Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies.

Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in 'omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the "Transcriptomes of 1,000 Fishes" (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes.

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L.

Genomic variation among populations of threatened coral: Acropora cervicornis.

Background: Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species' ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions.

Corrigendum: Relationship Between L-DOPA-Induced Reduction in Motor and Exploratory Activity and Striatal Dopamine D2 Receptor Binding in the Rat.

[This corrects the article on p. 352 in vol. 9, PMID: 26778989.

Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds.

The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 avian whole genomes representing all major extant bird clades.

Using probabilities of enterococci exceedance and logistic regression to evaluate long term weekly beach monitoring data.

Recreational water quality surveillance involves comparing bacterial levels to set threshold values to determine beach closure. Bacterial levels can be predicted through models which are traditionally based upon multiple linear regression. The objective of this study was to evaluate exceedance probabilities, as opposed to bacterial levels, as an alternate method to express beach risk.

A sphingolipid mechanism for behavioral extinction.

Reward-dependent instrumental behavior must continuously be re-adjusted according to environmental conditions. Failure to adapt to changes in reward contingencies may incur psychiatric disorders like anxiety and depression. When an expected reward is omitted, behavior undergoes extinction.

Relationship Between L-DOPA-Induced Reduction in Motor and Exploratory Activity and Striatal Dopamine D2 Receptor Binding in the Rat.

Purpose: The present study assessed the influence of L-DOPA administration on neostriatal dopamine (DA) D2 receptor binding in relation to motor and exploratory behaviors in the rat.

Methods: D2 receptor binding was measured in baseline, after challenge with the aromatic L-amino acid decarboxylase inhibitor benserazide, and after challenge with either 5 or 10 mg/kg L-DOPA plus benserazide. Additional rats received injections of saline.

Surfactant-associated bacteria in the near-surface layer of the ocean.

Certain marine bacteria found in the near-surface layer of the ocean are expected to play important roles in the production and decay of surface active materials; however, the details of these processes are still unclear. Here we provide evidence supporting connection between the presence of surfactant-associated bacteria in the near-surface layer of the ocean, slicks on the sea surface, and a distinctive feature in the synthetic aperture radar (SAR) imagery of the sea surface. From DNA analyses of the in situ samples using pyrosequencing technology, we found the highest abundance of surfactant-associated bacterial taxa in the near-surface layer below the slick.

Genetic Evidence for Contrasting Wetland and Savannah Habitat Specializations in Different Populations of Lions (Panthera leo).

South-central Africa is characterized by an archipelago of wetlands, which has evolved in time and space since at least the Miocene, providing refugia for animal species during Pleistocene arid episodes. Their importance for biodiversity in the region is reflected in the evolution of a variety of specialist mammal and bird species, adapted to exploit these wetland habitats. Populations of lions (Panthera leo) across south-central and east Africa have contrasting signatures of mitochondrial DNA haplotypes and biparental nuclear DNA in wetland and savannah habitats, respectively, pointing to the evolution of distinct habitat preferences.

Genomic legacy of the African cheetah, Acinonyx jubatus.

Background: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.

Results: Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.

The Population Origins and Expansion of Feral Cats in Australia.

The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [~200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.

Rheological properties, gelling behavior and texture characteristics of polysaccharide from Enteromorpha prolifera.

Polysaccharide from Enteromorpha prolifera (PE) which is the most common green algae is gradually becoming an attractive candidate with novel functions by virtue of its unique chemical and physicochemical properties. The infrared spectrum (FT-IR) of PE confirmed that it is a distinctive, sulfated heteropolysaccharide. Dynamic rheology was systematically conducted to investigate the effect of concentration, temperature, pH, and electrolytes on PE.

The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.

Background: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.

ZnO Nanoparticles Treatment Induces Apoptosis by Increasing Intracellular ROS Levels in LTEP-a-2 Cells.

