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.     

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.     

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.

     

I can produce more offspring as you can imagine: first records on exceptionally large litters in roe deer in central/southern Europe

Most roe deer females produce twins and more rarely singletons and triplets. Some very rare reported cases of litters above three offspring refer to quadruplets which are, however, very much an exception in roe deer reproduction (only some tens of documented cases can be found in the scientific literature). In this paper, we present the first firm evidence that roe deer females are able to produce even five offspring. By examination of large sample set (n = 4690) of roe deer uteri and ovaries in two neighbouring countries in southern/central Europe (Italy and Slovenia), we found ten females that either carried or had potential to produce quadruplets, and in three does the (potential) litter size was even five. While one doe from Slovenia had five corpora lutea, two does from Tuscany, Italy, carried five foetuses. In both cases, all foetuses were normally and equally developed, indicating that none of them had predominant exposure to resorption/abortion. Six out of 13 females with exceptionally large potential litters (>3 offspring) had significantly higher body mass in comparison with mean body mass of all does harvested in the same hunting management district and in the same period, while five of them were significantly lighter. This indicates that some roe deer females can produce exceptionally large litters even when their phenotypic quality is not higher than the average in the population, and that such large litters are a stochastic episode rather than a reproductive performance of a very vital individual(s).     

Minimizing the time and cost of production of transgenic alfalfa libraries using the highly efficient completely sequenced vector pPZP200BAR

Alfalfa is the most important forage legume worldwide. However, similar to other minor forage crops, it is usually harvested along with weeds, which decrease its nutrient quality and thus reduce its high value in the market. In addition, weeds reduce alfalfa yield by about 50 %. Although weeds are the limiting factor for alfalfa production, little progress has been made in the incorporation of herbicide-tolerant traits into commercial alfalfa. This is partially due to the high times and costs needed for the production of vast numbers of transgenic alfalfa events as an empirical approach to bypass the random transgenic silencing and for the identification of an event with optimal transgene expression. In this focus article, we report the complete sequence of pPZP200BAR and the extremely high efficiency of this binary vector in alfalfa transformation, opening the way for rapid and inexpensive production of transgenic events for alfalfa improvement public programs.     

Human granulocyte surface molecules identified by murine monoclonal antibodies

We have investigated the nature of the antigens recognized by four classes of mouse anti-human monoclonal antibodies that characteristically reacted with neutrophilic granulocytes and their precursor cells, but not with monocytes or other normal hemopoietic cells. The antigenic targets of the majority (9/12) of the independently isolated monoclonal antibodies were present on two surface glycoproteins (Mr 145,000 and 105,000) and glycolipids. This antigen(s) was also detected on granulocyte precursor cells, including the bone marrow granulocyte/monocyte progenitor cells (CFU-GM). The same antigen(s) detected by these monoclonal antibodies was also present in non-hemopoietic cell lines (colon carcinoma and neuroblastoma). Three other antigens, defined by monoclonal antibodies AHN-8, L12.2, and L13.1 and present on granulocytes and their mid-late precursor cells, could not be identified as proteins but were detected in a protein-free glycolipid extract of these cells. The diversity of the antigens was confirmed by cross-competition experiments and by the identification of their different patterns of reactivity with cell lines and bone marrow cells.