Quantifying Florida Bay Habitat Suitability for Fishes and Invertebrates Under Climate Change Scenarios

The Florida Bay ecosystem supports a number of economically important ecosystem services, including several recreational fisheries, which may be affected by changing salinity and temperature due toclimate change. In this paper, we use a combination of physical models and habitat suitability index models to quantify the effects of potential climate change scenarios on a variety of juvenile fish and lobster species in Florida Bay. The climate scenarios include alterations in sea level, evaporation and precipitation rates, coastal runoff, and water temperature. We find that the changes in habitat suitability vary in both magnitude and direction across the scenarios and species, but are on average small. Only one of the seven species we investigate (Lagodon rhomboides, i.e., pinfish) sees a sizable decrease in optimal habitat under any of the scenarios. This suggests that the estuarine fauna of Florida Bay may not be as vulnerable to climate change as other components of the ecosystem, such as those in the marine/terrestrial ecotone. However, these models are relatively simplistic, looking only at single species effects of physical drivers without considering the many interspecific interactions that may play a key role in the adjustment of the ecosystem as a whole. More complex models that capture the mechanistic links between physics and biology, as well as the complex dynamics of the estuarine food web, may be necessary to further understand the potential effects of climate change on the Florida Bay ecosystem

Estimating the Redshift Distribution of Faint Galaxy Samples

We present an empirical method for estimating the underlying redshift distribution N(z) of galaxy photometric samples from photometric observables. The method does not rely on photometric redshift (photo-z) estimates for individual galaxies, which typically suffer from biases. Instead, it assigns weights to galaxies in a spectroscopic subsample such that the weighted distributions of photometric observables (e.g., multi-band magnitudes) match the corresponding distributions for the photometric sample. The weights are estimated using a nearest-neighbor technique that ensures stability in sparsely populated regions of color-magnitude space. The derived weights are then summed in redshift bins to create the redshift distribution. We apply this weighting technique to data from the Sloan Digital Sky Survey as well as to mock catalogs for the Dark Energy Survey, and compare the results to those from the estimation of photo-z's derived by a neural network algorithm. We find that the weighting method accurately recovers the underlying redshift distribution, typically better than the photo-z reconstruction, provided the spectroscopic subsample spans the range of photometric observables covered by the photometric sample.Comment: 14 pages, 9 figures, submitted to MNRA

Crossing the Phantom Divide: Theoretical Implications and Observational Status

If the dark energy equation of state parameter w(z) crosses the phantom divide line w=-1 (or equivalently if the expression d(H^2(z))/dz - 3\Omega_m H_0^2 (1+z)^2 changes sign) at recent redshifts, then there are two possible cosmological implications: Either the dark energy consists of multiple components with at least one non-canonical phantom component or general relativity needs to be extended to a more general theory on cosmological scales. The former possibility requires the existence of a phantom component which has been shown to suffer from serious theoretical problems and instabilities. Therefore, the later possibility is the simplest realistic theoretical framework in which such a crossing can be realized. After providing a pedagogical description of various dark energy observational probes, we use a set of such probes (including the Gold SnIa sample, the first year SNLS dataset, the 3-year WMAP CMB shift parameter, the SDSS baryon acoustic oscillations peak (BAO), the X-ray gas mass fraction in clusters and the linear growth rate of perturbations at z=0.15 as obtained from the 2dF galaxy redshift survey) to investigate the priors required for cosmological observations to favor crossing of the phantom divide. We find that a low \Omega_m prior (0.2<\Omega_m <0.25) leads, for most observational probes (except of the SNLS data), to an increased probability (mild trend) for phantom divide crossing. An interesting degeneracy of the ISW effect in the CMB perturbation spectrum is also pointed out.Comment: Accepted in JCAP (to appear). Comments added, typos corrected. 19 pages (revtex), 8 figures. The numerical analysis files (Mathematica + Fortran) with instructions are available at http://leandros.physics.uoi.gr/pdl-cross/pdl-cross.htm . The ppt file of a relevant talk may be downloaded from http://leandros.physics.uoi.gr/pdl-cross/pdl2006.pp

f(R) theories

Over the past decade, f(R) theories have been extensively studied as one of the simplest modifications to General Relativity. In this article we review various applications of f(R) theories to cosmology and gravity - such as inflation, dark energy, local gravity constraints, cosmological perturbations, and spherically symmetric solutions in weak and strong gravitational backgrounds. We present a number of ways to distinguish those theories from General Relativity observationally and experimentally. We also discuss the extension to other modified gravity theories such as Brans-Dicke theory and Gauss-Bonnet gravity, and address models that can satisfy both cosmological and local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in Relativity, Published version, Comments are welcom

siRNA Off-Target Effects Can Be Reduced at Concentrations That Match Their Individual Potency

Small interfering RNAs (siRNAs) are routinely used to reduce mRNA levels for a specific gene with the goal of studying its function. Several studies have demonstrated that siRNAs are not always specific and can have many off-target effects. The 3′ UTRs of off-target mRNAs are often enriched in sequences that are complementary to the seed-region of the siRNA. We demonstrate that siRNA off-targets can be significantly reduced when cells are treated with a dose of siRNA that is relatively low (e.g. 1 nM), but sufficient to effectively silence the intended target. The reduction in off-targets was demonstrated for both modified and unmodified siRNAs that targeted either STAT3 or hexokinase II. Low concentrations reduced silencing of transcripts with complementarity to the seed region of the siRNA. Similarly, off-targets that were not complementary to the siRNA were reduced at lower doses, including up-regulated genes that are involved in immune response. Importantly, the unintended induction of caspase activity following treatment with a siRNA that targeted hexokinase II was also shown to be a concentration-dependent off-target effect. We conclude that off-targets and their related phenotypic effects can be reduced for certain siRNA that potently silence their intended target at low concentrations

Family History of Alcoholism and Childhood Adversity: Joint Effects on Alcohol Consumption and Dependence

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65494/1/j.1530-0277.1994.tb00085.x.pd

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

Two bursts of gene gains occurred on the mammalian X chromosome contribute to an age-dependent chromosomal distribution of male-biased genes

Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution

Ensembl 2011

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types