Intersection of selenoproteins and kinase signalling

The small, obscure group of selenoprotein oxidoreductases and the huge clan of kinases, the workhorses of cellular signalling, are rarely discussed together. Focusing on selenoproteins of unknown structures, we predict a thioredoxin-like fold for the Selenoprotein N (SelN) family and use the structure to rationalise effects of the muscular myopathy-linked mutations in the gene coding SelN. Discussing the recent prediction of a protein kinase-like domain in the Selenoprotein O (SelO), we reiterate evidence for an oxidoreductase function alongside the predicted kinase domain. Thus, we propose that SelO, the strongly conserved kinase-cum-tentative-oxidoreductase may reflect oxidoreductase regulation of kinase networks. Also, we use bibliometric and systems biology approach to explore the kinase–selenoprotein relationships that begin to emerge from the literature. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).     

Optimized perfusion‐based CUBIC protocol for the efficient whole‐body clearing and imaging of rat organs

Whole‐organ and whole‐body optical tissue clearing methods allowing imaging in 3 dimensions are an area of profound research interest. Originally developed to study nervous tissue, they have been successfully applied to all murine organs, yet clearing and imaging of rat peripheral organs is less advanced. Here, a modification of CUBIC clearing protocol is presented. It provides a rapid and simple approach to clear the entire adult rat organism and thus all organs within as little as 4 days. Upgraded perfusion‐based rat CUBIC protocol preserves both anatomical structure of organs and signal from proteinaceous fluorophores, and furthermore is compatible with antibody staining. Finally, it enables also volumetric cells analyses and is tailored for staining of calcium deposits within unsectioned soft tissues.      

Corpora amylacea from multiple sclerosis brain tissue consists of aggregated neuronal cells

In this report, we describe proteomic analysis of corpora amylacea collected by postmortem laser microdissection from multiple sclerosis (MS) brain lesions. Using low level protein loads (about 30 microg), a combination of two-dimensional electrophoresis with matrix-assisted laser desorption/ionization-time of flight mass spectrometry and database interrogations we identified 24 proteins of suspected neuronal origin. In addition to major cytoskeletal proteins like actin, tubulin, and vimentin, we identified a variety of proteins implicated specifically in cellular motility and plasticity (F-actin capping protein), regulation of apoptosis and senescence (tumor rejection antigen-1, heat shock proteins, valosin-containing protein, and ubiquitin-activating enzyme E1), and enzymatic pathways (glyceraldehyde-3-dehydrogenase, protein disulfide isomerase, protein disulfide isomerase related protein 5, lactate dehydrogenase). Samples taken from regions in the vicinity of corpora amylacea showed only traces of cellular proteins suggesting that these bodies may represent remnants of neuronal aggregates with highly polymerized cytoskeletal material. Our data provide evidence supporting the concept that biogenesis of corpora amylacea involves degeneration and aggregation of cells of neuronal origin.     

Pattern visual evoked potentials in the early diagnosis of optic neuropathy in the course of Graves' ophthalmopathy

THE AIM OF THE STUDY: To investigate by means of pattern visual evoked potentials (PVEPs) early neuropathic changes in Graves' ophthalmopathy (GO) patients without any clinical symptoms of optic neuropathy in order to evaluate the prevalence of subclinical optic neuropathy in GO patients and to elucidate whether there is a relationship between PVEP (P100 and N75 latency), intraocular pressure (IOP) and exophthalmometry. MATERIAL AND METHODS: Two groups of patients were examined: 15 patients with GO without clinical signs of dysthyroid optic neuropathy (DON) and 12 healthy controls. The correlations between the N75 and P100 latencies, IOP and Hertel exophthalmometry were investigated. RESULTS: The mean PVEP N75 and P100 latencies were significantly delayed in the GO uncomplicated with DON in comparison with controls (LP100- 106.2 +/- 4.4 ms vs. 102.4 +/- 2.7 ms, p < 0.01 and LN75- 79.0 +/- 3.7 ms vs. 73.9 +/- 2.8 ms, p < 0.001). In GO patients we documented a positive correlation between the LN75 latency and exophthalmometric readings (R = 0.51; p < 0.01). The value of LP100 and LN75 was above the normal limit in 5/30 eyes (17%) and in 3/30 eyes (10%) respectively. CONCLUSIONS: The assessment of PVEPs (especially the P100 latency) in GO patients without clinical signs of DON is a useful tool for the early diagnosis of optic nerve involvement.     

Vascular endothelial growth factor--structure and functions

Vascular endothelial cell growth factor (VEGF), originally described as a vascular permeability factor, is currently known as one of the main factors which regulate angiogenesis. It plays an important role in the regulation of normal as well as pathological angiogenesis. In this paper we try to shortly review the actual knowledge on VEGF protein family, its expression, VEGF receptors and role of VEGF in signal transduction. The aim of this review is also to summarize recent achievements in research on biological functions of vascular endothelial growth factor and their clinical applications.     

Characterization of Genomic Deletion Efficiency Mediated by Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 Nuclease System in Mammalian Cells

The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 nuclease system has provided a powerful tool for genome engineering. Double strand breaks may trigger nonhomologous end joining repair, leading to frameshift mutations, or homology-directed repair using an extrachromosomal template. Alternatively, genomic deletions may be produced by a pair of double strand breaks. The efficiency of CRISPR/Cas9-mediated genomic deletions has not been systematically explored. Here, we present a methodology for the production of deletions in mammalian cells, ranging from 1.3 kb to greater than 1 Mb. We observed a high frequency of intended genomic deletions. Nondeleted alleles are nonetheless often edited with inversions or small insertion/deletions produced at CRISPR recognition sites. Deleted alleles also typically include small insertion/deletions at predicted deletion junctions. We retrieved cells with biallelic deletion at a frequency exceeding that of probabilistic expectation. We demonstrate an inverse relationship between deletion frequency and deletion size. This work suggests that CRISPR/Cas9 is a robust system to produce a spectrum of genomic deletions to allow investigation of genes and genetic elements.     

Characterization of adducts formed in reactions of acrolein with thymidine and calf thymus DNA

Acrolein, an important industrial chemical and environmental contaminant, has been shown to interact with nucleic acids in vitro and in vivo. In this study, we examined the reactivity of acrolein towards thymidine and calf-thymus double- and single-stranded DNA in aqueous buffered solutions. LC-MS Analyses of the reaction mixture of acrolein with thymidine showed the formation of five structurally different adducts. The structures of the products were determined on the basis of mass spectrometry, UV absorbance, and (1)H- and (13)C-NMR spectroscopy. The adducts were identified as 3-(3-oxopropyl)thymidine (dT1), 3-[(tetrahydro-2,4-dihydroxypyran-3-yl)methyl]thymidine (dT2), 2-(hydroxymethyl)-5-(thymidin-3-yl)pent-2-enal (dT3), 3-hydroxy-2-methylidene-5-(thymidin-3-yl)pentanal (dT4), and 2-[(thymidin-3-yl)methyl]penta-2,4-dienal (dT5). The adducts dT2-dT5 were formed in reaction of dT1 with acrolein. In the reaction of acrolein with calf-thymus DNA, dT1 was the only adduct detected in the DNA hydrolysate.