Intra-genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria,Radiolaria) assessed by Sanger,MinION and Illumina sequencing

Ribosomal RNA (rRNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large-scale exploration of environmental microbial diversity through metabarcoding approaches has been focused mainly on the V4 and V9 regions of the 18S rRNA gene. The accurate interpretation of such environmental surveys is hampered by technical (e.g. PCR and sequencing errors) and biological biases (e.g. intra-genomic variability). Here we explored the intra-genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with Illumina and Oxford Nanopore Technologies (MinION). Our analysis determined that intra-genomic variability of Nassellaria and Spumellaria is generally low, yet some Spumellaria specimens showed two different copies of the V4 with <97% similarity. Of the different sequencing methods, Illumina showed the highest number of contaminations (i.e. environmental DNA, cross-contamination, tag-jumping), revealed by its high sequencing depth; and MinION showed the highest sequencing rate error (~14%). Yet the long reads produced by MinION (~2900 bp) allowed accurate phylogenetic reconstruction studies. These results highlight the requirement for a careful interpretation of Illumina-based metabarcoding studies, in particular regarding low abundant amplicons, and open future perspectives towards full-length rDNA environmental metabarcoding surveys.     

Characterization of the anti-tissue transglutaminase antibody response in nonobese diabetic mice

Type 1 diabetes mellitus is an autoimmune disorder characterized by destruction of insulin-producing pancreatic beta cells by T lymphocytes. In nonobese diabetic (NOD) mice, a role has been hypothesized for dietary gluten proteins in the onset of diabetes, and because gluten dependence is the major feature of celiac disease, together with production of Abs to the autoantigen tissue transglutaminase (tTG), we looked for the presence of anti-tTG Abs in the serum of NOD mice and, to establish their origin, analyzed the Ab repertoire of NOD mice using phage display Ab libraries. We found significant levels of serum anti-tTG Abs and were able to isolate single-chain Ab fragments to mouse tTG mainly from the Ab libraries made from intestinal lymphocytes and to a lesser extent from splenocytes. Data from NOD mice on a gluten-free diet suggest that the anti-tTG response is not gluten-dependent. The intestinal Ab response to tTG is a feature of NOD mice, but the underlying mechanisms remain obscure.     

Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes

Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are important contributors to global primary production occupying a key position at the base of marine food webs. The genetically diverse nature of each genus is likely an important reason for their successful colonization of vast tracts of the world's oceans, a feature that has led to detailed analysis of the distribution of these genetic lineages at the local and ocean basin scale. Here, we extend these analyses to the global dimension, using new data from cruises in the Pacific, Indian and Arctic Oceans in combination with data from previous studies in the Atlantic Ocean, Arabian Sea, Red Sea and a circumnavigation of the southern hemisphere to form a data set which comprises most of the world's major ocean systems. We show that the distribution patterns of Prochlorococcus and Synechococcus lineages are remarkably similar in different ocean systems with comparable environmental conditions, but producing a strikingly different 'signature' in the four major ocean domains or biomes (the Polar Domain, Coastal Boundary Domain, Trade Winds Domain and Westerly Winds Domain). This clearly reiterates the idea of spatial partitioning of individual cyanobacterial lineages, but at the global scale.     

Mucosal tissue transglutaminase expression in celiac disease

Tissue transglutaminase (tTG) plays an important role in celiac disease pathogenesis and antibodies to tTG are a diagnostic marker of gluten-sensitive enteropathy. The aim of this study was to investigate the localization of tTG in the duodenal mucosa in control tissues and in different histological stages of celiac disease by using a commercial and a novel set of anti-tTG monoclonal antibodies, to see whether this assessment can be useful for diagnostic purpose. The distribution of tTG was firstly evaluated in 18 untreated celiac patients by using a commercial monoclonal antibody (CUB7402) against tissue transglutaminase enzyme and directed against the loop-core region of the enzyme. Thereafter, in further 30 untreated celiac patients we employed three newly characterized anti-tTG monoclonal antibodies produced against recombinant human-tTG. The epitopes recognized are located in three distinct domains of the protein corresponding to the core, C1 and C2 protein structure. Eleven age- and sex-matched patients with chronic duodenitis acted as controls. All subjects underwent upper endoscopy to obtain biopsy samples from the duodenum. Overall, we found that ( i ) tTG is equally expressed in CD at different stages of disease; ( ii ) tTG is expressed, at similar level, in CD and controls with duodenitis. Assessment of tTG level in biopsy samples by immunohistochemical methods is not useful in the clinical diagnostic work-up of CD.     

