Metabarcoding of marine zooplankton: prospects, progress and pitfalls

Metabarcoding (large-scale taxonomic identification of complex samples via analysis of one or few orthologous DNA regions, called barcodes) is revolutionizing analysis of biodiversity of marine zooplankton assemblages. Metabarcoding relies on high-throughput DNA sequencing (HTS) technologies, which yield millions of DNA sequences in parallel and allow large-scale analysis of environmental samples. Metabarcoding studies of marine zooplankton have used various regions of nuclear small- (18S) and large-subunit (28S) rRNA, which allow accurate classification of novel sequences and reliable amplification with consensus primers, but- due to their relatively conserved nature- may underestimate species diversity in a community. To discriminate species, more variable genes are needed. A limited number of metabarcoding studies have used mitochondrial cytochrome oxidase I (COI), which ensures detection of species-level diversity, but may require group-specific primers and thus result in inconsistent amplification success rates. Reference databases with sequences for accurately-identified species are critically needed to allow taxonomic designation of molecular operational taxonomic units (MOTU) and comparison with previous studies of zooplankton diversity. Potential and promising applications of metabarcoding include rapid detection of impacts of climate change, monitoring and assessment of ecosystem health, calculation of biotic indices, characterization of food webs and detection of introduced, non-indigenous species

Experimental validation of a rans-vof numerical model of the wave generation and propagation in a 2d wave flume

This paper focus on the study of free surface variation in a Numerical Wave Flume (NWF) due to a paddle movement. The NWF is the numerical representation of a 12.5 meters long Experimental Wave Flume (EWF) of the laboratory of the University of the Basque Country. The experiments and the numerical simulations are performed in several depths (0.3, 0.4 and 0.5 meters). Besides different velocities for the paddle movement are induced between 0.064 and 0.1 m/s. The numerical simulations are based on an Eulerian Multiphase of two fluids, air and water, more concretely the Volume of Fluid model. The surface variation in two points (6.0 and 6.3 meters from the wave flume start) is studied in both numerical and experimental wave flumes and compared its variation through the experiment time. Besides, the experiments will be analyzed in the wave maker theory. The results show the models quality in the first moments of the experiments, where the reflection does not appear, in which the results from both experimental and numerical simulations are pretty similar

Connectivity, neutral theories and the assessment of species vulnerability to global change in temperate estuaries

One of the main adaptation strategies to global change scenarios, aiming to preserve ecosystem functioning and biodiversity, is to maximise ecosystem resilience. The resilience of a species metapopulation can be improved by facilitating connectivity between local populations, which will prevent demographic stochasticity and inbreeding. The objective of this investigation is to estimate the degree of connectivity among estuarine species along the north-eastern Iberian coast, in order to assess community vulnerability to global change scenarios. To address this objective, two connectivity proxy types have been used based upon genetic and ecological drift processes: 1) DNA markers for the bivalve cockle (Cerastoderma edule) and seagrass Zostera noltei, and 2) the decrease in the number of species shared between two sites with geographic distance; neutral biodiversity theory predicts that dispersal limitation modulates this decrease, and this has been explored in estuarine plants and macroinvertebrates. Results indicate dispersal limitation for both saltmarsh plants and seagrass beds community and Z. noltei populations; this suggests they are especially vulnerable to expected climate changes on their habitats. In contrast, unstructured spatial pattern found in macroinvertebrate communities and in C. edule genetic populations in the area suggests that estuarine soft-bottom macroinvertebrates with planktonic larval dispersal strategies may have a high resilience capacity to moderate changes within their habitats. Our findings can help environmental managers to prioritise the most vulnerable species and habitats to be restored

Primary systemic therapy in HER2-positive operable breast cancer using trastuzumab and chemotherapy: efficacy data, cardiotoxicity and long-term follow-up in 142 patients diagnosed from 2005 to 2016 at a single institution

