Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.)

Molecular phylogenetic analyses of aligned 18S rDNA gene sequences from articulate and inarticulate brachiopods representing all major extant lineages, an enhanced set of phoronids and several unrelated protostome taxa, confirm previous indications that in such data, brachiopod and phoronids form a well-supported clade that (on previous evidence) is unambiguously affiliated with protostomes rather than deuterostomes. Within the brachiopod-phoronid clade, an association between phoronids and inarticulate brachiopods is moderately well supported, whilst a close relationship between phoronids and craniid inarticulates is weakly indicated. Brachiopod-phoronid monophyly is reconciled with the most recent Linnaean classification of brachiopods by abolition of the phylum Phoronida and rediagnosis of the phylum Brachiopoda to include tubiculous, shell-less forms. Recognition that brachiopods and phoronids are close genealogical allies of protostome phyla such as molluscs and annelids, but are much more distantly related to deuterostome phyla such as echinoderms and chordates, implies either (or both) that the morphology and ontogeny of blastopore, mesoderm and coelom formation have been widely misreported or misinterpreted, or that these characters have been subject to extensive homoplasy. This inference, if true, undermines virtually all morphology-based reconstructions of phylogeny made during the past century or more

Small ribosomal-subunit RNA and the phylogeny of Mollusca

We determined the complete sequence of the small ribosomal subunit RNA of the pulmonate snail Onchidella celtica. This sequence and the one recently determined for the chiton Acanthopleura japonica were added to an alignment of 25 18S rRNA sequences of Metazoa, including three other Mollusca. The data set was used to assess certain aspects of molluscan phylogeny by distance matrix and character state methods. The trees obtained were tested for effects of random and systematic errors. The results of our analyses support: (a) molluscan monophyly; (b) gastropod monophyly; (c) bivalve monophyly; (d) a sister group relationship of Gastropoda and Polyplacophora. The position of the phylum among other Metazoa remains uncertain due to a lack of representatives of many invertebrate phyla in our data set. Most of our results are congruent with existing hypotheses

TRIB2 as a biomarker for diagnosis and progression of melanoma

Malignant melanoma is the most deadly form of skin cancer. There is a critical need to identify the patients that could be successfully treated by surgery alone and those that require adjuvant treatment. In this study, we demonstrate that the expression of tribbles2 (TRIB2) strongly correlates with both the presence and progression of melanocyte-derived malignancies. We examined the expression of TRIB2 in addition to 12 previously described melanoma biomarkers across three independent full genome microarray studies. TRIB2 expression was consistently and significantly increased in benign nevi and melanoma, and was highest in samples from patients with metastatic melanoma. The expression profiles for the 12 biomarkers were poorly conserved throughout these studies with only TYR, S100B and SPP1 showing consistently elevated expression in metastatic melanoma versus normal skin. Strikingly we confirmed these findings in 20 freshly obtained primary melanoma tissue samples from metastatic lesions where the expression of these biomarkers were evaluated revealing that TRIB2 expression correlated with disease stage and clinical prognosis. Our results suggest that TRIB2 is a meaningful biomarker reflecting diagnosis and progression of melanoma, as well as predicting clinical response to chemotherapy.Fundacao para a Ciencia e a Tecnologia (FCT) [PEst-OE/EQB/LA0023/2012, SFRH/BPD/84634/2012, SFRH/BPD/70718/2010]info:eu-repo/semantics/publishedVersio

Frequent detection of human polyomavirus 6 in keratoacanthomas

BACKGROUND: The recent discovery of the Merkel cell polyomavirus and its consistent association with Merkel cell carcinoma has drawn attention to the numerous recently discovered polyomaviruses and their possible involvement in the etiopathogenesis of non-melanoma skin cancer (NMSC). Data on the recently discovered human polyomavirus 6 (HPyV6) and its role in NMSC are sparse and in part controversial. METHODS: In the present study we tested a large number (n = 299) of NMSC specimens for the presence of human polyomavirus 6 (HPyV6) by DNA PCR and HPyV6 fluorescence in situ hybridization (FISH). In detail, 59 keratoacanthomas (KA), 109 basal cell carcinomas (BCC), 86 squamous cell carcinomas (SCC) and 45 trichoblastomas (TB) were tested for the presence of HPyV6. RESULTS: HPyV6 DNA PCR and subsequent sequence analysis revealed that 25 KAs (42.3 %), 23 BCCs (21.1 %), 8 SCCs (9.3 %) and 10 TBs (22.2 %) were HPyV6 positive. The presence of HPyV6 DNA was visualized and validated on the single cell level within the histomorphological context by HPyV6 fluorescence in situ hybridization. CONCLUSIONS: The high frequency of HPyV6 DNA in 42.3 % of KA possibly points to a role for HPyV6 in the etiopathogenesis of KAs. Although the detection rate of HPyV6 DNA in BCCs and TBs is within the previously reported detection range in normal skin, it does not exclude a possible role for HPyV6 in the carcinogenesis in a significant subset of these skin tumors

Phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit 1 gene from 13 sipunculan genera: intra- and interphylum relationships

Sipunculans are a phylum of non-segmented, marine worms. Although they are well characterized morphologically, relationships within the phylum and the relationship of Sipuncula to other spiralian phyla have been strongly debated. I analyzed representatives of 13 of 17 described genera using a 654-bp fragment of the mitochondrial gene, cytochrome c oxidase subunit I, to construct the first intraphylum phylogenetic hypothesis for sipunculans based on molecular sequence data. Within the phylum, tree topologies are loosely congruent with a previously published morphological analysis, except that the monotypic genus Phascolopsis occurred within the Golfingiaformes as a sister group to, or nested within, the Themistidae. Phylogenetic analyses, including 30 sequences from additional invertebrate taxa, suggest that sipunculans are most closely related to the Annelida (including Echiura). A previously proposed sipunculan-molluscan relationship is not supported. While not universally accepted, this hypothesis is consistent with other recent and past data on phylum-level relationships.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75669/1/j.1744-7410.2003.tb00089.x.pd

An Efficient Method for Genomic DNA Extraction from Different Molluscs Species

The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills) or quantity of tissue, can explain the lack of efficiency (quality and yield) in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia) and Muricidae (Gastropoda), with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others