The Extragalactic Distance Database: Color-Magnitude Diagrams

The CMDs/TRGB (Color-Magnitude Diagrams/Tip of the Red Giant Branch) section of the Extragalactic Distance Database contains a compilation of observations of nearby galaxies from the Hubble Space Telescope. Approximately 250 (and increasing) galaxies in the Local Volume have CMDs and the stellar photometry tables used to produce them available through the web. Various stellar populations that make up a galaxy are visible in the CMDs, but our primary purpose for collecting and analyzing these galaxy images is to measure the TRGB in each. We can estimate the distance to a galaxy by using stars at the TRGB as standard candles. In this paper we describe the process of constructing the CMDs and make the results available to the public.Comment: 8 pages, 5 figures, 1 long table, submitted to Astronomical Journa

Mahi-mahi (Coryphaena hippurus) life development: morphological, physiological, behavioral and molecular phenotypes.

BackgroundMahi-mahi (Coryphaena hippurus) is a commercially and ecologically important fish species that is widely distributed in tropical and subtropical waters. Biological attributes and reproductive capacities of mahi-mahi make it a tractable model for experimental studies. In this study, life development of cultured mahi-mahi from the zygote stage to adult has been described.ResultsA comprehensive developmental table has been created reporting development as primarily detailed observations of morphology. Additionally, physiological, behavioral, and molecular landmarks have been described to significantly contribute in the understanding of mahi life development.ConclusionRemarkably, despite the vast difference in adult size, many developmental landmarks of mahi map quite closely onto the development and growth of Zebrafish and other warm-water, active Teleost fishes

Corresponding morphological and molecular indicators of crude oil toxicity to the developing hearts of mahi mahi

Crude oils from distinct geological sources worldwide are toxic to developing fish hearts. When oil spills occur in fish spawning habitats, natural resource injury assessments often rely on conventional morphometric analyses of heart form and function. The extent to which visible indicators correspond to molecular markers for cardiovascular stress is unknown for pelagic predators from the Gulf of Mexico. Here we exposed mahi (Coryphaena hippurus) embryos to field-collected crude oil samples from the 2010 Deepwater Horizon disaster. We compared visible heart defects (edema, abnormal looping, reduced contractility) to changes in expression of cardiac-specific genes that are diagnostic of heart failure in humans or associated with loss-of-function zebrafish cardiac mutants. Mahi exposed to crude oil during embryogenesis displayed typical symptoms of cardiogenic syndrome as larvae. Contractility, looping, and circulatory defects were evident, but larval mahi did not exhibit downstream craniofacial and body axis abnormalities. A gradation of oil exposures yielded concentration-responsive changes in morphometric and molecular responses, with relative sensitivity being influenced by age. Our findings suggest that 1) morphometric analyses of cardiac function are more sensitive to proximal effects of crude oil-derived chemicals on the developing heart, and 2) molecular indicators reveal a longer-term adverse shift in cardiogenesis trajectory

A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)

As metagenomic studies continue to increase in their number, sequence volume and complexity, the scalability of biological analysis frameworks has become a rate-limiting factor to meaningful data interpretation. To address this issue, we have developed JCVI Metagenomics Reports (METAREP) as an open source tool to query, browse, and compare extremely large volumes of metagenomic annotations. Here we present improvements to this software including the implementation of a dynamic weighting of taxonomic and functional annotation, support for distributed searches, advanced clustering routines, and integration of additional annotation input formats. The utility of these improvements to data interpretation are demonstrated through the application of multiple comparative analysis strategies to shotgun metagenomic data produced by the National Institutes of Health Roadmap for Biomedical Research Human Microbiome Project (HMP) (http://nihroadmap.nih.gov). Specifically, the scalability of the dynamic weighting feature is evaluated and established by its application to the analysis of over 400 million weighted gene annotations derived from 14 billion short reads as predicted by the HMP Unified Metabolic Analysis Network (HUMAnN) pipeline. Further, the capacity of METAREP to facilitate the identification and simultaneous comparison of taxonomic and functional annotations including biological pathway and individual enzyme abundances from hundreds of community samples is demonstrated by providing scenarios that describe how these data can be mined to answer biological questions related to the human microbiome. These strategies provide users with a reference of how to conduct similar large-scale metagenomic analyses using METAREP with their own sequence data, while in this study they reveal insights into the nature and extent of variation in taxonomic and functional profiles across body habitats and individuals. Over one thousand HMP WGS datasets and the latest open source code are available at http://www.jcvi.org/hmp-metarep

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe

Interactions Between Water Chemistry and Waterborne Lead Exposure to Freshwater Organisms

