Primer extension based quantitative polymerase chain reaction reveals consistent differences in the methylation status of the MGMT promoter in diffusely infiltrating gliomas (WHO grade II-IV) of adults

Diffusely infiltrating gliomas (WHO grade II-IV) are the most common primary brain tumours in adults. These tumours are not amenable to cure by surgery alone, so suitable biomarkers for adjuvant modalities are required to guide therapeutic decision-making. Epigenetic silencing of the O(6)-methylguanine-DNA methyltransferase (MGMT) gene by promoter methylation has been associated with longer survival of patients with high-grade gliomas who receive alkylating chemotherapy; and molecular testing for the methylation status of the MGMT promoter sequence is regarded as among the most relevant of such markers. We have developed a primer extension-based assay adapted to formalin-fixed paraffin-embedded tissues that enables quantitative assessment of the methylation status of the MGMT promoter. The assay is very sensitive, highly reproducible, and provides valid test results in nearly 100% of cases. Our results indicate that oligodendrogliomas, empirically known to have a relatively favourable prognosis, are also the most homogeneous entities in terms of MGMT promoter methylation. Conversely, astrocytomas, which are more prone to spontaneous progression to higher grade malignancy, are significantly more heterogeneous. In addition, we show that the degree of promoter methylation correlates with the prevalence of loss of heterozygosity on chromosome arm 1p in the oligodendroglioma group, but not the astrocytoma group. Our results may have potentially important implications for clinical molecular diagnosis.

Selective Formation of Diblock Copolymers Using Radical Trap-Assisted Atom Transfer Radical Coupling

Polystyrene (PSt) radicals and poly(methyl acrylate) (PMA) radicals, derived from their monobrominated precursors prepared by atom transfer radical polymerization (ATRP), were formed in the presence of the radical trap 2-methyl-2-nitrosopropane (MNP), selectively forming PSt-PMA diblock copolymers with an alkoxyamine at the junction between the block segments. This radical trap-assisted, atom transfer radical coupling (RTA-ATRC) was performed in a single pot at low temperature (35 °C), while analogous traditional ATRC reactions at this temperature, which lacked the radical trap, resulted in no observed coupling and the PStBr and PMABr precursors were simply recovered. Selective formation of the diblock under RTA-ATRC conditions is consistent with the PStBr and PMABr having substantially different KATRP values, with PSt radicals initially being formed and trapped by the MNP and the PMA radicals being trapped by the in situ-formed nitroxide end-capped PSt. The midchain alkoxyamine functionality was confirmed by thermolysis of the diblock copolymer, resulting in recovery of the PSt segment and degradation of the PMA block at the relatively high temperatures (125 °C) required for thermal cleavage. A PSt-PMA diblock formed by chain extenstion ATRP using PStBr as the macroinitiator (thus lacking the alkoxyamine between the PSt-PMA segements) was inert to thermolysis. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3619–3626

Selective Formation of Diblock Copolymers Using Radical Trap-Assisted Atom Transfer Radical Coupling

Polystyrene (PSt) radicals and poly(methyl acrylate) (PMA) radicals, derived from their monobrominated precursors prepared by atom transfer radical polymerization (ATRP), were formed in the presence of the radical trap 2-methyl-2-nitrosopropane (MNP), selectively forming PSt-PMA diblock copolymers with an alkoxyamine at the junction between the block segments. This radical trap-assisted, atom transfer radical coupling (RTA-ATRC) was performed in a single pot at low temperature (35 degrees C), while analogous traditional ATRC reactions at this temperature, which lacked the radical trap, resulted in no observed coupling and the PStBr and PMABr precursors were simply recovered. Selective formation of the diblock under RTA-ATRC conditions is consistent with the PStBr and PMABr having substantially different K-ATRP values, with PSt radicals initially being formed and trapped by the MNP and the PMA radicals being trapped by the in situ-formed nitroxide end-capped PSt. The midchain alkoxyamine functionality was confirmed by thermolysis of the diblock copolymer, resulting in recovery of the PSt segment and degradation of the PMA block at the relatively high temperatures (125 degrees C) required for thermal cleavage. A PSt-PMA diblock formed by chain extenstion ATRP using PStBr as the macroinitiator (thus lacking the alkoxyamine between the PSt-PMA segements) was inert to thermolysis. (c) 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3619-3626

