Cluster analysis of multiplex ligation-dependent probe amplification data in choroidal melanoma.

PurposeTo determine underlying correlations in multiplex ligation-dependent probe amplification (MLPA) data and their significance regarding survival following treatment of choroidal melanoma (CM).MethodsMLPA data were available for 31 loci across four chromosomes (1p, 3, 6, and 8) in tumor material obtained from 602 patients with CM treated at the Liverpool Ocular Oncology Center (LOOC) between 1993 and 2012. Data representing chromosomes 3 and 8q were analyzed in depth since their association with CM patient survival is well-known. Unsupervised k-means cluster analysis was performed to detect latent structure in the data set. Principal component analysis (PCA) was also performed to determine the intrinsic dimensionality of the data. Survival analyses of the identified clusters were performed using Kaplan-Meier (KM) and log-rank statistical tests. Correlation with largest basal tumor diameter (LTD) was investigated.ResultsChromosome 3: A two-cluster (bimodal) solution was found in chromosome 3, characterized by centroids at unilaterally normal probe values and unilateral deletion. There was a large, significant difference in the survival characteristics of the two clusters (log-rank, p<0.001; 5-year survival: 80% versus 40%). Both clusters had a broad distribution in LTD, although larger tumors were characteristically in the poorer outcome group (Mann-Whitney, p<0.001). Threshold values of 0.85 for deletion and 1.15 for gain optimized the classification of the clusters. PCA showed that the first principal component (PC1) contained more than 80% of the data set variance and all of the bimodality, with uniform coefficients (0.28±0.03). Chromosome 8q: No clusters were found in chromosome 8q. Using a conventional threshold-based definition of 8q gain, and in conjunction with the chromosome 3 clusters, three prognostic groups were identified: chromosomes 3 and 8q both normal, either chromosome 3 or 8q abnormal, and both chromosomes 3 and 8q abnormal. KM analysis showed 5-year survival figures of approximately 97%, 80%, and 30% for these prognostic groups, respectively (log-rank, p<0.001). All MLPA probes within both chromosomes were significantly correlated with each other (Spearman, p<0.001).ConclusionsWithin chromosome 3, the strong correlation between the MLPA variables and the uniform coefficients from the PCA indicates a lack of evidence for a signature gene that might account for the bimodality we observed. We hypothesize that the two clusters we found correspond to binary underlying states of complete monosomy or disomy 3 and that these states are sampled by the complete ensemble of probes. Consequently, we would expect a similar pattern to emerge in higher-resolution MLPA data sets. LTD may be a significant confounding factor. Considering chromosome 8q, we found that chromosome 3 cluster membership and 8q gain as traditionally defined have an indistinguishable impact on patient outcome

Chrome-spinel geochemistry of the northern Oman-United Arab Emirates ophiolite

The Oman ophiolite is the largest and best preserved ophiolite in the world and records a switch from mid-ocean ridge (MOR) to supra-subduction zone (SSZ) setting. This study investigates the geochemical variability of chrome-spinel in the mantle sequence of the poorly known United Arab Emirates (U.A.E.) part of the northern Oman-U.A.E. ophiolite. Extensive field work was carried out and 260 samples collected for petrogenetic studies and geochemical mapping of the U.A.E. mantle. Chrome-spinel geochemistry provides valuable information on bom the residual mantle and on the nature and extent of melt-rock reaction. In particular, it is used to fingerprint the compositions of the magmas that interacted with the mantle lithosphere. This study also develops a new method to analyse gallium in chrome-spinel by Laser Ablation-ICP-MS, and successfully uses it to improve the tectonic discrimination of chrome-spinel. The results show that the U.A.E. mantle lithosphere formed at a MOR-type setting and was modified by melt-rock reaction with MORB-type and SSZ-type melts. This history of melt infiltration strongly resembles the magmatic history of the crustal sequence in each of the Aswad and Khawr Fakkan Blocks. Geochemical mapping illustrates a strong spatial control on the pattern of melt infiltration in the mantle and constrains the proximity of each mantle domain with respect to the subduction zone. The Khawr Fakkan mantle extensively interacted with boninitic melts during subduction initiation. Thus, it was closer to the subduction zone than the Aswad mantle which predominantly interacted with island-arc tholeiite melts. Importantly, this work demonstrates for the first time that the Dibba Zone peridotites originate from pre-existing 'true' MOR mantle lithosphere between the trench and the main body of the ophiolite. A further important conclusion is that the mantle lithosphere of the northern Oman-U.A.E. ophiolite was not the source region for the SSZ magmatism. Previous workers proposed that the plane of detachment and the subduction zone were the same, which implies that the mantle of the ophiolite was the source of the SSZ magmatism. Instead, this study proposes that detachment of the ophiolite took place at a shallower level than the plane of the subduction zone and thus provides strong evidence for a subduction zone at a still deeper level. During detachment, the ophiolite incorporated slices of ultramafic rock near the trench (i.e. the Dibba Zone peridotites) as it bulldozed its way over the underlying plate and onto the continental margin of Arabia.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Aluminum modulation of proteolytic activities

The effect of aluminum ions on the activity of proteolyic activities, mainly serine proteases and calpains, has been examined. Aluminum affects the biological activity of proteolytic activities either through a direct effect on the enzyme molecule or through a deregulation of the control mechanisms acting on them. Binding of the ion, most likely results in molecular rearrangements affecting both the substrates binding site and the site involved in the recognition of macromolecular inhibitors. As whole, the data reported clearly indicate that aluminum significatively affects the intracellular protein turnover, most likely triggering catastrophic events for the cellular life. The physiopathological significance of these effects has been discussed, in particular for neurological disorders (the Alzheimer's disease included) where an imbalance of proteolytic as well as antiproteolytic systems appears a crucial event both for the formation of neuritic plaques and neurofibrillary tangles which are the major hallmarks of the disease. © 2002 Elsevier Science B.V. All rights reserved

Acid-Stable Serine Proteinase Inhibitors in the Urine of Alzheimer Disease Subjects

A comparative study of the levels of acid-stable proteinase inhibitors (kallikrein and trypsin inhibitors) in the urine of healthy and Alzheimer subjects, of both sexes, has been performed. A preliminary characterization of the purified inhibitors indicates that the urinary antitryptic activity is accounted for by the presence of the well known Urinary Trypsin Inhibitor (UTI) while an apparently new molecule appears to be responsible for the anti kallikrein activity. The urinary levels of kallikrein inhibitors are very similar in healthy and sick subjects while the levels of trypsin inhibitors appear significatively increased in Alzheimer subjects of both sexes. The data presented here support the hypothesis that unpaired proteolytic processes could be involved in the pathogenesis of Alzheimer's disease and suggest that the levels of urinary acid-stable inhibitors may prove to be useful markers of the disease

Structure/activity virtual screening and in vitro testing of small molecule inhibitors of 8-hydroxy-5-deazaflavin:NADPH oxidoreductase from gut methanogenic bacteria

Virtual screening techniques and in vitro binding/inhibitory assays were used to search within a set of more than 8,000 naturally occurring small ligands for candidate inhibitors of 8-hydroxy-5-deazaflavin:NADPH oxidoreductase (FNO) from Methanobrevibacter smithii, the enzyme that catalyses the bidirectional electron transfer between NADP+ and F420H2 during the intestinal production of CH4 from CO2. In silico screening using molecular docking classified the ligand-enzyme complexes in the range between − 4.9 and − 10.5 kcal/mol. Molecular flexibility, the number of H-bond acceptors and donors, the extent of hydrophobic interactions, and the exposure to the solvent were the major discriminants in determining the affinity of the ligands for FNO. In vitro studies on a group of these ligands selected from the most populated/representative clusters provided quantitative kinetic, equilibrium, and structural information on ligands’ behaviour, in optimal agreement with the predictive computational results

50 Hz Extremely Low Frequency Electromagnetic Fields Enhance Protein Carbonyl Groups Content in Cancer Cells: Effects on Proteasomal Systems

Electromagnetic fields are an assessed cause of prolonging free radicals lifespan. This study was carried out to investigate the influence of extremely low frequency electromagnetic fields on protein oxidation and on the 20S proteasome functionality, the complex responsible for the degradation of oxidized proteins. Caco 2 cells were exposed, for 24–72 hours, to 1 mT, 50 Hz electromagnetic fields. The treatment induced a time-dependent increase both in cell growth and in protein oxidation, more evident in the presence of TPA, while no changes in cell viability were detected. Exposing the cells to 50 Hz electromagnetic fields caused a global activation of the 20S proteasome catalytic components, particularly evident at 72 hours exposure and in the presence of TPA. The finding that EGCG, a natural antioxidant compound, counteracted the field-related pro-oxidant effects demonstrates that the increased proteasome activity was due to an enhancement in intracellular free radicals

Aerobic training and angiogenesis activation in patients with stable chronic heart failure: a preliminary report.

The pathophysiology of chronic heart failure (CHF) involves multiple hystologic and molecular alterations. To determine the effects of physical training on circulating endothelial progenitor cells (EPCs), angiogenesis (angiogenin, angiopoietin-1 and -2, VEGF, Tie-2, SDF-1α) and inflammation (IL-6, CRP), we compared data obtained from 11 CHF pts before and after 3 months aerobic exercise training, to those from 10 non trained CHF pts (CHF-C group, age 64 + 2 years, NYHA 2). At the end of the study, EPCs count and AP-2 serum levels significantly increased in the CHF-TR group. These preliminary data suggest a significant effect of even a short program of physical training on angiogenic activation and endothelial dysfunction

Karyological and flow cytometric evidence of triploid specimens in Bufo viridis (Amphibia Anura)

Karyological and flow cytometric (FCM) analyses were performed on a group of 14 green toads of the Bufo viridis species from seven Eurasian populations. Both approaches gave concordant results concerning the DNA ploidy level. All the populations examined were represented exclusively by diploid or tetraploid specimens, except one, where triploids were found. Results evidenced an interpopulation variability in DNA content against the same ploidy level, as well as an unusually high number of triploids in a particular reproductive place. The origin of polyploidy and the presence and persistence of a high number of triploids in a particular population are discussed