Molecular taxonomic identification in the absence of a ‘barcoding gap’: a test with the endemic flora of the Canarian oceanic hotspot

We use a comprehensive subset of Canarian angiosperms corresponding to 23 families, 35 genera and 60 Canarian endemic taxa to test whether this flora is suitable to taxonomic identification with the two proposed plant DNA barcode sequences and whether these sequences may reveal the existence of cryptic species overlooked by morphology. The rate of discrimination success between the insular congeneric samples using the rbcL+matK combination and a ‘character‐based’ approach (where we use only the combination of nucleotide positions in an alignment that allows unambiguous species identification) is higher (82.29%) than that obtained with the ‘distance‐based’ approach (80.20%) used by the CBOL Plant Working Group in 2009 and also when compared with tests conducted in other floras. This suggests that the molecular identification of the Canarian endemic flora can be achieved as successfully as in other floras where the incidence of radiation is not as relevant. The facts that (i) a distance‐based criterion was unable to discriminate between congeneric and conspecific comparisons and (ii) only the character‐based discrimination criterion resolved cases that the distance‐based criterion did not, further support the use of a character discrimination approach for a more efficient DNA barcoding of floras from oceanic islands like the Canaries. Thus, a barcoding gap seems not to be necessary for the correct molecular characterization of the Canarian flora. DNA barcodes also suggest the possible existence of cryptic taxa to be further investigated by morphology and that the current taxonomic status of some of the taxa analysed may need revision.     

Lysosomal dysfunction in Parkinson disease: ATP13A2 gets into the groove

Mutations in ATP13A2 (PARK9) cause an autosomal recessive form of early-onset parkinsonism with pyramidal degeneration and dementia called Kufor-Rakeb Syndrome (KRS). The ATP13A2 gene encodes a transmembrane lysosomal P5-type ATPase (ATP13A2) whose physiological function in mammalian cells, and hence its potential role in Parkinson disease (PD), remains elusive. In this context, we have recently shown that KRS-linked mutations in ATP13A2 leads to several lysosomal alterations in ATP13A2 KRS patient-derived fibroblasts, including impaired lysosomal acidification, decreased proteolytic processing of lysosomal enzymes, reduced degradation of lysosomal substrates and diminished lysosomal-mediated clearance of autophagosomes (AP). Similar alterations are observed in stable ATP13A2-knockdown dopaminergic cell lines, which are associated with cell death. Restoration of ATP13A2 levels in ATP13A2-mutant/depleted cells is able to restore lysosomal function and attenuate cell death. Relevant to PD, we have determined that ATP13A2 levels are decreased in dopaminergic nigral neurons from sporadic PD patients. Interestingly in these patients, the main signal of ATP13A2 is detected in the Lewy bodies. Our results unravel an instrumental role of ATP13A2 in lysosomal function and in cell viability. Altogether, our results validate ATP13A2 as a likely therapeutic target against PD degeneration.     

Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2 > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.     

The xipotl mutant of Arabidopsis reveals a critical role for phospholipid metabolism in root system development and epidermal cell integrity

Phosphocholine (PCho) is an essential metabolite for plant development because it is the precursor for the biosynthesis of phosphatidylcholine, which is the major lipid component in plant cell membranes. The main step in PCho biosynthesis in Arabidopsis thaliana is the triple, sequential N-methylation of phosphoethanolamine, catalyzed by S-adenosyl-l-methionine:phosphoethanolamine N-methyltransferase (PEAMT). In screenings performed to isolate Arabidopsis mutants with altered root system architecture, a T-DNA mutagenized line showing remarkable alterations in root development was isolated. At the seedling stage, the mutant phenotype is characterized by a short primary root, a high number of lateral roots, and short epidermal cells with aberrant morphology. Genetic and biochemical characterization of this mutant showed that the T-DNA was inserted at the At3g18000 locus (XIPOTL1), which encodes PEAMT (XIPOTL1). Further analyses revealed that inhibition of PCho biosynthesis in xpl1 mutants not only alters several root developmental traits but also induces cell death in root epidermal cells. Epidermal cell death could be reversed by phosphatidic acid treatment. Taken together, our results suggest that molecules produced downstream of the PCho biosynthesis pathway play key roles in root development and act as signals for cell integrity.     

