Genetic Insights into the Giant Keyhole Limpet (), an Eastern Pacific Coastal Endemic: Complete Mitogenome, Phylogenetics, Phylogeography, and Historical Demography.

Background: The giant keyhole limpet is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. is socioeconomically important as it produces a potent immune-stimulating protein, called Keyhole Limpet Hemocyanin, which is extracted in vivo and utilized for vaccine development. However, ecological studies are scarce and genetic knowledge of the species needs to be improved.

Spirochaete genome identified in red abalone sample represents a novel genus Haliotispira gen. nov. within the order .

A fully assembled spirochaete genome was identified as a contaminating scaffold in our red abalone () genome assembly. In this paper, we describe the analysis of this bacterial genome. The assembled spirochaete genome is 3.

Seascape genomics of the pink abalone (Haliotis corrugata): An insight into a cross-border species in the northeast Pacific coast.

Seascape genomics gives insight into the geographic and environmental factors shaping local adaptations. It improves the understanding of the potential effects of climate change, which is relevant to provide the basis for the international management of fishery resources. The pink abalone (Haliotis corrugata) is distributed from California, United States to Baja California Sur, Mexico, exposed to a latitudinal environmental gradient in the California Current System.

Quantifying the kinematic features of dexterous finger movements in nonhuman primates with markerless tracking.

Research using nonhuman primate models for human disease frequently requires behavioral observational techniques to quantify functional outcomes. The ability to assess reaching and grasping patterns is of particular interest in clinical conditions that affect the motor system (e.g.

Regions of genetic divergence in depth-separated Sebastes rockfish species pairs: Depth as a potential driver of speciation.

Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation-driving adaptations, particularly along a depth gradient.

Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation.

Albacore () support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific.

Stable isotope turnover rates and fractionation in captive California yellowtail (Seriola dorsalis): insights for application to field studies.

Stable isotope analysis (SIA) measurements from long-term captivity studies provide required parameters for interpretation of consumer SIA data. We raised young-of-the-year (14-19 cm) California yellowtail (Seriola dorsalis) on a low δN and δC diet (pellet aquaculture feed) for 525 days, then switched to a high δN and δC diet (mackerel and squid) for 753 days. Yellowtail muscle was sequentially sampled from each individual after the diet switch (0 to 753 days) and analyzed for δN and δC, allowing for calculation of diet-tissue discrimination factors (DTDFs) from two isotopically different diets (low δN and δC: pellets; high δN and δC: fish/squid) and turnover rates of N and C.

An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species.

Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2.

Transcriptomic analysis of short-term 17α-ethynylestradiol exposure in two Californian sentinel fish species sardine (Sardinops sagax) and mackerel (Scomber japonicus).

Endocrine disrupting chemicals (EDCs) are substances which disrupt normal functioning of the endocrine system by interfering with hormone regulated physiological pathways. Aquatic environments provide the ultimate reservoir for many EDCs as they enter rivers and the ocean via effluent discharges and accumulate in sediments. One EDC widely dispersed in municipal wastewater effluent discharges is 17α-ethynylestradiol (EE2), which is one of the most widely prescribed medicines.

De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, , , and .

The monitoring of marine species as sentinels for ecosystem health has long been a valuable tool worldwide, providing insight into how both anthropogenic pollution and naturally occurring phenomena (i.e., harmful algal blooms) may lead to human and animal dietary concerns.

Erratum: KAREN E. UNDERKOFFLER, MEAGAN A. LUERS, JOHN R. HYDE MATTHEW T. CRAIG (2018) A taxonomic review of Lampris guttatus (Brünnich 1788) (Lampridiformes; Lampridae) with descriptions of three new species. Zootaxa, 4413: 551-565.

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A taxonomic review of Lampris guttatus (Brünnich 1788) Lampridiformes; Lampridae) with descriptions of three new species.

The genus Lampris (Lampridae) currently comprises two species, Lampris guttatus (Brünnich 1788) and L. immaculatus (Gilchrist 1905) commonly known as Opah and Southern Opah, respectively. Hyde et al.

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.

Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90.

Insights into teleost sex determination from the Seriola dorsalis genome assembly.

Background: The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for species in culture, such as the California Yellowtail (Seriola dorsalis), the likely candidate for the establishment of commercial offshore aquaculture production in southern California. Genomic resource development for this species will improve the understanding of sex and other phenotypic traits, and allow for rapid increases in genetic improvement for and economic gain in culture production.

Larval abundances of rockfishes that were historically targeted by fishing increased over 16 years in association with a large marine protected area.

