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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Collisional Cross-Sections with T-Wave Ion Mobility Spectrometry without Experimental Calibration

A method for relating traveling-wave ion mobility spectrometry (TWIMS) drift times with collisional cross-sections using computational simulations is presented. This method is developed using SIMION modeling of the TWIMS potential wave and equations that describe the velocity of ions in gases induced by electric fields. The accuracy of this method is assessed by comparing the collisional cross-sections of 70 different reference ions obtained using this method with those obtained from static drift tube ion mobility measurements. The cross-sections obtained here with low wave velocities are very similar to those obtained using static drift (average difference?=?0.3%) for ions formed from both denaturing and buffered aqueous solutions. In contrast, the cross-sections obtained with high wave velocities are significantly greater, especially for ions formed from buffered aqueous solutions. These higher cross-sections at high wave velocities may result from high-order factors not accounted for in the model presented here or from the protein ions unfolding during TWIMS. Results from this study demonstrate that collisional cross-sections can be obtained from single TWIMS drift time measurements, but that low wave velocities and gentle instrument conditions should be used in order to minimize any uncertainties resulting from high-order effects not accounted for in the present model and from any protein unfolding that might occur. Thus, the method presented here eliminates the need to calibrate TWIMS drift times with collisional cross-sections measured using other ion mobility devices.

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Determination of gold and palladium in rocks and ores by atomic absorption spectrometry using two-stage probe atomization

The efficiency of two-stage probe atomization for the determination of gold and palladium in geological samples by electrothermal atomic absorption spectrometry is studied. The effects of temperature–time program and the position of the probe in an atomizer on the fractionation of sample components and the magnitude of the analytical signal are studied. It is demonstrated that gold and palladium can be quantitatively determined by atomic absorption spectrometry in rocks and ores, using a two-stage probe atomization with the limits of detection for gold and palladium 0.01 and 0.04 g/t, respectively.     

An electrochemical aptasensor for cytochrome C,based on pillar[5]arene modified with Neutral Red

An electrochemical aptasensor is developed for the highly sensitive determination of cytochrome C, using a change in the redox current of Neutral Red covalently bound to terminal carboxyl groups of decasubstituted pillar[5]arene as a signal. The inclusion of the analyte into the complex with an aptamer reduces peaks of redox current of the dye through the dissociation of electron transfer chain in the surface layer. The aptasensor enables the determination of 1 nM to 1.0 mM of cytochrome C in the presence of 1000-fold excesses of albumin, polyethylene glycol, and lysozyme as models of interfering components in biological fluids.     

Synthesis and properties of 1-(R-adamant-1-yl)-3-(1-propionylpiperidin-4-yl)ureas and 4-({4-[3-(R-adamant-1-yl)ureido]cyclohexyl}oxy)benzoic acids,efficient target-oriented human soluble epoxide hydrolase inhibitors

A reaction of R-adamant-1-yl isocyanates with 4-[(4-aminocyclohexyl)oxy]benzoic acid and 1-(4-aminopiperidin-1-yl)propan-1-one in DMF afforded corresponding ureas in 90—95% yield, the target-oriented inhibitors of epoxide hydrolase sEH. The ureas are characterized by reduced melting points and increased solubility in water, as well as by inhibitory activity in the range of 0.5—4.0 nmol L^–1.     

The importance of glyceraldehyde radiolysis in chemical evolution

Studies in chemical evolution are intended to demonstrate how compounds of biological importance are generated from substances that could have been found in abiotic conditions on the primitive Earth or in extraterrestrial environments. In this context, the aim of the present work was to examine the behavior of dl-glyceraldehyde in both aqueous solution and solid samples under gamma irradiation. We irradiated dl-glyceraldehyde at different doses and temperatures with a gamma source; even at low doses and temperature (77 K), free radicals were detected. Among the products formed were ethylene glycol and glycolaldehyde. Some sugar-like compounds were also detected.

     

Sulphur content estimation of Venezuelan heavy oil by fast neutron and gamma transmission technique

A compact and modern equipment for implementing the fast neutron and γ-ray transmission technique (FNGT) has been developed in order to estimate the sulphur content of crude oil. FNGT is employed for non- destructive analysis of different kinds of samples. The compact system presented in this work represents an improvement of our previous experimental set-up [1, 2]. It makes use of a ²⁵²Cf source, an EJ-301 liquid scintillator detector (2″ × 2″) with excellent n/γ discrimination capabilities, and modern nuclear electronics based on fast digitizers. The fast neutron and gamma transmission technique was employed to study a system for on-line sulphur concentration measurement in Venezuelan heavy sour oil. The range of sulphur concentrations investigated is between 0.1 and 6.5 wt%. The equipment performances and limitations are compared with those predicted by a Monte Carlo model built in GEANT4 v10.01. The results show the possibility to implement a compact unit for on-line determination of sulphur concentration in crude oil.

     

Chromatographic separation of americium from europium using bis-2,6-(5,6,7,8-tetrahydro-5,9,9-trimethyl-5,8-methano-1,2,4-benzotriazin-3-yl) pyridine

The separation of americium(III) from europium(III) was achieved utilizing a bis-2,6-(5,6,7,8-tetrahydro-5,9,9-trimethyl-5,8-methano-1,2,4-benzotriazin-3-yl) pyridine (CA-BTP) chromatographic resin. The extraction chromatographic materials were prepared using various concentrations of CA-BTP. This new, hydrolytically stable extractant was impregnated on an inert polymeric support at 40% loading. The uptake of Am(III) and Eu(III) by this material from 0.1 to 4.0 M aqueous HNO₃ solutions was measured. The resulting dry weight distribution ratios, D _w , indicated a strong preference for Am(III) with little affinity for Eu(III). These results are similar to recently reported solvent extraction studies indicating a maximum uptake of Am(III) in the 0.5–1.0 M HNO₃ range. The resin preparation, performance, and characterization of the Am/Eu separation are reported herein.

     

On the geometric–arithmetic index by decompositions-CMMSE

The concept of geometric–arithmetic index was introduced in the chemical graph theory recently, but it has shown to be useful. There are many papers studying different kinds of indices (as Wiener, hyper–Wiener, detour, hyper–detour, Szeged, edge–Szeged, PI, vertex–PI and eccentric connectivity indices) under particular cases of decompositions. The main aim of this paper is to show that the computation of the geometric-arithmetic index of a graph G is essentially reduced to the computation of the geometric-arithmetic indices of the so-called primary subgraphs obtained by a general decomposition of G. Furthermore, using these results, we obtain formulas for the geometric-arithmetic indices of bridge graphs and other classes of graphs, like bouquet of graphs and circle graphs. These results are applied to the computation of the geometric-arithmetic index of Spiro chain of hexagons, polyphenylenes and polyethene.