Objective: The aim of this study was to evaluate the efficacy, cardiotoxicity profile and long-term benefits of neoadjuvant therapy in human epidermal growth factor receptor 2-positive operable breast cancer patients. Patients and methods: A total of 142 patients diagnosed from 2005 to 2016 were included in the study. The treatment consisted of a sequential regimen of taxanes and anthracyclines plus trastuzumab. The clinical and pathological responses were evaluated and correlated with clinical and biological factors. The cardiotoxicity profile and long-term benefits were analyzed. Results: The median age was 49 years, and 4%, 69% and 27% of patients had stage I, II and III breast cancer, respectively, while 10% had inflammatory breast cancer at diagnosis. Hormone receptor (HR) status was negative in 43%, and 62% had grade III breast cancer. The clinical complete response rate was 49% and 63% as assessed using ultrasound and magnetic resonance imaging, respectively, and this allowed a high rate of conservative surgery (66%). The pathological complete response (pCR) rate was 52%, and it was higher in HR-negative (64%) patients than in HR-positive (41%) patients and in grade III breast cancer (53%) patients than in grade I-II breast cancer (45%) patients. Patients who achieved pCR had longer disease-free survival and a trend toward improved overall survival. A total of 2% of patients showed a 10% decrease in left ventricular ejection fraction to <50% during treatment. All patients except one recovered after discontinuation of trastuzumab. Conclusion: A sequential regimen of taxanes and anthracyclines plus trastuzumab was effective, with high pCR rates and long-term benefit, and had a very good cardiotoxicity profile

DNA methylation epigenotypes in breast cancer molecular subtypes

12 páginas, 3 figuras, 3 tablas.-- et al.[Introduction]: Identification of gene expression-based breast cancer subtypes is considered a critical means of prognostication. Genetic mutations along with epigenetic alterations contribute to gene-expression changes occurring in breast cancer. So far, these epigenetic contributions to sporadic breast cancer subtypes have not been well characterized, and only a limited understanding exists of the epigenetic mechanisms affected in those particular breast cancer subtypes. The present study was undertaken to dissect the breast cancer methylome and to deliver specific epigenotypes associated with particular breast cancer subtypes. [Methods]: By using a microarray approach, we analyzed DNA methylation in regulatory regions of 806 cancer-related genes in 28 breast cancer paired samples. We subsequently performed substantial technical and biologic validation by pyrosequencing, investigating the top qualifying 19 CpG regions in independent cohorts encompassing 47 basal-like, 44 ERBB2+ overexpressing, 48 luminal A, and 48 luminal B paired breast cancer/adjacent tissues. With the all-subset selection method, we identified the most subtype-predictive methylation profiles in multivariable logistic regression analysis. [Results]: The approach efficiently recognized 15 individual CpG loci differentially methylated in breast cancer tumor subtypes. We further identified novel subtype-specific epigenotypes that clearly demonstrate the differences in the methylation profiles of basal-like and human epidermal growth factor 2 (HER2)-overexpressing tumors. [Conclusions]: Our results provide evidence that well-defined DNA methylation profiles enable breast cancer subtype prediction and support the utilization of this biomarker for prognostication and therapeutic stratification of patients with breast cancer.This work was supported by grants from project CGL2008-01131 (Departamento de Sanidad del Gobierno Vasco), S-PE08UN45 and PE09BF02 (Departamento de Ciencia y Tecnologia del Gobierno Vasco), BIO2008-04212, and RD06/0020/1019 (Red Tematica de Investigacion Cooperativa en Cancer, RTICC) from the MICINN. The CIBER de Enfermedades Raras is an initiative of the ISCIII. NGB had a doctoral fellowship from the Basque Government (Departamento de Educacion, Universidades e Investigacion).Peer reviewe

Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts

Molecular detection of plaice remains in the stomachs of potential predators on a flatfish nursery ground

