Genetic diversity of eukaryotic ultraphytoplankton in the Gulf of Naples during an annual cycle

Eukaryotic ultraphytoplankton (<5 μm) are an important component of phytoplankton populations, Dot blot hybridisation analysis using class level 16S rRNA gene probes as well as clone libraries were used to investigate the diversity of these ultraphytoplankton during a 15 mo period (2003 to 2004) in the Gulf of Naples. Hybridisation data showed the presence of 3 main classes, Cryptophyceae, Chrysophyceae and Prymnesiophyceae, along with lower signals from the Pelagophyceae. Clone libraries also contained these 4 classes as well as sequences from the Dictyochophyceae, Bacillariophyceae and Prasinophyceae. However, the Prymnesiophyceae gave the dominant hybridisation signal and constituted the majority of each clone library. Their diversity, with a total of 190 sequences belonging to 114 operational taxonomic units (OTUs), probably allows them to dominate the ultraphytoplankton throughout the whole year under differing environmental conditions. Over 100 of these OTUs were unique to different libraries, suggesting a succession of different taxa during the year. The Cryptophyceae were present most of the year with 1 OTU, corresponding to a Plagioselmis prolonga strain from the Gulf of Naples, being the dominant taxon (28 % of sequences). A striking result was the high hybridisation signal from the Chrysophyceae, which showed a preference for the summer months. The Pelagophyceae were present between December and March. Most (80 %) of the sequences found in the clone libraries were not identical to available 16S rRNA gene sequences, indicating a high amount of hidden diversity for these algal classes. However, sequences from Prasinophyceae Clade II (Mamiellales) were not detected in the clone libraries

Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

Background: Flagella have been lost in the vegetative phase of the diatom life cycle, but they are still present in male gametes of centric species, thereby representing a hallmark of sexual reproduction. This process, besides maintaining and creating new genetic diversity, in diatoms is also fundamental to restore the maximum cell size following its reduction during vegetative division. Nevertheless, sexual reproduction has been demonstrated in a limited number of diatom species, while our understanding of its different phases and of their genetic control is scarce. Results: In the transcriptome of Leptocylindrus danicus, a centric diatom widespread in the world's seas, we identified 22 transcripts related to the flagella development and confirmed synchronous overexpression of 6 flagellum-related genes during the male gamete formation process. These transcripts were mostly absent in the closely related species L. aporus, which does not have sexual reproduction. Among the 22 transcripts, L. danicus showed proteins that belong to the Intra Flagellar Transport (IFT) subcomplex B as well as IFT-A proteins, the latter previously thought to be absent in diatoms. The presence of flagellum-related proteins was also traced in the transcriptomes of several other centric species. Finally, phylogenetic reconstruction of the IFT172 and IFT88 proteins showed that their sequences are conserved across protist species and have evolved similarly to other phylogenetic marker genes. Conclusion: Our analysis describes for the first time the diatom flagellar gene set, which appears to be more complete and functional than previously reported based on the genome sequence of the model centric diatom, Thalassiosira pseudonana. This first recognition of the whole set of diatom flagellar genes and of their activation pattern paves the way to a wider recognition of the relevance of sexual reproduction in individual species and in the natural environment

The dual impact of Ostreopsis cf. ovata on Mytilus galloprovincialis and Paracentrotus lividus: Toxin accumulation and pathological aspects

Blooms of the toxic dinoflagellates Ostreopsis have become common along rocky shores of the Mediterranean Sea. In addition to health problems for beach-goers, Ostreopsis toxins may accumulate in benthic marine animals used for human consumption, which however at times have shown signals of stress and even mortality. In order to elucidate the actual relationships between Ostreopsis and benthic invertebrates, we exposed mussels Mytilus galloprovincialis and sea urchins Paracentrotus lividus from the Gulf of Naples to cultures and natural material of O. cf. ovata and assessed feeding and adverse effects on the animals, along with their acquired toxicity. Mussels exposed to O. cf. ovata for 24 hours filtered the microalgae at different rates, depending on both mussel size and microalgal density, and became weakly toxic in some cases. Under longer exposure most animals died and all survivors were toxic. Detoxification of a naturally toxic mussel populations from an area affected by O. cf. ovata blooms took more than two weeks. Sea urchins fed with the red alga Asparagopsis taxiformis epiphytised by O. cf. ovata did not show damages and became mildly toxic in some cases. However, the direct exposure of sea urchins to O. cf. ovata cultures caused the partial or total loss of the spines in a density-dependent way, with the death of the animals at the highest microalgal concentrations. Milder effects were registered with sonicated cultures or toxin extracts. Our results indicate that the balance between toxicity and animal health in these invertebrates depends on the mode and intensity of exposure to the toxic microalga, while the response varies between the two species but also within the same species. This scenario matches the variety of responses of benthic populations recorded in the natural environment in areas affected by O. cf. ovata blooms

