Feedback on a c omparative metatranscriptomic analysis

National audienceThe progress of next generation sequencing favors the development of more comprehensive ecosystem studies thanks to metatranscriptomic approaches. These latter can indeed provide access to functional information at a good analysis depth. Through a study of anaerobic digesters treating anionic surfactant contaminated wastewater [1] (namely the linear alkylbenzene sulfonate, LAS), we developed a bioinformatics pipeline to perform the RNAseq data analysis for shotgun metatranscriptomics data.In this pipe-line, the raw data are cleaned and pre-processed. Reads corresponding to rRNA are detected and discarded from the datasets. After a normalization step based on k-mer counts, the mRNA reads from the datasets are de novo co-assembled using the Trinity software. Coding regions of the metatranscriptomic assembly are subsequently predicted and annotated. For functional annotation, sequences with matches to the eggNOG and KEGG GENES databases are retrieved to establish functional categories and reconstruct the metabolic pathways. For taxonomic classification, the sequences are assigned by comparing them to a NCBI-nr database. For each dataset individually, reads are mapped back to the co-assembled contigs. Eventually, a count table is constructed; it contains, for each predicted gene, the counts obtained by samples, as well as the associated taxonomic and functional annotations.After aggregation and statistical analysis, this study enabled detecting active genes likely involved in each step of LAS biodegradation and exploring the microbial active core related to LAS degradation.We developed a bioinformatics pipeline to perform the RNAseq data analysis for shotgun metatranscriptomics data, through a study of anaerobic digesters treating anionic surfactant contaminated wastewater.In this pipeline, the raw data are cleaned and pre-processed. Reads corresponding to rRNA are detected and discarded from the datasets. After a normalization step based on k-mer counts, the mRNA reads from the datasets are de novo co-assembled. Coding regions of the metatranscriptomic assembly are subsequently predicted and annotated. Taxonomic and functional annotations are obtained by comparison to public reference databases. The latter are used to define functional categories and reconstruct metabolic pathways. For each dataset individually, reads are mapped back to the co-assembled contigs. Finally, a count table is constructed; it contains, for each predicted gene, the counts obtained by samples, as well as the associated taxonomic and functional annotations.After aggregation and statistical analysis, this study enabled detecting active genes likely involved in each step of the anionic surfactant degradation and exploring the associated microbial activse core

Feedback on a c omparative metatranscriptomic analysis

National audienceThe progress of next generation sequencing favors the development of more comprehensive ecosystem studies thanks to metatranscriptomic approaches. These latter can indeed provide access to functional information at a good analysis depth. Through a study of anaerobic digesters treating anionic surfactant contaminated wastewater [1] (namely the linear alkylbenzene sulfonate, LAS), we developed a bioinformatics pipeline to perform the RNAseq data analysis for shotgun metatranscriptomics data.In this pipe-line, the raw data are cleaned and pre-processed. Reads corresponding to rRNA are detected and discarded from the datasets. After a normalization step based on k-mer counts, the mRNA reads from the datasets are de novo co-assembled using the Trinity software. Coding regions of the metatranscriptomic assembly are subsequently predicted and annotated. For functional annotation, sequences with matches to the eggNOG and KEGG GENES databases are retrieved to establish functional categories and reconstruct the metabolic pathways. For taxonomic classification, the sequences are assigned by comparing them to a NCBI-nr database. For each dataset individually, reads are mapped back to the co-assembled contigs. Eventually, a count table is constructed; it contains, for each predicted gene, the counts obtained by samples, as well as the associated taxonomic and functional annotations.After aggregation and statistical analysis, this study enabled detecting active genes likely involved in each step of LAS biodegradation and exploring the microbial active core related to LAS degradation.We developed a bioinformatics pipeline to perform the RNAseq data analysis for shotgun metatranscriptomics data, through a study of anaerobic digesters treating anionic surfactant contaminated wastewater.In this pipeline, the raw data are cleaned and pre-processed. Reads corresponding to rRNA are detected and discarded from the datasets. After a normalization step based on k-mer counts, the mRNA reads from the datasets are de novo co-assembled. Coding regions of the metatranscriptomic assembly are subsequently predicted and annotated. Taxonomic and functional annotations are obtained by comparison to public reference databases. The latter are used to define functional categories and reconstruct metabolic pathways. For each dataset individually, reads are mapped back to the co-assembled contigs. Finally, a count table is constructed; it contains, for each predicted gene, the counts obtained by samples, as well as the associated taxonomic and functional annotations.After aggregation and statistical analysis, this study enabled detecting active genes likely involved in each step of the anionic surfactant degradation and exploring the associated microbial activse core

Broadly tunable linewidth-invariant Raman Stokes comb for selective resonance photoionization

