On the Sensitivity of 3-D Thermal Convection Codes to Numerical Discretization: A Model Intercomparison

Fully 3-D numerical simulations of thermal convection in a spherical shell have become a standard for studying the dynamics of pattern formation and its stability under perturbations to various parameter values. The question arises as to how does the discretization of the governing equations affect the outcome and thus any physical interpretation. This work demonstrates the impact of numerical discretization on the observed patterns, the value at which symmetry is broken, and how stability and stationary behavior is dependent upon it. Motivated by numerical simulations of convection in the Earth\u27s mantle, we consider isoviscous Rayleigh-Bénard convection at infinite Prandtl number, where the aspect ratio between the inner and outer shell is 0.55. We show that the subtleties involved in development mantle convection models are considerably more delicate than has been previously appreciated, due to the rich dynamical behavior of the system. Two codes with different numerical discretization schemes: an established, community-developed, and benchmarked finite element code (CitcomS) and a novel spectral method that combines Chebyshev polynomials with radial basis functions (RBF) are compared. A full numerical study is investigated for the following three cases. The first case is based on the cubic (or octahedral) initial condition (spherical harmonics of degree ℓ =4). How variations in the behavior of the cubic pattern to perturbations in the initial condition and Rayleigh number between the two numerical discrezations is studied. The second case investigates the stability of the dodecahedral (or icosahedral) initial condition (spherical harmonics of degree ℓ = 6). Although both methods converge first to the same pattern, this structure is ultimately unstable and systematically degenerates to cubic or tetrahedral symmetries, depending on the code used. Lastly, a new steady state pattern is presented as a combination of order 3 and 4 spherical harmonics leading to a five cell or a hexahedral pattern and stable up to 70 times the critical Rayleigh number. This pattern can provide the basis for a new accuracy benchmark for 3-D spherical mantle convection codes

The Tetraodon nigroviridis reference transcriptome: Developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome

Pufferfish such as fugu and tetraodon carry the smallest genomes among all vertebrates and are ideal for studying genome evolution. However, comparative genomics using these species is hindered by the poor annotation of their genomes. We performed RNA sequencing during key stages of maternal to zygotic transition of Tetraodon nigroviridis and report its first developmental transcriptome. We assembled 61,033 transcripts (23,837 loci) representing 80% of the annotated gene models and 3816 novel coding transcripts from 2667 loci. We demonstrate the similarities of gene expression profiles between pufferfish and zebrafish during maternal to zygotic transition and annotated 1120 long non-coding RNAs (lncRNAs) many of which differentially expressed during development. The promoters for 60% of the assembled transcripts result validated by CAGE-seq. Despite the extreme compaction of the tetraodon genome and the dramatic loss of transposons, the length of lncRNA exons remain comparable to that of other vertebrates and a small set of lncRNAs appears enriched for transposable elements suggesting a selective pressure acting on lncRNAs length and composition. Finally, a set of lncRNAs are microsyntenic between teleost and vertebrates, which indicates potential regulatory interactions between lncRNAs and their flanking coding genes. Our work provides a fundamental molecular resource for vertebrate comparative genomics and embryogenesis studies

Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements

Background: Long non-coding RNAs (lncRNA) are a major class of non-coding RNAs. They are involved in diverse intra-cellular mechanisms like molecular scaffolding, splicing and DNA methylation. Through these mechanisms they are reported to play a role in cellular differentiation and development. They show an enriched expression in the brain where they are implicated in maintaining cellular identity, homeostasis, stress responses and plasticity. Low sequence conservation and lack of functional annotations make it difficult to identify homologs of mammalian lncRNAs in other vertebrates. A computational evaluation of the lncRNAs through systematic conservation analyses of both sequences as well as their genomic architecture is required.Results: Our results show that a subset of mouse candidate lncRNAs could be distinguished from random sequences based on their alignment with zebrafish phastCons elements. Using ROC analyses we were able to define a measure to select significantly conserved lncRNAs. Indeed, starting from ~2,800 mouse lncRNAs we could predict that between 4 and 11% present conserved sequence fragments in fish genomes. Gene ontology (GO) enrichment analyses of protein coding genes, proximal to the region of conservation, in both organisms highlighted similar GO classes like regulation of transcription and central nervous system development. The proximal coding genes in both the species show enrichment of their expression in brain. In summary, we show that interesting genomic regions in zebrafish could be marked based on their sequence homology to a mouse lncRNA, overlap with ESTs and proximity to genes involved in nervous system development.Conclusions: Conservation at the sequence level can identify a subset of putative lncRNA orthologs. The similar protein-coding neighborhood and transcriptional information about the conserved candidates provide support to the hypothesis that they share functional homology. The pipeline herein presented represents a proof of principle showing that a portion between 4 and 11% of lncRNAs retains region of conservation between mammals and fishes. We believe this study will result useful as a reference to analyze the conservation of lncRNAs in newly sequenced genomes and transcriptomes. \uc2\ua9 2013 Basu et al.; licensee BioMed Central Ltd

