Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools

An integrated 4249 marker FISH/RH map of the canine genome

BACKGROUND: The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral traits, often generated by deliberate crossing of closely related individuals, leading to a high rate of genetic disease in many breeds. Understanding the genetic basis of both phenotypic variation and disease susceptibility in the dog provides new ways in which to dissect the genetics of human health and biology. RESULTS: To facilitate both genetic mapping and cloning efforts, we have constructed an integrated canine genome map that is both dense and accurate. The resulting resource encompasses 4249 markers, and was constructed using the RHDF5000-2 whole genome radiation hybrid panel. The radiation hybrid (RH) map features a density of one marker every 900 Kb and contains 1760 bacterial artificial chromosome clones (BACs) localized to 1423 unique positions, 851 of which have also been mapped by fluorescence in situ hybridization (FISH). The two data sets show excellent concordance. Excluding the Y chromosome, the map features an RH/FISH mapped BAC every 3.5 Mb and an RH mapped BAC-end, on average, every 2 Mb. For 2233 markers, the orthologous human genes have been established, allowing the identification of 79 conserved segments (CS) between the dog and human genomes, dramatically extending the length of most previously described CS. CONCLUSIONS: These results provide a necessary resource for the canine genome mapping community to undertake positional cloning experiments and provide new insights into the comparative canine-human genome maps

YAC contigs of the Rab1 and wobbler (wr) spinal muscular atrophy gene region on proximal mouse chromosome 11 and of the homologous region on human chromosome 2p

powerful tool to advance the identi®cation of gene com-Despite rapid progress in the physical characteriza- plexes and of disease genes. In this respect, the analysis tion of murine and human genomes, little molecular in- of human chromosomes 16 and 19 (Nowak, 1995) and formation is available on certain regions, e.g., proximal mouse chromosomes 1 (Hunter et al., 1994) and 17 (Cox mouse chromosome 11 (Chr 11) and human chromosome et al., 1993) as well as of human and murine X chromo-2p (Chr 2p). We have localized the wobbler spinal atrophy somes is particularly far advanced (Hamvas et al., 1993). gene wr to proximal mouse Chr 11, tightly linked toRab1, On the other hand, such extensive information is not a gene coding for a small GTP-binding protein, and Glns- available for mouse proximal chromosome 11 (Chr 11) ps1, an intronless pseudogene of the glutamine synthe- and human chromosome 2p (Chr 2p) (Fig. 1; cf. Berry et tase gene. We have now used these markers to construct al., 1995; Nowak, 1995), known to share at least the genesa 1.3-Mb yeast arti®cial chromosome (YAC) contig of the for the reticuloendotheliosis oncogene (Brownell et al.,Rab1 region on mouse Chr 11. Four YAC clones isolated 1985), for a brain-speci®cb-spectrin isoform (Bloom et al.,from two independent YAC libraries were characterized 1992), and for cytoplasmic malate dehydrogenase (Ball etby rare-cutting analysis, ¯uorescence in situ hybridiza-al., 1994). However, comparing the segregation map oftion (FISH), and sequence-tagged site (STS) isolation and the mouse with the human cytogenetic map, a colinearmapping. Rab1 and Glns-ps1 were found to be only 20

A Fast Parameterized Algorithm for Co-Path Set

The k-CO-PATH SET problem asks, given a graph G and a positive integer k, whether one can delete k edges from G so that the remainder is a collection of disjoint paths. We give a linear-time fpt algorithm with complexity O^*(1.588^k) for deciding k-CO-PATH SET, significantly improving the previously best known O^*(2.17^k) of Feng, Zhou, and Wang (2015). Our main tool is a new O^*(4^{tw(G)}) algorithm for CO-PATH SET using the Cut&Count framework, where tw(G) denotes treewidth. In general graphs, we combine this with a branching algorithm which refines a 6k-kernel into reduced instances, which we prove have bounded treewidth

Separating E and B types of polarization on an incomplete sky

Detection of magnetic-type ($B$-type) polarization in the Cosmic Microwave Background (CMB) radiation plays a crucial role in probing the relic gravitational wave (RGW) background. In this paper, we propose a new method to deconstruct a polarization map on an incomplete sky in real space into purely electric and magnetic polarization type maps, ${\mathcal{E}}(\hat{\gamma})$ and ${\mathcal{B}}(\hat{\gamma})$, respectively. The main properties of our approach are as follows: Firstly, the fields ${\mathcal{E}}(\hat{\gamma})$ and ${\mathcal{B}}(\hat{\gamma})$ are constructed in real space with a minimal loss of information. This loss of information arises due to the removal of a narrow edge of the constructed map in order to remove various numerical errors, including those arising from finite pixel size. Secondly, this method is fast and can be efficiently applied to high resolution maps due to the use of the fast spherical harmonics transformation. Thirdly, the constructed fields, ${\mathcal{E}}(\hat{\gamma})$ and ${\mathcal{B}}(\hat{\gamma})$, are scalar fields. For this reason various techniques developed to deal with temperature anisotropy maps can be directly applied to analyze these fields. As a concrete example, we construct and analyze an unbiased estimator for the power spectrum of the $B$-mode of polarization $C_{\ell}^{BB}$. Basing our results on the performance of this estimator, we discuss the RGW detection ability of two future ground-based CMB experiments, QUIET and POLARBEAR.Comment: 43 pages, 15 figures, 1 table. The finial version, will appear in PR

Matching post-Newtonian and numerical relativity waveforms: systematic errors and a new phenomenological model for non-precessing black hole binaries

We present a new phenomenological gravitational waveform model for the inspiral and coalescence of non-precessing spinning black hole binaries. Our approach is based on a frequency domain matching of post-Newtonian inspiral waveforms with numerical relativity based binary black hole coalescence waveforms. We quantify the various possible sources of systematic errors that arise in matching post-Newtonian and numerical relativity waveforms, and we use a matching criteria based on minimizing these errors; we find that the dominant source of errors are those in the post-Newtonian waveforms near the merger. An analytical formula for the dominant mode of the gravitational radiation of non-precessing black hole binaries is presented that captures the phenomenology of the hybrid waveforms. Its implementation in the current searches for gravitational waves should allow cross-checks of other inspiral-merger-ringdown waveform families and improve the reach of gravitational wave searches.Comment: 22 pages, 11 figure