We demonstrate a continuously tunable, multi-Stokes Raman laser operating in the visible range (420 - 600 nm). Full spectral coverage was achieved by efficiently cascading the Raman shifted output of a tunable, frequency-doubled Ti:Sapphire laser. Using an optimized hemi-spherical external Raman cavity composed only of a diamond crystal and a single reflecting mirror, producing high power output at high conversion efficiency (>60 % from pump to Stokes) for a broad range of wavelengths across the visible. Enhancement of the cascading was achieved by controlling the polarization state of the pump and Stokes orders. The Stokes outputs exhibited a linewidth of 11 ± 1 GHz for each order, resembling the pump laser linewidth, enabling its use for the intended spectroscopic applications. Furthermore, the Raman laser performance was demonstrated by applying it for the resonance excitation of atomic transitions in calcium

Zonação de comunidade bêntica do entremarés em molhes sob diferente hidrodinamismo na costa norte do estado do Rio de Janeiro, Brasil Zonation of intertidal benthic communities on breakwaters of different hydrodynamics in the north coast of the state of Rio de Janeiro, Brazil

O presente estudo pretende comparar a distribuição vertical da comunidade bêntica na zona entremarés em dois locais compostos por matacões graníticos caracterizados por hidrodinâmica distinta, reflexo da diferença na orientação dos molhes nas praias do Farol de São Tomé (Píer) e na Barra do Furado (Barra), norte do Estado do Rio de Janeiro. Quadrados de 400 cm² foram sobrepostos ao longo de três perfis verticais de ambos os sítios e amostrados através do método de fotoquadrats, desde o nível 0,2 m da maré até o limite superior de Littorina spp. O limite superior dos organismos marinhos foi ampliado na Barra (3,8 m) em relação ao Píer (2,2 m). Quanto à composição taxonômica, nove espécies foram comuns. Chaetomorpha sp., Chondracanthus teedii (Mertens ex Roth) Fredericq e Grateloupia sp. foram exclusivas na Barra, enquanto Tetraclita stalactifera (Lamarck, 1818), Fissurella clench, Gracilaria domingensis (Kützing) Sonder ex Dickie e Hypnea musciformis (Wulfen in Jacqu.) Lamouroux ocorreram somente no Píer. Em ambos os locais, a riqueza e a diversidade de espécies foram superiores nos quadrados intermediários. Os maiores valores foram registrados na Barra. As maiores diferenças nos agrupamentos entre faixas equivalentes de locais distintos ocorreram na faixa eulitorânea superior, seguida pela faixa eulitorânea inferior e franja sublitorânea. Apenas a orla litorânea não revelou diferença significativa entre os locais, mas uma maior extensão desta franja e da faixa eulitorânea superior era bastante evidente. As demais faixas na Barra do Furado foram caracterizadas em grande parte por espécies típicas de ambientes mais expostos como Chaetomorpha sp. na faixa eulitorânea superior e Perna perna (Linnaeus, 1758) na eulitorânea inferior, além de C. teedii e Ulva fasciata Delile, 1813 na franja sublitorânea. No Píer, as diferentes faixas apresentavam distribuição eqüitativa, refletindo um ambiente menos estressante. As diferenças observadas na distribuição vertical dos organismos bênticos, principalmente na extensão das faixas superiores, evidenciam condições de exposição a ondas variáveis.<br>The present study aims to compare the vertical distribution of intertidal benthic communities in two sites composed by granitic boulders with distint hydrodynamics due to different wave swells at Farol de São Tomé (Pier) and Barra do Furado beaches (Barra), both in northern state of Rio de Janeiro. Quadrats of 400 cm² were overlapped along three vertical profiles on each site and were sampled by the photoquadrat method from 0.2 m of the tide level to the upper limit of Littorina spp. The upper limit of the marine organisms was higher at Barra site (3.8 m) than at Píer site (2.2 m). Nine species were common to both sites. Chaetomorpha sp., Chondracanthus teedii (Mertens ex Roth) Fredericq, and Grateloupia sp. were unique to Barra, whereas Tetraclita stalactifera (Lamarck, 1818), Fissurella clench, Gracilaria domingensis (Kützing) Sonder ex Dickie, and Hypnea musciformis (Wulfen in Jacqu.) Lamouroux occurred only at Píer boulders. On both sites species richness and diversity were superior at the intermediate quadrats of the intertidal zone. The highest values were recorded at Barra. The most pronounced assemblage differences between equivalent areas of either site occurred on the lower upper eulittoral band followed by the lower eulittoral and the sub-littoral fringe, respectively. The littoral fringe assemblage was the only one that did not show significant differences among the studied sites, yet a larger range of this fringe and the upper eulittoral band at Barra was quite evident. This site was mostly characterized by species of more exposed areas, such as Chaetomorpha sp. and Perna perna (Linnaeus, 1758) on upper and lower eulittoral bands, and by C. teedii and Ulva fasciata Delile, 1813 on the sub-littoral fringe. At Píer, the intertidal zone showed an even distribution, reflecting a less stressful environment. The differences on vertical distribution of the local benthic, particularly in the extent of the upper bands, indicate the variable conditions of wave exposure