Identity by descent mapping of founder mutations in cancer using high-resolution tumor SNP data

Dense genotype data can be used to detect chromosome fragments inherited from a common ancestor in apparently unrelated individuals. A disease-causing mutation inherited from a common founder may thus be detected by searching for a common haplotype signature in a sample population of patients. We present here FounderTracker, a computational method for the genome-wide detection of founder mutations in cancer using dense tumor SNP profiles. Our method is based on two assumptions. First, the wild-type allele frequently undergoes loss of heterozygosity (LOH) in the tumors of germline mutation carriers. Second, the overlap between the ancestral chromosome fragments inherited from a common founder will define a minimal haplotype conserved in each patient carrying the founder mutation. Our approach thus relies on the detection of haplotypes with significant identity by descent (IBD) sharing within recurrent regions of LOH to highlight genomic loci likely to harbor a founder mutation. We validated this approach by analyzing two real cancer data sets in which we successfully identified founder mutations of well-characterized tumor suppressor genes. We then used simulated data to evaluate the ability of our method to detect IBD tracts as a function of their size and frequency. We show that FounderTracker can detect haplotypes of low prevalence with high power and specificity, significantly outperforming existing methods. FounderTracker is thus a powerful tool for discovering unknown founder mutations that may explain part of the "missing" heritability in cancer. This method is freely available and can be used online at the FounderTracker website.     

Temperature-, SDS-, and pH-induced conformational changes in protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus: a dynamic simulation and fourier transform infrared spectroscopic study

The effect of SDS, pD, and temperature on the structure and stability of the protein disulfide oxidoreductase from Pyrococcus furiosus (PfPDO) was investigated by molecular dynamic (MD) simulations and FT-IR spectroscopy. pD affects the thermostability of alpha-helices and beta-sheets differently, and 0.5% or higher SDS concentration influences the structure significantly. The experiments allowed us to detect a secondary structural reorganization at a definite temperature and pD which may correlate with a high ATPase activity of the protein. The MD simulations supported the infrared data and revealed the different behavior of the N and C terminal segments, as well as of the two active sites.     

Uncommon and fatal case of cystoisosporiasis in a non HIV-immunosuppressed patient from a non-endemic country

Cystoisospora belli (previously known as Isospora belli) is a tropical coccidian parasite sometimes leading to severe diarrhea in immunocompromised patients. Here we describe a fatal case of cystoisosporiasis in a non HIV-immunocompromised 71-year-old female with no recent travel history. Infection was either latent or potentially caused by the consumption of contaminated imported food from Asia. Diagnosis was made by microscopical detection of numerous C. belli oocysts in stools without specific staining. Treatment with TMP-SMZ slightly improved diarrhea within 3 days, but dehydration subsequently led to acute decompensated heart failure and a fatal evolution. This report illustrates the possibility of severe cystoisosporiasis in non HIV-immunocompromised patients in a non-endemic country and highlights the risk of transmission through imported contaminated food consumption.     

Oxylipin analysis methods

Practical guidelines for monitoring and measuring compounds such as jasmonates, ketols, ketodi(tri)enes and hydroxy-fatty acids as well as detecting the presence of novel oxylipins are presented. Additionally, a protocol for the penetrant analysis of non-enzymatic lipid oxidation is described. Each of the methods, which employ gas chromatography/mass spectrometry, can be applied without specialist knowledge or recourse to the latest analytical instrumentation. Additional information on oxylipin quantification and novel protocols for preparing oxygen isotope-labelled internal standards are provided. Four developing areas of research are identified: (i) profiling of the unbound cellular pools of oxylipins; (ii) profiling of esterified oxylipins and/or monitoring of their release from parent lipids; (iii) monitoring of non-enzymatic lipid oxidation; (iv) analysis of unstable and reactive oxylipins. The methods and protocols presented herein are designed to give technical insights into the first three areas and to provide a platform from which to enter the fourth area.     