Spring-time dynamics of diatom communities in landfast and underlying platelet ice in Terra Nova Bay, Ross Sea, Antarctica

We investigated the composition of diatom communities in annual fast ice and their variations over time during the 1999 austral spring in Terra Nova Bay (Ross Sea, Antarctica). Diatoms varied along the ice core in both cell abundance and species composition, with a minimum in the lower layer and a peak in the platelet ice. Planktonic species constituted in total about 98% of the diatom assemblage in the surface layers of the ice core down to the thickness of 220 cm. In the bottom ice and the underlying platelet-ice layer, the contribution of planktonic diatoms was lower (60% and 65%, respectively) at the beginning of the sampling period, and then decreased further to reach 30% in the bottom ice, where a remarkable biomass increase over time was caused by in situ growth and accumulation of benthic species. By contrast in the platelet-ice layer only small changes were recorded in the composition of the diatom assemblage, which was mainly constituted by the bloom of Fragilariopsis nana. The benthic species are generally not found in the water column, while species in the platelet-ice layer presumably constitute the seed for the initial plankton bloom during the ice-free periods in Terra Nova Bay

Intraspecific diversity in the cold stress response of transposable elements in the diatom leptocylindrus aporus

Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the possible involvement of TEs in their response to changing temperature conditions. At low temperature (13 \ub0C) several stress response proteins were overexpressed, confirming low temperature to be unfavorable for L. aporus, while TE-related transcripts of the LTR retrotransposon superfamily were the most enriched transcripts. Their expression levels, as well as most of the stress-related proteins, were found to vary significantly among strains, and even within the same strains analysed at different times. The lack of overexpression after many months of culturing suggests a possible role of physiological plasticity in response to growth under controlled laboratory conditions. While further investigation on the possible central role of TEs in the diatom stress response is warranted, the strain-specific responses and possible role of in-culture evolution draw attention to the interplay between the high intraspecific variability and the physiological plasticity of diatoms, which can both contribute to the adaptation of a species to a wide range of conditions in the marine environment

Paradoxical expression of INK4c in proliferative multiple myeloma tumors: bi-allelic deletion vs increased expression

BACKGROUND: A high proliferative capacity of tumor cells usually is associated with shortened patient survival. Disruption of the RB pathway, which is critically involved in regulating the G1 to S cell cycle transition, is a frequent target of oncogenic events that are thought to contribute to increased proliferation during tumor progression. Previously, we determined that p18INK4c, an essential gene for normal plasma cell differentiation, was bi-allelically deleted in five of sixteen multiple myeloma (MM) cell lines. The present study was undertaken to investigate a possible role of p18INK4c in increased proliferation of myeloma tumors as they progress. RESULTS: Thirteen of 40 (33%) human myeloma cell lines do not express normal p18INK4c, with bi-allelic deletion of p18 in twelve, and expression of a mutated p18 fragment in one. Bi-allelic deletion of p18, which appears to be a late progression event, has a prevalence of about 2% in 261 multiple myeloma (MM) tumors, but the prevalence is 6 to10% in the 50 tumors with a high expression-based proliferation index. Paradoxically, 24 of 40 (60%) MM cell lines, and 30 of 50 (60%) MM tumors with a high proliferation index express an increased level of p18 RNA compared to normal bone marrow plasma cells, whereas this occurs in only five of the 151 (3%) MM tumors with a low proliferation index. Tumor progression is often accompanied by increased p18 expression and an increased proliferation index. Retroviral-mediated expression of exogenous p18 results in marked growth inhibition in three MM cell lines that express little or no endogenous p18, but has no effect in another MM cell line that already expresses a high level of p18. CONCLUSION: Paradoxically, although loss of p18 appears to contribute to increased proliferation of nearly 10% of MM tumors, most MM cell lines and proliferative MM tumors have increased expression of p18. Apart from a small fraction of cell lines and tumors that have inactivated the RB1 protein, it is not yet clear how other MM cell lines and tumors have become insensitive to the anti-proliferative effects of increased p18 expression

