An EvoDevo Study of Salmonid Visual Opsin Dynamics and Photopigment Spectral Sensitivity

Salmonids are ideal models as many species follow a distinct developmental program from demersal eggs and a large yolk sac to hatching at an advanced developmental stage. Further, these economically important teleosts inhabit both marine- and freshwaters and experience diverse light environments during their life histories. At a genome level, salmonids have undergone a salmonid-specific fourth whole genome duplication event (Ss4R) compared to other teleosts that are already more genetically diverse compared to many non-teleost vertebrates. Thus, salmonids display phenotypically plastic visual systems that appear to be closely related to their anadromous migration patterns. This is most likely due to a complex interplay between their larger, more gene-rich genomes and broad spectrally enriched habitats; however, the molecular basis and functional consequences for such diversity is not fully understood. This study used advances in genome sequencing to identify the repertoire and genome organization of visual opsin genes (those primarily expressed in retinal photoreceptors) from six different salmonids [Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Chinook salmon (Oncorhynchus tshawytcha), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka)] compared to the northern pike (Esox lucius), a closely related non-salmonid species. Results identified multiple orthologues for all five visual opsin classes, except for presence of a single short-wavelength-sensitive-2 opsin gene. Several visual opsin genes were not retained after the Ss4R duplication event, which is consistent with the concept of salmonid rediploidization. Developmentally, transcriptomic analyzes of Atlantic salmon revealed differential expression within each opsin class, with two of the long-wavelength-sensitive opsins not being expressed before first feeding. Also, early opsin expression in the retina was located centrally, expanding dorsally and ventrally as eye development progressed, with rod opsin being the dominant visual opsin post-hatching. Modeling by spectral tuning analysis and atomistic molecular simulation, predicted the greatest variation in the spectral peak of absorbance to be within the Rh2 class, with a ∼40 nm difference in λmax values between the four medium-wavelength-sensitive photopigments. Overall, it appears that opsin duplication and expression, and their respective spectral tuning profiles, evolved to maximize specialist color vision throughout an anadromous lifecycle, with some visual opsin genes being lost to tailor marine-based vision.publishedVersio

J.S. Bell's Concept of Local Causality

John Stewart Bell's famous 1964 theorem is widely regarded as one of the most important developments in the foundations of physics. It has even been described as "the most profound discovery of science." Yet even as we approach the 50th anniversary of Bell's discovery, its meaning and implications remain controversial. Many textbooks and commentators report that Bell's theorem refutes the possibility (suggested especially by Einstein, Podolsky, and Rosen in 1935) of supplementing ordinary quantum theory with additional ("hidden") variables that might restore determinism and/or some notion of an observer-independent reality. On this view, Bell's theorem supports the orthodox Copenhagen interpretation. Bell's own view of his theorem, however, was quite different. He instead took the theorem as establishing an "essential conflict" between the now well-tested empirical predictions of quantum theory and relativistic \emph{local causality}. The goal of the present paper is, in general, to make Bell's own views more widely known and, in particular, to explain in detail Bell's little-known mathematical formulation of the concept of relativistic local causality on which his theorem rests. We thus collect and organize many of Bell's crucial statements on these topics, which are scattered throughout his writings, into a self-contained, pedagogical discussion including elaborations of the concepts "beable", "completeness", and "causality" which figure in the formulation. We also show how local causality (as formulated by Bell) can be used to derive an empirically testable Bell-type inequality, and how it can be used to recapitulate the EPR argument.Comment: 19 pages, 4 figure

The properties and luminosity function of extremely low luminosity galaxies

We examine a sample of low redshift (10 < d < 150 Mpc) galaxies including galaxies with r-band absolute magnitudes as faint as -12.5 (for h=1), selected from the Sloan Digital Sky Survey Data Release 2 (SDSS). The sample is unique in containing galaxies of extremely low luminosities in a wide range of environments, selected with uniform and well-understood criteria. We present the luminosity function as well as the broad-band properties of low luminosity galaxies in this sample. A Schechter function is an insufficient parameterization of the r-band luminosity function; there is an upturn in the slope at low luminosities. The resulting slope at low luminosities in this sample is around -1.3. However, we almost certainly miss a large number of galaxies at very low luminosities due to low surface brightness selection effects, and we estimate that the true low luminosity slope may be as steep or steeper than -1.5. The results here are consistent with previous SDSS results and, in the g-band, roughly consistent with the results of the Two degree Field Galaxy Redshift Survey. Extremely low luminosity galaxies are predominantly blue, low surface brightness, exponential disks.Comment: accepted by ApJ; full resolution figures available at http://sdss.physics.nyu.edu/vagc/lowlum.ps.gz; associated data files available at http://sdss.physics.nyu.edu/vagc/lowz.htm

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species.

Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present "haplotagging," a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations

The SAMI Galaxy Survey: a new method to estimate molecular gas surface densities from star formation rates

Stars form in cold molecular clouds. However, molecular gas is difficult to observe because the most abundant molecule (H_2) lacks a permanent dipole moment. Rotational transitions of CO are often used as a tracer of H_2, but CO is much less abundant and the conversion from CO intensity to H2 mass is often highly uncertain. Here we present a new method for estimating the column density of cold molecular gas (Σ_(gas)) using optical spectroscopy. We utilize the spatially resolved Hα maps of flux and velocity dispersion from the Sydney-AAO Multi-object Integral field spectrograph (SAMI) Galaxy Survey. We derive maps of Σ_(gas) by inverting the multi-freefall star formation relation, which connects the star formation rate surface density (Σ_(SFR)) with Σ_(gas) and the turbulent Mach number (M). Based on the measured range of Σ_(SFR) = 0.005-1.5M⊙ yr^(−1) kpc^(−2) and M=18–130, we predict Σ_(gas) = 7–200 M⊙ pc^(−2) in the star-forming regions of our sample of 260 SAMI galaxies. These values are close to previously measured Σ_(gas) obtained directly with unresolved CO observations of similar galaxies at low redshift. We classify each galaxy in our sample as ‘star-forming’ (219) or ‘composite/AGN/shock’ (41), and find that in ‘composite/AGN/shock’ galaxies the average Σ_(SFR), M and Σ_(gas) are enhanced by factors of 2.0, 1.6 and 1.3, respectively, compared to star-forming galaxies. We compare our predictions of Σ_(gas) with those obtained by inverting the Kennicutt–Schmidt relation and find that our new method is a factor of 2 more accurate in predicting Σ_(gas), with an average deviation of 32 per cent from the actual Σ_(gas)

Effects of oral adenosine 5'-triphosphate and adenosine in enteric-coated capsules on indomethacin-induced permeability changes in the human small intestine: a randomized cross-over study

<p>Abstract</p> <p>Background</p> <p>It is well-known that nonsteroidal anti-inflammatory drugs (NSAIDs) can cause damage to the small bowel associated with disruption of mucosal barrier function. In healthy human volunteers, we showed previously that topical administration of adenosine 5'-triphosphate (ATP) by naso-intestinal tube attenuated a rise in small intestinal permeability induced by short-term challenge with the NSAID indomethacin. This finding suggested that ATP may be involved in the preservation of intestinal barrier function. Our current objective was to corroborate the favourable effect of ATP on indomethacin-induced permeability changes in healthy human volunteers when ATP is administered via enteric-coated capsules, which is a more practically feasible mode of administration. Since ATP effects may have been partly mediated through its breakdown to adenosine, effects of encapsulated adenosine were tested also.</p> <p>Methods</p> <p>By ingesting a test drink containing 5 g lactulose and 0.5 g L-rhamnose followed by five-hour collection of total urine, small intestinal permeability was assessed in 33 healthy human volunteers by measuring the urinary lactulose/rhamnose excretion ratio. Urinary excretion of lactulose and L-rhamnose was determined by fluorescent detection high-pressure liquid chromatography (HPLC). Basal permeability of the small intestine was assessed as a control condition (no indomethacin, no ATP/adenosine). As a model of increased small intestinal permeability, two dosages of indomethacin were ingested at 10 h (75 mg) and 1 h (50 mg) before ingesting the lactulose/rhamnose test drink. At 1.5 h before indomethacin ingestion, two dosages of placebo, ATP (2 g per dosage) or adenosine (1 g per dosage) were administered via enteric-coated hydroxypropyl methylcellulose (HPMC) capsules with Eudragit^©L30D-55.</p> <p>Results</p> <p>Median urinary lactulose/rhamnose excretion ratio (g/g) in the control condition was 0.032 (interquartile range: 0.022–0.044). Compared to the control condition, lactulose/rhamnose ratio after ingestion of indomethacin plus placebo was significantly increased to 0.039 (0.035–0.068); P < 0.01). The indomethacin-induced increase was neither affected by administration of encapsulated ATP (0.047 (0.033–0.065)) nor adenosine (0.050 (0.030–0.067)). Differences in L/R ratios between the conditions with indomethacin plus placebo, ATP or adenosine were not significant.</p> <p>Conclusion</p> <p>In this study, either ATP or adenosine administered via enteric-coated capsules had no effect on indomethacin-induced small intestinal permeability changes in healthy human volunteers. The observed lack of effect of encapsulated ATP/adenosine may have been caused by opening of the enteric-coated supplement at a site distal from the indomethacin-inflicted site. Further studies on site-specific effectiveness of ATP/adenosine on intestinal permeability changes are warranted.</p

