Intersession reproducibility of mass spectrometry profiles and its effect on accuracy of multivariate classification models

MOTIVATION: The 'reproducibility' of mass spectrometry proteomic profiling has become an intensely controversial topic. The mere mention of concern over the 'reproducibility' of data generated from any particular platform can lead to the anxiety over the generalizability of its results and its role in the future of discovery proteomics. In this study, we examine the reproducibility of proteomic profiles generated by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) across multiple data-generation sessions. We analyze the problem in terms of the reproducibility of signals, reproducibility of discriminative features and reproducibility of multivariate classification models on profiles for serum samples from early lung cancer and healthy control subjects. RESULTS: Proteomic profiles in individual data-generation sessions experience within-session variability. We show that combining data from multiple sessions introduces additional (inter-session) noise. While additional noise can affect the discriminative analysis, we show that its average effect on profiles in our study is relatively small. Moreover, for the purposes of prediction on future (previously unseen) data, classifiers trained on multi-session data are able to adapt to inter-session noise and improve their classification accuracy.     

Overexpression of Cystathionine γ-Lyase Suppresses Detrimental Effects of Spinocerebellar Ataxia Type 3

Spinocerebellar ataxia type 3 (SCA3) is a polyglutamine (polyQ) disorder caused by a CAG repeat expansion in the ataxin-3 (ATXN3) gene resulting in toxic protein aggregation. Inflammation and oxidative stress are considered secondary factors contributing to the progression of this neurodegenerative disease. There is no cure that halts or reverses the progressive neurodegeneration of SCA3. Here we show that overexpression of cystathionine γ-lyase, a central enzyme in cysteine metabolism, is protective in a Drosophila model for SCA3. SCA3 flies show eye degeneration, increased oxidative stress, insoluble protein aggregates, reduced levels of protein persulfidation and increased activation of the innate immune response. Overexpression of Drosophila cystathionine γ-lyase restores protein persulfidation, decreases oxidative stress, dampens the immune response and improves SCA3-associated tissue degeneration. Levels of insoluble protein aggregates are not altered; therefore, the data implicate a modifying role of cystathionine γ-lyase in ameliorating the downstream consequence of protein aggregation leading to protection against SCA3-induced tissue degeneration. The cystathionine γ-lyase expression is decreased in affected brain tissue of SCA3 patients, suggesting that enhancers of cystathionine γ-lyase expression or activity are attractive candidates for future therapies.     

Glial cells in (patho)physiology

Neuroglial cells define brain homeostasis and mount defense against pathological insults. Astroglia regulate neurogenesis and development of brain circuits. In the adult brain, astrocytes enter into intimate dynamic relationship with neurons, especially at synaptic sites where they functionally form the tripartite synapse. At these sites, astrocytes regulate ion and neurotransmitter homeostasis, metabolically support neurons and monitor synaptic activity; one of the readouts of the latter manifests in astrocytic intracellular Ca(2+) signals. This form of astrocytic excitability can lead to release of chemical transmitters via Ca(2+) -dependent exocytosis. Once in the extracellular space, gliotransmitters can modulate synaptic plasticity and cause changes in behavior. Besides these physiological tasks, astrocytes are fundamental for progression and outcome of neurological diseases. In Alzheimer's disease, for example, astrocytes may contribute to the etiology of this disorder. Highly lethal glial-derived tumors use signaling trickery to coerce normal brain cells to assist tumor invasiveness. This review not only sheds new light on the brain operation in health and disease, but also points to many unknowns.     

Synthesis and cytotoxic activities of estrone and estradiol cis-dichloroplatinum(II) complexes

Sixteen platinum(II) complexes of estrone and estradiol were synthesized in this work to evaluate their cytotoxic activity against several cancer cell lines including estrogen dependent and independent ones. The synthesis of all the complexes was done in three steps. The reaction of steroids with dibromoalkanes was followed by a reaction of the bromoalkyl steroids with 2-(aminomethyl)pyridine or 2-(2-aminoethyl)pyridine. The last step was a reaction of steroidal diamino ligands with potassium tetrachloroplatinate to obtain the desired platinum(II) complexes. Cytotoxicity assays showed that most of the complexes prepared are active against the cancer cell lines used—CEM, U-2 OS, MCF7, MCF7 AL, MDA-MB-468, BT-474, BT-549, and BJ fibroblasts. The six-membered platinum complexes are more active than five-membered ones.     