Owing to the wide use of novel nanoparticles (NPs) such as zinc oxide (ZnO) in all aspects of life, toxicological research on ZnO NPs is receiving increasing attention in these days. In this study, the toxicity of ZnO NPs in a human pulmonary adenocarcinoma cell line LTEP-a-2 was tested in vitro. Log-phase cells were exposed to different levels of ZnO NPs for hours, followed by colorimetric cell viability assay using tetrazolium salt and cell survival rate assay using trypan blue dye.

Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND).

Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S.

Vansoestia caribensis gen. nov., sp. nov.: first report of the family Ianthellidae (Verongida, Demospongiae) in the Caribbean.

A thin fiber-less sponge from Caribbean reefs (Bocas del Toro, Panama) with close genetic affinities (based on 18S and 28S nuclear ribosomal RNA gene sequences) to large fan-shaped fiber-bearing sponges (Ianthella and Anomoianthella) from the Indo-Pacific Ocean is here presented. We describe its overall external morphology, histological features, and ultrastructure. Its genetic distance from the only previously known fiber-less verongid genus, Hexadella, prompted the need to erect a new genus to classify this species.

Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species.

The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids.

Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida.

Olfactory receptors (ORs) govern a prime sensory function. Extant birds have distinct olfactory abilities, but the molecular mechanisms underlining diversification and specialization remain mostly unknown. We explored OR diversity in 48 phylogenetic and ecologically diverse birds and 2 reptiles (alligator and green sea turtle).

Using Pooled Local Expert Opinions (PLEO) to Discern Patterns in Sightings of Live and Dead Manatees (Trichechus senegalensis, Link 1785) in Lower Sanaga Basin, Cameroon.

We aimed at unveiling patterns in live and dead manatee sightings in the Lower Sanaga Basin, Cameroon. For this purpose, the expert opinions of 133 local fishers were collected during in-person interviews, distilled using categorical data analysis, and checked against scientific literature. The five main results are as follows: manatees were sighted averagely once a week in lakes, rivers, and the coast & estuaries, mostly in group sizes of 2-3; the odds of sighting live manatees (respectively dead manatees) decreased (respectively increased) from inland lakes to estuaries and the coast, via rivers; manatee carcasses were reported in all habitats, albeit more frequently in rivers; a distribution map based on fishers' reports show two manatee concentration areas: Lake Ossa and the Malimba-Mbiako section of River Sanaga; the number of manatees was perceived as increasing despite incidental and directed catches.

Dietary administration of the probiotic SpPdp11: Effects on the intestinal microbiota and immune-related gene expression of farmed Solea senegalensis treated with oxytetracycline.

Few antimicrobials are currently authorised in the aquaculture industry to treat infectious diseases. Among them, oxytetracycline (OTC) is one of the first-choice drugs for nearly all bacterial diseases. The objective of this study was to evaluate the effect of the dietary administration of OTC both alone and jointly with the probiotic Shewanella putrefaciens Pdp11 (SpPdp11) on the intestinal microbiota and hepatic expression of genes related to immunity in Senegalese sole (Solea senegalensis) juveniles.

Oceanic Sink and Biogeochemical Controls on the Accumulation of Polychlorinated Dibenzo-p-dioxins, Dibenzofurans, and Biphenyls in Plankton.

Polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs) and dioxin-like polychlorinated biphenyls (dl-PCBs) were measured in plankton samples from the Atlantic, Pacific, and Indian Oceans collected during the Malaspina circumnavigation cruise. The concentrations of PCDD/Fs and dl-PCBs in plankton averaged 14 and 240 pg gdw(-1), respectively, but concentrations were highly variable. The global distribution of PCDD/Fs and dl-PCBs was not driven by proximity to continents but significantly correlated with plankton biomass, with higher plankton phase PCDD/F and dl-PCB concentrations at lower biomass.

Towards a common oil spill risk assessment framework – Adapting ISO 31000 and addressing uncertainties.

Oil spills are a transnational problem, and establishing a common standard methodology for Oil Spill Risk Assessments (OSRAs) is thus paramount in order to protect marine environments and coastal communities. In this study we firstly identified the strengths and weaknesses of the OSRAs carried out in various parts of the globe. We then searched for a generic and recognized standard, i.