Soluble interleukin-15 receptor alpha (IL-15R alpha)-sushi as a selective and potent agonist of IL-15 action through IL-15R beta/gamma. Hyperagonist IL-15 x IL-15R alpha fusion proteins

Interleukin-15 (IL-15) is crucial for the generation of multiple lymphocyte subsets (natural killer (NK), NK-T cells, and memory CD8 T cells), and transpresentation of IL-15 by monocytes and dendritic cells has been suggested to be the dominant activating process of these lymphocytes. We have previously shown that a natural soluble form of IL-15R alpha chain corresponding to the entire extracellular domain of IL-15R alpha behaves as a high affinity IL-15 antagonist. In sharp contrast with this finding, we demonstrate in this report that a recombinant, soluble sushi domain of IL-15R alpha, which bears most of the binding affinity for IL-15, behaves as a potent IL-15 agonist by enhancing its binding and biological effects (proliferation and protection from apoptosis) through the IL-15R beta/gamma heterodimer, whereas it does not affect IL-15 binding and function of the tripartite IL-15R alpha/beta/gamma membrane receptor. Our results suggest that, if naturally produced, such soluble sushi domains might be involved in the IL-15 transpresentation mechanism. Fusion proteins (RLI and ILR), in which IL-15 and IL-15R alpha-sushi are attached by a flexible linker, are even more potent than the combination of IL-15 plus sIL-15R alpha-sushi. After binding to IL-15R beta/gamma, RLI is internalized and induces a biological response very similar to the IL-15 high affinity response. Such hyper-IL-15 fusion proteins appear to constitute potent adjuvants for the expansion of lymphocyte subsets.     

Discriminant haplotypes of avirulence genes of Phytophthora sojae lead to a molecular assay to predict phenotypes

The soybean–Phytophthora sojae interaction operates on a gene-for-gene relationship, where the product of a resistance gene (Rps) in the host recognizes that of an avirulence gene (Avr) in the pathogen to generate an incompatible reaction. To exploit this form of resistance, one must match with precision the appropriate Rps gene with the corresponding Avr gene. Currently, this association is evaluated by phenotyping assays that are labour-intensive and often imprecise. To circumvent this limitation, we sought to develop a molecular assay that would reveal the avirulence allele of the seven main Avr genes (Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a, and Avr6) in order to diagnose with precision the pathotypes of P. sojae isolates. For this purpose, we analysed the genomic regions of these Avr genes in 31 recently sequenced isolates with different virulence profiles and identified discriminant mutations between avirulence and virulence alleles. Specific primers were designed to generate amplicons of a distinct size, and polymerase chain reaction conditions were optimized in a final assay of two parallel runs. When tested on the 31 isolates of known virulence, the assay accurately revealed all avirulence alleles. The test was further assessed and compared to a phenotyping assay on 25 isolates of unknown virulence. The two assays matched in 97% (170/175) of the interactions studied. Interestingly, the sole cases of discrepancy were obtained with Avr3a, which suggests a possible imperfect interaction with Rps3a. This molecular assay offers a powerful and reliable tool to exploit and study with greater precision soybean resistance against P. sojae.     

Relationship between reversed sexual dimorphism,breeding investment and foraging ecology in a pelagic seabird,the masked booby

Reversed sexual dimorphism (RSD) may be related to different roles in breeding investment and/or foraging, but little information is available on foraging ecology. We studied the foraging behaviour and parental investment by male and female masked boobies, a species with RSD, by combining studies of foraging ecology using miniaturised activity and GPS data loggers of nest attendance, with an experimental study where flight costs were increased. Males attended the chick more often than females, but females provided more food to the chick than males. Males and females foraged during similar periods of the day, had similar prey types and sizes, diving depths, durations of foraging trips, foraging zones and ranges. Females spent a smaller proportion of the foraging trip sitting on the water and had higher diving rate than males, suggesting higher foraging effort by females. In females, trip duration correlated with mass at departure, suggesting a flexible investment through control by body mass. The experimental study showed that handicapped females and female partners of handicapped males lost mass compared to control birds, whereas there was no difference for males. These results indicate that the larger female is the main provisioner of the chick in the pair, and regulates breeding effort in relation to its own body mass, whereas males have a fixed investment. The different breeding investment between the sexes is associated with contrasting foraging strategies, but no clear niche differentiation was observed. The larger size of the females may be advantageous for provisioning the chick with large quantities of energy and for flexible breeding effort, while the smaller male invests in territory defence and nest guarding, a crucial task when breeding at high densities. In masked boobies, division of labour appears to be maximal during chick rearing—the most energy-demanding period—and may be related to evolution of RSD.     

Pollen morphology of Lathyrus (Fabaceae) taxa in the Platystylis section from Turkey

In this study, the pollen morphology of 18 wild taxa of Lathyrus L. grown in Turkey: L. pallescens (Bieb.) Koch, L. brachypterus Cel., L. haussknechtii Sirj., L. karsianus P. H. Davis, L. satdaghensis P. H. Davis, L. nivalis Hand.-Mazz, L. atropatanus (Grossh.) Sir., L. armenus (Boiss. and Huet) Sirj., L. cyaneus (Stev.) Koch var. cyaneus, L. cyaneus var. pinnatus?Davis, L. digitatus (Bieb.) Fiori, L. tukhtensis Czecz., L. variabilis (Boiss. and Ky.) Maly, L. spathulatus Cel. L. elongatus (Bornm.) Sirj., L. cilicicus Hayek and Siehe, L. boissieri Sirj., and L. bitlisicus Pe?men was examined by light microscopy and scanning electron microscopy. The pollen grains were 3-zonocolporate, of spheroidal-subprolate-prolate (P/E?=?0.957?C1.252) types, and medium in size. Equatorial view: rectangular or elliptical-obtuse-convex, polar view: circular, triangular or quinquangular-obtuse-convex. The smallest pollen grains belonged to L. elongatus (P?=?36.972/E?=?38.636) and the largest to L. cyaneus var. cyaneus (P?=?46.332/E?=?32.864). The ornamentation was perforate-foveolate or slightly reticulate. Some photographs included in this work were taken using both light microscopy and scanning electron microscopy.     

Retro-nasal aroma release is correlated with variations in the in-mouth air cavity volume after empty deglutition

We hypothesized that interindividual differences in motor activities during chewing and/or swallowing were determining factors for the transfer of volatile aroma from the in-mouth air cavity (IMAC) toward the olfactory mucosa. In our first experiment, we looked for changes in IMAC volume after saliva deglutition in 12 healthy subjects. The mean IMAC volume was measured after empty deglutition using an acoustic pharyngometer device. Based on the time course of the IMAC volume after swallowing, we discerned two groups of subjects. The first group displayed a small, constant IMAC volume (2.26 mL ±0.62) that corresponded to a high tongue position. The second group displayed a progressive increase in IMAC (from 6.82 mL ±2.37 to 22.82 mL ±3.04) that corresponded to a progressive lowering of the tongue to its resting position. In our second experiment, we investigated the relationship between IMAC volume changes after deglutition and the level of aroma release at the nostril. For this purpose, the release of menthone was measured at the nostril level in 25 subjects who consumed similar amounts of a mint tablet. The subjects were separated into two groups corresponding to two levels of menthone release: high (H) and low (L). The mean volume of IMAC was measured during and after empty deglutition. Group H displayed a small, constant amplitude of IMAC volume change after deglutition, while Group L displayed a progressive increase in IMAC. It is likely that Group H continuously released the aroma through the veloglossal isthmus as the mint was consumed, while Group L trapped the aroma in the oral cavity and then released it into the nasal cavity upon swallowing. These results show that the in vivo aroma release profile in humans depends closely on the different motor patterns at work during empty deglutition.