Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.

We present the first results from a study designed to test whether, given high-quality spectrophotometry spanning the mid-ultraviolet-optical wavelength regime, it is possible to distinguish the metal content and star formation history of individual elliptical galaxies with sufficient accuracy to establish whether their formation history is linked to their detailed morphology and position on the Fundamental Plane.

It is widely believed that ultraluminous infrared (IR) galaxies and active galactic nuclei (AGN) activity are triggered by galaxy interactions and merging, with the peak of activity occurring at z similar to 2, where submillimetre galaxies are thousands of times more numerous than local ULIRGs. In this evolutionary picture, submillimetre galaxies (SMGs) would host an AGN, which would eventually grow a black hole (BH) strong enough to blow off all of the gas and dust leaving an optically luminous QSO. To probe this evolutionary sequence we have focussed on the 'missing link' sources, which demonstrate both strong starburst (SB) and AGN signatures, in order to determine if the SB is the main power source even in SMGs when we have evidence that an AGN is present from their IRAC colours. The best way to determine if a dominant AGN is present is to look for their signatures in the mid-infrared with the Spitzer IRS, since often even deep X-ray observations miss identifying the presence of AGN in heavily dust-obscured SMGs. We present the results of our audit of the energy balance between star-formation and AGN within this special sub-population of SMGs - where the BH has grown appreciably to begin heating the dust emission.

We investigate the stellar populations of Ly alpha emitters (LAEs) at z = 3.1 and 3.7 in 0.65 deg2 of the Subaru/XMM-Newton Deep Field, based on rest-frame ultraviolet-to-optical photometry obtained from the Subaru/XMM-Newton Deep Survey, the UKIRT Infrared Deep Sky Survey/Ultra Deep Survey (UKIDSS/UDS), and the Spitzer legacy survey of the UKIDSS/UDS. Among a total of 302 LAEs (224 for z = 3.1 and 78 for z = 3.7), only 11 are detected in the K band, i.e. brighter than K(3 Sigma) = 24.1 mag. Eight of the 11 K-detected LAEs are spectroscopically confirmed. In our stellar population analysis, we treat K-detected objects individually, while K-undetected objects are stacked at each redshift. We find that the K-undetected objects, which should closely represent the LAE population as a whole, have low stellar masses of similar to 108-108.5 M(circle dot), modest star formation rates (SFRs) of 1-100 M(circle dot) yr-1, and modest dust extinction of E(B - V)(star) < 0.2. The K-detected objects are massive, M(star) similar to 109-1010.5 M(circle dot), and have significant dust extinction with a median of E(B - V)(star) similar or equal to 0.3. Four K-detected objects with the reddest spectral energy distributions, two of which are spectroscopically confirmed, are heavily obscured with E(B - V)(star) similar to 0.65, and their continua resemble those of some local ultraluminous infrared galaxies (ULIRGs). Interestingly, they have large Ly alpha equivalent widths similar or equal to 70-250 A. If these four are excluded, our sample has a weak anticorrelation between Ly alpha equivalent width and M(star). We compare the stellar masses and the specific SFRs (sSFRs) of LAEs with those of Lyman-break galaxies (LBGs), distant red galaxies, submillimetre galaxies, and I- or K-selected galaxies with photometric redshifts of z(phot) similar to 3. We find that the LAE population is the least massive among all the galaxy populations in question, but with relatively high sSFRs, while near-infrared (NIR)-detected LAEs have M(star) and sSFR similar to LBGs. Our reddest four LAEs have very high sSFRs in spite of large M(star), thus occupying a unique region in the M(star) versus sSFR space.

Spitzer spectroscopy has revealed that similar or equal to 80% of submm galaxies (SMGs) are starburst (SB)-dominated in the mid-infrared. Here we focus on the remaining similar or equal to 20% that show signs of harboring powerful active galactic nuclei (AGNs). We have obtained Spitzer-InfraRed Spectrograph spectroscopy of a sample of eight SMGs that are candidates for harboring powerful AGNs on the basis of IRAC color selection (S(8 mu m)/S(4.5 mu m) > 2, i.e., likely power-law mid-infrared spectral energy distributions). SMGs with an AGN dominating (greater than or similar to 50%) their mid-infrared emission could represent the "missing link" sources in an evolutionary sequence involving a major merger. First of all, we detect polycyclic aromatic hydrocarbon (PAH) features in all of the SMGs, indicating redshifts from 2.5 to 3.4, demonstrating the power of the mid-infrared to determine redshifts for these optically faint dusty galaxies. Second, we see signs of both star formation (from the PAH features) and AGN activity (from continuum emission) in our sample: 62% of the sample are AGN-dominated in the mid-infrared with a median AGN content of 56%, compared with <30% on average for typical SMGs, revealing that our IRAC color selection has successfully singled out sources with proportionately more AGN emission than typical SB-dominated SMGs. However, we find that only about 10% of these AGNs dominate the bolometric emission of the SMG when the results are extrapolated to longer infrared wavelengths, implying that AGNs are not a significant power source to the SMG population overall, even when there is evidence in the mid-infrared for substantial AGN activity. When existing samples of mid-infrared AGN-dominated SMGs are considered, we find that S(8 mu m)/S(4.5 mu m) > 1.65 works well at selecting mid-infrared energetically dominant AGNs in SMGs, implying a duty cycle of similar to 15% if all SMGs go through a subsequent mid-infrared AGN-dominated phase in the proposed evolutionary sequence.