Freshwater protists: unveiling the unexplored in a large floodplain system

Protists play a fundamental role in all ecosystems, but we are still far from estimating the total diversity of many lineages, in particular in highly diverse environments, such as freshwater. Here, we survey the protist diversity of the Paraná River using metabarcoding, and we applied an approach that includes sequence similarity and phylogeny to evaluate the degree of genetic novelty of the protists' communities against the sequences described in the reference database PR². We observed that ~28% of the amplicon sequence variants were classified as novel according to their similarity with sequences from the reference database; most of them were related to heterotrophic groups traditionally overlooked in freshwater systems. This lack of knowledge extended to those groups within the green algae (Archaeplastida) that are well documented such as Mamiellophyceae, and also to the less studied Pedinophyceae, for which we found sequences representing novel deep-branching clusters. Among the groups with potential novel protists, Bicosoecida (Stramenopiles) were the best represented, followed by Codosiga (Opisthokonta), and the Perkinsea (Alveolata). This illustrates the lack of knowledge on freshwater planktonic protists and also the need for isolation and/or cultivation of new organisms to better understand their role in ecosystem functioning.     

Spatial distribution of the Tintinnina (Ciliophora, Protista) in the North Sea, spring of 1986

Tintinnids were identified in 256 samples from 60 stations inthe North Sea investigated by a German multidisciplinary [Zirkulationund Schadstoffumsatz in der Nordsee (ZISCH)] program, duringlate spring of 1986. Tbe distribution of the most frequentlyoccurring species. Parafavella elegans, P.denticulatn, Acanthostomellanorvegica, Helicostomella subulata, Prychocylis unurla, Stenosemellanivalis, Tintinnopsis beroidea and T.parvula, was described.Some species showed a similar horizontal distribution. However,a vertical division was evidenced after analyzing species abundancesagainst temperature, salinity, depth and     

Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probes

Very few studies have analysed the niches of pelagic protist in details. This is because for most protists, both an accurate species definition and methods for routine detection and quantification of cells are lacking. The morphospecies Micromonas pusilla , a marine unicellular green alga, is the most ubiquitous and cosmopolitan picoeukaryote described to date. This species comprises several independent genetic lineages or clades, which are not currently distinguishable based on comparison of their morphology or biogeographical distribution. Molecular probes were used to detect and quantify the genetic clades of M. pusilla in samples from temperate, polar and tropical environments in order to assess potential ecological niche partitioning. The three clades were detected in all biogeographical regions studied and were commonly found in sympatry. Cell abundances recorded for clades A and B were high, especially at coastal stations. Clade C, when detected, was always at low abundances and is suggested to be a low-light clade. Shifts in the contribution of clades to total M. pusilla abundance were observed along environmental gradients, both at local and basin-wide scales. This suggests that the phylogenetic clades occupy specific niches and confirms the existence of cryptic species within the morphospecies M. pusilla . Parameters which can precisely explain the distribution of these cryptic species remain to be elucidated.     

New Cytotoxic Triterpenoid Saponins from the Roots of Albizia gummifera (J.F.Gmel.) C.A.Sm.

As part of our search for new bioactive saponins from Cameroonian medicinal plants, two new oleanane‐type saponins, named gummiferaosides D and E ( 1 and 2 ), along with one known saponin, julibroside J₈ ( 3 ), were isolated from the roots of Albizia gummifera. Their structures were established on the basis of extensive 1D‐ and 2D‐NMR (¹H‐ and ¹³C‐NMR, DEPT, COSY, TOCSY, NOESY, HSQC, HSQC‐TOCSY, and HMBC) and HR‐ESI‐MS studies, and by chemical evidence. The apoptotic effect of saponins 1  –  3 was evaluated on the A431 human epidermoid cancer cell. Flow cytometric analyses showed that saponins 1  –  3 induced apoptosis of human epidermoid cancer cell (A431) in a dose‐dependent manner.     

A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are widely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence data set of the complete SSU rRNA gene from 298 specimens, representing all known extant reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora and Alveopora) compared to other corals. The V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished. A time‐calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages. The use of this data set as a valuable reference for investigating aspects of ecology, biology, molecular taxonomy and evolution of scleractinian corals is discussed.