Otolith shape analysis for three <Emphasis Type="Italic">Sicyopterus</Emphasis> (Teleostei: Gobioidei: Sicydiinae) species from New Caledonia and Vanuatu

Otolith shape analysis has been used in a number of studies as an inexpensive and powerful method for categorising fish in individual stocks. Elliptical Fourier analysis was used on three different amphidromous Sicyopterus species. Sicyopterus lagocephalus is a widespread species while the other two have a limited distribution area, Sicyopterus aiensis being endemic to Vanuatu, and Sicyopterus sarasini to New Caledonia. Both endemics live in sympatry with the widespread species. The otolith shape of all fish sampled was a clear species differentiator, thereby demonstrating that otolith shape is species-specific. At an intraspecific level there are different river populations within samples from Vanuatu, indicating a western group and an eastern “central” group.These results are congruent both for the endemic species, S. aiensis and for the cosmopolitan species. Finally, we found that, for S. lagocephalus, the cosmopolitan species, New Caledonian samples are close to western Vanuatu samples, the latter two being well differentiated from the eastern “central” Vanuatu samples. The explanation for these results may lay either in the influence of environmental factors on the otolith shape, or in the influence of common early life history thus reflecting genetic factors, or a combination of both.     

Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish

A group of ten Arcobacter isolates (Gram negative, slightly curved motile rods, oxidase positive) was recovered from mussels (nine) and from clams (one). These isolates could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR). The aim of this study is to establish the taxonomic position of these isolates. The 16S rRNA gene sequence similarity of mussel strain F4(T) to the type strains of all other Arcobacter species ranged from 91.1% to 94.8%. The species most similar to the clams' strain F67-11(T) were Arcobacter defluvii (CECT 7697(T), 97.1%) and Arcobacter ellisii (CECT 7837(T), 97.0%). On the basis of phylogenetic analyses with 16S rRNA, rpoB, gyrB and hsp60 genes, the mussel and clam strains formed two different, new lineages within the genus Arcobacter. These data, together with their different phenotypic characteristics and MALDI-TOF mass spectra, revealed that these strains represent two new species, for which the names Arcobacter bivalviorum (type strain F4(T)=CECT 7835(T)=LMG 26154(T)) and Arcobacter venerupis (type strain F67-11(T)=CECT 7836(T)=LMG 26156(T)) are proposed.     

A promoter DNA demethylation landscape of human hematopoietic differentiation

Global mechanisms defining the gene expression programs specific for hematopoiesis are still not fully understood. Here, we show that promoter DNA demethylation is associated with the activation of hematopoietic-specific genes. Using genome-wide promoter methylation arrays, we identified 694 hematopoietic-specific genes repressed by promoter DNA methylation in human embryonic stem cells and whose loss of methylation in hematopoietic can be associated with gene expression. The association between promoter methylation and gene expression was studied for many hematopoietic-specific genes including CD45, CD34, CD28, CD19, the T cell receptor (TCR), the MHC class II gene HLA-DR, perforin 1 and the phosphoinositide 3-kinase (PI3K) and results indicated that DNA demethylation was not always sufficient for gene activation. Promoter demethylation occurred either early during embryonic development or later on during hematopoietic differentiation. Analysis of the genome-wide promoter methylation status of induced pluripotent stem cells (iPSCs) generated from somatic CD34(+) HSPCs and differentiated derivatives from CD34(+) HSPCs confirmed the role of DNA methylation in regulating the expression of genes of the hemato-immune system, and indicated that promoter methylation of these genes may be associated to stemness. Together, these data suggest that promoter DNA demethylation might play a role in the tissue/cell-specific genome-wide gene regulation within the hematopoietic compartment.     

