Mouse Genome-Wide Association Mapping Needs Linkage Analysis to Avoid False-Positive Loci

We carried out genome-wide association (GWA) studies in inbred mouse strains characterized for their lung tumor susceptibility phenotypes (spontaneous or urethane-induced) with panels of 12,959 (13K) or 138,793 (140K) single-nucleotide polymorphisms (SNPs). Above the statistical thresholds, we detected only SNP rs3681853 on Chromosome 5, two SNPs in the pulmonary adenoma susceptibility 1 (Pas1) locus, and SNP rs4174648 on Chromosome 16 for spontaneous tumor incidence, urethane-induced tumor incidence, and urethane-induced tumor multiplicity, respectively, with the 13K SNP panel, but only the Pas1 locus with the 140K SNP panel. Haplotype analysis carried out in the latter panel detected four additional loci. Loci reported in previous GWA studies failed to replicate. Genome-wide genetic linkage analysis in urethane-treated (BALB/c×C3H/He)F2, (BALB/c×SWR/J)F2, and (A/J×C3H/He)F2 mice showed that Pas1, but none of the other loci detected previously or herein by GWA, had a significant effect. The Lasc1 gene, identified by GWA as a functional element (Nat. Genet., 38:888–95, 2006), showed no genetic effects in the two independent intercross mouse populations containing both alleles, nor was it expressed in mouse normal lung or lung tumors. Our results indicate that GWA studies in mouse inbred strains can suffer a high rate of false-positive results and that such an approach should be used in conjunction with classical linkage mapping in genetic crosses.     

Reticulate evolution in stick insects: the case of <Emphasis Type="Italic">Clonopsis</Emphasis> (Insecta Phasmida)

Background  

Phasmids show noteworthy abilities to overcome species-specific reproductive isolation mechanisms, including hybridization, polyploidy, parthenogenesis, hybridogenesis and androgenesis. From an evolutionary standpoint, such tangled reproductive interactions lead to the complex phyletic relationships known as "reticulate evolution". Moroccan stick insects of the genus Clonopsis include one bisexual (C. felicitatis) and two closely related parthenogenetic forms (C. gallica, C. soumiae), which represent a polyploid series in chromosome number, but with apparent diploid karyotypes. Moreover, two Clonopsis strains of ameiotic males have been described, C. androgenes-35 and C. androgenes-53. As a consequence, Clonopsis stick insects may have experienced complex micro-evolutionary events, which we try to disentangle in this study.     

Inflammatory signalling pathways involved in astroglial activation by unconjugated bilirubin

During neonatal hyperbilirubinaemia, astrocytes activated by unconjugated bilirubin (UCB) may contribute to brain toxicity through the production of cytokines. As a first step in addressing the signal transduction cascades involved in the UCB-induced astroglial immunological response, we tested whether tumour necrosis factor (TNF)-alpha receptor 1 (TNFR1), mitogen-activated protein kinase (MAPK) and nuclear factor kappaB (NF-kappaB) would be activated in astrocytes exposed to UCB, and examined the profile of cytokine production. Astrocyte cultures stimulated with UCB showed a rapid rise in TNFR1 protein levels, followed by activation of the MAPKs p38, Jun N-terminal kinase1/2 and extracellular signal-regulated kinase1/2, and NF-kappaB. Interestingly, the induction of these signal effectors preceded the early up-regulation of TNF-alpha and interleukin (IL)-1beta mRNAs, and later secretion of TNF-alpha, IL-1beta and IL-6. Treatment of astrocytes with UCB also induced cell death, with levels comparable to those obtained after exposure of astrocytes to recombinant TNF-alpha and IL-1beta. Moreover, loss of cell viability and cytokine secretion were reduced when the NF-kappaB signal transduction pathway was inhibited, suggesting a key role for NF-kappaB in the astroglial response to UCB. These results demonstrate the complexity of the molecular mechanisms involved in cell injury by UCB during hyperbilirubinaemia and provide a basis for the development of novel therapeutic strategies.     

