Cosmoglobe: Towards end-to-end CMB cosmological parameter estimation without likelihood approximations

We implement support for a cosmological parameter estimation algorithm as proposed by Racine et al. (2016) in Commander, and quantify its computational efficiency and cost. For a semi-realistic simulation similar to Planck LFI 70 GHz, we find that the computational cost of producing one single sample is about 60 CPU-hours and that the typical Markov chain correlation length is $\sim$100 samples. The net effective cost per independent sample is $\sim$6 000 CPU-hours, in comparison with all low-level processing costs of 812 CPU-hours for Planck LFI and WMAP in Cosmoglobe Data Release 1. Thus, although technically possible to run already in its current state, future work should aim to reduce the effective cost per independent sample by at least one order of magnitude to avoid excessive runtimes, for instance through multi-grid preconditioners and/or derivative-based Markov chain sampling schemes. This work demonstrates the computational feasibility of true Bayesian cosmological parameter estimation with end-to-end error propagation for high-precision CMB experiments without likelihood approximations, but it also highlights the need for additional optimizations before it is ready for full production-level analysis.Comment: 10 pages, 8 figures. Submitted to A&

Characterization of Arabidopsis thaliana lines with T-DNA insertions in the mitochondrial ribosomal protein genes Rps14 and Rps19

In Arabidopsis, most of the genes encoding mitochondrial ribosomal proteins are located in the nucleus and only seven are present in the mitochondrial genome. Assembly of a functional ribosome requires coordinated expression of ribosomal protein encoding genes located in both these organelles. Genes and promoters of nuclear encoded mitochondrial ribosomal protein coding genes of plants have not been well characterized so far. In the present study we have characterized Arabidopsis thaliana SALK mutant lines with T-DNA insertion in Rps14 or Rps19 gene. The location of T-DNA insertion in the mutant lines was confirmed and plants homozygous and hemizygous for TDNA insertion were identified for both Rps14 and Rps19 genes. In homozygous T-DNA mutant lines of both Rps14 and Rps19 genes, the expression was estimated using RTPCR. Rps14 and Rps19 transcripts similar to wild type were present in homozygous mutant plants of Rps14 and Rps19 which indicated that T-DNA insertion has not affected their expression.</jats:p

<span style="font-size:11.0pt;font-family: "Times New Roman";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: Mangal;mso-ansi-language:EN-GB;mso-fareast-language:EN-US;mso-bidi-language: HI" lang="EN-GB">Assessment of <i style="mso-bidi-font-style:normal">Arabidopsis thaliana <span style="mso-bidi-font-style:italic">CENH3</span></i> promoter in <i style="mso-bidi-font-style:normal">Brassica juncea</i> for development of haploid inducer lines</span>

425-430<span style="font-size:11.0pt;font-family: " times="" new="" roman";mso-fareast-font-family:"times="" roman";mso-bidi-font-family:="" mangal;mso-ansi-language:en-gb;mso-fareast-language:en-us;mso-bidi-language:="" hi;mso-bidi-font-weight:bold"="" lang="EN-GB">Centromeres are epigenetically specified by the centromeric histone H3 protein (CENH3). The timing and level of expression of CENH3 is tightly regulated to match the demands of the host cell. So far in plants, only CENH3 promoter of Arabidopsis thaliana (L.) Heynh. has been characterized. However, whether CENH3 promoters retain their characteristic mode of regulation in other species remains to be established. In the present study, activity of AtCENH3 promoter was investigated using reporter gene assay in <i style="mso-bidi-font-style: normal">Brassica juncea (L.) Czern. A 1156 bp promoter fragment of AtCENH3 gene (<i style="mso-bidi-font-style: normal">At1g01370) including the first 111 nucleotides of the coding sequence was amplified and cloned into the pORE-R2 binary vector to ensure translation fusion with the uidA coding sequences. The Agrobacterium tumefaciens strain GV3101 harbouring the recombinant construct was used to transform B. juncea cv. RLM198 hypocotyl explants. Histochemical assay of T0 and T1 transgenics showed GUS expression in shoot apical meristem, leaf, sepal, flower pedicel and root tip. Intense GUS expression was observed in meristematic tissues, particularly at shoot and root apices. However, mature leaves, flowers, pollen and ovules exhibited very low or no GUS expression. Our results showed that AtCENH3 promoter regulates cognate gene expression in Brassica juncea as it does in A. thaliana, and hence a suitable candidate for developing haploid inducer line in <i style="mso-bidi-font-style: normal">B. juncea. </span

Genetically Modified Crops: Need for Rational Evaluation

14-17GM technology holds promise to solve some of the basic problems related to agriculture

Cloning, characterization and expression analysis of <em>APETALA2</em> genes of <em>Brassica juncea</em> (L.) Czern.

604-610The APETALA2/Ethylene-Responsive Factor (AP2/ERF) is one of the largest gene families encoding several plant specific transcription factors. It plays significant roles in growth and development process, biotic and abiotic stresses, and responses to hormones. AP2 is a homeotic gene governing floral meristem specification, floral organ determination and floral homeotic gene expression in Arabidopsis. The basic structure of AP2 gene was unchanged during evolution in diploid species. The present study was undertaken to find whether AP2 has undergone any change in structure or expression pattern during evolution of allopolyploid Brassica juncea. We cloned AP2 orthologs and c-DNAs from B. juncea and B. nigra. B. juncea was found to carry three AtAP2 orthologs. Comparison of BjAP2 genes with AP2 orthologs from progenitor species, B. rapa and B. nigra showed that two of the BjAP2 genes were derived from B. rapa and one from B. nigra. BjAP2 genes have retained its characteristic AP2 domain and miR172 complementary sequences. mRNAs originated from three AP2 orthologs were detected in all the tissues examined, namely, leaf, flower buds and seedling, indicating absence of sub-functionalization of AP2 during polyploid evolution. However, one of the B. rapa copies gave alternatively spliced AP2 transcript which lacked the second exon. Consequently, the splice variant could not be translated into functional AP2 protein. Considering that miR172 suppresses translation of AP2 transcripts, the alternatively spliced transcript could still play important regulatory role by limiting the availability of miR172 molecules to bind to functional AP2 transcripts. qRT-PCR analysis of BjAP2 expression in different accessions of B. juncea with contrasting seed size indicated that BjAP2 is not a major determinant of seed size in mustard