Spherical Collapse and Cluster Counts in Modified Gravity Models

Modifications to the gravitational potential affect the nonlinear gravitational evolution of large scale structures in the Universe. To illustrate some generic features of such changes, we study the evolution of spherically symmetric perturbations when the modification is of Yukawa type; this is non-trivial, because we should not and do not assume that Birkhoff's theorem applies. We then show how to estimate the abundance of virialized objects in such models. Comparison with numerical simulations shows reasonable agreement: When normalized to have the same fluctuations at early times, weaker large scale gravity produces fewer massive halos. However, the opposite can be true for models that are normalized to have the same linear theory power spectrum today, so the abundance of rich clusters potentially places interesting constraints on such models. Our analysis also indicates that the formation histories and abundances of sufficiently low mass objects are unchanged from standard gravity. This explains why simulations have found that the nonlinear power-spectrum at large k is unaffected by such modifications to the gravitational potential. In addition, the most massive objects in CMB-normalized models with weaker gravity are expected to be similar to the high-redshift progenitors of the most massive objects in models with stronger gravity. Thus, the difference between the cluster and field galaxy populations is expected to be larger in models with stronger large-scale gravity.Comment: 9 pages, 8 figures Accepted by Phys. Rev.

On the equivalence between the effective cosmology and excursion set treatments of environment

In studies of the environmental dependence of structure formation, the large scale environment is often thought of as providing an effective background cosmology: e.g. the formation of structure in voids is expected to be just like that in a less dense universe with appropriately modified Hubble and cosmological constants. However, in the excursion set description of structure formation which is commonly used to model this effect, no explicit mention is made of the effective cosmology. Rather, this approach uses the spherical evolution model to compute an effective linear theory growth factor, which is then used to predict the growth and evolution of nonlinear structures. We show that these approaches are, in fact, equivalent: a consequence of Birkhoff's theorem. We speculate that this equivalence will not survive in models where the gravitational force law is modified from an inverse square, potentially making the environmental dependence of clustering a good test of such models.Comment: 4 pages, 0 figures, accepted to MNRA

PhyleasProg: a user-oriented web server for wide evolutionary analyses

Evolutionary analyses of biological data are becoming a prerequisite in many fields of biology. At a time of high-throughput data analysis, phylogenetics is often a necessary complementary tool for biologists to understand, compare and identify the functions of sequences. But available bioinformatics tools are frequently not easy for non-specialists to use. We developed PhyleasProg (http://phyleasprog.inra.fr), a user-friendly web server as a turnkey tool dedicated to evolutionary analyses. PhyleasProg can help biologists with little experience in evolutionary methodologies by analysing their data in a simple and robust way, using methods corresponding to robust standards. Via a very intuitive web interface, users only need to enter a list of Ensembl protein IDs and a list of species as inputs. After dynamic computations, users have access to phylogenetic trees, positive/purifying selection data (on site and branch-site models), with a display of these results on the protein sequence and on a 3D structure model, and the synteny environment of related genes. This connection between different domains of phylogenetics opens the way to new biological analyses for the discovery of the function and structure of proteins

BLAST Observations of the South Ecliptic Pole field: Number Counts and Source Catalogs

We present results from a survey carried out by the Balloon-borne Large Aperture Submillimeter Telescope (BLAST) on a 9 deg^2 field near the South Ecliptic Pole at 250, 350 and 500 {\mu}m. The median 1{\sigma} depths of the maps are 36.0, 26.4 and 18.4 mJy, respectively. We apply a statistical method to estimate submillimeter galaxy number counts and find that they are in agreement with other measurements made with the same instrument and with the more recent results from Herschel/SPIRE. Thanks to the large field observed, the new measurements give additional constraints on the bright end of the counts. We identify 132, 89 and 61 sources with S/N>4 at 250, 350, 500 {\mu}m, respectively and provide a multi-wavelength combined catalog of 232 sources with a significance >4{\sigma} in at least one BLAST band. The new BLAST maps and catalogs are available publicly at http://blastexperiment.info.Comment: 25 pages, 6 figures, 4 tables, Accepted by ApJS. Maps and catalogs available at http://blastexperiment.info