The Effect of Surface Nanometre-Scale Morphology on Protein Adsorption

Background

Protein adsorption is the first of a complex series of events that regulates many phenomena at the nano-bio interface, e.g. cell adhesion and differentiation, in vivo inflammatory responses and protein crystallization. A quantitative understanding of how nanoscale morphology influences protein adsorption is strategic for providing insight into all of these processes, however this understanding has been lacking until now.

Methodology/Principal Findings

Here we introduce novel methods for quantitative high-throughput characterization of protein-surface interaction and we apply them in an integrated experimental strategy, to study the adsorption of a panel of proteins on nanostructured surfaces. We show that the increase of nanoscale roughness (from 15 nm to 30 nm) induces a decrease of protein binding affinity (≤90%) and a relevant increase in adsorbed proteins (≤500%) beyond the corresponding increase of specific area. We demonstrate that these effects are caused by protein nucleation on the surface, which is promoted by surface nanoscale pores.

Conclusions/Significance

These results show that the adsorption of proteins depends significantly on surface nanostructure and that the relevant morphological parameter regulating the protein adsorption process is the nanometric pore shape. These new findings improve our understanding of the role of nanostructures as a biomaterial design parameter and they have important implications for the general understanding of cell behavior on nanostructured surfaces.     

Rat Cerebellar Slice Cultures Exposed to Bilirubin Evidence Reactive Gliosis,Excitotoxicity and Impaired Myelinogenesis that Is Prevented by AMPA and TNF-α Inhibitors

The cerebellum is one of the most affected brain regions in the course of bilirubin-induced neurological dysfunction. We recently demonstrated that unconjugated bilirubin (UCB) reduces oligodendrocyte progenitor cell (OPC) survival and impairs oligodendrocyte (OL) differentiation and myelination in co-cultures of dorsal root ganglia neurons and OL. Here, we used organotypic cerebellar slice cultures, which replicate many aspects of the in vivo system, to dissect myelination defects by UCB in the presence of neuroimmune-related glial cells. Our results demonstrate that treatment of cerebellar slices with UCB reduces the number of myelinated fibres and myelin basic protein mRNA expression. Interestingly, UCB addition to slices increased the percentage of OPC and decreased mature OL content, whereas it decreased Olig1 and increased Olig2 mRNA expression. These UCB effects were associated with enhanced gliosis, revealed by an increased burden of both microglia and astrocytes. Additionally, UCB treatment led to a marked increase of tumor necrosis factor (TNF)-α and glutamate release, in parallel with a decrease of interleukin (IL)-6. No changes were observed relatively to IL-1β and S100B secretion. Curiously, both α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor antagonist and TNF-α antibody partially prevented the myelination defects that followed UCB exposure. These data point to a detrimental role of UCB in OL maturation and myelination together with astrocytosis, microgliosis, and both inflammatory and excitotoxic responses, which collectively may account for myelin deficits following moderate to severe neonatal jaundice.     

Action of the nematophagous fungus Pochonia chlamydosporia on Dioctophyma renale eggs

The ovicidal action of the nematophagous fungus Pochonia chlamydosporia (VC4) was evaluated on Dioctophyma renale eggs under laboratory conditions (Assay A). Next, the enzymatic action of proteases and chitinases produced by P. chlamydosporia (VC4) was evaluated on D. renale eggs, under laboratory conditions (Assay B). At the end of the experiment, there was difference (p < 0.01) in the destruction of eggs in the four concentrations tested in relation to control group at each interval studied. On the other hand, no difference was observed (p > 0.01) among the concentrations in the destruction of eggs. However, there was a trend of increasing mortality with increased concentration. Then (Assay B), it was observed that in the 24-hour interval, the proteases and chitinases of P. chlamydosporia (VC4), either individually or together, caused a significant percentage reduction (p < 0.01) on the number of viable eggs of D. renale, compared to control, with the following reduction values: 27.8% (proteases), 29.4% (chitinases) and 43.4% (proteases + chitinases). Thus, the constant search for alternatives that may help combat the various infectious forms (or eggs and larvae) of potentially zoonotic nematodes is important, as in the use of fungi destroyers of eggs. Therefore, it is suggested that the application of P. chlamydosporia would be an approach in the biological control of nematodes.     