We report the discovery of a galaxy cluster at z = 1.62 located in the Spitzer Wide-Area Infrared Extragalactic survey XMM-LSS field. This structure was selected solely as an overdensity of galaxies with red Spitzer/Infrared Array Camera colors, satisfying ([3.6] - [4.5]) AB > -0.1 mag. Photometric redshifts derived from the Subaru XMM Deep Survey (BV iz bands), the UKIRT Infrared Deep Survey-Ultra-Deep Survey (UKIDSS-UDS, JK bands), and from the Spitzer Public UDS survey (3.6-8.0 mu m) show that this cluster corresponds to a surface density of galaxies at z approximate to 1.6 that is >20 sigma above the mean at this redshift. We obtained optical spectroscopic observations of galaxies in the cluster region using IMACS on the Magellan telescope. We measured redshifts for seven galaxies in the range z = 1.62-1.63 within 2.8 arcmin (<1.4 Mpc) of the astrometric center of the cluster. A posteriori analysis of the XMM data in this field reveal a weak (4 sigma) detection in the [0.5-2 keV] band compatible with the expected thermal emission from such a cluster. The color-magnitude diagram of the galaxies in this cluster shows a prominent red sequence, dominated by a population of red galaxies with (z - J) > 1.7 mag. The photometric-redshift probability distributions for the red galaxies are strongly peaked at z = 1.62, coincident with the spectroscopically confirmed galaxies. The rest-frame (U - B) color and scatter of galaxies on the red sequence are consistent with a mean luminosity-weighted age of 1.2 +/- 0.1 Gyr, yielding a formation redshift (z(f)) over bar = 2.35 +/- 0.10, and corresponding to the last significant star formation period in these galaxies.

We measure the rest-frame colors (dust-corrected), infrared luminosities, star formation rates, and stellar masses of 92 galaxies in a Spitzer-selected cluster at z = 1.62. By fitting spectral energy distributions (SEDs) to 10-band photometry (0.4 mu m < lambda(obs) < 8 mu m) and measuring 24 mu m fluxes for the 12 spectroscopically confirmed and 80 photometrically selected members, we discover an exceptionally high level of star formation in the cluster core of similar to 1700 M(circle dot) yr(-1) Mpc(-2). The cluster galaxies define a strong blue sequence in (U-V) color and span a range in color. We identify 17 members with L(IR) > 10(11) L(circle dot), and these IR luminous members follow the same trend of increasing star formation with stellar mass that is observed in the field at z similar to 2. Using rates derived from both the 24 mu m imaging and SED fitting, we find that the relative fraction of star-forming members triples from the lowest to highest galaxy density regions; e.g., the IR luminous fraction increases from similar to 8% at Sigma similar to 10 gal Mpc(-2) to similar to 25% at Sigma greater than or similar to 100 gal Mpc(-2). The observed increase is a reversal of the well-documented trend at z < 1 and signals that we have reached the epoch when massive cluster galaxies are still forming a substantial fraction of their stars.

Gravitational lensing is a powerful astrophysical and cosmological probe and is particularly valuable at submillimeter wavelengths for the study of the statistical and individual properties of dusty star-forming galaxies. However, the identification of gravitational lenses is often time-intensive, involving the sifting of large volumes of imaging or spectroscopic data to find few candidates. We used early data from the Herschel Astrophysical Terahertz Large Area Survey to demonstrate that wide-area submillimeter surveys can simply and easily detect strong gravitational lensing events, with close to 100% efficiency.

We investigate the stellar populations of Ly alpha emitters (LAEs) at z = 5.7 and 6.6 in a 0.65 deg(2) sky of the Subaru/XMM-Newton Deep Survey (SXDS) Field, using deep images taken with the Subaru/Suprime-Cam, United Kingdom Infrared Telescope/Wide Field Infrared Camera, and Spitzer/Infrared Array Camera (IRAC). We produce stacked multiband images at each redshift from 165 (z = 5.7) and 91 (z = 6.6) IRAC-undetected objects to derive typical spectral energy distributions (SEDs) of z similar to 6-7 LAEs for the first time. The stacked LAEs have as blue UV continua as the Hubble Space Telescope (HST)/Wide Field Camera 3 (WFC3) z-dropout galaxies of similar M-UV, with a spectral slope beta similar to -3, but at the same time they have red UV-to-optical colors with detection in the 3.6 mu m band. Using SED fitting we find that the stacked LAEs have low stellar masses of similar to(3-10) x 10(7) M-circle dot, very young ages of similar to 1-3 Myr, negligible dust extinction, and strong nebular emission from the ionized interstellar medium, although the z = 6.6 object is fitted similarly well with high-mass models without nebular emission; inclusion of nebular emission reproduces the red UV-to-optical colors while keeping the UV colors sufficiently blue. We infer that typical LAEs at z similar to 6-7 are building blocks of galaxies seen at lower redshifts. We find a tentative decrease in the Lya escape fraction from z = 5.7 to 6.6, which may imply an increase in the intergalactic medium neutral fraction. From the minimum contribution of nebular emission required to fit the observed SEDs, we place an upper limit on the escape fraction of ionizing photons of f(esc)(ion) similar to 0.6 at z = 5.7 and similar to 0.9 at z = 6.6. We also compare the stellar populations of our LAEs with those of stacked HST/WFC3 z-dropout galaxies.