Gain and loss of phosphorylation sites in human cancer

MOTIVATION: Coding-region mutations in human genes are responsible for a diverse spectrum of diseases and phenotypes. Among lesions that have been studied extensively, there are insights into several of the biochemical functions disrupted by disease-causing mutations. Currently, there are more than 60 000 coding-region mutations associated with inherited disease catalogued in the Human Gene Mutation Database (HGMD, August 2007) and more than 70 000 polymorphic amino acid substitutions recorded in dbSNP (dbSNP, build 127). Understanding the mechanism and contribution these variants make to a clinical phenotype is a formidable problem. RESULTS: In this study, we investigate the role of phosphorylation in somatic cancer mutations and inherited diseases. Somatic cancer mutation datasets were shown to have a significant enrichment for mutations that cause gain or loss of phosphorylation when compared to our control datasets (putatively neutral nsSNPs and random amino acid substitutions). Of the somatic cancer mutations, those in kinase genes represent the most enriched set of mutations that disrupt phosphorylation sites, suggesting phosphorylation target site mutation is an active cause of phosphorylation deregulation. Overall, this evidence suggests both gain and loss of a phosphorylation site in a target protein may be important features for predicting cancer-causing mutations and may represent a molecular cause of disease for a number of inherited and somatic mutations.     

Role of heat shock protein 27 in cytoskeletal remodeling of the airway smooth muscle cell.

Remodeling of the airway smooth muscle (ASM) cell has been proposed to play an important role in airway hyperresponsiveness. Using a functional assay, we have assessed remodeling of the cultured rat ASM cell and the role of heat shock protein (HSP) 27 in that process. To probe remodeling dynamics, we measured spontaneous motions of an individual Arg-Gly-Asp-coated microbead that was anchored to the cytoskeleton. We reasoned that the bead could not move unless the microstructure to which it is attached rearranged; if so, then its mean square displacement (MSD) would report ongoing internal reorganizations over time. Each bead displayed a random, superdiffusive motion; MSD increased with time as approximately t(1.7), whereas an exponent of unity would be expected for a simple passive diffusion. Increasing concentrations of cytochalasin-D or latrunculin-A caused marked increases in the MSD, whereas colchicine did not. Treatments with PDGF or IL-1beta, but not transforming growth factor-beta, caused decreases in the MSD, the extent of which rank-ordered with the relative potency of these agents in eliciting the phosphorylation of HSP27. The chemical stressors anisomycin and arsenite each increased the levels of HSP27 phosphorylation and, at the same time, decreased bead motions. In particular, arsenite prevented and even reversed the effects of cytochalasin-D on bead motions. Finally, ASM cells overexpressing phospho-mimicking human HSP27, but not wild-type or phosphorylation-deficient HSP27, exhibited decreases in bead motions that were comparable to the arsenite response. Taken together, these results show that phosphorylated HSP27 favors reduced bead motions that are probably due to stabilization of the actin cytoskeleton.     

Pentadecapeptide BPC 157 and its effects on a NSAID toxicity model: diclofenac-induced gastrointestinal, liver, and encephalopathy lesions

AimsWe attempted to fully antagonize the extensive toxicity caused by NSAIDs (using diclofenac as a prototype).Main methodsHerein, we used the stable gastric pentadecapeptide BPC 157 (GEPPPGKPADDAGLV, MW 1419), an anti-ulcer peptide shown to be efficient in inflammatory bowel disease clinical trials (PL 14736) and various wound treatments with no toxicity reported. This peptide was given to antagonize combined gastrointestinal, liver, and brain toxicity induced by diclofenac (12.5 mg/kg intraperitoneally, once daily for 3 days) in rats.Key findingsAlready considered a drug that can reverse the toxic side effects of NSAIDs, BPC 157 (10 μg/kg, 10 ng/kg) was strongly effective throughout the entire experiment when given (i) intraperitoneally immediately after diclofenac or (ii) per-orally in drinking water (0.16 μg/mL, 0.16 ng/mL). Without BPC 157 treatment, at 3 h following the last diclofenac challenge, we encountered a complex deleterious circuit of diclofenac toxicity characterized by severe gastric, intestinal and liver lesions, increased bilirubin, aspartate transaminase (AST), alanine transaminase (ALT) serum values, increased liver weight, prolonged sedation/unconsciousness (after any diclofenac challenge) and finally hepatic encephalopathy (brain edema particularly located in the cerebral cortex and cerebellum, more in white than in gray matter, damaged red neurons, particularly in the cerebral cortex and cerebellar nuclei, Purkinje cells and less commonly in the hippocampal neurons).SignificanceThe very extensive antagonization of diclofenac toxicity achieved with BPC 157 (μg-/ng-regimen, intraperitoneally, per-orally) may encourage its further use as a therapy to counteract diclofenac- and other NSAID-induced toxicity.     

