The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses.

Understanding how genotypes are linked to phenotypes is important in biomedical and evolutionary studies. The chaperone heat-shock protein 90 (HSP90) buffers genetic variation by stabilizing proteins with variant sequences, thereby uncoupling phenotypes from genotypes. Here we report an unexpected role of HSP90 in buffering cis-regulatory variation affecting gene expression.

Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease.

Background: The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's disease (PD) and other neurodegenerative diseases has not yet been systematically evaluated.

Results: We have used a systems genomics approach to characterize the SH-SY5Y cell line using whole-genome sequencing to determine the genetic content of the cell line and used transcriptomics and proteomics data to determine molecular correlations.

Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching.

Background: The robust identification of isotope patterns originating from peptides being analyzed through mass spectrometry (MS) is often significantly hampered by noise artifacts and the interference of overlapping patterns arising e.g. from post-translational modifications.

Xanthohumol, a prenylated chalcone from hops, modulates hepatic expression of genes involved in thyroid hormone distribution and metabolism.

In the present study, we analyzed the influence of xanthohumol (XN) on thyroid hormone (TH) distribution and metabolism in rats. A potent and selective competition of XN for thyroxine (T4) binding to transthyretin (IC(50)=1 microM at 1.7 nM [(125)I]T4) was found in human and rat sera in vitro.

Signal processing in proteomics.

Computational proteomics applications are often imagined as a pipeline, where information is processed in each stage before it flows to the next one. Independent of the type of application, the first stage invariably consists of obtaining the raw mass spectrometric data from the spectrometer and preparing it for use in the later stages by enhancing the signal of interest while suppressing spurious components. Numerous approaches for preprocessing MS data have been described in the literature.