Marine protected areas (MPAs) can facilitate recovery of diminished stocks by protecting reproductive adults. To effectively augment fisheries, however, reproductive output must increase within the bounds of MPAs so that larvae can be exported to surrounding areas and seed the region. In response to dramatic declines of rockfishes ( spp.

Estimating fish abundance at spawning aggregations from courtship sound levels.

Sound produced by fish spawning aggregations (FSAs) permits the use of passive acoustic methods to identify the timing and location of spawning. However, difficulties in relating sound levels to abundance have impeded the use of passive acoustics to conduct quantitative assessments of biomass. Here we show that models of measured fish sound production versus independently measured fish density can be generated to estimate abundance and biomass from sound levels at FSAs.

Population genomics reveals high gene flow in grass rockfish (Sebastes rastrelliger).

Variation at the genomic level is important for understanding a species' demographic and phylogenetic history, in addition to identifying candidate regions that may be under selection and important to local adaptation. We used restriction-site associated DNA (RAD) sequencing to sample single nucleotide polymorphisms (SNPs) from the grass rockfish genome (Sebastes rastrelliger) to assess range-wide patterns of population structure and test for signatures of selection (i.e.

Malaria in the Era of Food Fortification With Folic Acid.

Food fortified with folic acid has been available for consumption in North America for over a decade. This strategy has led to an increase in folate levels in the general population and, more importantly, a significant decrease in the incidence of neural tube defects. However, this increase in folate intake has been associated with a greater risk of cancer disease.

Animal physiology. Whole-body endothermy in a mesopelagic fish, the opah, Lampris guttatus.

Endothermy (the metabolic production and retention of heat to warm body temperature above ambient) enhances physiological function, and whole-body endothermy generally sets mammals and birds apart from other animals. Here, we describe a whole-body form of endothermy in a fish, the opah (Lampris guttatus), that produces heat through the constant "flapping" of wing-like pectoral fins and minimizes heat loss through a series of counter-current heat exchangers within its gills. Unlike other fish, opah distribute warmed blood throughout the body, including to the heart, enhancing physiological performance and buffering internal organ function while foraging in the cold, nutrient-rich waters below the ocean thermocline.

Genetic diversity and population structure of the pelagic thresher shark (Alopias pelagicus) in the Pacific Ocean: evidence for two evolutionarily significant units.

There has been an increasing concern about shark overexploitation in the last decade, especially for open ocean shark species, where there is a paucity of data about their life histories and population dynamics. Little is known regarding the population structure of the pelagic thresher shark, Alopias pelagicus. Though an earlier study using mtDNA control region data, showed evidence for differences between eastern and western Pacific populations, the study was hampered by low sample size and sparse geographic coverage, particularly a lack of samples from the central Pacific.

DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus).

The cornerstone of fisheries management relies on a solid taxonomic base and an understanding of how animals can be grouped into coherent management units. Surprisingly, little is known about the basic biology and ecology of opah (Lampris guttatus), a globally distributed species that is commercially exploited and regionally common in the North Pacific. Recent efforts to collect life history data on this species uncovered evidence of two North Pacific morphotypes.

Folate metabolism in human malaria parasites--75 years on.

Malaria still poses one of the most serious threats to human health worldwide and the prevailing lack of effective, clinically licensed, vaccines means that prophylaxis and treatment depend heavily on a small number of compounds whose efficacies are progressively compromised at varying rates by the inevitable emergence of drug-resistant parasite populations. Of these antimalarials, those inhibiting steps in folate metabolism, along with chloroquine, are the oldest synthetic compounds, with origins dating back three-quarters of a century. Despite widespread parasite resistance, the antifolates still play an important role in malaria control, and our understanding of the underlying mechanisms of folate metabolism and genesis of drug resistance has increased considerably over the last twenty years.

Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci.

Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high gene-flow marine species off the west coast of North America that experienced strong population decline over the past 3 decades. We used 18 anonymous and 13 gene-associated simple sequence repeat (SSR) loci (expressed sequence tag [EST]-SSRs) to characterize range-wide population structure with temporal replicates.

A mass spectrometric strategy for absolute quantification of Plasmodium falciparum proteins of low abundance.

Selected reaction monitoring mass spectrometry has been combined with the use of an isotopically labelled synthetic protein, made up of proteotypic tryptic peptides selected from parasite proteins of interest. This allows, for the first time, absolute quantification of proteins from Plasmodium falciparum. This methodology is demonstrated to be of sufficient sensitivity to quantify, even within whole cell extracts, proteins of low abundance from the folate pathway as well as more abundant "housekeeping" proteins.