Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus

The characterization of candidate loci is a critical step in obtaining insight into adaptation and acclimation of organisms. In this study of two non-model tropical (to sub-tropical) congeneric perciformes (Lates calcarifer and Lates niloticus) we characterized both coding and non-coding regions of lactate dehydrogenase-B (ldh-b), a locus which exhibits temperature-adaptive differences among temperate and sub-tropical populations of the North American killifish Fundulus heteroclitus. Ldh-b was 5,004 and 3,527 bp in length in L. calcarifer and L. niloticus, respectively, with coding regions comprising 1,005 bp in both species. A high level of sequence homology existed between species for both coding and non-coding regions of ldh-b (> 97% homology), corresponding to a 98.5% amino acid sequence homology. All six known functional sites within the encoded protein sequence (LDH-B) were conserved between the two Lates species. Ten simple sequence repeat (SSR) motifs (mono-, di-, tri- and tetranucleotide) and thirty putative microRNA elements (miRNAs) were identified within introns 1, 2, 5 and 6 of both Lates species. Five single nucleotide polymorphisms (SNPs) were also identified within miRNA containing intron regions. Such SNPs are implicated in several complex human conditions and/or diseases (as demonstrated by extensive genome-wide association studies). This novel characterization serves as a platform to further examine how non-model species may respond to changes in their native temperatures, which are expected to increase by up to 6°C over the next century

Can environmental DNA be used to detect first arrivals of the cane toad, Rhinella marina, into novel locations?

Eradicating invasive species is difficult, but success is more likely when populations are small after arrival. The cane toad, Rhinella marina, is an invasive pest species that threatens native fauna worldwide. Increasingly, environmental DNA (eDNA) is used as a technique to monitor the presence of invasive species given its power to detect low numbers of individuals. We aimed to investigate eDNA persistence in freshwater at three different temperatures (25, 30 and 35°C) and eDNA detection thresholds for R. marina using controlled experiments in aquaria. For the latter, two water volumes and two cane toad exposure times were used (800 or 200 L volume with 5 or 30 min exposure). A 15‐ml water sample was collected from each replicated aquaria and preserved with 5 ml Longmire's buffer. Environmental DNA was extracted and four technical quantitative PCR replicates were analyzed targeting the cane toad 16S rDNA mitochondrial gene. Environmental DNA decayed rapidly in water and was reliably detected for up to 3 days after cane toad removal, regardless of the temperature treatment. Also, cane toad eDNA was detected in the water after a 5‐min initial exposure of a single individual in 800 L of water. Under the physical parameters tested here, a positive detection means that a cane toad has been in contact with the water body between 1 and 3 days prior to the sampling event. The results of the present study show the importance of eDNA for determining the presence of a species that occurs at low abundance in a small water body, such as at the onset of a cane toad invasion

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology

Modelling the Pan-Spectral Energy Distribution of Starburst Galaxies: III. Emission Line Diagnostics of Ensembles of Evolving HII Regions

We build, as far as theory will permit, self consistent model HII regions around central clusters of aging stars. These produce strong emission line diagnostics applicable to either individual HII regions in galaxies, or to the integrated emission line spectra of disk or starburst galaxies. The models assume that the expansion and internal pressure of individual HII regions is driven by the net input of mechanical energy from the central cluster, be it through winds or supernova events. This eliminates the ionization parameter as a free variable, replacing it with a parameter which depends on the ratio of the cluster mass to the pressure in the surrounding interstellar medium. These models explain why HII regions with low abundances have high excitation, and demonstrate that at least part of the warm ionized medium is the result of overlapping faint, old, large, and low pressure HII regions. We present line ratios (at both optical and IR wavelengths) which provide reliable abundance diagnostics for both single HII regions or for integrated galaxy spectra, and we find a number that can be used to estimate the mean age of the cluster stars exciting individual HII regions.Comment: 22 pages. 18 figures. Accepted for publication in Astrophysical journal Supplements. Electronic tabular material is available on request to [email protected]

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

Period and Cohort Changes in Americans’ Support for Marijuana Legalization: Convergence and Divergence across Social Groups

We cast fresh light on how and why Americans’ views on marijuana legalization shifted between 1973 and 2014. Results from age-period-cohort models show a strong negative effect of age and relatively high levels of support for legalization among baby boom cohorts. Despite the baby boom effect, the large increase in support for marijuana legalization is predominantly a broad, period-based change in the population. Additional analyses demonstrate that differences in support for legalization by education, region, and religion decline, that differences by political party increase, and that differences between whites and African Americans reverse direction. We conclude by discussing the implications of these findings and by identifying promising directions for future research on this topic

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Predicted norovirus resurgence in 2021-2022 due to the relaxation of nonpharmaceutical interventions associated with COVID-19 restrictions in England: a mathematical modeling study.

BACKGROUND: To reduce the coronavirus disease burden in England, along with many other countries, the government implemented a package of non-pharmaceutical interventions (NPIs) that have also impacted other transmissible infectious diseases such as norovirus. It is unclear what future norovirus disease incidence is likely to look like upon lifting these restrictions. METHODS: Here we use a mathematical model of norovirus fitted to community incidence data in England to project forward expected incidence based on contact surveys that have been collected throughout 2020-2021. RESULTS: We report that susceptibility to norovirus infection has likely increased between March 2020 and mid-2021. Depending upon assumptions of future contact patterns incidence of norovirus that is similar to pre-pandemic levels or an increase beyond what has been previously reported is likely to occur once restrictions are lifted. Should adult contact patterns return to 80% of pre-pandemic levels, the incidence of norovirus will be similar to previous years. If contact patterns return to pre-pandemic levels, there is a potential for the expected annual incidence to be up to 2-fold larger than in a typical year. The age-specific incidence is similar across all ages. CONCLUSIONS: Continued national surveillance for endemic diseases such as norovirus will be essential after NPIs are lifted to allow healthcare services to adequately prepare for a potential increase in cases and hospital pressures beyond what is typically experienced

Spatial Patterns of Parrotfish Corallivory in the Caribbean: The Importance of Coral Taxa, Density and Size

The past few decades have seen an increase in the frequency and intensity of disturbance on coral reefs, resulting in shifts in size and composition of coral populations. These changes have lead to a renewed focus on processes that influence demographic rates in corals, such as corallivory. While previous research indicates selective corallivory among coral taxa, the importance of coral size and the density of coral colonies in influencing corallivory are unknown. We surveyed the size, taxonomy and number of bites by parrotfish per colony of corals and the abundance of three main corallivorous parrotfish (Sparisoma viride, Sparisoma aurofrenatum, Scarus vetula) at multiple spatial scales (reefs within islands: 1–100 km, and between islands: >100 km) within the Bahamas Archipelago. We used a linear mixed model to determine the influence of coral taxa, colony size, colony density, and parrotfish abundance on the intensity of corallivory (bites per m2 of coral tissue). While the effect of colony density was significant in determining the intensity of corallivory, we found no significant influence of colony size or parrotfish abundance (density, biomass or community structure). Parrotfish bites were most frequently observed on the dominant species of reef building corals (Montastraea annularis, Montastraea faveolata and Porites astreoides), yet our results indicate that when the confounding effects of colony density and size were removed, selective corallivory existed only for the less dominant Porites porites. As changes in disturbance regimes result in the decline of dominant frame-work building corals such as Montastraea spp., the projected success of P. porites on Caribbean reefs through high reproductive output, resistance to disease and rapid growth rates may be attenuated through selective corallivory by parrotfish