Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer

With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient’s pathology based diagnosis of “poorly differentiated SqCC”. Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic.

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CZE study on adsorption processes of aliphatic and aromatic amines on PMMA chip

Adsorption processes on a PMMA chip linked with CZE separations of a group of 13 aliphatic and aromatic mono‐ and di‐amines were studied. Due to the lack of chromophores within aliphatic amines, contact conductivity detection implemented directly onto the chip was used for monitoring of cationic CZE separations. To prevent an adsorption of studied amines to the chip channels, the surface of PMMA chip was modified by dynamic coating. Different surface modifiers, such as aliphatic oligoamines (diethylenetriamine and triethylenetetramine), were added to the BGE solutions filling the chip channels. The effect of various concentrations of surface modifiers on peak profiles and separation parameters of amines was monitored. Of these, mainly, aliphatic di‐amines and aromatic mono‐amines adversely affected the CZE resolution of a whole group of analytes by their strong adsorption to the chip channels. A propionate BGE with pH 3.2 containing 100 μM triethylenetetramine and 25 mM 18‐crown‐6‐ether was found suitable for CZE resolution of 12 from a total of 13 amines studied. Simple dynamic modification of the surface of PMMA chip enabled fast (analysis time lasted 9 min), sensitive (sub‐μM LODs reached) and reproducible (1–3% RSD of the peak areas) CZE analysis of the aliphatic and aromatic amines.     

Synthesis,Photophysics and Nonlinear Optical Properties of Stilbenoid Pyrimidine‐Based Dyes Bearing Methylenepyran Donor Groups

The nonlinear properties and the photophysical behavior of two π‐conjugated chromophores that incorporate an electron‐deficient pyrimidine core (A) and γ‐methylenepyrans as terminal donor (D) groups have been thoroughly investigated. Both dipolar and quadrupolar branching strategies are explored and rationalized on the basis of the Frenkel exciton model. Even though a cooperative effect is clearly observed if the dimensionality is increased, the nonlinear optical (NLO) response of this series is moderate if one considers the nature of the D/A couple and the size of the chromophores (as measured by the number of π electrons). This effect was attributed to a disruption in the electronic conjugation within the dyes’ scaffold for which the geometry deviates from planarity owing to a noticeable twisting of the pyranylidene end‐groups. This latter structural parameter also has a strong influence on the excited‐state dynamics, which leads to a very efficient fluorescence quenching.     

Jack Superpolynomials with Negative Fractional Parameter: Clustering Properties and Super-Virasoro Ideals

The Jack polynomials ${P_\lambda^{(\alpha)}}$ at ???= ?(k?+?1)/(r ? 1) indexed by certain (k, r, N)-admissible partitions are known to span an ideal ${I_{N}^{(k,r)}}$ of the space of symmetric functions in N variables. The ideal ${I_{N}^{(k,r)}}$ is invariant under the action of certain differential operators which include half the Virasoro algebra. Moreover, the Jack polynomials in ${I_{N}^{(k,r)}}$ admit clusters of size at most k: they vanish when k?+?1 of their variables are identified, and they do not vanish when only k of them are identified. We generalize most of these properties to superspace using orthogonal eigenfunctions of the supersymmetric extension of the trigonometric Calogero-Moser-Sutherland model known as Jack superpolynomials. In particular, we show that the Jack superpolynomials ${P_\lambda^{(\alpha)}}$ at ???= ?(k?+?1)/(r ? 1) indexed by certain (k, r, N)-admissible superpartitions span an ideal ${\mathcal{I}_{N}^{(k,r)}}$ of the space of symmetric polynomials in N commuting variables and N anticommuting variables. We prove that the ideal ${\mathcal{I}_{N}^{(k,r)}}$ is stable with respect to the action of the negative-half of the super-Virasoro algebra. In addition, we show that the Jack superpolynomials in ${\mathcal {I}_{N}^{(k,r)}}$ vanish when k?+?1 of their commuting variables are equal, and conjecture that they do not vanish when only k of them are identified. This allows us to conclude that the standard Jack polynomials with prescribed symmetry should satisfy similar clustering properties. Finally, we conjecture that the elements of ${\mathcal{I}_{N}^{(k,2)}}$ provide a basis for the subspace of symmetric superpolynomials in N variables that vanish when k?+?1 commuting variables are set equal to each other.     