Evolutionary Implications of Dental Eruption in Dasypus (Xenarthra)

Late eruption of the permanent dentition was recently proposed as a shared anatomical feature of endemic African mammals (Afrotheria), with anecdotal reports indicating that it is also present in dasypodids (armadillos). In order to clarify this question, and address the possiblity that late eruption is shared by afrotherians and dasypodids, we quantified the eruption of permanent teeth in Dasypus, focusing on growth series of D. hybridus and D. novemcinctus. This genus is the only known xenarthran that retains two functional generations of teeth. Its adult dentition typically consists of eight upper and eight lower ever-growing (or euhypsodont) molariforms, with no premaxillary teeth. All but the posterior-most tooth are replaced, consistent with the identification of a single molar locus in each series. Comparison of dental replacement and skull metrics reveals that most specimens reach adult size with none or few erupted permanent teeth. This pattern of growth occurring prior to the full eruption of the dentition is similar to that observed in most afrotherians. The condition observed in Dasypus and many afrotherians differs from that of most other mammals, in which the permanent dentition erupts during (not after) growth, and is complete at or near the attainment of sexual maturity and adult body size. The suture closure sequence of basicranial and postcranial epiphyses does not correlate well with dental eruption. The basal phylogenetic position of the taxon within dasypodids suggests that diphyodonty and late dental replacement represent the condition of early xenarthrans. Additionally, the inferred reduction in the number of molars to a single locus and the multiplication of premolars represent rare features for any living mammal, but may represent apomorphic characters for Dasypus.     

Synergistic inhibition of pancreatic adenocarcinoma cell growth by trichostatin A and gemcitabine

We investigated the ability of the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) to interact with gemcitabine (GEM) in inducing pancreatic cancer cell death. The combined treatment with TSA and GEM synergistically inhibited growth of four pancreatic adenocarcinoma cell lines and induced apoptosis. This effect was associated with the induction of reactive oxygen species (ROS) by GEM, increased expression of the pro-apoptotic BIM gene by both TSA and GEM and downregulation of the 5'-nucleotidase UMPH type II gene by TSA. The expression of other genes critical for GEM resistance (nucleoside transporters, deoxycytidine kinase, cytidine deaminase, and ribonucleotide reductase genes) was not affected by TSA. The functional role of ROS in cell growth inhibition by GEM was supported by (i) a significantly reduced GEM-associated growth inhibition by the free radical scavenger N-acetyl-L-cysteine, and (ii) a positive correlation between the basal level of ROS and sensitivity to GEM in 10 pancreatic cancer cell lines. The functional role of both Bim and 5'-nucleotidase UMPH type II in cell growth inhibition by TSA and GEM was assessed by RNA interference assays. In vivo studies on xenografts of pancreatic adenocarcinoma cells in nude mice showed that the association of TSA and GEM reduced to 50% the tumour mass and did not cause any apparent form of toxicity, while treatments with TSA or GEM alone were ineffective. In conclusion, the present study demonstrates a potent anti-tumour activity of TSA/GEM combination against pancreatic cancer cells in vitro and in vivo, strongly supporting the use of GEM in combination with an HDAC inhibitor for pancreatic cancer therapy.     

The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies

Background

Urothelial bladder cancer is a highly heterogeneous disease. Cancer cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression.

Results

Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events.

Conclusions

Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1450-3) contains supplementary material, which is available to authorized users.     

Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae)

The implementation of the phylogeographic approach for the study of biodiversity is critical in poorly sampled regions like the montane systems of Middle America, as complex evolutionary histories often result in the presence of independent lineages not properly considered by traditional taxonomy. Herein we sequenced 2370 bp of mtDNA (ND2, cyt b and ATPase) from 81 individuals of Ergaticus, a complex of birds endemic to the montane forests of Middle America. Although current taxonomy recognizes two species, the results reveal considerable genetic structure with the presence of four mtDNA lineages. Two of these lineages within Ergaticus ruber evidence the need of a revaluation of the species limits for this taxon. The general phylogeographic pattern can be explained as a consequence of relative isolation of the populations in different mountain ranges separated by low elevation barriers. Most population groups did not show signals of demographic expansion with the exception of the one corresponding to clade 1. The divergence time estimates point to the Pleistocene as an important time period for the diversification of this complex.