Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species

Genetic taxonomic assignment can be more sensitive than morphological taxonomic assignment, particularly for small, cryptic or rare species. Sequence processing is essential to taxonomic assignment, but can also produce errors because optimal parameters are not known a priori. Here, we explored how sequence processing parameters influence taxonomic assignment of 18S sequences from bulk zooplankton samples produced by 454 pyrosequencing. We optimized a sequence processing pipeline for two common research goals, estimation of species richness and early detection of aquatic invasive species (AIS), and then tested most optimal models’ performances through simulations. We tested 1,050 parameter sets on 18S sequences from 20 AIS to determine optimal parameters for each research goal. We tested optimized pipelines’ performances (detectability and sensitivity) by computationally inoculating sequences of 20 AIS into ten bulk zooplankton samples from ports across Canada. We found that optimal parameter selection generally depends on the research goal. However, regardless of research goal, we found that metazoan 18S sequences produced by 454 pyrosequencing should be trimmed to 375–400 bp and sequence quality filtering should be relaxed (1.5 ≤ maximum expected error ≤ 3.0, Phred score = 10). Clustering and denoising were only viable for estimating species richness, because these processing steps made some species undetectable at low sequence abundances which would not be useful for early detection of AIS. With parameter sets optimized for early detection of AIS, 90% of AIS were detected with fewer than 11 target sequences, regardless of whether clustering or denoising was used. Despite developments in next-generation sequencing, sequence processing remains an important issue owing to difficulties in balancing false-positive and false-negative errors in metabarcoding data

Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns

Epigenetic processes, including DNA methylation (DNAm), are among the mechanisms allowing integration of genetic and environmental factors to shape cellular function. While many studies have investigated either environmental or genetic contributions to DNAm, few have assessed their integrated effects. Here we examine the relative contributions of prenatal environmental factors and genotype on DNA methylation in neonatal blood at variably methylated regions (VMRs) in 4 independent cohorts (overall n = 2365). We use Akaike’s information criterion to test which factors best explain variability of methylation in the cohort-specific VMRs: several prenatal environmental factors (E), genotypes in cis (G), or their additive (G + E) or interaction (GxE) effects. Genetic and environmental factors in combination best explain DNAm at the majority of VMRs. The CpGs best explained by either G, G + E or GxE are functionally distinct. The enrichment of genetic variants from GxE models in GWAS for complex disorders supports their importance for disease risk

Nitrogen kinetics of algal populations in two gulfs adjoining the Attica peninsula, one receiving effluents

4 pagesPeer reviewe

Variaciones en la actividad de reductasa de nitrato en el fitoplancton

11 pages, 4 figures, 2 tables[EN] The study of biochemical processes in the ocean can be facilitated by analysis of the enzyme systems that control them. Such analysis may provide explanations for oceanographic phenomena by facilitating the location of the sites and the determination of the rates of nitrate reduction, sulfate reduction, ammonia oxidation, photosynthesis, and respiration. [...] Skeletonema costatum, Amphora sp., Platymoras sp., Corethron histrix, Rhizosolenia fragilissima [...][ES] Uno de los procesos más importantes en el mar es la asimilación del nitrato por el fitoplancton. El análisis de la actividad de las enzimas que reducen el nitrato en fitoplancton puede permitir conocer su capacidad para asimilar nitrato y la velocidad de esta asimilación. [...

Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports

Aim: The urgent need for large-scale spatio-temporal assessments of biodiversity in the face of rapid environmental change prompts technological advancements in species identification and biomonitoring such as metabarcoding. The high-throughput DNA sequencing of bulk samples offers many advantages over traditional morphological identification for describing community composition. Our objective was to evaluate the applicability of metabarcoding to identify species in taxonomically complex samples, evaluate biodiversity trends across broad geographical and temporal scales and facilitate cross-study comparisons. Location: Marine and freshwater ports along Canadian coastlines (Pacific, Arctic and Atlantic) and the Great Lakes. Methods: We used metabarcoding of bulk zooplankton samples to identify species and profile biodiversity across habitats and seasons in busy commercial ports. A taxonomic assignment approach circumventing sequence clustering was implemented to provide increased resolution and accuracy compared to pre-clustering. Results: Taxonomic classification of over seven million sequences identified organisms spanning around 400 metazoan families and complements previous surveys based on morphological identification. Metabarcoding revealed over 30 orders that were previously not reported, while certain taxonomic groups were underrepresented because of depauperate reference databases. Despite the limitations of assigning metabarcoding data to the species level, zooplankton communities were distinct among coastlines and significantly divergent among marine, freshwater and estuarine habitats even at the family level. Furthermore, biodiversity varied substantially across two seasons reaching a beta diversity of 0.9 in a sub-Arctic port exposed to high vessel traffic. Main Conclusions: Metabarcoding offers a powerful and sensitive approach to conduct large-scale biodiversity surveys and allows comparability across studies when rooted in taxonomy. We highlight ways of overcoming current limitations of metabarcoding for identifying species and assessing biodiversity, which has important implications for detecting organisms at low abundance such as endangered species and early invaders. Our study conveys pertinent and timely considerations for future large-scale monitoring surveys in relationship to environmental change. © 2016 John Wiley & Sons Ltd

Primary production cycle in an upwelling center

The cycle of nitrogen and carbon productivity of phytoplankton in an upwelling center at 15°S on the coast of Peru was studied during the JOINT-II expedition of the Coastal Upwelling Ecosystems Analysis program. The productivity cycle was characterized by repeated stations at various locations in the upwelling plume, a time series of stations in mid plume, and stations located along drogue tracks. Four zones of physiological condition were distinguished along the axis of the upwelling plume. In Zone I phytoplankton upwelled with nutrient-rich water were initially ‘shifted-down’; in Zone II they underwent light induced ‘shift-up’ to increased nutrient uptake, photosynthesis, and synthesis of macromolecules. In Zone III ambient nutrient concentrations were rapidly reduced, there was a rapid accumulation of phytoplankton biomass in the water column, and rate processes proceeded at maximal rates. In Zone IV ambient nutrient concentrations were significantly decreased, phytoplankton biomass remained high, and limitation of phytoplankton processes was beginning to be observed. Phytoplankton responded to the altered environment by undergoing ‘shift-down’ to lower rates of nutrient uptake, photosynthesis, and macromolecule synthesis. The time and space domain where this entire sequence occurs was relatively small; the cycle from initial upwelling to ‘shift-down’ was completed in 8 to 10 days within 30 to 60 km off the coastThis is a contribution of the Coastal Upwelling Ecosystem Analysis (CUEA) program of the International Decade of Ocean Exploration Office of the U.S. National Science Foundation. We thank our CUEA colleagues for contributing ideas and data and we thank Cocos Foundation for support for the synthesis of these ideas and data. We especially thank Burton H. Jones and Frances P. Wilkerson of the University of Southern California and Jane E. Kogelschatz of Duke University for their efforts in preparation of the manuscriptPeer reviewe

Quarterly list of Welsh health circulars - April to June 2002

SIGLEAvailable from British Library Document Supply Centre-DSC:9294.517((2002)81) / BLDSC - British Library Document Supply CentreGBUnited Kingdo