Mathematical modelling and process optimization of a continuous 5-stage bioreactor cascade for production of poly[-(R)-3-hydroxybutyrate] by Cupriavidus necator

A multistage system for poly(hydroxyalkanoate) (PHA) production consisting of five continuous stirred tank reactors in series (5-CSTR) with Cupriavidus necator DSM 545 as production strain was modelled using formal kinetic relations. Partially growth-associated production of PHA under nitrogen limited growth was chosen as modelling strategy, thus the Luedeking-Piret’s model of partial growth-associated product synthesis was applied as working hypothesis. Specific growth rate relations adjusted for double substrate (C and N source) limited growth according to Megee et al. and Mankad-Bungay relation were tested. The first stage of the reactor cascade was modelled according to the principle of nutrient balanced continuous biomass production system, the second one as two substrate controlled process, while the three subsequent reactors were adjusted to produce PHB under continuous C source fed and nitrogen deficiency. Simulated results of production obtained by the applied mathematical models and computational optimization indicate that PHB productivity of the whole system could be significantly increased (from experimentally achieved 2.14 g L^?1 h^?1 to simulated 9.95 g L^?1 h^?1) if certain experimental conditions would have been applied (overall dilution rate, C and N source feed concentration). Additionally, supplemental feeding strategy for switching from batch to continuous mode of cultivation was proposed to avoid substrate inhibition.     

Polyhydroxyalkanoate production from whey by Pseudomonas hydrogenovora

Whey permeate from dairy industry was hydrolyzed enzymatically to cleave its main carbon source, lactose, to glucose and galactose. The hydrolysis products were chosen as carbon sources for the production of poly-3-hydroxybutyric acid (PHB) by Pseudomonas hydrogenovora. In shaking flask experiments, the utilization of whey permeate as a cheap substrate was compared to the utilization of pure glucose and galactose for bacterial growth under balanced conditions as well as for the production of PHB under nitrogen limitation. After determination of the inhibition constant Ki for sodium valerate on biomass production (Ki=1.84 g/l), the biosynthesis of PHA co-polyesters containing 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) units from hydrolyzed whey permeate and valerate was investigated. The application of hydrolyzed whey permeate turned out to be advantageous compared with the utilization of pure sugars. Therefore, fermentation under controlled conditions in a bioreactor was performed with hydrolyzed whey permeate to obtain detailed kinetic data (maximum specific growth rate, mu max=0.291/h, maximum polymer concentration, 1.27 g/l PHB), values for molecular mass distribution (weight average molecular weight Mw=353.5 kDa, polydispersity index PDI=3.8) and thermo analytical data. The fermentation was repeated with co-feeding of valerate (maximum specific growth rate, mu(max)=0.201/h, maximum polymer concentration, 1.44 g/l poly-(3HB-co-21%-3HV), weight average molecular weight M(w)=299.2 kDa, polydispersity index PDI=4.3).     