Stomach contents of potential predators from a flatfish nursery ground on the Scot- tish west coast were examined visually and probed using a TaqMan real-time PCR based assay designed to detect plaice Pleuronectes platessa DNA. Stomachs from 1137 brown shrimp Crangon crangon, along with a lesser number of shore crab Carcinus maenas, grey gurnard Eutrigla gurnardus and Gobiidae were analysed. Overall 45% of shrimp tested positive for plaice DNA, a proportion considerably higher than in stomachs containing visually identifiable flatfish remains. When scaled to the population level, predation by shrimp generated an estimated mortality of ~9% d–1 , which compares with a decline in plaice abundance from mid-May to mid-June of ~4.4% d−1 . The discrepancy between mortality estimates based on molecular and catch-curve analysis might be due to sampling being conducted at low water between dusk and dawn, which would concentrate predators and prey at times coincident with peaks of shrimp feeding. In addition, the sensitivity of the TaqMan assay could have led to some over-estimation because non-fatal interac- tions may also have been detected, e.g. shrimp are known to nibble the fins of flatfish, that might result in a positive TaqMan result but not necessarily in mortality for the fish. The percentage of shrimp testing positive for presence of plaice DNA in their stomachs was also related to plaice density in a positive, linear manner. For less abundant predators, stomachs of 6% of shore crabs, 40% of gurnards and 11% of large gobies also tested positive.A.A. was supported by a Postdoctoral fellowship from the Education, Universities and Research Department of the Basque Country Government. C.J.F. was supported by NERC Oceans 2025 Program, Theme 4, Work package 4.4 Predators and prey. Probe development and testing was financially supported by Defra (UK Department for Environment, Food and Rural Affairs) under research project MF0432 (Detecting predation on fish eggs and larvae) and by a Small Research Grant award of the Fisheries Society of the British Isles awarded to M.I.T

Spring zooplankton distribution in the Bay of Biscay from 1998 to 2006 in relation with anchovy recruitment

The objective of this study was to investigate whether successive recruitment failures in the anchovy fishery in the Bay of Biscay were due to changes in the zooplankton biomass or composition. Image analysis and automatic recognition were used to analyse zooplankton samples collected during diel egg production method spring surveys from 1998 to 2006. We were not able to detect any trend in zooplankton biomass during this period. The zooplankton spatial distribution showed permanent features with large organisms being more abundant over the shelf break and outer areas. Finally, we found a negative correlation between anchovy recruitment and zooplankton biomass which suggests that the 2002-2006 failures in anchovy recruitment in the Bay of Biscay are not due to a decrease in mesozooplankton biomass

Survey of the chemical defence potential of diatoms: Screening of fifty one species for alphabetagammadelta-unsaturated aldehydes

In recent years a negative influence of diatom-derived α,β,γ,δ-unsaturated aldehydes (PUA) on the reproductive success of copepods and invertebrates has been suggested. Since adverse chemical properties of diatoms would question the traditional view of the marine food web, this defense mechanism has been investigated in detail, but the PUA-release by test organisms has only been determined in a few cases. The observed effects were nevertheless frequently discussed from a general point of view often leading to contradictory conclusions. We have examined the PUA-production of 50 diatom species (71 isolates) in order to provide a basis for the interpretation of laboratory and field results on the influence of diatom food on the reproductive success of their consumers. PUA-production is species and strain dependent. Thirty-six percent of the investigated species (38% of the cultivated isolates) release α,β,γ,δ-unsaturated aldehydes upon cell disruption in concentrations from 0.01 to 9.8 fmol per cell. Thalassiosira rotula and Thalassiosira pacifica, major spring-bloom forming diatoms isolated from Roscoff (Bretagne, English Channel, France) and Puget Sound (Washington, USA) were among the PUA-producing strains

Survey of the chemical defence potential of diatoms: screening of fifty one species for alpha,beta,gamma,delta-unsaturated aldehydes

Max Planck Institute for Chemical Ecology, Hans-Knoill-Str. 8, D-07745 Jena, Germany. In recent years a negative influence of diatom-derived alpha,beta,gamma,delta-unsaturated aldehydes (PUA) on the reproductive success of copepods and invertebrates has been suggested. Since adverse chemical properties of diatoms would question the traditional view of the marine food web, this defense mechanism has been investigated in detail, but the PUA-release by test organisms has only been determined in a few cases. The observed effects were nevertheless frequently discussed from a general point of view often leading to contradictory conclusions. We have examined the PUA-production of 51 diatom species (71 isolates) in order to provide a basis for the interpretation of laboratory and field results on the influence of diatom food on the reproductive success of their consumers. PUA-production is species and strain dependent. Thirty-six percent of the investigated species (38% of the cultivated isolates) release alpha,beta,gamma,delta-unsaturated aldehydes upon cell disruption in concentrations from 0.01 to 9.8 fmol per cell. Thalassiosira rotula and Thalassiosira pacifica, major spring-bloom forming diatoms isolated from Roscoff (Bretagne, English Channel, France) and Puget Sound (Washington, USA) were among the PUA-producing strains