Radical Chain Reduction of Alkylboron Compounds with Catechols

The conversion of alkylboranes to the corresponding alkanes is classically performed via protonolysis of alkylboranes. This simple reaction requires the use of severe reaction conditions, that is, treatment with a carboxylic acid at high temperature (>150 degrees C). We report here a mild radical procedure for the transformation of organoboranes to alkalies. 4-tert-Butylcatechol, a well-established radical inhibitor and antioxidant, is acting as a source of hydrogen atoms. An efficient chain reaction is observed due to the exceptional reactivity of phenoxyl radicals toward alkylboranes. The reaction has been applied to a wide range of organoboron derivatives such as B-alkylcatecholboranes, trialkylboranes, pinacolboronates, and alkylboronic acids. Furthermore, the so far elusive rate constants for the hydrogen transfer between secondary alkyl radical and catechol derivatives have been experimentally determined. Interestingly, they are less than 1 order of magnitude slower than that of tin hydride at 80 degrees C, making catechols particularly attractive for a wide range of transformations involving C-C bond formation.

Cathepsin D primes caspase-8 activation by multiple intra-chain proteolysis

During the resolution of inflammatory responses, neutrophils rapidly undergo apoptosis. A direct and fast activation of caspase-8 by cathepsin D was shown to be crucial in the initial steps of neutrophil apoptosis. Nevertheless, the activation mechanism of caspase-8 remains unclear. Here, by using site-specific mutants of caspase-8, we show that both cathepsin D-mediated proteolysis and homodimerization of caspase-8 are necessary to generate an active caspase-8. At acidic pH, cathepsin D specifically cleaved caspase-8 but not the initiator caspase-9 or -10 and significantly increased caspase-8 activity in dimerizing conditions. These events were completely abolished by pepstatin A, a pharmacological inhibitor of cathepsin D. The cathepsin D intra-chain proteolysis greatly stabilized the active site of caspase-8. Moreover, the main caspase-8 fragment generated by cathepsin D cleavage could be affinity-labeled with the active site probe biotin-VAD-fluoromethyl ketone, suggesting that this fragment is enzymatically active. Importantly, in an in vitro cell-free assay, the addition of recombinant human caspase-8 protein, pre-cleaved by cathepsin D, was followed by caspase-3 activation. Our data therefore indicate that cathepsin D is able to initiate the caspase cascade by direct activation of caspase-8. As cathepsin D is ubiquitously expressed, this may represent a general mechanism to induce apoptosis in a variety of immune and nonimmune cells.

Synthesis of Mid-Chain Functionalized Polymers

Polymers with mid-chain alkoxyamine functionality were synthesized by activating monohalogenated polymers in the presence of nitroso or nitrone radical traps. The resulting polymers were either polystyrene (PSt) homopolymers with a mid-chain alkoxyamine or PSt-poly(methyl acrylate) (PMA) diblock copolymers with an alkoxyamine unit at the junction between the segments. Monohalogenated polymers where synthesized by atom transfer radical polymerization (ATRP) and were then reacted to form polymer radicals in the presence of a radical trap, nitrone or nitroso. When only polystyrene radicals were reacted with the radical trap a dimer was formed with an alkoxyamine functionality in the center of the polymer chain. This functionality allowed the polymer chain to be cleaved in order to visualize the extent of the alkoxyamine functionality incorporation into the polymer chains. It was found that near quantitative alkoxyamine mid-chain functionality could be achieved by activating the PStBr in the presence of 10 equivalents of nitrone, 5 equivalents of copper bromide, and 2 equivalents of copper metal. Further reducing the amount of copper metal led to incomplete coupling, while increasing the equivalents beyond 2 generated polymer dimers with less than quantitative mid-chain functionality. Monochlorinated polystyrene (PStCl) precursors gave much poorer coupling results compared to reactions with PStBr, which is consistent with the stronger C-Cl bond resisting activation and the formation of the polystyryl radicals. When poly (methyl acrylate) (PMABr) is reacted with PStBr in the presence of a nitroso group at reduced temperatures (30 oC) block copolymers were selectively formed with an alkoxyamine functionality in the center. This was done by first activating the PSt-Br to form a polymer radical that would react with the radical trap to form a persistent radical on the oxygen. The PMA-Br, once activated, reacted with the radical on the oxygen to form the block copolymer. To test the amount of functionality incorporated, a coupling reaction was performed with no nitroso present, and found that no reaction occurred. This showed that the radical trap is essential for the coupling to occur, and cleavage of the diblock indicated that the alkoxyamine functionality was indeed incorporated into the diblock.