Comparative structural analysis of haemagglutinin proteins from type A influenza viruses: conserved and variable features

Background

Genome variation is very high in influenza A viruses. However, viral evolution and spreading is strongly influenced by immunogenic features and capacity to bind host cells, depending in turn on the two major capsidic proteins. Therefore, such viruses are classified based on haemagglutinin and neuraminidase types, e.g. H5N1. Current analyses of viral evolution are based on serological and primary sequence comparison; however, comparative structural analysis of capsidic proteins can provide functional insights on surface regions possibly crucial to antigenicity and cell binding.

Results

We performed extensive structural comparison of influenza virus haemagglutinins and of their domains and subregions to investigate type- and/or domain-specific variation. We found that structural closeness and primary sequence similarity are not always tightly related; moreover, type-specific features could be inferred when comparing surface properties of haemagglutinin subregions, monomers and trimers, in terms of electrostatics and hydropathy. Focusing on H5N1, we found that variation at the receptor binding domain surface intriguingly relates to branching of still circulating clades from those ones that are no longer circulating.

Conclusions

Evidence from this work suggests that integrating phylogenetic and serological analyses by extensive structural comparison can help in understanding the ‘functional evolution’ of viral surface determinants. In particular, variation in electrostatic and hydropathy patches can provide molecular evolution markers: intriguing surface charge redistribution characterizing the haemagglutinin receptor binding domains from circulating H5N1 clades 2 and 7 might have contributed to antigenic escape hence to their evolutionary success and spreading.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0363-5) contains supplementary material, which is available to authorized users.     

Carbonate facies dominated by syndepositional cements: a key component of Middle Triassic platforms. The Marmolada case history (Dolomites, Italy)

Summary This article deals with the discussion of the role of the syndepositional cementation for the growth of the Middle Triassic pre-volcanic carbonate platforms of the Dolomites (Southern Alps, Northern Italy). The study is concentrated on the Marmolada Buildup, which escaped the facies destroying dolomitization which affected many surrounding platforms. The investigations took place within an almost isochronous uppermost Anisian palcogeographic transect, ranging from the platform-top to the margin and the upper slope. Methods used include geological mapping, sedimentological and paleontological studies, evaluation of the microfacies, as well as SEM and EDS epifluorescence analyses. The well bedded platform-top succession consists of intra-bioclast calcarenites and calcirudites, interbedded with subordinate boundstones, and organized in shallowing upward, meter scale depositional cycles, sometimes capped by subaerial surfaces. The platform margin belt is rich in boundstones and lacks a primary framework formed by organisms; metazoan skeletons form less then 5% of the rock volume. The outer margin and the uppermost slope are characterized by decimeter-scale boundstone blocks, coated and linked to each other by huge amounts of radiaxial fibrous calcite cements, arranged in concentric crusts. These cements (“evinospongiac”) represent the main component of the margin and upper slope facies. Epifluorescence analyses suggest the existence of abundant organic residual matter associated not only with the bioclasts and peloids, but also with the syndepositional cements. Organic matter likely played a significant role in carbonate cementation and was a key factor for the early lithification of the platform as well as for the sediment production. Minor element microanalyses reveal an uniform Mg content in different calcite types (2–4 Mole % MgCO₃), independently from the primary nature of the components. Late diagenetic sparry calcites exhibit similar Mg values but no iron. These data point to a homogenization of minor element distribution, probably associated with a slow but long-lasting semi-closed fluid circulation, possibly related with the Neogene uplifting of the Dolomite Mountains.