Biological CO2-methanation: An approach to standardization

Power-to-Methane as one part of Power-to-Gas has been recognized globally as one of the key elements for the transition towards a sustainable energy system. While plants that produce methane catalytically have been in operation for a long time, biological methanation has just reached industrial pilot scale and near-term commercial application. The growing importance of the biological method is reflected by an increasing number of scientific articles describing novel approaches to improve this technology. However, these studies are diffcult to compare because they lack a coherent nomenclature. In this article, we present a comprehensive set of parameters allowing the characterization and comparison of various biological methanation processes. To identify relevant parameters needed for a proper description of this technology, we summarized existing literature and defined system boundaries for Power-to-Methane process steps. On this basis, we derive system parameters providing information on the methanation system, its performance, the biology and cost aspects. As a result, three different standards are provided as a blueprint matrix for use in academia and industry applicable to both, biological and catalytic methanation. Hence, this review attempts to set the standards for a comprehensive description of biological and chemical methanation processes

f(R) theories

Over the past decade, f(R) theories have been extensively studied as one of the simplest modifications to General Relativity. In this article we review various applications of f(R) theories to cosmology and gravity - such as inflation, dark energy, local gravity constraints, cosmological perturbations, and spherically symmetric solutions in weak and strong gravitational backgrounds. We present a number of ways to distinguish those theories from General Relativity observationally and experimentally. We also discuss the extension to other modified gravity theories such as Brans-Dicke theory and Gauss-Bonnet gravity, and address models that can satisfy both cosmological and local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in Relativity, Published version, Comments are welcom

Crossing the Phantom Divide: Theoretical Implications and Observational Status

If the dark energy equation of state parameter w(z) crosses the phantom divide line w=-1 (or equivalently if the expression d(H^2(z))/dz - 3\Omega_m H_0^2 (1+z)^2 changes sign) at recent redshifts, then there are two possible cosmological implications: Either the dark energy consists of multiple components with at least one non-canonical phantom component or general relativity needs to be extended to a more general theory on cosmological scales. The former possibility requires the existence of a phantom component which has been shown to suffer from serious theoretical problems and instabilities. Therefore, the later possibility is the simplest realistic theoretical framework in which such a crossing can be realized. After providing a pedagogical description of various dark energy observational probes, we use a set of such probes (including the Gold SnIa sample, the first year SNLS dataset, the 3-year WMAP CMB shift parameter, the SDSS baryon acoustic oscillations peak (BAO), the X-ray gas mass fraction in clusters and the linear growth rate of perturbations at z=0.15 as obtained from the 2dF galaxy redshift survey) to investigate the priors required for cosmological observations to favor crossing of the phantom divide. We find that a low \Omega_m prior (0.2<\Omega_m <0.25) leads, for most observational probes (except of the SNLS data), to an increased probability (mild trend) for phantom divide crossing. An interesting degeneracy of the ISW effect in the CMB perturbation spectrum is also pointed out.Comment: Accepted in JCAP (to appear). Comments added, typos corrected. 19 pages (revtex), 8 figures. The numerical analysis files (Mathematica + Fortran) with instructions are available at http://leandros.physics.uoi.gr/pdl-cross/pdl-cross.htm . The ppt file of a relevant talk may be downloaded from http://leandros.physics.uoi.gr/pdl-cross/pdl2006.pp

Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

<p>Abstract</p> <p>Background</p> <p>Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions. Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered. Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated. This inefficient approach to primer design is further intensified in a high-throughput laboratory, where hundreds of genes may be targeted in one experiment.</p> <p>Results</p> <p>We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline. Investigators may specify target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. In the process of improving our sequencing success rate, which currently exceeds 95% for exons, we have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. We reveal the laboratory protocols and their associated, empirically determined computational parameters, as well as describe the novel computational methods which may benefit others in future primer design research.</p> <p>Conclusion</p> <p>The high-throughput PCR primer design pipeline has been very successful in providing the basis for high-quality directed sequencing results and for minimizing costs associated with labor and reprocessing. The modular architecture of the primer design software has made it possible to readily integrate additional primer critique tests based on iterative feedback from the laboratory. As a result, the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing.</p

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

Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution