Functional normalization of 450k methylation array data improves replication in large cancer studies

We propose an extension to quantile normalization that removes unwanted technical variation using control probes. We adapt our algorithm, functional normalization, to the Illumina 450k methylation array and address the open problem of normalizing methylation data with global epigenetic changes, such as human cancers. Using data sets from The Cancer Genome Atlas and a large case–control study, we show that our algorithm outperforms all existing normalization methods with respect to replication of results between experiments, and yields robust results even in the presence of batch effects. Functional normalization can be applied to any microarray platform, provided suitable control probes are available.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0503-2) contains supplementary material, which is available to authorized users.     

Cd uptake by intact wheat plants

Abstract. An investigation of the uptake of Cd by intact wheat plants has been carried out. The accumulation of Cd in the roots as a function of time and external Cd concentration was determined. Since the transport of Cd to the grains and shoots was found to be small, only uptake into the root was examined further. An appreciable fraction of the Cd absorbed by the roots can be desorbed and consequently constitutes the freely diffusible and exchangeable fraction.
The effect of temperature and of metabolic inhibitors on the absorption provides evidence that another Cd fraction is taken up by metabolically mediated processes. The absorption of this Cd fraction was found to be inhibited by Cu and Zn. The inhibitory effect of Cu and Zn on Cd absorption was comparable.     

Three-Dimensional Reconstruction of Rabbit-Derived Pneumocystis carinii from Serial-Thin Sections I: Trophozoite

The highly complex ultrastructural morphology of the endomembrane system in Pneumocystis carinii led us to perform three-dimensional reconstruction from serial-thin sections using the CATIA (Conception Assistée Tridimensionnelle Inter Active) Dassault system program. The three-dimensional reconstruction of a small trophozoite made it possible to better understand the morphological relationship among organelles and to suggest cytophysiological hypotheses. By reconstructing other parasite stages, we gathered information about the evolution of organelles during the life cycle and about their physiology.     

Chromosomal introgression in house mice from the hybrid zone between M. m. domesticus and M. m. musculus in Denmark

The recent discovery of Robertsonian (Rb) translocations in Danish mice from the hybrid zone between Mus musculus musculus and M. m. domesticus stimulated the chromosomal analysis of populations along a north-south transect through this zone. G-Banding identified the Rb fusions as Rb(3.8), Rb(2.5) and Rb(6.9). The cytogenetic results show that there is a gradual decrease in the number of fusions as one proceeds north, the translocations abruptly ending in populations from the centre of the hybrid zone determined by seven diagnostic allozymic markers. These results indicate that Rb fusions are present only in domesticus or predominantly domesticus-genotype mice and that they do not introgress into M. m. musculus . To test if genie incompatibilities between the musculus genetic background and Rb fusions were involved in the systematic elimination of the latter, predominantly musculus mice from the hybrid zone were crossed with Rb domesticus mice carrying Rb(3.8). The karyotypic analysis of the progeny showed no distortion of the transmission ratio of this fusion.
The chromosomal and allozymic analysis of these mice further indicates that (i) recombination is not suppressed between metacentrics and their acrocentric homologues and (ii) specific domesticus chromosomal segments are tolerated in the musculus genomes whereas the Rb centromeres are not.     

Bleomycin Induces Molecular Changes Directly Relevant to Idiopathic Pulmonary Fibrosis: A Model for “Active” Disease

The preclinical model of bleomycin-induced lung fibrosis, used to investigate mechanisms related to idiopathic pulmonary fibrosis (IPF), has incorrectly predicted efficacy for several candidate compounds suggesting that it may be of limited value. As an attempt to improve the predictive nature of this model, integrative bioinformatic approaches were used to compare molecular alterations in the lungs of bleomycin-treated mice and patients with IPF. Using gene set enrichment analysis we show for the first time that genes differentially expressed during the fibrotic phase of the single challenge bleomycin model were significantly enriched in the expression profiles of IPF patients. The genes that contributed most to the enrichment were largely involved in mitosis, growth factor, and matrix signaling. Interestingly, these same mitotic processes were increased in the expression profiles of fibroblasts isolated from rapidly progressing, but not slowly progressing, IPF patients relative to control subjects. The data also indicated that TGFβ was not the sole mediator responsible for the changes observed in this model since the ALK-5 inhibitor SB525334 effectively attenuated some but not all of the fibrosis associated with this model. Although some would suggest that repetitive bleomycin injuries may more effectively model IPF-like changes, our data do not support this conclusion. Together, these data highlight that a single bleomycin instillation effectively replicates several of the specific pathogenic molecular changes associated with IPF, and may be best used as a model for patients with active disease.     