Morphogenesis and molecular mechanisms involved in human kidney development

The development of the human kidney is a complex process that requires interactions between epithelial and mesenchymal cells, eventually leading to the coordinated growth and differentiation of multiple highly specialized stromal, vascular, and epithelial cell types. The application of molecular biology and immunocytochemistry to the study of cell types involved in renal morphogenesis is leading to a better understanding of nephrogenesis, which requires a fine balance of many factors that can be disturbed by various prenatal events in humans. The aim of this paper is to review human kidney organogenesis, with particular emphasis on the sequence of morphological events, on the immunohistochemical peculiarities of nephron progenitor populations and on the molecular pathways regulating the process of mesenchymal to epithelial transition. Kidney development can be subdivided into five steps: (i) the primary ureteric bud (UB); (ii) the cap mesenchyme; (iii) the mesenchymal-epithelial transition; (iv) glomerulogenesis and tubulogenesis; (v) the interstitial cells. Complex correlations between morphological and molecular events from the origin of the UB and its branching to the metanephric mesenchyme, ending with the maturation of nephrons, have been reported in different animals, including mammals. Marked differences, observed among different species in the origin and the duration of nephrogenesis, suggest that morphological and molecular events may be different in different animal species and mammals. Further studies must be carried out in humans to verify at the morphological, immunohistochemical, and molecular levels if the outcome in humans parallels that previously described in other species.     

IRF5 risk polymorphisms contribute to interindividual variance in pattern recognition receptor-mediated cytokine secretion in human monocyte-derived cells

Monocyte-derived cells display highly variable cytokine secretion upon pattern recognition receptor (PRR) stimulation across individuals; such variability likely affects interindividual inflammatory/autoimmune disease susceptibility. To define mechanisms for this heterogeneity, we examined PRR-induced monocyte-derived cell cytokine secretion from a large cohort of healthy individuals. Although cytokine secretion ranged widely among individuals, the magnitude of cytokine induction after individual nucleotide-binding oligomerization domain 2 (Nod2) and TLR2 stimulation (a cohort of 86 individuals) or stimulation of multiple TLRs (a cohort of 77 individuals), either alone or in combination with Nod2, was consistent intraindividually across these stimuli. Nod2 and TLRs signal through IFN regulatory factor 5 (IRF5), and common IRF5 polymorphisms confer risk for autoimmunity. We find that cells from rs2004640 IRF5 risk-associated allele carriers secrete increased cytokines upon individual or synergistic PRR stimulation in a gene dose- and ligand dose-dependent manner in both monocyte-derived dendritic cells and monocyte-derived macrophages. IRF5 expression knockdown in IRF5 risk allele carrier cells significantly decreases PRR-induced cytokines. Moreover, we find that IRF5 knockdown profoundly decreases Nod2-mediated MAPK and NF-κB pathway activation, whereas the PI3K and mammalian target of rapamycin pathways are not impaired. Finally, the IRF5 rs2004640 polymorphism is a major determinant of the variance (r(2) = 0.53) in Nod2-induced cytokine secretion by monocyte-derived cells from different individuals. We therefore show a profound contribution of a single gene to the variance in interindividual PRR-induced cytokines. The hyperresponsiveness of IRF5 disease-associated polymorphisms to a wide spectrum of microbial triggers has broad implications on global immunological responses, host defenses against pathogens, and inflammatory/autoimmune disease susceptibility.     

The fission yeast MRN complex tethers dysfunctional telomeres for NHEJ repair

Telomeres protect the natural ends of chromosomes from being repaired as deleterious DNA breaks. In fission yeast, absence of Taz1 (homologue of human TRF1 and TRF2) renders telomeres vulnerable to DNA repair. During the G1 phase, when non‐homologous end joining (NHEJ) is upregulated, taz1Δ cells undergo telomere fusions with consequent loss of viability. Here, we show that disruption of the fission yeast MRN (Rad23^MRE11‐Rad50‐Nbs1) complex prevents NHEJ at telomeres and, as a result, rescues taz1Δ lethality in G1. Neither Tel1^ATM activation nor 5′‐end resection was required for telomere fusion. Nuclease activity of Rad32^MRE11 was also dispensable for NHEJ. Mutants unable to coordinate metal ions required for nuclease activity were proficient in NHEJ repair. In contrast, Rad32^MRE11 mutations that affect binding and/or positioning of DNA ends leaving the nuclease function largely unaffected also impaired NHEJ at telomeres and restored the viability of taz1Δ in G1. Consistently, MRN structural integrity but not nuclease function is also required for NHEJ of independent DNA ends in a novel split‐molecule plasmid assay. Thus, MRN acts to tether unlinked DNA ends, allowing for efficient NHEJ.     

