Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

A comparison between Zooglider and shipboard net and acoustic mesozooplankton sensing systems

Some planktonic patches have markedly higher concentrations of organisms compared to ambient conditions and are <5 m in thickness (i.e. thin layers). Conventional net sampling techniques are unable to resolve this vertical microstructure, while optical imaging systems can measure it for limited durations. Zooglider, an autonomous zooplankton-sensing glider, uses a low-power optical imaging system (Zoocam) to resolve mesozooplankton at a vertical scale of 5 cm while making concurrent physical and acoustic measurements (Zonar). In March 2017, Zooglider was compared with traditional nets (MOCNESS) and ship-based acoustics (Simrad EK80). Zoocam recorded significantly higher vertically integrated abundances of smaller copepods and appendicularians, and larger gelatinous predators and mineralized protists, but similar abundances of chaetognaths, euphausiids, and nauplii. Differences in concentrations and size-frequency distributions are attributable to net extrusion and preservation artifacts, suggesting advantages of in situ imaging of organisms by Zooglider. Zoocam detected much higher local concentrations of copepods and appendicularians (53 000 and 29 000 animals m-3, respectively) than were resolvable by nets. The EK80 and Zonar at 200 kHz agreed in relative magnitude and distribution of acoustic backscatter. The profiling capability of Zooglider allows for deeper high-frequency acoustic sampling than conventional ship-based acoustics

Juvenile Albacore tuna (Thunnus alalunga) foraging ecology varies with environmental conditions in the California Current Large Marine Ecosystem

Juvenile North Pacific Albacore tuna (Thunnus alalunga) support commercial and recreational fisheries in the California Current Large Marine Ecosystem (CCLME), where they forage during summer and fall. The distributions of the commercial and recreational fisheries and estimates of forage availability have varied substantially over the past century. Time-series quantifying Albacore diet can help link forage composition to variability in Albacore abundance and distribution and, consequently, their availability to fishers. Previous diet studies in the CCLME are of relatively short duration, and long-term variability in Albacore diet remains poorly understood. We describe the diets of juvenile Albacore from three regions in the CCLME from 2007 to 2019 and use classification and regression tree analysis to explore environmental drivers of variability. Important prey include Northern Anchovy (Engraulis mordax), rockfishes (Sebastes spp.), Boreal Clubhook Squid (Onychoteuthis borealijaponica), euphausiids (Order: Euphausiidae), and amphipods (Order: Amphipoda), each contributing >5% mean proportional abundance. Most prey items were short lived species or young-of-the-year smaller than 10 cm. Diet variability was related to environmental conditions over the first 6 months of the year (PDO, sea surface temperature, and NPGO) and conditions concurrent with Albacore capture (region and surface nitrate flux). We describe foraging flexibility over regional and annual scales associated with these environmental influences. Continuous, long-term studies offer the opportunity to identify flexibility in Albacore foraging behavior and begin to make a predictive link between environmental conditions early in the year and Albacore foraging during summer and fall

Trait-based indicators of resource selection by albacore tuna in the California Current Large Marine Ecosystem

As global climate change reorganizes marine ecosystems, understanding how predators will respond to variable prey resources is critical to forecasting future community dynamics. Prey traits that affect the foraging process and recur across unrelated taxa offer a means to better anticipate predator resource use by simplifying complex foraging dynamics. Here we compare taxonomic and trait-based indicators of resource use and selection for albacore tuna (Thunnus alalunga), a commercially valuable pelagic predator undergoing climate-driven range shifts. We synthesized datasets from 2005 to 2019 to evaluate diets of albacore tuna in relation to prey availability estimates from shipboard surveys in the California Current Large Marine Ecosystem. Analyses with these data reveal that albacore and trawl surveys sample different aspects of the pelagic system, with albacore consuming a subset of taxa identified within trawls. Albacore consistently selected coastal prey that are schooling, undefended, silvered and countershaded, and have high energy density — suggesting that ecological mechanisms driving albacore foraging outcomes may be conserved across time and space. Ecological traits mediating predator-prey interactions consistently distinguished albacore diets from assemblages sampled by trawls across years and regions. We demonstrate that a traits-based approach simplifies taxonomically diverse predator-prey interactions and may be a valuable tool to facilitate predictions of prey resource use in changing environments

