Tasting Phenylthiocarbamide (PTC): A New Integrative Genetics Lab with an Old Flavor

First reported in the early 1930s, variation in the ability to taste phenylthiocarbamide (PTC) has since become one of the most widely studied of all human genetic traits. Guo and Reed (2001) provide an excellent review of work on this polymorphism prior to the identification and sequencing of the PTC gene by Kim et al. (2003), and Wooding (2006) provides a stimulating historical review of the role various scientists have played in the study of PTC taste sensitivity and the importance of these studies in relation to natural selection. Identification of the PTC gene and a number of subsequent publications (Wooding et al., 2004; Kim et al., 2005; Wooding et al., 2006) have provided the basis for a new, integrative laboratory investigation of PTC taste sensitivity. This genetics laboratory culminates in the use of the polymerase chain reaction (PCR) and restriction endonuclease digestion to determine the PTC genotype of each student. But “getting there is half the fun” and, in this case, “getting there” requires students to use not only their knowledge of molecular techniques in genetics but also their knowledge of Mendelian genetics, population genetics, probability, and pedigree analysis. The other “half the fun” in this case is that in determining their PTC phenotypes and genotypes, students are learning something about themselves

Infrared Galaxies in the Field of the Massive Cluster Abell S1063: Discovery of a Luminous Kiloparsec-Sized HII Region in a Gravitationally Lensed IR-Luminous Galaxy at z=0.6z=0.6

Using the Spitzer Space Telescope and Herschel Space Observatory, we have conducted a survey of infrared galaxies in the field of the galaxy cluster Abell S1063 (AS1063) at $z=0.347$, which is one of the most massive clusters known and a target of the HST CLASH and Frontier-Field surveys. The Spitzer/MIPS 24 $\mu$m and Herschel/PACS & SPIRE images revealed that the core of AS1063 is surprisingly devoid of infrared sources, showing only a few detectable sources within the central r$\sim1^{\prime}$. There is, however, one particularly bright source (2.3 mJy at 24 $\mu$m; 106 mJy at 160 $\mu$m), which corresponds to a background galaxy at $z=0.61$. The modest magnification factor (4.0$\times$) implies that this galaxy is intrinsically IR-luminous (L$_{\rm IR}=3.1\times10^{11}\ \rm L_{\odot}$). What is particularly interesting about this galaxy is that HST optical/near-infrared images show a remarkably bright and large (1 kpc) clump at one edge of the disk. Our follow-up optical/near-infrared spectroscopy shows Balmer (H$\alpha$-H8) and forbidden emission from this clump ([OII] $\lambda$3727, [OIII] $\lambda\lambda$4959,5007, [NII] $\lambda\lambda$6548,6583), indicating that it is a HII region. The HII region appears to have formed in-situ, as kinematically it is part of a rotating disk, and there is no evidence of nearby interacting galaxies. With an extinction correction of A$_{\rm V}=1.5$ mag, the star formation rate of this giant HII region is $\sim$10 M$_{\odot}$ yr$^{-1}$, which is exceptionally large, even for high redshift HII regions. Such a large and luminous HII region is often seen at $z\sim2$ but quite rare in the nearby Universe.Comment: Accepted for publication in the Astrophysical Journal. 29 pages, 15 figure

The DEEP2 Redshift Survey: Lyman Alpha Emitters in the Spectroscopic Database

We present the first results of a search for Lyman-alpha emitters (LAEs) in the DEEP2 spectroscopic database that uses a search technique that is different from but complementary to traditional narrowband imaging surveys. We have visually inspected ~20% of the available DEEP2 spectroscopic data and have found nine high-quality LAEs with clearly asymmetric line profiles and an additional ten objects of lower quality, some of which may also be LAEs. Our survey is most sensitive to LAEs at z=4.4-4.9 and that is indeed where all but one of our high-quality objects are found. We find the number density of our spectroscopically-discovered LAEs to be consistent with those found in narrowband imaging searches. The combined, averaged spectrum of our nine high-quality objects is well fit by a two-component model, with a second, lower-amplitude component redshifted by ~420 km/s with respect to the primary Lyman-alpha line, consistent with large-scale outflows from these objects. We conclude by discussing the advantages and future prospects of blank-sky spectroscopic surveys for high-z LAEs.Comment: Accepted for publication in Ap

Adaptive Autoimmunity and Foxp3-Based Immunoregulation in Zebrafish

Background: Jawed vertebrates generate their immune-receptor repertoire by a recombinatorial mechanism that has the potential to produce harmful autoreactive lymphocytes. In mammals, peripheral tolerance to self-antigens is enforced by Foxp3+ regulatory T cells. Recombinatorial mechanisms also operate in teleosts, but active immunoregulation is thought to be a late incorporation to the vertebrate lineage. Methods/Principal Findings: Here we report the characterization of adaptive autoimmunity and Foxp3-based immunoregulation in the zebrafish. We found that zebrafish immunization with an homogenate of zebrafish central nervous system (zCNS) triggered CNS inflammation and specific antibodies. We cloned the zebrafish ortholog for mammalian Foxp3 (zFoxp3) which induced a regulatory phenotype on mouse T cells and controlled IL-17 production in zebrafish embryos. Conclusions/Significance: Our findings demonstrate the acquisition of active mechanisms of self-tolerance early in vertebrate evolution, suggesting that active regulatory mechanisms accompany the development of the molecular potential for adaptive autoimmunity. Moreover, they identify the zebrafish as a tool to study the molecular pathways controlling adaptive immunity