Synthesis Of Triblock Copolymers By Radical Trap Assisted-Atom Transfer Radical Coupling

Monobrominated diblock copolymers composed of poly(styrene) (PSt), poly(methylacrylate) (PMA), or poly(methyl methacrylate) (PMMA) were synthesized by consecutive atom transfer radical polymerizations (ATRP). The brominated diblocks were utilized in atom transfer radical coupling (ATRC) and radical trap-assisted ATRC (RTA-ATRC) reactions to form ABA type triblock copolymers. Once PMMA-PStBr and PSt-PMABrBr were produced by ATRP, the synthes of PSt-PMA-PSt and PMMA-PSt- PMMA by ATRC and also by RTA-ATRC were attempted. The coupling methods were compared and it was found that RTA-ATRC succeeded in synthesizing PSt-PMA-PSt where ATRC could not, and that RTA-ATRC improved coupling over ATRC for PMMAPSt- PMMA. Incorporation of the radical trap 2-methyl-2-nitrosopropane (MNP) midchain allowed for simple thermal cleavage of the triblock to confirm the RTA-ATRC pathway occurred in preference over the head to head radical coupling pathway of ATRC. Triblocks made by ATRC did not cleave under our conditions, as no MNP was present and thus no labile C-O bond was incorporated. The RTA-ATRC pathway allowed for lower catalyst amounts (2 molar equivalents of copper(I)bromide and 2 molar equivalents of copper metal) and a high degree of coupling at lower temperatures (40°C). The RTA-ATRC improved upon ATRC because of its ability to generate a persistent radical and proceed by first order kinetics with respect to the chain end radical.

Dimerization of Poly(methyl methacrylate) Chains Using Radical Trap-Assisted Atom Transfer Radical Coupling

End-brominated poly(methyl methacrylate) (PMMABr) was prepared by atom transfer radical polymerization (ATRP) and employed in a series of atom transfer radical coupling (ATRC) and radical trap-assisted ATRC (RTA-ATRG) reactions. When coupling reactions were performed in the absence of a nitroso radical trap-traditional ATRC condition-very little coupling of the PMMA chains was observed, consistent with disproportionation as the major termination pathway for two PMMA chain-end radicals in our reactions. When 2-methyl-2-nitrosopropane (MNP) was used as the radical trap, coupling of the PMMA chains in this attempted RTA-ATRC reaction was again unsuccessful, owing to capping of the PMMA chains with a bulky nitroxide and preventing further coupling. Analogous reactions performed using nitrosobenzene (NBz) as the radical trap showed significant dimerization, as observed by gel permeation chromatography (GPC) by a shift in the apparent molecular weight compared to the PMMABr precursors. The extent of coupling was found to depend on the concentrion of NBz compared to the PMMABr chain ends, as well as the temperature and time of the coupling reaction. To a lesser extent, the concentrations of copper(I) bromide (CuBr), nitrogen ligand (N,N,N',N',N"-pentamethyldiethylenetriamine = PMDETA), and elemental copper (Cu) were also found to play a role in the success of the RTA-ATRC reaction. The highest levels of dimerization were observed when the coupling reaction was carried out at 80 degrees C for 0.5h, with ratio of 1:4:2.5:8:1 equiv of NBz: CuBr:Cu:PMDETA:PMMABr.

Fragmentation with a Cut on Thrust: Predictions for B-factories

When high-energy single-hadron production takes place inside an identified jet, there are important correlations between the fragmentation and phase-space cuts. For example, when one-hadron yields are measured in on-resonance B-factory data, a cut on the thrust event shape T is required to remove the large b-quark contribution. This leads to a dijet final-state restriction for the light-quark fragmentation process. Here, we complete our analysis of unpolarized fragmentation of (light) quarks and gluons to a light hadron h with energy fraction z in e+e−→dijet+h at the center-of-mass energy Q=10.58  GeV. In addition to the next-to-next-to-leading order resummation of the logarithms of 1−T, we include the next-to-leading order nonsingular

