Cosmological Applications of Gravitational Lensing

The last decade has seen an enormous increase of activity in the field of gravitational lensing, mainly driven by improvements of observational capabilities. I will review the basics of gravitational lens theory, just enough to understand the rest of this contribution, and will then concentrate on several of the main applications in cosmology. Cluster lensing, and weak lensing, will constitute the main part of this review.Comment: 26 pages, including 2 figures (a third figure can be obtained from the author by request) gziped and uuencoded postscript file; to be published in Proceedings of the Laredo Advanced Summer School, Sept. 9

Gravitational Collapse and Disk Formation in Magnetized Cores

We discuss the effects of the magnetic field observed in molecular clouds on the process of star formation, concentrating on the phase of gravitational collapse of low-mass dense cores, cradles of sunlike stars. We summarize recent analytic work and numerical simulations showing that a substantial level of magnetic field diffusion at high densities has to occur in order to form rotationally supported disks. Furthermore, newly formed accretion disks are threaded by the magnetic field dragged from the parent core during the gravitational collapse. These disks are expected to rotate with a sub-Keplerian speed because they are partially supported by magnetic tension against the gravity of the central star. We discuss how sub-Keplerian rotation makes it difficult to eject disk winds and accelerates the process of planet migration. Moreover, magnetic fields modify the Toomre criterion for gravitational instability via two opposing effects: magnetic tension and pressure increase the disk local stability, but sub-Keplerian rotation makes the disk more unstable. In general, magnetized disks are more stable than their nonmagnetic counterparts; thus, they can be more massive and less prone to the formation of giant planets by gravitational instability.Comment: Chapter 16 in "Magnetic Fields in Diffuse Media", Springer-Verlag, eds. de Gouveia Dal Pino, E., Lazarian, A., Melioli,

Gene and repetitive sequence annotation in the Triticeae

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes