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.

Open image in new window

Graphical Abstract ?

     

Cyclization of protected N-acylhydroxyguanidine to 3-amino-1,2,4-oxadiazole

The acid mediated cyclization of a protected N-acylhydroxyguanidine into the corresponding 3-amino-1,2,4-oxadiazole and confirmation of its structure by single crystal X-ray crystallography is reported herein. The yield of the cyclization is comparable to literature reports utilizing alternative procedures. Importantly, these new conditions provide complementary chemoselectivity to current synthetic procedures which may be useful for the synthesis of 3-amino-1,2,4-oxadiazoles in general.     

Aggregation and dispersion of silver nanoparticles in exposure media for aquatic toxicity tests

Silver nanoparticles (AgNPs) are currently being very widely used in industry, mainly because of their anti-bacterial properties, with applications in many areas. Once released into the environment, the mobility, bioavailability, and toxicity of AgNPs in any ecosystem are dominated by colloidal stability. There have been studies on the stability or the aggregation of various nanoparticles (NPs) under a range of environmental conditions, but there is little information on fully characterised AgNPs in media used in (eco)toxicity studies. In this study, monodisperse 7, 10 and 20 nm citrate-stabilised AgNPs were synthesised, characterised and then fractionated and sized by flow field-flow fractionation (FFF) and measured with dynamic light scattering (DLS) in different dilutions of the media recommended by OECD for Daphnia magna (water flea) toxicity testing. Stability of NPs was assessed over 24 h, and less so over 21 days, similar time periods to the OECD acute and chronic toxicity tests for D. magna. All particles aggregated quickly in the media with high ionic strength (media1), resulting in a loss of colour from the solution. The size of particles could be measured by DLS in most cases after 24h, although a fractogram by FFF could not be obtained due to aggregation and polydispersity of the sample. After diluting the media by a factor of 2, 5 or 10, aggregation was reduced, although the smallest NPs were unstable under all media conditions. Media diluted up to 10-fold in the absence of AgNPs did not induce any loss of mobility or fecundity in D. magna. These results confirm that standard OECD media causes aggregation of AgNPs, which result in changes in organism exposure levels and the nature of the exposed particles compared to exposure to fully dispersed particles. Setting aside questions of dose metrics, significant and substantial reduction in concentration over exposure period suggests that literature data are in the main improperly interpreted and nanoparticles are likely to have far greater biological effects than suggested thus far by poorly controlled exposures. We recommend that the standard OECD media is diluted by a factor of ca. 10 for use with these NPs and this test media, which reduces AgNP aggregation without affecting the viability of the text organism.     

Cavity Volume and Free Energy in Many-Body Systems

Most models for the spread of an invasive species into a new environment are based on Fisher’s reaction–diffusion equation. They assume that habitat quality is independent of the presence or absence of the invading population. Ecosystem engineers are species that modify their environment to make it (more) suitable for them. A potentially more appropriate modeling approach for such an invasive species is to adapt the well-known Stefan problem of melting ice. Ahead of the front, the habitat is unsuitable for the species (the ice); behind the front, the habitat is suitable (the open water). The engineering action of the population moves the boundary ahead (the melting). This approach leads to a free boundary problem. In this paper, we study the well-posedness of a novel free boundary model for the spread of ecosystem engineers that was recently derived from an individual random walk model. The Stefan condition for the moving boundary is replaced by a biologically derived two-sided condition that models the movement behavior of individuals at the boundary as well as the process by which the population moves the boundary to expand their territory. Our proofs consist of several new and novel ideas that can be used in broader contexts. We assign a convex functional to this problem so that the evolution system governed by this convex potential is exactly the system of evolution equations describing the above model. We then apply variational and fixed-point methods to deal with this free boundary problem.

     

Modified Bridgman anvils for high pressure synthesis and neutron scattering

ABSTRACT

A simple modified Bridgman design for large volume pressure anvils usable in the Paris-Edinburgh (PE) press has been demonstrated at Oak Ridge National Laboratory Spallation Neutron Source. The design shows advantages over the toroidal anvils typically used in the PE press, mainly rapid compression/decompression rates, complete absence of blow-outs upon drastic phase transitions, simplified cooling, high reliability, and relative low loads (～40 tons) corresponding to relatively high pressures (～20?GPa). It also shows advantages over existing large-volume diamond cells as sample volumes of ～2–3?mm³ can be easily and rapidly synthesized. The anvils thus allow sample sizes sufficient for in situ neutron diffraction as well as rapid synthesis of adequate amounts of new materials for ex situ analysis via total neutron scattering and neutron spectroscopy.     

Enzymatic hydrolysis of steam-exploded and ethanol organosolv-pretreated douglas-fir by novel and commercial fungal cellulases

Softwood residues are the most abundant feedstock available for bioconversion in many northern countries. However, the high costs for delignification and enzymatic hydrolysis currently deter commercialization of softwood bioconversion processes. This study evaluates the abilities of two novel fungal preparations (MSUBC1 and MSUBC2) and two commercial cellulase preparations (TR1 and TR2) to hydrolyze cellulose in Douglas-fir pretreated by steam explosion or ethanol organosolv process. MSUBC1 showed significantly better performance than the other preparations on both lignocellulosic substrates. In particular, MSUBC1 achieved >76% cellulose conversion for hydrolysis of steam-exploded Douglas-fir (～44% lignin) after 72 h at low enzyme loading (10 filter paper units/g of cellulose) and without β-glucosidase supplementation.     

Micro-emulsion synthesis of monodisperse surface stabilized silicon nanocrystals

Silicon nanocrystals with a uniform size distribution were synthesized in inverse micelles using powerful hydride reducing agents. The silicon nanocrystals surfaces were then stabilized with 1-heptene to produce particles with strong blue photoluminescence.