Synthesis and antiproliferative activity of two new tiazofurin analogues with 2'-amido functionalities

Two novel tiazofurin analogues 2 and 3 were synthesized starting from d-glucose. The key step of the synthesis was the efficient one-step hydrogen sulfide-mediated conversion of 2-azido-3-O-acyl-ribofuranosyl cyanides to the corresponding 2-amido thiocarboxamides. Compounds 2 and 3 were evaluated for their in vitro antiproliferative activity against certain human tumour cell lines. Remarkably, compound 2 was found to be 570-fold more potent than tiazofurin against MCF-7 cells, while compound 3 showed the most powerful cytotoxicity against HT-29 cancer cells, being almost 100-fold more active than tiazofurin.     

Impact of Previous Virological Treatment Failures and Adherence on the Outcome of Antiretroviral Therapy in 2007

Background

Combination antiretroviral treatment (cART) has been very successful, especially among selected patients in clinical trials. The aim of this study was to describe outcomes of cART on the population level in a large national cohort.

Methods

Characteristics of participants of the Swiss HIV Cohort Study on stable cART at two semiannual visits in 2007 were analyzed with respect to era of treatment initiation, number of previous virologically failed regimens and self reported adherence. Starting ART in the mono/dual era before HIV-1 RNA assays became available was counted as one failed regimen. Logistic regression was used to identify risk factors for virological failure between the two consecutive visits.

Results

Of 4541 patients 31.2% and 68.8% had initiated therapy in the mono/dual and cART era, respectively, and been on treatment for a median of 11.7 vs. 5.7 years. At visit 1 in 2007, the mean number of previous failed regimens was 3.2 vs. 0.5 and the viral load was undetectable (<50 copies/ml) in 84.6% vs. 89.1% of the participants, respectively. Adjusted odds ratios of a detectable viral load at visit 2 for participants from the mono/dual era with a history of 2 and 3, 4, >4 previous failures compared to 1 were 0.9 (95% CI 0.4–1.7), 0.8 (0.4–1.6), 1.6 (0.8–3.2), 3.3 (1.7–6.6) respectively, and 2.3 (1.1–4.8) for >2 missed cART doses during the last month, compared to perfect adherence. From the cART era, odds ratios with a history of 1, 2 and >2 previous failures compared to none were 1.8 (95% CI 1.3–2.5), 2.8 (1.7–4.5) and 7.8 (4.5–13.5), respectively, and 2.8 (1.6–4.8) for >2 missed cART doses during the last month, compared to perfect adherence.

Conclusions

A higher number of previous virologically failed regimens, and imperfect adherence to therapy were independent predictors of imminent virological failure.     

Effect of alternating the magnetic field on phosphate metabolism in the nervous system of Helix pomatia

The effect of extremely low frequency magnetic fields (50 Hz, 0.5 mT) - ELF-MF, on phosphate metabolism has been studied in the isolated ganglions of the garden snail Helix pomatia, after 7 and 16 days of snail exposure to ELF-MF. The influence of ELF-MF on the level of phosphate compounds and intracellular pH was monitored by 31P NMR spectroscopy. Furthermore, the activity of enzymes involved in phosphate turnover, total ATPases, Na+/K+-ATPase and acid phosphatase has been measured. The exposure of snails to the ELF-MF for the period of 7 days shifted intracellular pH toward more alkaline conditions, and increased the activity of investigated enzymes. Prolonged exposure to the ELF-MF for the period of 16 days caused a decrease of PCr and ATP levels and decreased enzyme activity, compared to the 7-day treatment group. Our results can be explained in terms of: 1. increase in phosphate turnover by exposure to the ELF-MF for the period of 7 days, and 2. adaptation of phosphate metabolism in the nervous system of snails to prolonged ELF-MF exposure.     