Assessment of in vitro biofilm formation by Candida species isolates from vulvovaginal candidiasis and ultrastructural characteristics

Vulvovaginal candidiasis (VVC) is a very common cause of fungal infection that remains a significant problem worldwide, especially concerning its complex pathogenicity. Biofilm dynamics from vaginal isolates requires further investigation. Different assays, such as cell surface hydrophobicity (CSH), biofilm production, fungal metabolism by 2H-tetrazolium-5-carboxanilide (XTT) and phenazine methosulfate (PMS), scanning electron microscopy (SEM) and confocal scanning laser microscopy (CSLM) were used in order to determine the ability of five Candida species isolates from VVC patients to form in vitro biofilms and their ultrastructural characteristics. All yeasts demonstrated the ability to produce biofilm and showed viability up to 48 h after the completion of assay, confirmed by SEM and CSLM, but differences were observed between them. SEM and CSLM also revealed that all VVC isolates adhered only in blastoconidia form, except for Candida parapsilosis. Even though, only one isolate from each Candida species has been used, the results of high biofilm formation, metabolic activity and CSH showed by Candida albicans and C. parapsilosis, as well as by the ultrastructural characteristics, suggest that these species exhibit greater ability of adherence in relation to the others. Ours results support the theory that virulence potential is multifactorial and that other factors not evaluated in this study could be involved in the CVV physiopathogeny.     

Extraction optimization for antioxidant phenolic compounds in red grape jam using ultrasound with a response surface methodology

Optimization of the extraction methodology for antioxidant phenolic compounds in red grape jam was performed with an ultrasound-assisted system. The antioxidant phenolic compounds were extracted and analyzed by determining the total phenolic content (Folin Ciocalteu), as well as by employing free radical DPPH and the beta-carotene/linoleic acid system. To optimize the parameters of solvent concentration, time and extraction temperature, the experiments were carried out using the central composite rotatable design (CCRD) method. Using response surface methodology (RSM), the best combinations achieved were with 60% ethanol and water for 20 min at 50 °C. The optimized parameters for this method were compared to an extraction method that has been commonly noted in the literature, which used to be the standard method, and the results were expressed in the milligram equivalent of quercetin per gram of jam (mg E.Q/g Jam). With the new method, the antioxidant potential measured by DPPH was 70% higher than that obtained with the standard extraction method, and the antioxidant potential measured using the beta-carotene/linoleic acid system was 65% higher. In addition, a significant decrease in the total analysis time was achieved (from 10 h to 30 min), when compared to the standard method.     

Determination of organometallic compounds in surface water and sediment samples with SPME-CGC-ICPMS

Organometal compounds of tin, mercury and lead were simultaneously determined in environmental water and sediment samples by CGC-ICPMS. Instead of classical liquid/liquid extractions, solid phase microextraction was used as sampling technique. In this method, the organometallic compounds arein situ derivatised in the aqueous phase and simultaneously extracted onto a polydimethylsiloxane fiber, so that organic solvents are no longer necessary. The sorbed organometals are subsequently released from the fiber in the GC injection liner by thermal desorption. By sampling from the headspace, only the species of interest are sampled and no interfering matrix components are coextracted. With this new method, derivatisation, extraction, preconcentration and injection into the GC takes only 10 min with a minimum of handling steps. Owing to the very low detection limits (0.13–3.7 ng/1 as metal) only small sample amounts (25 ml of water, 0.5 g of sediment) are needed for one analysis. Finally, SPME is an inexpensive sampling technique that can be used with standard split/splitless injection systems.     

Equi-surjective systems of linear operators and applications

In this paper we study a system of linear operators between finite-dimensional Euclidean spaces. Emphasis is made on unbounded systems and sufficient conditions are established for their equi-surjectivity. An application is presented in which a system of approximate Jacobian matrices is used to obtain a parametric interior mapping theorem. A multiplier rule for vector problems is also derived.     

Isotopic characteristics of the Garonne River and its tributaries

The Garonne is the largest river in the south‐west of France, and its drainage basin stretches between the Pyrénées and the Massif Central mountains. Until now, no water stable isotope study has been performed on the whole Garonne river basin which is composed of different geological substrata, and where the water resources are limited during the dry summer period. This study focuses on the Garonne river and its tributaries from the Pyrénées foothill upstream to its confluence with the Lot River downstream. The aim of the study is to determine the origins of the surface waters using their chemical and stable isotopic compositions (¹⁸O, D and ¹³C), to better understand their circulation within the drainage basin and to assess the anthropogenic influences. The Garonne displays a specific ¹⁸O seasonal effect, and keeps its Pyrénean characteristics until its confluence with the Tarn River. The difference in the dissolved inorganic carbon (DIC) comes mainly from the change in lithology between the Pyrénées and the Massif Central mountains. Agriculture activity is only detected in the small tributaries. Copyright © 2009 John Wiley & Sons, Ltd.