Trait-based indicators of resource selection by albacore tuna in the California Current Large Marine Ecosystem

As global climate change reorganizes marine ecosystems, understanding how predators will respond to variable prey resources is critical to forecasting future community dynamics. Prey traits that affect the foraging process and recur across unrelated taxa offer a means to better anticipate predator resource use by simplifying complex foraging dynamics. Here we compare taxonomic and trait-based indicators of resource use and selection for albacore tuna (Thunnus alalunga), a commercially valuable pelagic predator undergoing climate-driven range shifts. We synthesized datasets from 2005 to 2019 to evaluate diets of albacore tuna in relation to prey availability estimates from shipboard surveys in the California Current Large Marine Ecosystem. Analyses with these data reveal that albacore and trawl surveys sample different aspects of the pelagic system, with albacore consuming a subset of taxa identified within trawls. Albacore consistently selected coastal prey that are schooling, undefended, silvered and countershaded, and have high energy density — suggesting that ecological mechanisms driving albacore foraging outcomes may be conserved across time and space. Ecological traits mediating predator-prey interactions consistently distinguished albacore diets from assemblages sampled by trawls across years and regions. We demonstrate that a traits-based approach simplifies taxonomically diverse predator-prey interactions and may be a valuable tool to facilitate predictions of prey resource use in changing environments

Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer

Contains fulltext : 118378.pdf (publisher's version ) (Open Access)HNF1B is overexpressed in clear cell epithelial ovarian cancer, and we observed epigenetic silencing in serous epithelial ovarian cancer, leading us to hypothesize that variation in this gene differentially associates with epithelial ovarian cancer risk according to histological subtype. Here we comprehensively map variation in HNF1B with respect to epithelial ovarian cancer risk and analyse DNA methylation and expression profiles across histological subtypes. Different single-nucleotide polymorphisms associate with invasive serous (rs7405776 odds ratio (OR)=1.13, P=3.1 x 10(-10)) and clear cell (rs11651755 OR=0.77, P=1.6 x 10(-8)) epithelial ovarian cancer. Risk alleles for the serous subtype associate with higher HNF1B-promoter methylation in these tumours. Unmethylated, expressed HNF1B, primarily present in clear cell tumours, coincides with a CpG island methylator phenotype affecting numerous other promoters throughout the genome. Different variants in HNF1B associate with risk of serous and clear cell epithelial ovarian cancer; DNA methylation and expression patterns are also notably distinct between these subtypes. These findings underscore distinct mechanisms driving different epithelial ovarian cancer histological subtypes

Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31

Contains fulltext : 118576.pdf (publisher's version ) (Open Access)Epithelial ovarian cancer (EOC) has a heritable component that remains to be fully characterized. Most identified common susceptibility variants lie in non-protein-coding sequences. We hypothesized that variants in the 3' untranslated region at putative microRNA (miRNA)-binding sites represent functional targets that influence EOC susceptibility. Here, we evaluate the association between 767 miRNA-related single-nucleotide polymorphisms (miRSNPs) and EOC risk in 18,174 EOC cases and 26,134 controls from 43 studies genotyped through the Collaborative Oncological Gene-environment Study. We identify several miRSNPs associated with invasive serous EOC risk (odds ratio=1.12, P=10(-8)) mapping to an inversion polymorphism at 17q21.31. Additional genotyping of non-miRSNPs at 17q21.31 reveals stronger signals outside the inversion (P=10(-10)). Variation at 17q21.31 is associated with neurological diseases, and our collaboration is the first to report an association with EOC susceptibility. An integrated molecular analysis in this region provides evidence for ARHGAP27 and PLEKHM1 as candidate EOC susceptibility genes