Zooming-in on floral nectar: a first exploration of nectar-associated bacteria in wild plant communities

Floral nectar of some animal-pollinated plants usually harbours highly adapted yeast communities which can profoundly alter nectar characteristics and, therefore, potentially have significant impacts on plant reproduction through their effects on insect foraging behaviour. Bacteria have also been occasionally observed in floral nectar, but their prevalence, phylogenetic diversity and ecological role within plant-pollinator-yeast systems remains unclear. Here we present the first reported survey of bacteria in floral nectar from a natural plant community. Culturable bacteria occurring in a total of 71 nectar samples collected from 27 South African plant species were isolated and identified by 16S rRNA gene sequencing. Rarefaction-based analyses were used to assess operational taxonomic units (OTUs) richness at the plant community level using nectar drops as sampling units. Our results showed that bacteria are common inhabitants of floral nectar of South African plants (53.5% of samples yielded growth), and their communities are characterized by low species richness (18 OTUs at a 16S rRNA gene sequence dissimilarity cut-off of 3%) and moderate phylogenetic diversity, with most isolates belonging to the Gammaproteobacteria. Furthermore, isolates showed osmotolerance, catalase activity and the ability to grow under microaerobiosis, three traits that might help bacteria to overcome important factors limiting their survival and/or growth in nectar.     

Adsorption of Adenine and Thymine on Zeolites: FT-IR and EPR Spectroscopy and X-Ray Diffractometry and SEM Studies

The interactions of adenine and thymine with and adsorption on zeolites were studied using different techniques. There were two main findings. First, as shown by X-ray diffractometry, thymine increased the decomposition of the zeolites (Y, ZSM-5) while adenine prevented it. Second, zeolite Y adsorbed almost the same amount of adenine and thymine, thus both nucleic acid bases could be protected from hydrolysis and UV radiation and could be available for molecular evolution. The X-ray diffractometry and SEM showed that artificial seawater almost dissolved zeolite A. The adsorption of adenine on ZSM-5 zeolite was higher than that of thymine (Student-Newman-Keuls test-SNK p<0.05). Adenine was also more greatly adsorbed on ZSM-5 zeolite, when compared to other zeolites (SNK p<0.05). However the adsorption of thymine on different zeolites was not statistically different (SNK p>0.05). The adsorption of adenine and thymine on zeolites did not depend on pore size or Si/Al ratio and it was not explained only by electrostatic forces; rather van der Waals interactions should also be considered.     

Chorusing Behaviour in the Lusitanian Toadfish: Should I Match My Neighbours' Calling Rate?

Choruses have been described mostly in birds, anurans and insects but have been poorly studied in fish. Research in batrachoidid (toadfishes) species suggest vocal facilitation among neighbouring males, but whether chorusing fish present more complex interactions is unknown. In this study, we test the hypothesis that chorusing fish males compete actively to increase attractiveness to females. We first describe vocal interactions in natural choruses of Lusitanian toadfish males. Our analysis found positive correlations between the calling rates of neighbouring males in several occasions. However, we also found that males that showed an overall low vocal activity throughout the observation period exhibited peaks of increased calling activity when neighbours decreased their calling rate, suggesting an opportunistic maximisation of attractiveness. We further test with playback experiments how toadfish males adjust calling activity relative to their neighbours'. We observed that males silent at the time of the playbacks but who had an overall high vocal performance tended to start calling when exposed to playbacks in contrast to low‐activity males. Playback experiments further showed that males initially calling at a high rate adjust their calling rate according to the neighbour's vocal activity level, that is, they increased calling rate when exposed to a high calling rate and decreased it when confronted with a low calling rate. However, males calling at a low rate did not significantly alter their calling rate when presented with a low (similar) or higher calling rate, probably due to temporary physiological and/or ecological constraints. We argue that Lusitanian toadfish males tend to optimise calling effort in relation to their neighbours when they are actively advertising. Further studies are necessary to better understand vocal behaviour with increased chorus size.