OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data

Background  

Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform.     

Aryl- and heteroaryl-substituted aminobenzo[a]quinolizines as dipeptidyl peptidase IV inhibitors

Synthesis and SAR are described for a structurally distinct class of DPP–IV inhibitors based on aminobenzo[a]quinolizines bearing (hetero-)aromatic substituents in the S1 specificity pocket. The m-(fluoromethyl)-phenyl derivative (S,S,S)-2g possesses the best fit in the S1 pocket. However, (S,S,S)-2i, bearing a more hydrophilic 5-methyl-pyridin-2-yl residue as substituent for the S1 pocket, displays excellent in vivo activity and superior drug-like properties.     

Evidence for genetic differentiation and divergent selection in an autotetraploid forage grass (Arrhenatherum elatius)

The use of local provenances in restoration, agriculture and forestry has been identified as measure to sustain biological diversity and to improve local productivity. However, the delineation of regional provenances is challenging because it requires the identification of well-defined groups based on spatiogenetic differentiation and/or the evidence of local adaptation. In this study, we investigate genetic variation at 186 AFLP loci in 46 European accessions of the important grassland species Arrhenatherum elatius and ask (1) whether genetic variation within accessions differs between European geographical regions; (2) at which spatial scale populations are structured across Europe and (3) whether putatively adaptive markers contribute to this pattern and whether these markers can be related to climatic site conditions. Basic expectations of population genetics are likely to be altered in autotetraploid species, thus, we adopted a band-based approach to estimate genetic diversity and structuring. Compared to other grasses A. elatius showed high genetic diversity and considerable differentiation among accessions (Φ_ST = 0.24). Accessions separated in a Western European and a Central/Eastern European group, without further structure within groups. A genome scan approach identified four potentially adaptive loci, whose band frequencies correlated significantly with climatic parameters, suggesting that genetic differentiation in A. elatius is also the result of adaptive processes. Knowledge on adaptive loci might in the long run also help to adapt ecosystems to adverse climate change effects through assisted migration of ecotypes rather than introduction of new species.     

Acetylation reduces SOX9 nuclear entry and ACAN gene transactivation in human chondrocytes

Changes in the content of aggrecan, an essential proteoglycan of articular cartilage, have been implicated in the pathophysiology of osteoarthritis (OA), a prevalent age‐related, degenerative joint disease. Here, we examined the effect of SOX9 acetylation on ACAN transactivation in the context of osteoarthritis. Primary chondrocytes freshly isolated from degenerated OA cartilage displayed lower levels of ACAN mRNA and higher levels of acetylated SOX9 compared with cells from intact regions of OA cartilage. Degenerated OA cartilage presented chondrocyte clusters bearing diffused immunostaining for SOX9 compared with intact cartilage regions. Primary human chondrocytes freshly isolated from OA knee joints were cultured in monolayer or in three‐dimensional alginate microbeads (3D). SOX9 was hypo‐acetylated in 3D cultures and displayed enhanced binding to a ?10 kb ACAN enhancer, a result consistent with higher ACAN mRNA levels than in monolayer cultures. It also co‐immunoprecipitated with SIRT1, a major deacetylase responsible for SOX9 deacetylation. Finally, immunofluorescence assays revealed increased nuclear localization of SOX9 in primary chondrocytes treated with the NAD SIRT1 cofactor, than in cells treated with a SIRT1 inhibitor. Inhibition of importin β by importazole maintained SOX9 in the cytoplasm, even in the presence of NAD. Based on these data, we conclude that deacetylation promotes SOX9 nuclear translocation and hence its ability to activate ACAN.     

Caveolin-1 is required for fatty acid translocase (FAT/CD36) localization and function at the plasma membrane of mouse embryonic fibroblasts

Several lines of evidence suggest that lipid rafts are involved in cellular fatty acid uptake and influence fatty acid translocase (FAT/CD36) function. However, it remains unknown whether caveolae, a specialized raft type, are required for this mechanism. Here, we show that wild-type (WT) mouse embryonic fibroblasts (MEFs) and caveolin-1 knockout (KO) MEFs, which are devoid of caveolae, have comparable overall expression of FAT/CD36 protein but altered subcellular FAT/CD36 localization and function. In WT MEFs, FAT/CD36 was isolated with both lipid raft enriched detergent-resistant membranes (DRMs) and detergent-soluble membranes (DSMs), whereas in cav-1 KO cells it was exclusively associated with DSMs. Subcellular fractionation demonstrated that FAT/CD36 in WT MEFs was localized intracellularly and at the plasma membrane level while in cav-1 KO MEFs it was absent from the plasma membrane. This mistargeting of FAT/CD36 in cav-1 KO cells resulted in reduced fatty acid uptake compared to WT controls. Adenoviral expression of caveolin-1 in KO MEFs induced caveolae formation, redirection of FAT/CD36 to the plasma membrane and rescue of fatty acid uptake. In conclusion, our data provide evidence that caveolin-1 is necessary to target FAT/CD36 to the plasma membrane. Caveolin-1 may influence fatty acid uptake by regulating surface availability of FAT/CD36.     

A stochastic model for estimation of mutation rates in multiple-replication proliferation processes

In this paper we propose a stochastic model based on the branching process for estimation and comparison of the mutation rates in proliferation processes of cells or microbes. We assume in this model that cells or microbes (the elements of a population) are reproduced by generations and thus the model is more suitably applicable to situations in which the new elements in a population are produced by older elements from the previous generation rather than by newly created elements from the same current generation. Cells and bacteria proliferate by binary replication, whereas the RNA viruses proliferate by multiple replication. The model is in terms of multiple replications, which includes the special case of binary replication. We propose statistical procedures for estimation and comparison of the mutation rates from data of multiple cultures with divergent culture sizes. The mutation rate is defined as the probability of mutation per replication per genome and thus can be assumed constant in the entire proliferation process. We derive the number of cultures for planning experiments to achieve desired accuracy for estimation or desired statistical power for comparing the mutation rates of two strains of microbes. We establish the efficiency of the proposed method by demonstrating how the estimation of mutation rates would be affected when the culture sizes were assumed similar but actually diverge.      

New chemotypes for wALADin1-like inhibitors of delta-aminolevulinic acid dehydratase from Wolbachia endobacteria

Substituted benzimidazoles of the wALADin1-family have recently been identified as a new class of species-selective inhibitors of delta-aminolevulinic acid dehydratase (ALAD) from Wolbachia endobacteria of parasitic filarial worms. Due to its Wolbachia-dependent antifilarial activity, wALADin1 is a starting point for the development of new drugs against filarial nematodes. We now present several other chemotypes of ALAD inhibitors that have been identified based upon their molecular similarity to wALADin1. A tricyclic quinoline derivative (wALADin2) with a different inhibitory mechanism and improved inhibitory potency and selectivity may represent an improved drug lead candidate.