Gene transfer of hepatocyte growth factor by electroporation reduces bleomycin-induced lung fibrosis

Abnormal alveolar wound repair contributes to the development of pulmonary fibrosis after lung injury. Hepatocyte growth factor (HGF) is a potent mitogenic factor for alveolar epithelial cells and may therefore improve alveolar epithelial repair in vitro and in vivo. We hypothesized that HGF could increase alveolar epithelial repair in vitro and improve pulmonary fibrosis in vivo. Alveolar wound repair in vitro was determined using an epithelial wound repair model with HGF-transfected A549 alveolar epithelial cells. Electroporation-mediated, nonviral gene transfer of HGF in vivo was performed 7 days after bleomycin-induced lung injury in the rat. Alveolar epithelial repair in vitro was increased after transfection of wounded epithelial monolayers with a plasmid encoding human HGF, pCikhHGF [human HGF (hHGF) gene expressed from the cytomegalovirus (CMV) immediate-early promoter and enhancer] compared with medium control. Electroporation-mediated in vivo HGF gene transfer using pCikhHGF 7 days after intratracheal bleomycin reduced pulmonary fibrosis as assessed by histology and hydroxyproline determination 14 days after bleomycin compared with controls treated with the same vector not containing the HGF sequence (pCik). Lung epithelial cell proliferation was increased and apoptosis reduced in hHGF-treated lungs compared with controls, suggesting increased alveolar epithelial repair in vivo. In addition, profibrotic transforming growth factor-beta1 (TGF-beta1) was decreased in hHGF-treated lungs, indicating an involvement of TGF-beta1 in hHGF-induced reduction of lung fibrosis. In conclusion, electroporation-mediated gene transfer of hHGF decreases bleomycin-induced pulmonary fibrosis, possibly by increasing alveolar epithelial cell proliferation and reducing apoptosis, resulting in improved alveolar wound repair.

Checking Assumptions in Latent Class Regression Models via a Markov Chain Monte Carlo Estimation Approach: An Application to Depression and Socio-Economic Status

Latent class regression models are useful tools for assessing associations between covariates and latent variables. However, evaluation of key model assumptions cannot be performed using methods from standard regression models due to the unobserved nature of latent outcome variables. This paper presents graphical diagnostic tools to evaluate whether or not latent class regression models adhere to standard assumptions of the model: conditional independence and non-differential measurement. An integral part of these methods is the use of a Markov Chain Monte Carlo estimation procedure. Unlike standard maximum likelihood implementations for latent class regression model estimation, the MCMC approach allows us to calculate posterior distributions and point estimates of any functions of parameters. It is this convenience that allows us to provide the diagnostic methods that we introduce. As a motivating example we present an analysis focusing on the association between depression and socioeconomic status, using data from the Epidemiologic Catchment Area study. We consider a latent class regression analysis investigating the association between depression and socioeconomic status measures, where the latent variable depression is regressed on education and income indicators, in addition to age, gender, and marital status variables. While the fitted latent class regression model yields interesting results, the model parameters are found to be invalid due to the violation of model assumptions. The violation of these assumptions is clearly identified by the presented diagnostic plots. These methods can be applied to standard latent class and latent class regression models, and the general principle can be extended to evaluate model assumptions in other types of models.

Translocation of GPIb and Fc receptor gamma-chain to cytoskeleton in mucetin-activated platelets

Recent studies have implied that GPIb-IX-V as well as functioning as an adhesion receptor may also induce signaling to mediate binding of platelets to damaged vessel wall to prevent bleeding. Reorganization of the cytoskeleton and redistribution of platelet structural proteins and signaling molecules are thought to be important in this early activation process, though the molecular mechanisms remain to be fully defined. In this study, we have used mucetin, a snake venom lectin protein that activates platelets via GPIb, to study the redistribution of GPIb in platelets. In unstimulated platelets, a minor portion of GPIb localized to Triton-insoluble cytoskeleton fractions (TIC). This portion increased considerably after platelet activation by mucetin. We also find increased contents of the FcRgamma chain in TIC. Anti-GPIb antibodies, mocarhagin or cytochalasin D completely inhibited the cytoskeletal translocation. In addition, BAPTA-AM, a cytoplasmic calcium chelator, strongly inhibited this process. On the other hand, inhibitors of alphaIIbbeta3, PLCgamma, PKC, tyrosine kinases, ADP receptor, PI3-kinase or EDTA are effective in preventing GPIb relocation in convulxin- but not in mucetin-activated platelets. We propose that cytoskeletal translocation of GPIb is upstream of alphaIIbbeta3 activation and cross-linking of GPIb is sufficient to induce this event in mucetin-activated platelets.

