ALBERT

Description: We correlate the positions of radio galaxies in the FIRST survey with the cosmic microwave background lensing convergence estimated from the Atacama Cosmology Telescope over 470 deg 2 to determine the bias of these galaxies. We remove optically cross-matched sources below redshift z  = 0.2 to preferentially select active galactic nuclei (AGN). We measure the angular cross-power spectrum $C_l^{\kappa g}$ at 4.4 significance in the multipole range 100 〈  l  〈 3000, corresponding to physical scales within 2–60 Mpc at an effective redshift z eff  = 1.5. Modelling the AGN population with a redshift-dependent bias, the cross-spectrum is well fitted by the Planck best-fitting cold dark matter cosmological model. Fixing the cosmology and assumed redshift distribution of sources, we fit for the overall bias model normalization, finding b ( z eff ) = 3.5 ± 0.8 for the full galaxy sample and b ( z eff ) = 4.0 ± 1.1(3.0 ± 1.1) for sources brighter (fainter) than 2.5 mJy. This measurement characterizes the typical halo mass of radio-loud AGN: we find $\log (M_{\rm halo} / \,\mathrm{M}_{\odot }) = 13.6^{+0.3}_{-0.4}$ .

Description: Background: Long-read sequencing technologies were launched a few years ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing. However, existing long-read technologies still have several limitations that complicate their use for most research laboratories, as well as in large and/or complex genome projects. In 2014, Oxford Nanopore released the MinION® device, a small and low-cost single-molecule nanopore sequencer, which offers the possibility of sequencing long DNA fragments. Results: The assembly of long reads generated using the Oxford Nanopore MinION® instrument is challenging as existing assemblers were not implemented to deal with long reads exhibiting close to 30% of errors. Here, we presented a hybrid approach developed to take advantage of data generated using MinION® device. We sequenced a well-known bacterium, Acinetobacter baylyi ADP1 and applied our method to obtain a highly contiguous (one single contig) and accurate genome assembly even in repetitive regions, in contrast to an Illumina-only assembly. Our hybrid strategy was able to generate NaS (Nanopore Synthetic-long) reads up to 60 kb that aligned entirely and with no error to the reference genome and that spanned highly conserved repetitive regions. The average accuracy of NaS reads reached 99.99% without losing the initial size of the input MinION® reads. Conclusions: We described NaS tool, a hybrid approach allowing the sequencing of microbial genomes using the MinION® device. Our method, based ideally on 20x and 50x of NaS and Illumina reads respectively, provides an efficient and cost-effective way of sequencing microbial or small eukaryotic genomes in a very short time even in small facilities. Moreover, we demonstrated that although the Oxford Nanopore technology is a relatively new sequencing technology, currently with a high error rate, it is already useful in the generation of high-quality genome assemblies.

Description: We correlate the positions of radio galaxies in the FIRST survey with the cosmic microwave background lensing convergence estimated from the Atacama Cosmology Telescope over 470 deg 2 to determine the bias of these galaxies. We remove optically cross-matched sources below redshift z  = 0.2 to preferentially select active galactic nuclei (AGN). We measure the angular cross-power spectrum $C_l^{\kappa g}$ at 4.4 significance in the multipole range 100 〈  l  〈 3000, corresponding to physical scales within 2–60 Mpc at an effective redshift z eff  = 1.5. Modelling the AGN population with a redshift-dependent bias, the cross-spectrum is well fitted by the Planck best-fitting cold dark matter cosmological model. Fixing the cosmology and assumed redshift distribution of sources, we fit for the overall bias model normalization, finding b ( z eff ) = 3.5 ± 0.8 for the full galaxy sample and b ( z eff ) = 4.0 ± 1.1(3.0 ± 1.1) for sources brighter (fainter) than 2.5 mJy. This measurement characterizes the typical halo mass of radio-loud AGN: we find $\log (M_{\rm halo} / \,\mathrm{M}_{\odot }) = 13.6^{+0.3}_{-0.4}$ .

Description: Background: Metatranscriptomics is rapidly expanding our knowledge of gene expression patterns and pathway dynamics in natural microbial communities. However, to cope with the challenges of environmental sampling, various rRNA removal and cDNA synthesis methods have been applied in published microbial metatranscriptomic studies, making comparisons arduous. Whereas efficiency and biases introduced by rRNA removal methods have been relatively well explored, the impact of cDNA synthesis and library preparation on transcript abundance remains poorly characterized. The evaluation of potential biases introduced at this step is challenging for metatranscriptomic samples, where data analyses are complex, for example because of the lack of reference genomes. Results: Herein, we tested four cDNA synthesis and Illumina library preparation protocols on a simplified mixture of total RNA extracted from four bacterial species. In parallel, RNA from each microbe was tested individually. cDNA synthesis was performed on rRNA depleted samples using the TruSeq Stranded Total RNA Library Preparation, the SMARTer Stranded RNA-Seq, or the Ovation RNA-Seq V2 System. A fourth experiment was made directly from total RNA using the Encore Complete Prokaryotic RNA-Seq. The obtained sequencing data were analyzed for: library complexity and reproducibility; rRNA removal efficiency and bias; the number of genes detected; coverage uniformity; and the impact of protocols on expression biases. Significant variations, especially in organism representation and gene expression patterns, were observed among the four methods. TruSeq generally performed best, but is limited by its requirement of hundreds of nanograms of total RNA. The SMARTer method appears the best solution for smaller amounts of input RNA. For very low amounts of RNA, the Ovation System provides the only option; however, the observed biases emphasized its limitations for quantitative analyses. Conclusions: cDNA and library preparation methods may affect the outcome and interpretation of metatranscriptomic data. The most appropriate method should be chosen based on the available quantity of input RNA and the quantitative or non-quantitative objectives of the study. When low amounts of RNA are available, as in most metatranscriptomic studies, the SMARTer method seems to be the best compromise to obtain reliable results. This study emphasized the difficulty in comparing metatranscriptomic studies performed using different methods.

Description: The adiabatic evolution of the temperature of the cosmic microwave background (CMB) is a key prediction of standard cosmology. We study deviations from the expected adiabatic evolution of the CMB temperature of the form T ( z ) =  T 0 (1 + z ) 1 – α using measurements of the spectrum of the Sunyaev–Zel'dovich effect with the South Pole Telescope (SPT). We present a method for using the ratio of the Sunyaev–Zel'dovich signal measured at 95 and 150 GHz in the SPT data to constrain the temperature of the CMB. We demonstrate that this approach provides unbiased results using mock observations of clusters from a new set of hydrodynamical simulations. We apply this method to a sample of 158 SPT-selected clusters, spanning the redshift range 0.05 〈 z  〈 1.35, and measure $\alpha = 0.017^{+0.030}_{-0.028}$, consistent with the standard model prediction of α = 0. In combination with other published results, we find α = 0.005 ± 0.012, an improvement of ~10 per cent over published constraints. This measurement also provides a strong constraint on the effective equation of state in models of decaying dark energy w eff  = –0.994 ± 0.010.