How old is this mutation? - a study of three Ashkenazi Jewish founder mutations

Background

Several founder mutations leading to increased risk of cancer among Ashkenazi Jewish individuals have been identified, and some estimates of the age of the mutations have been published. A variety of different methods have been used previously to estimate the age of the mutations. Here three datasets containing genotype information near known founder mutations are reanalyzed in order to compare three approaches for estimating the age of a mutation. The methods are: (a) the single marker method used by Risch et al., (1995); (b) the intra-allelic coalescent model known as DMLE, and (c) the Goldgar method proposed in Neuhausen et al. (1996), and modified slightly by our group. The three mutations analyzed were MSH2*1906 G->C, APC*I1307K, and BRCA2*6174delT.

Results

All methods depend on accurate estimates of inter-marker recombination rates. The modified Goldgar method allows for marker mutation as well as recombination, but requires prior estimates of the possible haplotypes carrying the mutation for each individual. It does not incorporate population growth rates. The DMLE method simultaneously estimates the haplotypes with the mutation age, and builds in the population growth rate. The single marker estimates, however, are more sensitive to the recombination rates and are unstable. Mutation age estimates based on DMLE are 16.8 generations for MSH2 (95% credible interval (13, 23)), 106 generations for I1037K (86-129), and 90 generations for 6174delT (71-114).

Conclusions

For recent founder mutations where marker mutations are unlikely to have occurred, both DMLE and the Goldgar method can give good results. Caution is necessary for older mutations, especially if the effective population size may have remained small for a long period of time.

     

Monoclonal Antibodies Identify a Subset of Dense Granules in Cryptosporidium parvum Zoites and Gamonts

ABSTRACT. Two monoclonal antibodies raised against purified oocysts and excysted sporozoites of Cryptosporidium parvum identified antigens located in the anterior half of sporozoites by indirect immunofluorescence microscopic assay. The monoclonal antibodies also reacted with Triton X-100-insoluble antigens of asexual and sexual stage parasites developing in epithelial cells in vitro and identified a 110 kilodalton antigen on immunoblots of sodium dodecyl sulfate-extracted oocysts. Immunoblotting reactivity was abolished by prior treatment of blotted antigen with periodic acid suggesting that the monoclonal antibodies recognize a carbohydrate or carbohydrate-dependent epitope(s). By immunoelectron microscopy, the antibodies reacted with a family of small, electron-dense granules located predominantly in the central region of merozoites and also with a population of cytoplasmic inclusions in macrogamonts. In addition, the monoclonal antibodies prominently labeled the parasitophorous vacuole membrane of all intracellular stages examined suggesting that the corresponding antigen(s) may be exocytosed from the granules to become associated with Triton X-100-insoluble components of the vacuolar membrane or cytoskeleton.     

Behavioural circadian rhythms measured in real-time by automatic image analysis: applications in parasitoid insects

Abstract. A video analysis system was developed to study behavioural circadian rhythms in insects. Technical innovations were performed in image analysis and in the use of robotics. In image analysis, both the automatic detection of the insect and the calculation of several variables (linear and angular speed, locomotor activity, etc.) are carried out in real-time, which saves time and allows long-term studies without any intervention of the operator. The displacement of the camera by robotics allows the simultaneous study of many individuals (i.e. sixty individuals for the study of locomotor activity of adult insects, more than 400 individuals for the study of the emergence of adult parasitoids from their host). Four applications of this new device are presented. They deal with circadian rhythms in parasitoid insects: locomotor activity and time variation in locomotory parameters, daily distribution of the emergence and onset of the locomotor activity in adults. The adaptability of the system to several experimental materials and situations is discussed and the interest of the study of behavioural rhythms in the approach of host-parasitoid associations is emphasized.