Proteomic analysis in aortic media of patients with Marfan syndrome reveals increased activity of calpain 2 in aortic aneurysms

BACKGROUND: Marfan syndrome (MFS) is a heritable disorder of connective tissue, affecting principally skeletal, ocular, and cardiovascular systems. The most life-threatening manifestations are aortic aneurysm and dissection. We investigated changes in the proteome of aortic media in patients with and without MFS to gain insight into molecular mechanisms leading to aortic dilatation. METHODS AND RESULTS: Aortic samples were collected from 46 patients. Twenty-two patients suffered from MFS, 9 patients had bicuspid aortic valve, and 15 patients without connective tissue disorder served as controls. Aortic media was isolated and its proteome was analyzed in 12 patients with the use of 2-dimensional difference gel electrophoresis and mass spectrometry. We found higher amounts of filamin A C-terminal fragment, calponin 1, vinculin, microfibril-associated glycoprotein 4, and myosin-10 heavy chain in aortic media of MFS aneurysm samples than in controls. Regulation of filamin A C-terminal fragmentation was validated in all patient samples by immunoblotting. Cleavage of filamin A and the calpain substrate spectrin was increased in the MFS and bicuspid aortic valve groups. Extent of cleavage correlated positively with calpain 2 expression and negatively with the expression of its endogenous inhibitor calpastatin. CONCLUSIONS: Our observation demonstrates for the first time upregulation of the C-terminal fragment of filamin A in dilated aortic media of MFS and bicuspid aortic valve patients. In addition, our results present evidence that the cleavage of filamin A is highly likely the result of the protease calpain. Increased calpain activity might explain, at least in part, histological alterations in dilated aorta.

Habitat fragmentation and adaptation: a reciprocal replant-transplant experiment among 15 populations of Lychnis flos-cuculi

1. Habitat fragmentation and variation in habitat quality can both affect plant performance, but their effects have rarely been studied in combination. We thus examined plant performance in response to differences in habitat quality for a species subject to habitat fragmentation, the common but declining perennial herb Lychnis flos-cuculi. 2. We reciprocally transplanted plants between 15 fen grasslands in north-east Switzerland and recorded plant performance for 4 years. 3. Variation between the 15 target sites was the most important factor and affected all measures of plant performance in all years. This demonstrates the importance of plastic responses to habitat quality for plant performance. 4. Plants from smaller populations produced fewer rosettes than plants from larger populations in the first year of the replant-transplant experiment. 5. Plant performance decreased with increasing ecological difference between grassland of origin and target grassland, indicating adaptation to ecological conditions. In contrast, plant performance was not influenced by microsatellite distance and hardly by geographic distance between grassland of origin and target grassland. 6. Plants originating from larger populations were better able to cope with larger ecological differences between transplantation site and site of origin. 7. Synthesis: In addition to the direct effects of target grasslands, both habitat fragmentation, through reduced population size, and adaptation to habitats of different quality, contributed to the performance of L. flos-cuculi. This underlines that habitat fragmentation also affects species that are still common. Moreover, it suggests that restoration projects involving L. flos-cuculi should use plant material from large populations living in habitats similar to the restoration site. Finally, our results bring into question whether plants in small habitat remnants will be able to cope with future environmental change.

Differentiating hippocampal subregions by means of quantitative magnetization transfer and relaxometry: preliminary results

The hippocampal formation (HF) of healthy control subjects and schizophrenic patients was examined using an MRI experiment that implements sequences for relaxometry and magnetization transfer (MT) quantification. In addition to the semi-quantitative magnetization transfer ratio (MTR), all of the observable properties of the binary spin bath model were included. The study demonstrates that, in contrast to the MTR, quantitative MT parameters (especially the T2 relaxation time of restricted protons, T2b) are capable to differentiate functionally significant subregions within the HF. The MT methodology appears to be a promising new tool for the differential microstructural evaluation of the HF in neuropsychiatric disorders accompanied by memory disturbances.