Creation of vortices in a Bose-Einstein condensate by a Raman technique

We propose a method for taking a Bose-Einstein condensate in the ground trap state simultaneously to a different atomic hyperfine state and to a vortex trap state. This can be accomplished through a Raman scheme in which one of the two copropagating laser beams has a higher-order Laguerre-Gaussian mode profile. Coefficients relating the beam waist, pulse area, and trap potentials for a complete transfer to the m = 1 vortex are calculated for a condensate in the non-interacting and strongly interacting regimes.Comment: RevTex, 4 pages, 2 PostScript figure

Detection of vorticity in Bose-Einstein condensed gases by matter-wave interference

A phase-slip in the fringes of an interference pattern is an unmistakable characteristic of vorticity. We show dramatic two-dimensional simulations of interference between expanding condensate clouds with and without vorticity. In this way, vortices may be detected even when the core itself cannot be resolved.Comment: 3 pages, RevTeX, plus 6 PostScript figure

Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses

Genomic data together with sequencing of tissue specific small RNA libraries reveals insights into the genome content, small RNA repertoire and evolutionary origins of the grass Miscanthus × giganteus

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.\ud •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.\ud •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.\ud •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms. •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137Keywords: recombination., allele frequency gradients, linkage disequilibrium (LD), population structure, black cottonwood (Populus trichocarpa), genome resequencin

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

PERTRAN: Genome-guided RNA-seq Read Assembler

As short RNA-seq reads become a standard, affordable input to any genome annotation project, a sensitive and accurate transcript assembler is an essential part of any gene prediction system. PERTRAN is a pipeline for assembling transcripts from RNA-seq reads which demonstrates higher sensitivity, with fewer fused exons (in most cases), and faster run times compared to other TOPHAT/CUFFLINKS and genome-guided Trinity. PERTRAN shows slightly lower specificity with increased gene fusions in some cases, discussed below. SAM files generated from PERTRAN can be used to compute expression level by cuffdiff and result is comparable to that from TOPHAT

InterMine Webservices for Phytozome (Rev2)

A datawarehousing framework for information provides a useful infrastructure for providers and users of genomic data. For providers, the infrastructure give them a consistent mechanism for extracting raw data. While for the users, the web services supported by the software allows them to make complex, and often unique, queries of the data. Previously, phytozome.net used BioMart to provide the infrastructure. As the complexity, scale and diversity of the dataset as grown, we decided to implement an InterMine web service on our servers. This change was largely motivated by the ability to have a more complex table structure and richer web reporting mechanism than BioMart. For InterMine to achieve its more complex database schema it requires an XML description of the data and an appropriate loader. Unlimited one-to-many and many-to-many relationship between the tables can be enabled in the schema.We have implemented support for:1.) Genomes and annotations for the data in Phytozome. This set is the 48 organisms currently stored in a back end CHADO datastore. The data loaders are modified versions of the CHADO data adapters from FlyMine. 2.) Interproscan results from all proteins in the Phytozome database. 3.) Clusters of proteins into a grouped heirarchically by similarity. 4.) Cufflinks results from tissue-specific RNA-Seq data of Phytozome organisms. 5.) Diversity data (GATK and SnpEFF results) from a set of individual organism. The last two datatypes are new in this implementation of our web services. We anticipate that the scale of these data will increase considerably in the near future