High-resolution, 3D radiative transfer modeling: I. The grand-design spiral galaxy M 51

International audienceContext. Dust reprocesses about half of the stellar radiation in galaxies. The thermal re-emission by dust of absorbed energy is considered to be driven merely by young stars so is often applied to tracing the star formation rate in galaxies. Recent studies have argued that the old stellar population might be responsible for a non-negligible fraction of the radiative dust heating.Aims. In this work, we aim to analyze the contribution of young (≲100 Myr) and old (~10 Gyr) stellar populations to radiative dust heating processes in the nearby grand-design spiral galaxy M 51 using radiative transfer modeling. High-resolution 3D radiative transfer (RT) models are required to describe the complex morphologies of asymmetric spiral arms and clumpy star-forming regions and to model the propagation of light through a dusty medium. Methods. In this paper, we present a new technique developed to model the radiative transfer effects in nearby face-on galaxies. We construct a high-resolution 3D radiative transfer model with the Monte-Carlo code SKIRT to account for the absorption, scattering, and non-local thermal equilibrium (NLTE) emission of dust in M 51. The 3D distribution of stars is derived from the 2D morphology observed in the IRAC 3.6 μm, GALEX FUV, Hα, and MIPS 24 μm wavebands, assuming an exponential vertical distribution with an appropriate scale height. The dust geometry is constrained through the far-ultraviolet (FUV) attenuation, which is derived from the observed total-infrared-to-far-ultraviolet luminosity ratio. The stellar luminosity, star formation rate, and dust mass have been scaled to reproduce the observed stellar spectral energy distribution (SED), FUV attenuation, and infrared SED.Results. The dust emission derived from RT calculations is consistent with far-infrared and submillimeter observations of M 51, implying that the absorbed stellar energy is balanced by the thermal re-emission of dust. The young stars provide 63% of the energy for heating the dust responsible for the total infrared emission (8−1000 μm), while 37% of the dust emission is governed through heating by the evolved stellar population. In individual wavebands, the contribution from young stars to the dust heating dominates at all infrared wavebands but gradually decreases towards longer infrared and submillimeter wavebands for which the old stellar population becomes a non-negligible source of heating. Upon extrapolation of the results for M 51, we present prescriptions for estimating the contribution of young stars to the global dust heating based on a tight correlation between the dust heating fraction and specific star formation rate

Galaxy And Mass Assembly (GAMA): stellar mass growth of spiral galaxies in the cosmic web

We look for correlated changes in stellar mass and star formation rate (SFR) along filaments in the cosmic web by examining the stellar masses and UV-derived SFRs of 1799 ungrouped and unpaired spiral galaxies that reside in filaments. We devise multiple distance metrics to characterize the complex geometry of filaments, and find that galaxies closer to the cylindrical centre of a filament have higher stellar masses than their counterparts near the periphery of filaments, on the edges of voids. In addition, these peripheral spiral galaxies have higher SFRs at a given mass. Complementing our sample of filament spiral galaxies with spiral galaxies in tendrils and voids, we find that the average SFR of these objects in different large-scale environments are similar to each other with the primary discriminant in SFR being stellar mass, in line with previous works. However, the distributions of SFRs are found to vary with large-scale environment. Our results thus suggest a model in which in addition to stellar mass as the primary discriminant, the large-scale environment is imprinted in the SFR as a second-order effect. Furthermore, our detailed results for filament galaxies suggest a model in which gas accretion from voids on to filaments is primarily in an orthogonal direction. Overall, we find our results to be in line with theoretical expectations of the thermodynamic properties of the intergalactic medium in different large-scale environments

Current Status of Pharmaceutical and Genetic Therapeutic Approaches to Treat DMD

Duchenne muscular dystrophy (DMD) is a genetic disease affecting about one in every 3,500 boys. This X-linked pathology is due to the absence of dystrophin in muscle fibers. This lack of dystrophin leads to the progressive muscle degeneration that is often responsible for the death of the DMD patients during the third decade of their life. There are currently no curative treatments for this disease but different therapeutic approaches are being studied. Gene therapy consists of introducing a transgene coding for full-length or a truncated version of dystrophin complementary DNA (cDNA) in muscles, whereas pharmaceutical therapy includes the use of chemical/biochemical substances to restore dystrophin expression or alleviate the DMD phenotype. Over the past years, many potential drugs were explored. This led to several clinical trials for gentamicin and ataluren (PTC124) allowing stop codon read-through. An alternative approach is to induce the expression of an internally deleted, partially functional dystrophin protein through exon skipping. The vectors and the methods used in gene therapy have been continually improving in order to obtain greater encapsidation capacity and better transduction efficiency. The most promising experimental approaches using pharmaceutical and gene therapies are reviewed in this article