Expression of PTRF in PC3 cells modulates cholesterol dynamics and the actin cytoskeleton impacting secretion pathways

Expression of caveolin-1 is up-regulated in prostate cancer metastasis and is associated with aggressive recurrence of the disease. Intriguingly, caveolin-1 is also secreted from prostate cancer cell lines and has been identified in secreted prostasomes. Caveolin-1 is the major structural component of the plasma membrane invaginations called caveolae. Co-expression of the coat protein Polymerase I and transcript release factor (PTRF) is required for caveolae formation. We recently found that expression of caveolin-1 in the aggressive prostate cancer cell line PC-3 is not accompanied by PTRF, leading to noncaveolar caveolin-1 lipid rafts. Moreover, ectopic expression of PTRF in PC-3 cells sequesters caveolin-1 into caveolae. Here we quantitatively analyzed the effect of PTRF expression on the PC-3 proteome using stable isotope labeling by amino acids in culture and subcellular proteomics. We show that PTRF reduced the secretion of a subset of proteins including secreted proteases, cytokines, and growth regulatory proteins, partly via a reduction in prostasome secretion. To determine the cellular mechanism accounting for the observed reduction in secreted proteins we analyzed total membrane and the detergent-resistant membrane fractions. Our data show that PTRF expression selectively impaired the recruitment of actin cytoskeletal proteins to the detergent-resistant membrane, which correlated with altered cholesterol distribution in PC-3 cells expressing PTRF. Consistent with this, modulating cellular cholesterol altered the actin cytoskeleton and protein secretion in PC-3 cells. Intriguingly, several proteins that function in ER to Golgi trafficking were reduced by PTRF expression. Taken together, these results suggest that the noncaveolar caveolin-1 found in prostate cancer cells generates a lipid raft microenvironment that accentuates secretion pathways, possibly at the step of ER sorting/exit. Importantly, these effects could be modulated by PTRF expression.

Prostate cancer biomarkers and the emerging proteomic techniques used in biomarker research

Prostate cancer (CaP) is the second leading cause of cancer-related deaths in North American males and the most common newly diagnosed cancer in men world wide. Biomarkers are widely used for both early detection and prognostic tests for cancer. The current, commonly used biomarker for CaP is serum prostate specific antigen (PSA). However, the specificity of this biomarker is low as its serum level is not only increased in CaP but also in various other diseases, with age and even body mass index. Human body fluids provide an excellent resource for the discovery of biomarkers, with the advantage over tissue/biopsy samples of their ease of access, due to the less invasive nature of collection. However, their analysis presents challenges in terms of variability and validation. Blood and urine are two human body fluids commonly used for CaP research, but their proteomic analyses are limited both by the large dynamic range of protein abundance making detection of low abundance proteins difficult and in the case of urine, by the high salt concentration. To overcome these challenges, different techniques for removal of high abundance proteins and enrichment of low abundance proteins are used. Their applications and limitations are discussed in this review. A number of innovative proteomic techniques have improved detection of biomarkers. They include two dimensional differential gel electrophoresis (2D-DIGE), quantitative mass spectrometry (MS) and functional proteomic studies, i.e., investigating the association of post translational modifications (PTMs) such as phosphorylation, glycosylation and protein degradation. The recent development of quantitative MS techniques such as stable isotope labeling with amino acids in cell culture (SILAC), isobaric tags for relative and absolute quantitation (iTRAQ) and multiple reaction monitoring (MRM) have allowed proteomic researchers to quantitatively compare data from different samples. 2D-DIGE has greatly improved the statistical power of classical 2D gel analysis by introducing an internal control. This chapter aims to review novel CaP biomarkers as well as to discuss current trends in biomarker research from two angles: the source of biomarkers (particularly human body fluids such as blood and urine), and emerging proteomic approaches for biomarker research.

TiO2 nanofibers of different crystal phases for transesterification of alcohols with dimethyl carbonate

TiO2 nanofibers with different crystal phases have been discovered to be efficient catalysts for the transesterification of alcohols with dimethyl carbonate to produce corresponding methyl carbonates. Advantages of this catalytic system include excellent selectivity (>99%), general suitability to alcohols, reusability and ease of preparation and separation of fibrous catalysts. Activities of TiO2 catalysts were found to correlate with their crystal phases which results in different absorption abilities and activation energies on the catalyst surfaces. The kinetic isotope effect (KIE) investigation identified the rate-determining step, and the isotope labeling of oxygen-18 of benzyl alcohol clearly demonstrated the reaction pathway. Finally, the transesterification mechanism of alcohols with dimethyl carbonate catalyzed by TiO2 nanofibers was proposed, in which the alcohol released the proton to form benzyl alcoholic anion, and subsequently the anion attacks the carbonyl carbon of dimethyl carbonate to produce the target product of benzyl methyl carbonate.

Isolation and characterization of charge-tagged phenylperoxyl radicals in the gas phase : direct evidence for products and pathways in low temperature benzene oxidation

The phenylperoxyl radical has long been accepted as a critical intermediate in the oxidation of benzene and an archetype for arylperoxyl radicals in combustion and atmospheric chemistry. Despite being central to many contemporary mechanisms underpinning these chemistries, reports of the direct detection or isolation of phenylperoxyl radicals are rare and there is little experimental evidence connecting this intermediate with expected product channels. We have prepared and isolated two charge-tagged phenyl radical models in the gas phase [i.e., 4-(N,N,N-trimethylammonium) phenyl radical cation and 4-carboxylatophenyl radical anion] and observed their reactions with dioxygen by ion-trap mass spectrometry. Measured reaction rates show good agreement with prior reports for the neutral system (k(2)[(Me3N+)C6H4 center dot + O-2] = 2.8 x 10(-11) cm(3) molecule(-1) s(-1), Phi = 4.9%; k(2)[(-O2C)C6H4 center dot + O-2] = 5.4 x 10(-1)1 cm(3) molecule(-1) s(-1), Phi = 9.2%) and the resulting mass spectra provide unequivocal evidence for the formation of phenylperoxyl radicals. Collisional activation of isolated phenylperoxyl radicals reveals unimolecular decomposition by three pathways: (i) loss of dioxygen to reform the initial phenyl radical; (ii) loss of atomic oxygen yielding a phenoxyl radical; and (iii) ejection of the formyl radical to give cyclopentadienone. Stable isotope labeling confirms these assignments. Quantum chemical calculations for both charge-tagged and neutral phenylperoxyl radicals confirm that loss of formyl radical is accessible both thermodynamically and entropically and competitive with direct loss of both hydrogen atom and carbon dioxide.

Base-induced decomposition of alkyl hydroperoxides in the gas phase. Part 3. Kinetics and dynamics in HO-+CH3OOH, C2H5OOH, and tert-C4H9OOH reactions

The E-CO(2) elimination reactions of alkyl hydroperoxides proceed via abstraction of an (x-hydrogen by a base: X- + (RRHCOOH)-R-1-H-2 -> HX + (RRC)-R-1-C-2=O + HO-. Efficiencies and product distributions for the reactions of the hydroxide anion with methyl, ethyl, and tert-butyl hydroperoxides are studied in the gas phase. On the basis of experiments using three isotopic analogues, HO- + CH3OOH, HO- + CD3OOH, and H18O- + CH3OOH. the overall intrinsic reaction efficiency is determined to be 80% or greater. The E(CO)2 decomposition is facile for these methylperoxide reactions, and predominates over competing proton transfer at the hydroperoxide moiety. The CH3CH2OOH reaction displays a similar E(CO)2 reactivity, whereas proton transfer and the formation of HOO- are the exclusive pathways observed for (CH3)(3)COOH, which has no (x-hydrogen. All results are consistent with the E-CO(2) mechanism, transition state structure, and reaction energy diagrams calculated using the hybrid density functional B3LYP approach. Isotope labeling for HO- + CH3OOH also reveals some interaction between H2O and HO- within the E(CO)2 product complex [H2O center dot center dot center dot CH2=O center dot center dot center dot HO-]. There is little evidence, however. for the formation of the most exothermic products H2O + CH2(OH)O-, which would arise from nuclephilic condensation of CH2=O and HO-. The results suggest that the product dynamics are not totally statistical but are rather direct after the E-CO(2) transition state. The larger HO- + CH3CH2OOH system displays more statistical behavior during complex dissociation.

Ion-molecule reactions of O,S-Dimethyl methylphosphonothioate : Evidence for intramolecular sulfur oxidation during VX perhydrolysis

The alkaline perhydrolysis of the nerve agent O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate (VX) was investigated by studying the ion-molecule reactions of HOO(-) with O,S-dimethyl methylphosphonothioate in a modified linear ion-trap mass spectrometer. In addition to simple proton transfer, two other abundant product ions are observed at m/z 125 and 109 corresponding to the S-methyl methylphosphonothioate and methyl methylphosphonate anions, respectively. The structure of these product ions is demonstrated by a combination of collision-induced dissociation and isotope-labeling experiments that also provide evidence for their formation by nucleophilic reaction pathways, namely, (i) S(N)2 at carbon to yield the S-methyl methylphosphonothioate anion and (ii) nucleophilic addition at phosphorus affording a reactive pentavalent intermediate that readily undergoes internal sulfur oxidation and concomitant elimination of CH(3)SOH to yield the methyl methylphosphonate anion. Consistent with previous Solution phase observations of VX perhydrolysis, the toxic P-O cleavage product is not observed in this VX model system and theoretical calculations identify P-O cleavage to be energetically uncompetitive. Conversely, intramolecular sulfur oxidation is calculated to be extremely exothermic and kinetically accessible explaining its competitiveness with the facile gas phase proton transfer process. Elimination of a sulfur moiety deactivates the nerve agent VX and thus the intramolecular sulfur oxidation process reported here is also able to explain the selective perhydrolysis of the nerve agent to relatively nontoxic products.

Unimolecular reaction chemistry of a charge-tagged beta-hydroxyperoxyl radical

β-Hydroxyperoxyl radicals are formed during atmospheric oxidation of unsaturated volatile organic compounds such as isoprene. They are intermediates in the combustion of alcohols. In these environments the unimolecular isomerization and decomposition of β-hydroxyperoxyl radicals may be of importance, either through chemical or thermal activation. We have used ion-trap mass spectrometry to generate the distonic charge-tagged β-hydroxyalkyl radical anion, ˙CH2C(OH)(CH3)CH2C(O)O−, and investigated its subsequent reaction with O2 in the gas phase under conditions that are devoid of complicating radical–radical reactions. Quantum chemical calculations and master equation/RRKM theory modeling are used to rationalize the results and discern a reaction mechanism. Reaction is found to proceed via initial hydrogen abstraction from the γ-methylene group and from the β-hydroxyl group, with both reaction channels eventually forming isobaric product ions due to loss of either ˙OH + HCHO or ˙OH + CO2. Isotope labeling studies confirm that a 1,5-hydrogen shift from the β-hydroxyl functionality results in a hydroperoxyalkoxyl radical intermediate that can undergo further unimolecular dissociations. Furthermore, this study confirms that the facile decomposition of β-hydroxyperoxyl radicals can yield ˙OH in the gas phase.

In search of a hidden long-term isolated sub-chondritic 142Nd/144Nd reservoir in the deep mantle : implications for the Nd isotope systematics of the Earth

Here we search for evidence of the existence of a sub-chondritic 142Nd/144Nd reservoir that balances the Nd isotope chemistry of the Earth relative to chondrites. If present, it may reside in the source region of deeply sourced mantle plume material. We suggest that lavas from Hawai’i with coupled elevations in 186Os/188Os and 187Os/188Os, from Iceland that represent mixing of upper mantle and lower mantle components, and from Gough with sub-chondritic 143Nd/144Nd and high 207Pb/206Pb, are favorable samples that could reflect mantle sources that have interacted with an Early-Enriched Reservoir (EER) with sub-chondritic 142Nd/144Nd. High-precision Nd isotope analyses of basalts from Hawai’i, Iceland and Gough demonstrate no discernable 142Nd/144Nd deviation from terrestrial standards. These data are consistent with previous high-precision Nd isotope analysis of recent mantle-derived samples and demonstrate that no mantle-derived material to date provides evidence for the existence of an EER in the mantle. We then evaluate mass balance in the Earth with respect to both 142Nd/144Nd and 143Nd/144Nd. The Nd isotope systematics of EERs are modeled for different sizes and timing of formation relative to ε143Nd estimates of the reservoirs in the μ142Nd = 0 Earth, where μ142Nd is ((measured 142Nd/144Nd/terrestrial standard 142Nd/144Nd)−1 * 10−6) and the μ142Nd = 0 Earth is the proportion of the silicate Earth with 142Nd/144Nd indistinguishable from the terrestrial standard. The models indicate that it is not possible to balance the Earth with respect to both 142Nd/144Nd and 143Nd/144Nd unless the μ142Nd = 0 Earth has a ε143Nd within error of the present-day Depleted Mid-ocean ridge basalt Mantle source (DMM). The 4567 Myr age 142Nd–143Nd isochron for the Earth intersects μ142Nd = 0 at ε143Nd of +8 ± 2 providing a minimum ε143Nd for the μ142Nd = 0 Earth. The high ε143Nd of the μ142Nd = 0 Earth is confirmed by the Nd isotope systematics of Archean mantle-derived rocks that consistently have positive ε143Nd. If the EER formed early after solar system formation (0–70 Ma) continental crust and DMM can be complementary reservoirs with respect to Nd isotopes, with no requirement for significant additional reservoirs. If the EER formed after 70 Ma then the μ142Nd = 0 Earth must have a bulk ε143Nd more radiogenic than DMM and additional high ε143Nd material is required to balance the Nd isotope systematics of the Earth.

Use of 3D visualisation to enhance groundwater stable isotope data and its interpretation, Lockyer Valley, southeast Queensland

The use of stable isotope ratios δ18O and δ2H are well established in assessment of groundwater systems and their hydrology. The conventional approach is based on x/y plots and relation to various MWL’s, and plots of either ratio against parameters such as Clor EC. An extension of interpretation is the use of 2D maps and contour plots, and 2D hydrogeological vertical sections. An enhancement of presentation and interpretation is the production of “isoscapes”, usually as 2.5D surface projections. We have applied groundwater isotopic data to a 3D visualisation, using the alluvial aquifer system of the Lockyer Valley. The 3D framework is produced in GVS (Groundwater Visualisation System). This format enables enhanced presentation by displaying the spatial relationships and allowing interpolation between “data points” i.e. borehole screened zones where groundwater enters. The relative variations in the δ18O and δ2H values are similar in these ambient temperature systems. However, δ2H better reflects hydrological processes, whereas δ18O also reflects aquifer/groundwater exchange reactions. The 3D model has the advantage that it displays borehole relations to spatial features, enabling isotopic ratios and their values to be associated with, for example, bedrock groundwater mixing, interaction between aquifers, relation to stream recharge, and to near-surface and return irrigation water evaporation. Some specific features are also shown, such as zones of leakage of deeper groundwater (in this case with a GAB signature). Variations in source of recharging water at a catchment scale can be displayed. Interpolation between bores is not always possible depending on numbers and spacing, and by elongate configuration of the alluvium. In these cases, the visualisation uses discs around the screens that can be manually expanded to test extent or intersections. Separate displays are used for each of δ18O and δ2H and colour coding for isotope values.

Tracking the magmatic evolution of island arc volcanism : insights from a high-precision Pb isotope record of Montserrat, Lesser Antilles

The volcanic succession on Montserrat provides an opportunity to examine the magmatic evolution of island arc volcanism over a ∼2.5 Ma period, extending from the andesites of the Silver Hills center, to the currently active Soufrière Hills volcano (February 2010). Here we present high-precision double-spike Pb isotope data, combined with trace element and Sr-Nd isotope data throughout this period of Montserrat's volcanic evolution. We demonstrate that each volcanic center; South Soufrière Hills, Soufrière Hills, Centre Hills and Silver Hills, can be clearly discriminated using trace element and isotopic parameters. Variations in these parameters suggest there have been systematic and episodic changes in the subduction input. The SSH center, in particular, has a greater slab fluid signature, as indicated by low Ce/Pb, but less sediment addition than the other volcanic centers, which have higher Th/Ce. Pb isotope data from Montserrat fall along two trends, the Silver Hills, Centre Hills and Soufrière Hills lie on a general trend of the Lesser Antilles volcanics, whereas SSH volcanics define a separate trend. The Soufrière Hills and SSH volcanic centers were erupted at approximately the same time, but retain distinctive isotopic signatures, suggesting that the SSH magmas have a different source to the other volcanic centers. We hypothesize that this rapid magmatic source change is controlled by the regional transtensional regime, which allowed the SSH magma to be extracted from a shallower source. The Pb isotopes indicate an interplay between subduction derived components and a MORB-like mantle wedge influenced by a Galapagos plume-like source.

Mechanical properties of graphene : effects of layer number, temperature and isotope

Herein the mechanical properties of graphene, including Young’s modulus, fracture stress and fracture strain have been investigated by molecular dynamics simulations. The simulation results show that the mechanical properties of graphene are sensitive to the temperature changes but insensitive to the layer numbers in the multilayer graphene. Increasing temperature exerts adverse and significant effects on the mechanical properties of graphene. However, the adverse effect produced by the increasing layer number is marginal. On the other hand, isotope substitutions in graphene play a negligible role in modifying the mechanical properties of graphene.

Modelling carbon membranes for gas and isotope separation

Molecular modelling has become a useful and widely applied tool to investigate separation and diffusion behavior of gas molecules through nano-porous low dimensional carbon materials, including quasi-1D carbon nanotubes and 2D graphene-like carbon allotropes. These simulations provide detailed, molecular level information about the carbon framework structure as well as dynamics and mechanistic insights, i.e. size sieving, quantum sieving, and chemical affinity sieving. In this perspective, we revisit recent advances in this field and summarize separation mechanisms for multicomponent systems from kinetic and equilibrium molecular simulations, elucidating also anomalous diffusion effects induced by the confining pore structure and outlining perspectives for future directions in this field.

Asymmetrically decorated, doped porous graphene as an effective membrane for hydrogen isotope separation

We propose a new route to hydrogen isotope separation which exploits the quantum sieving effect in the context of transmission through asymmetrically decorated, doped porous graphenes. Selectivities of D2 over H2 as well as rate constants are calculated based on ab initio interaction potentials for passage through pure and nitrogen functionalized porous graphene. One-sided dressing of the membrane with metal provides the critical asymmetry needed for an energetically favorable pathway.