinity of insecticides, leading to a decrease in sensitivity to the insecticides. Moreover, once these two genes were knocked down, the susceptibility of the beetles to dichlorvos or carbofuran was enhanced. Additionally, RNA interference (RNAi) targeting of lph followed by exposure to dichlorvos or carbofuran also caused the opposing expression levels of TcCSP10 and TcOBPC01 compared to the expression levels of wild-type larvae treated with insecticides alone. All these results indicate that lph is involved in insecticide susceptibility through positively regulating TcCSP10; and the susceptibility could also further partially compensated for through the negative regulation of TcOBPC01 when lph was knockdown in the red flour beetle. Our studies shed new light on the molecular regulatory mechanisms of lph related to insecticide susceptibility.
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