Effect of Wortmannin on the repair profiles of DNA double-strand breaks in the whole genome and in interstitial telomeric sequences of Chinese hamster cells

The DNA breakage detection-fluorescence in situ hybridization (DBD-FISH) procedure was applied to analyze the effect of Wortmannin (WM) in the rejoining kinetics of ionizing radiation-induced DNA double-strand breaks (DSBs) in the whole genome and in the long interstitial telomeric repeat sequence (ITRS) blocks from Chinese hamster cell lines. The results indicate that the ITRS blocks from wild-type Chinese hamster cell lines, CHO9 and V79B, exhibit a slower initial rejoining rate of ionizing radiation-induced DSBs than the genome overall. Neither Rad51C nor the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) activities, involved in homologous recombination (HR) and in non-homologous end-joining (NHEJ) pathways of DSB repair respectively, influenced the rejoining kinetics within ITRS in contrast to DNA sequences in the whole genome. Nevertheless, DSB removal rate within ITRS was decreased in the absence of Ku86 activity, though at a lower affectation level than in the whole genome, thus homogenizing both rejoining kinetics rates. WM treatment slowed down the DSB rejoining kinetics rate in ITRS, this effect being more pronounced in the whole genome, resulting in a similar pattern to that of the Ku86 deficient cells. In fact, no WM effect was detected in the Ku86 deficient Chinese hamster cells, so probably WM does not add further impairment in DSB rejoining than that resulted as a consequence of absence of Ku activity. The same slowing effect was also observed after treatment of Rad51C and DNA-PKcs defective hamster cells by WM, suggesting that: (1) there is no potentiation of the HR when the NHEJ is impaired by WM, either in the whole genome or in the ITRS, and (2) that this impairment may probably involve more targets than DNA-PKcs. These results suggest that there is an intragenomic heterogeneity in DSB repair, as well as in the effect of WM on this process.     

Population traits and colonization success of non-native Eurasian perch (<Emphasis Type="Italic">Perca fluviatilis</Emphasis>) 35 years after its first appearance in the Mediterranean Lake Skadar

Abundance, spatial distribution, population structure and growth of non-native Eurasian perch (Perca fluviatilis) were examined in the Lake Skadar, a large, unstratified lake in the Mediterranean region inhabited by several endemic, rare and threatened fish species. Fish were caught in the infra-littoral and littoral habitats of the northern and central parts of the lake using multi-mesh gill nets over three consecutive years. Eurasian perch was among the most dominant species in both habitats. The mean relative abundance is - NPUE (0.556 individuals m^?2) and relative biomass is - WPUE (23.56 g m^?2) (years and habitats combined). Its population consisted primarily of individuals in first, second and third year of life span (0+???2+ age classes). The youngest fish in first and second year showed low mortality rates, older fish in third, fourth, fifth and sixth year of life span (age classes 2+???5+) experienced great losses, with mortality rates ranging from 0.6–1.0. The von Bertalanffy growth curve formula, expressing the expected total length L _t ?=?36.98 (1-e^{-0.23 (t?+?1.018)}) with growth performance value Φ ^’ ?=?2.50, revealed fast growth-in-length. Length-to-weight relationship was W_t?=?6.2?×?10^?3 L _t ^3.27, indicating positive growth-in-weight. It has been concluded that 35 years after the first finding in the Lake Skadar, Eurasian perch adapted well to local conditions in this Mediterranean environment, with the life span changed in favor of fast growth and early maturation.     

The stacking interactions of bipyridine complexes: the influence of the metal ion type on the strength of interactions

The strength of the stacking interactions in the bipy complexes of nickel, palladium, and platinum, [M(CN)₂ bipy]₂ (M?=?Ni, Pd, Pt), was calculated using the ωB97xD/def2-TZVP method. The results show that for all considered geometries, interactions are the strongest for platinum, and weakest for nickel complexes, as a result of higher dispersion contributions of platinum over the palladium and nickel complexes. It was also shown that strength of interactions considerably rises with an increase of the stacking overlap area. As a consequence of the favorable electrostatic term, the strength of interactions also rises when metal atom and cyano ligands are involved in the overlap with bipy ligand. The strongest interaction was calculated in the platinum complex, for the geometry that has overlap of metal and cyano ligands with bipy ligand with an energy of -39.80 kcal mol^-1. The energies for similar geometries of palladium and nickel complexes are -34.60 and -32.45 kcal mol^-1. These energies, remarkably, exceed the strength of the stacking interactions between organic aromatic molecules. These results can be of importance in all systems with stacking interactions, from materials to biomolecules.