Assessing the quality of biogeochemical coastal data: a step-wise procedure

Coastal areas host valuable but vulnerable marine ecosystems subjected to increasing anthropogenic pressure and climate change consequences. To assess the impact of these pressures, monitoring programs have proliferated in coastal areas, but most of them follow locally established procedures for quality control (QC). The well-established QC procedure of open ocean data cannot simply be extended to the highly variable coastal area, for which there is the need to develop ad hoc QC approaches. This is particularly crucial for long-term time series, where different instrumentation and analytical methods have been applied over time. This study, based on the biogeochemical dataset collected over 30 years at the LTER MareChiara station (LTER-MC, Gulf of Naples, Mediterranean Sea), addresses potential discrepancies in a long-term dataset, identifying criteria and methods that could also be applied to other coastal datasets. We developed a serial step-wise procedure to characterize the quality of ~ 84,000 data-points, merging statistical tests and expert knowledge. The procedure included nine tests, each addressing potential problems in data generation and management, some of which of general application and others tailored to specific subsets of data. Based on these test, quality flags were assigned to individual data. Critical tests applied to two other independent datasets, showed that the procedure is not dataset dependent. These results contribute to bridge the gap between the need of objective QC criteria and the intrinsic noise of coastal datasets, promoting the discussion on this topic, and improving a proper management and sharing of coastal data

Time series and beyond: multifaceted plankton research at a marine Mediterranean LTER site

Plankton are a pivotal component of the diversity and functioning of coastal marine ecosystems. A long time-series of observations is the best tool to trace their patterns and variability over multiple scales, ultimately providing a sound foundation for assessing, modelling and predicting the effects of anthropogenic and natural environmental changes on pelagic communities. At the same time, a long time-series constitutes a formidable asset for different kinds of research on specific questions that emerge from the observations, whereby the results of these complementary studies provide precious interpretative tools that augment the informative value of the data collected. In this paper, we review more than 140 studies that have been developed around a Mediterranean plankton time series gathered in the Gulf of Naples at the station LTER-MC since 1984. These studies have addressed different topics concerning marine plankton, which have included: i) seasonal patterns and trends; ii) taxonomic diversity, with a focus on key or harmful algal species and the discovery of many new taxa; iii) molecular diversity of selected species, groups of species or the whole planktonic community; iv) life cycles of several phyto- and zooplankton species; and v) interactions among species through trophic relationships, parasites and viruses. Overall, the products of this research demonstrate the great value of time series besides the record of fluctuations and trends, and highlight their primary role in the development of the scientific knowledge of plankton much beyond the local scale

Mediterranean Azadinium dexteroporum (Dinophyceae) produces six novel azaspiracids and azaspiracid-35: a structural study by a multi-platform mass spectrometry approach

Azadinium dexteroporum is the first species of the genus described from the Mediterranean Sea and it produces different azaspiracids (AZA). The aims of this work were to characterize the toxin profile of the species and gain structural information on azaspiracids produced by the A. dexteroporum strain SZN-B848 isolated from the Gulf of Naples. Liquid chromatography-mass spectrometry (LC-MS) analyses were carried out on three MS systems having different ion source geometries (ESI, TurboIonSpray®, ESI ION MAX) and different MS analyzers operating either at unit resolution or at high resolution, namely a hybrid triple quadrupole-linear ion trap (Q-Trap MS), a time of flight (TOF MS), and a hybrid linear ion trap Orbitrap XL Fourier transform mass spectrometer (LTQ Orbitrap XL FTMS). As a combined result of these different analyses, A. dexteroporum showed to produce AZA-35, previously reported from Azadinium spinosum, and six compounds that represent new additions to the AZA-group of toxins, including AZA-54 to AZA-58 and 3-epiAZA-7, a stereoisomer of the shellfish metabolite AZA-7. Based on the interpretation of fragmentation patterns, we propose that all these molecules, except AZA-55, have the same A to I ring system as AZA-1, with structural modifications all located in the carboxylic side chain. Considering that none of the azaspiracids produced by the Mediterranean strain of A. dexteroporum is currently regulated by European food safety authorities, monitoring programs of marine biotoxins in the Mediterranean area should take into account the occurrence of the new analogues to avoid an underestimation of the AZA-related risk for seafood consumers

Relationship between West African ancestry with lung cancer risk and survival in African Americans

Purpose: African Americans, especially men, have a higher incidence of lung cancer compared with all other racial and ethnic groups in the US. Self-reported race is frequently used in genomic research studies to capture an individual's race or ethnicity. However, it is clear from studies of genetic admixture that human genetic variation does not segregate into the same biologically discrete categories as socially defined categories of race. Previous studies have suggested that the degree of West African ancestry among African Americans can contribute to cancer risk in this population, though few studies have addressed this question in lung cancer. Methods: Using a genetic ancestry panel of 100 SNPs, we estimated West African, European, and Native American ancestry in 1,407 self-described African Americans and 2,413 European Americans. Results: We found that increasing West African ancestry was associated with increased risk of lung cancer among African American men (ORQ5 vs Q1 = 2.55 (1.45-4.48), p = 0.001), while no association was observed in African American women (ORQ5 vs Q1 = 0.90 (0.51-1.59), p = 0.56). This relationship diminished following adjustment for income and education. Conclusions: Genetic ancestry is not a major contributor to lung cancer risk or survival disparities