Zinc‐induced oxidative stress in Verbascum thapsus is caused by an accumulation of reactive oxygen species and quinhydrone in the cell wall

Oxidative stress is one aspect of metal toxicity. Zinc, although unable to perform univalent oxido‐reduction reactions, can induce the oxidative damage of cellular components and alter antioxidative systems. Verbascum thapsus L. plants that were grown hydroponically were exposed to 1 and 5 mM Zn²⁺. Reactive oxygen species (ROS) accumulation was demonstrated by the fluorescent probe H₂DCFDA and EPR measurements. The extent of zinc‐induced oxidative damage was assessed by measuring the level of protein carbonylation. Activities and isoform profiles of some antioxidant enzymes and the changes in ascorbate and total phenolic contents of leaves and roots were determined. Stunted growth because of zinc accumulation, preferentially in the roots, was accompanied by H₂O₂ production in the leaf and root apoplasts. Increased EPR signals of the endogenous oxidant quinhydrone, ^?CH₃ and ^?OH, were found in the cell walls of zinc‐treated plants. The activities of the antioxidative enzymes ascorbate peroxidase (APX) (EC 1.11.1.11), soluble superoxide dismutase (SOD) (EC 1.15.1.1), peroxidase (POD), (EC 1.11.1.7) and monodehydroascorbate reductase (EC 1.6.5.4) were increased; those of glutathione reductase (EC 1.6.4.2), dehydroascorbate reductase (EC 1.8.5.1) and ascorbate oxidase (AAO) (EC 1.10.3.3) were decreased with zinc treatment. Zinc induced a cell‐wall‐bound SOD isoform in both organs. Leaves accumulated more ascorbate and phenolics in comparison to roots. We propose a mechanism for zinc‐promoted oxidative stress in V. thapsus L. through the generation of charge transfer complexes and quinhydrone because of phenoxyl radical stabilisation by Zn²⁺ in the cell wall. Our results suggest that the SOD and APX responses are mediated by ROS accumulation in the apoplast. The importance of the POD/Phe/AA (ascorbic acid) scavenging system in the apoplast is also discussed.     

Development of anthropometric and physical performance profiles of young elite male soccer players: a longitudinal study

The purpose of the present longitudinal study was to explore distinctive anthropometric and physical performance characteristics of young soccer players between the age of 11 and 14 and to reveal the performance at the age of 11, which contributes to the later success. Male players of the best national male squads of the 'cadet league' (14 years of age; n = 26) were annually tested starting from the age of 11 for body size and composition, flexibility, power, coordination, and agility. Randomly selected untrained but physically active age-matched boys (n = 63) were also tested over 4 consecutive years. The results revealed no difference between 2 groups regarding the body size and composition (p > 0.05). The differences in flexibility emerged only at the later age, whereas the differences regarding the explosive power (as assessed by various jumps) were moderate and partly inconsistent. The most prominent advantage of the soccer players over the control subjects during the entire tested age period appeared to be movement agility and coordination (p < 0.01). Therefore, the explosive muscle power and, in particular, the agility and coordination characterize elite soccer players of 11-14 years of age but not the body size and body composition. In addition, the agility and coordination could be among the crucial factors of future success in 11-year-old players and, therefore, should be used for early selection.     

Changes in liver protein abundance in inbred alcohol-preferring rats due to chronic alcohol exposure, as measured through a proteomics approach

This study compares the total liver proteome of inbred alcohol‐preferring line (iP) rats exposed to alcohol with iP rats without alcohol experience. Rat liver proteins were extracted using a three‐step procedure. Each of the three solutions solubilizes a different set of proteins. The extracted proteins were separated by 2‐DE. Scanned gels of two sample groups, alcohol‐exposed iP and alcohol‐naïve iP, were compared, revealing many protein spots with significantly higher or lower densities. These spots were cut from the gel, destained, and subjected to trypsin digestion and subsequent identification by LC‐MS/MS. Twenty‐four individual rats, 12 alcohol‐naïve, and 12 alcohol‐exposed, were used in this study. Two groups, each containing six naïve and six exposed animals, were created for statistical comparison. For the first group, 64 spots were observed to have statistically significant intensity differences upon alcohol exposure across all three extracts while 118 such spots were found in the second group. There were 113 unique proteins in both groups together. The majority of these proteins were enzymes. Significant changes are observed for three major metabolic pathways: glycolysis, gluconeogenesis, and fatty acid β‐oxidation. In addition, enzymes involved in protein synthesis and antioxidant activity show significant changes in abundance in response to alcohol exposure.