Transverse Sizes of CIV Absorption Systems Measured from Multiple QSO Sightlines

We present tomography of the circum-galactic metal distribution at redshift 1.7 to 4.5 derived from echellete spectroscopy of binary quasars. We find CIV systems at similar redshifts in paired sightlines more often than expected for sightline-independent redshifts. As the separation of the sightlines increases from 36 kpc to 907 kpc, the amplitude of this clustering decreases. At the largest separations, the CIV systems cluster similar to Lyman-break galaxies (Adelberger et al. 2005a). The CIV systems are significantly less correlated than these galaxies, however, at separations less than R_1 ~ 0.42 +/- 0.15 h-1 comoving Mpc. Measured in real space, i.e., transverse to the sightlines, this length scale is significantly smaller than the break scale estimated from the line-of-sight correlation function in redshift space (Scannapieco et al. 2006a). Using a simple model, we interpret the new real-space measurement as an indication of the typical physical size of enriched regions. We adopt this size for enriched regions and fit the redshift-space distortion in the line-of-sight correlation function. The fitted velocity kick is consistent with the peculiar velocity of galaxies as determined by the underlying mass distribution and places an upper limit on the outflow (or inflow) speed of metals. The implied time scale for dispersing metals is larger than the typical stellar ages of Lyman-break galaxies (Shapley et al. 2001), and we argue that enrichment by galaxies at z > 4.3 played a greater role in dispersing metals. To further constrain the growth of enriched regions, we discuss empirical constraints on the evolution of the CIV correlation function with cosmic time. This study demonstrates the potential of tomography for measuring the metal enrichment history of the circum-galactic medium.Comment: 22 pages, 15 figures, 1 tabl

The DEEP2 Galaxy Redshift Survey: Design, Observations, Data Reduction, and Redshifts

We describe the design and data sample from the DEEP2 Galaxy Redshift Survey, the densest and largest precision-redshift survey of galaxies at z ~ 1 completed to date. The survey has conducted a comprehensive census of massive galaxies, their properties, environments, and large-scale structure down to absolute magnitude M_B = -20 at z ~ 1 via ~90 nights of observation on the DEIMOS spectrograph at Keck Observatory. DEEP2 covers an area of 2.8 deg^2 divided into four separate fields, observed to a limiting apparent magnitude of R_AB=24.1. Objects with z < 0.7 are rejected based on BRI photometry in three of the four DEEP2 fields, allowing galaxies with z > 0.7 to be targeted ~2.5 times more efficiently than in a purely magnitude-limited sample. Approximately sixty percent of eligible targets are chosen for spectroscopy, yielding nearly 53,000 spectra and more than 38,000 reliable redshift measurements. Most of the targets which fail to yield secure redshifts are blue objects that lie beyond z ~ 1.45. The DEIMOS 1200-line/mm grating used for the survey delivers high spectral resolution (R~6000), accurate and secure redshifts, and unique internal kinematic information. Extensive ancillary data are available in the DEEP2 fields, particularly in the Extended Groth Strip, which has evolved into one of the richest multiwavelength regions on the sky. DEEP2 surpasses other deep precision-redshift surveys at z ~ 1 in terms of galaxy numbers, redshift accuracy, sample number density, and amount of spectral information. We also provide an overview of the scientific highlights of the DEEP2 survey thus far. This paper is intended as a handbook for users of the DEEP2 Data Release 4, which includes all DEEP2 spectra and redshifts, as well as for the publicly-available DEEP2 DEIMOS data reduction pipelines. [Abridged]Comment: submitted to ApJS; data products available for download at http://deep.berkeley.edu/DR4

Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline

Mapping genome-wide data to human subtelomeres has been problematic due to the incomplete assembly and challenges of low-copy repetitive DNA elements. Here, we provide updated human subtelomere sequence assemblies that were extended by filling telomere-adjacent gaps using clone-based resources. A bioinformatic pipeline incorporating multiread mapping for annotation of the updated assemblies using short-read data sets was developed and implemented. Annotation of subtelomeric sequence features as well as mapping of CTCF and cohesin binding sites using ChIP-seq data sets from multiple human cell types confirmed that CTCF and cohesin bind within 3 kb of the start of terminal repeat tracts at many, but not all, subtelomeres. CTCF and cohesin co-occupancy were also enriched near internal telomere-like sequence (ITS) islands and the nonterminal boundaries of subtelomere repeat elements (SREs) in transformed lymphoblastoid cell lines (LCLs) and human embryonic stem cell (ES) lines, but were not significantly enriched in the primary fibroblast IMR90 cell line. Subtelomeric CTCF and cohesin sites predicted by ChIP-seq using our bioinformatics pipeline (but not predicted when only uniquely mapping reads were considered) were consistently validated by ChIP-qPCR. The colocalized CTCF and cohesin sites in SRE regions are candidates for mediating long-range chromatin interactions in the transcript-rich SRE region. A public browser for the integrated display of short-read sequence–based annotations relative to key subtelomere features such as the start of each terminal repeat tract, SRE identity and organization, and subtelomeric gene models was established