This dissertation characterizes the influences of water chemistry on the acute toxicity of lead (Pb) to two of the long-standing sentinel test organisms commonly employed by the United States Environmental Protection Agency (USEPA), the fathead minnow (Pimephales promelas) and daphnid (Ceriodaphnia dubia), for parameterization of an acute Pb Biotic Ligand Model (BLM). In addition, a toxicogenomic approach was employed to identify genes that might serve as molecular markers of Pb exposure and long-term effects, as well as provide new insights as to the underlying toxic mechanisms of chronic Pb exposure in P. promelas. The endpoints of growth, reproduction, Pb accumulation, prey capture ability, and swimming performance of P. promelas were examined to assess the influences of water chemistry during chronic Pb exposures and to potentially link microarray-identified genes to outcomes of ecological significance. Importantly, this work revealed that calcium does not protect against acute toxicity to C. dubia or chronic Pb accumulation by P. promelas, indicating that current hardness-based regulations are inappropriate and provide further support for the need for alternative approaches to setting environmental regulations for Pb. The findings reported herein should facilitate the arrival of such an approach in the form of a new acute Pb BLM. However, different responses with respect to the influences of water chemistry on the acute toxicity of Pb were exhibited by these species suggesting that development of separate BLMs for P. promelas and C. dubia should be considered to ensure adequate protection for both species. Furthermore, the influences of water chemistry were found to be inconsistent during acute and chronic Pb exposures to P. promelas and thus caution against inferring chronic effects from acute exposures. A number of Pb-responsive genes were identified that exhibited a strong potential for serving as robust indicators of Pb exposure and accumulation in P. promelas. While these genes also provided insight as to the likely toxic mechanisms of Pb, additional work will be necessary to firmly link these genes to chronic outcomes of ecological relevance in the context of ambient water chemistry

Effects of acute and chronic waterborne lead exposure on the swimming performance and aerobic scope of fathead minnows (Pimephales promelas)

Fathead minnows were subjected to an incremental velocity test using swim tunnel respirometry for the analysis of aerobic scope and swimming performance, as critical aerobic swim speed (U(crit)), following chronic exposures (33-57 ) to 0.9±0.4, 157±18 or 689±66 nmol L⁻¹ Pb and an acute exposure (24 h) to 672±35 nmol L⁻¹ Pb (mean±SEM). Assessment of Pb-induced anemia and neurological impairment were evaluated by blood hemoglobin (Hb) concentrations and a cost of transport (COT) analysis, respectively. Fish from the acute 672±35 nmol L⁻¹ Pb (24.4±1.2 BL s⁻¹) and chronic 689±66 nmol L⁻¹ Pb (24.6±0.9 BL s⁻¹) treatments exhibited reduced U(crits) compared to control fish (27.6±0.8 BL s⁻¹). Aerobic scope was reduced by acute Pb exposure (8.6±2.6 μmol O₂ g⁻¹ h⁻¹ vs. 22.6±3.8 μmol O₂ g⁻¹ h⁻¹ from controls) owing to a decrease in maximum oxygen consumption rate (38.8±0.8 μmol O₂ g⁻¹ h⁻¹ vs. 54.0±4.2 μmol O₂ g⁻¹ h⁻¹ from controls). However, no effect on aerobic scope was observed with fish chronically exposed to Pb. Significant differences were not observed for Hb concentrations or COT. These findings suggest that the impaired swimming performances arising from acute and chronic Pb exposures reflect different mechanisms of toxicity

Swimming Performance Assessments of Fish Species of Greatest Conservation Need to Inform Future Stream Crossing Designs in Texas

Conventional structures associated with stream crossings such as bridges and culverts can lead to zones of high-velocity water flow that impede fish passage. Such obstacles are likely to harm native fish populations by impacting migrations critical to their life history strategies, causing habitat fragmentation and extirpation, thereby limiting population growth and distribution. Due to the high rates of human population growth and development occurring in Texas, this is an issue of particular concern for fish designated as species of greatest conservation need (SGCN). This project focused on four SGCN fishes native to the Edwards Plateau Ecoregion, namely the Guadalupe Bass, Guadalupe Roundnose Minnow, Guadalupe Darter, and Plateau Shiner, at both adult (all species) and juvenile (Guadalupe Bass only) life stages. Our primary aim was to aid in the design of future culverts associated with stream crossings (or the modification of existing culverts) so that the water velocities through these structures do not exceed the swimming capacities of our target SGCN fishes. To this end, we assessed their maximum sustained swimming speeds (Ucrit) under a typical range of Edwards Plateau stream temperatures (15, 22.5, and 30 °C) to be used in site-specific calculations of the maximum allowable culvert water velocities (Vf). A secondary objective was to collect physiological endpoints of relevance to the overall swimming performance including the maximum burst swimming speeds (Umax), metabolic rate measurements (i.e., standard metabolic rate (SMR), maximum metabolic rate (MMR), and aerobic scope (AS)), cost of transport (COT), and optimal swimming speed (Uopt). Temperature-related effects were observed that can be used to inform site-specific culvert designs. In general, the highest Ucrit values for the tested species were near, or possibly between, 22.5 and 30 °C, while Umax stayed relatively consistent among treatments