FIDEL—a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut

In this paper, we describe a Ty3-gypsy retrotransposon from allotetraploid peanut (Arachis hypogaea) and its putative diploid ancestors Arachis duranensis (A-genome) and Arachis ipaënsis (B-genome). The consensus sequence is 11,223 bp. The element, named FIDEL (Fairly long Inter-Dispersed Euchromatic LTR retrotransposon), is more frequent in the A- than in the B-genome, with copy numbers of about 3,000 (±950, A. duranensis), 820 (±480, A. ipaënsis), and 3,900 (±1,500, A. hypogaea) per haploid genome. Phylogenetic analysis of reverse transcriptase sequences showed distinct evolution of FIDEL in the ancestor species. Fluorescent in situ hybridization revealed disperse distribution in euchromatin and absence from centromeres, telomeric regions, and the nucleolar organizer region. Using paired sequences from bacterial artificial chromosomes, we showed that elements appear less likely to insert near conserved ancestral genes than near the fast evolving disease resistance gene homologs. Within the Ty3-gypsy elements, FIDEL is most closely related with the Athila/Calypso group of retrovirus-like retrotransposons. Putative transmembrane domains were identified, supporting the presence of a vestigial envelope gene. The results emphasize the importance of FIDEL in the evolution and divergence of different Arachis genomes and also may serve as an example of the role of retrotransposons in the evolution of legume genomes in general

De Novo assembly and transcriptome analysis of the mediterranean fruit fly ceratitis capitata early embryos

The agricultural pest Ceratitis capitata, also known as the Mediterranean fruit fly or Medfly, belongs to the Tephritidae family, which includes a large number of other damaging pest species. The Medfly has been the first non-drosophilid fly species which has been genetically transformed paving the way for designing geneticbased pest control strategies. Furthermore, it is an experimentally tractable model, in which transient and transgene-mediated RNAi have been successfully used. We applied Illumina sequencing to total RNA preparations of 8-10 hours old embryos of C. capitata, This developmental window corresponds to the blastoderm cellularization stage. In summary, we assembled 42,614 transcripts which cluster in 26,319 unique transcripts of which 11,045 correspond to protein coding genes; we identified several hundreds of long ncRNAs; we found an enrichment of transcripts encoding RNA binding proteins among the highly expressed transcripts, such as CcTRA-2, known to be necessary to establish and, most likely, to maintain female sex of C. capitata. Our study is the first de novo assembly performed for Ceratitis capitata based on Illumina NGS technology during embryogenesis and it adds novel data to the previously published C. capitata EST databases. We expect that it will be useful for a variety of applications such as gene cloning and phylogenetic analyses, as well as to advance genetic research and biotechnological applications in the Medfly and other related Tephritidae

Numerical modelling of subduction parameters' influence on partial melting

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References

www.geosci-model-dev-discuss.net/7/2033/2014

Constraints on thermal state and composition of the Earth's lower mantle from electromagnetic impedances and seismic data

International audienceDespite the tight constraints put by seismology on the elastic properties of the Earth's lower mantle, its mineralogical composition and thermal state remain poorly known because the interpretation of seismic measurements suffers from the trade-off between temperature, iron content, and mineralogical composition. In order to overcome this difficulty, we complement seismic data with electromagnetic induction data. The latter data are mostly sensitive to temperature and iron content, while densities and acoustic speeds mostly constrain the mineralogy. A 0.5 log unit increase in electrical conductivity can be caused either by a 400 K increase of the temperature or by an increase of iron content from 10% to 12.5%. Acoustic velocity is only marginally sensitive to temperature but it increases by 0.8 km s−1 on average as the perovskite fraction increases from 50% to 100%. Olsen's (1999) apparent resistivities in the period range [15 days, 11 years], and Preliminary reference Earth model (PREM) densities and acoustic speeds are jointly inverted in the depth range [800 km, 2600 km] by using a Monte Carlo Markov Chain method. Given the uncertainties on these data, estimates of perovskite fraction are well constrained over the whole depth range, but information on temperature and iron content is only obtained for depths less than 2000 km, corresponding to the penetration depth of the long-period electromagnetic field. All parameter values are determined with an uncertainty better than 15–20% at the 1σ confidence level. The temperature in the uppermost lower mantle (i.e., down to 1300 km depth) is close to a value of 2200 K and increases along a superadiabatic gradient of 0.4 K km−1 between 1300 and 2000 km depth. Extrapolation of this gradient at greater depth leads to a temperature close to 2800 K at 2600 km depth. The iron content of the lower mantle is found to be almost constant and equal to 10–11% whatever the depth, while a significant linear decrease of the perovskite content is observed throughout the whole depth range, from 80% at 800 km depth down to ∼65% at 2600 km depth