Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM? Platform

Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™. The robust bioinformatic pipeline allowed us to correctly call both Single Nucleotide Variants (SNVs) and indels with a detection limit of 5%, achieving 100% specificity and 96% sensitivity. This workflow was also validated in 13 FFPE NSCLC biopsies. Furthermore, a specific protocol for low input gDNA capable of producing good sequencing data with high coverage, high uniformity, and a low error rate was also optimized. In conclusion, we demonstrate the feasibility of obtaining gDNA from FFPE samples suitable for NGS by performing appropriate quality controls. The optimized workflow, capable of screening low input gDNA, highlights NGS as a potential tool in the detection, disease monitoring, and treatment of NSCLC.     

Laser‐induced surface structures on gold‐coated polymers: Influence of morphology on surface‐enhanced Raman scattering enhancement

The fabrication of highly sensitive and reproducible substrates for Surface‐Enhanced Raman Scattering (SERS) remains a challenging scientific and technological issue. In this work, laser‐induced periodic surface structures are generated on poly(trimethylen terephthalate) films upon laser irradiation with the linearly polarized beams of a Nd:YAG laser (4th harmonic, 266 nm), an ArF excimer laser (193 nm), and a Titanium:sapphire laser (795 nm), resulting in periods close to the laser wavelength when irradiating at normal incidence, and larger periods for different angles of incidence. Additional irradiation with a circularly polarized beam at 266 nm produces superficial circular structures. The nanostructured polymers are coated with a nanoparticle assembled gold layer by pulsed laser deposition at 213 nm. The capabilities of these substrates for SERS are evaluated using benzenethiol as a test molecule and different degrees of Raman signal enhancement are observed depending on the nanostructure type. The highest enhancement factor is obtained by for nanostructured substrates with the highest values of period, depth, and roughness. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 42770.     

Structural Determinants of the Selectivity of 3‐Benzyluracil‐1‐acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10

The human enzymes aldose reductase (AR) and AKR1B10 have been thoroughly explored in terms of their roles in diabetes, inflammatory disorders, and cancer. In this study we identified two new lead compounds, 2‐(3‐(4‐chloro‐3‐nitrobenzyl)‐2,4‐dioxo‐3,4‐dihydropyrimidin‐1(2H)‐yl)acetic acid (JF0048, 3 ) and 2‐(2,4‐dioxo‐3‐(2,3,4,5‐tetrabromo‐6‐methoxybenzyl)‐3,4‐dihydropyrimidin‐1(2H)‐yl)acetic acid (JF0049, 4 ), which selectively target these enzymes. Although 3 and 4 share the 3‐benzyluracil‐1‐acetic acid scaffold, they have different substituents in their aryl moieties. Inhibition studies along with thermodynamic and structural characterizations of both enzymes revealed that the chloronitrobenzyl moiety of compound 3 can open the AR specificity pocket but not that of the AKR1B10 cognate. In contrast, the larger atoms at the ortho and/or meta positions of compound 4 prevent the AR specificity pocket from opening due to steric hindrance and provide a tighter fit to the AKR1B10 inhibitor binding pocket, probably enhanced by the displacement of a disordered water molecule trapped in a hydrophobic subpocket, creating an enthalpic signature. Furthermore, this selectivity also occurs in the cell, which enables the development of a more efficient drug design strategy: compound 3 prevents sorbitol accumulation in human retinal ARPE‐19 cells, whereas 4 stops proliferation in human lung cancer NCI‐H460 cells.     

N‐Oligo(3‐hydroxybutyrate)‐functionalized polypyrroles: towards bio‐erodible conducting copolymers

New copolymer materials have been prepared by chemical grafting of oligomeric 3‐hydroxybutyric acid (OHB) onto polypyrrole (PPy) derivatives. The influence of grafting density and molecular weight of OHB brushes on the physicochemical properties of prepared copolymers was investigated. PPy substrates were prepared by FeCl₃‐driven oxidative homopolymerization of N‐(2‐carboxyethyl)pyrrole or its copolymerization with pyrrole. The grafting method employed involved controlled anionic polymerization of β‐butyrolactone on pyrrole‐tethered potassium carboxylate active sites. Obtained PPy‐g‐OHB copolymers of varying grafting density and pendant polyester chain length were characterized and the observed structure–property relationships discussed. The impact of real time exposure to phosphate‐buffered saline environment was investigated and the residue products were characterized. Cross‐correlation of spectroscopic, thermal, electrical and elemental analysis data afforded comprehensive evaluation of the structure of prepared materials and their behaviour in hydrolytic medium. Erosion and degradation pathways have been identified, indicating ways to consciously tailor the physicochemical properties of these new biomimetic materials. © 2016 Society of Chemical Industry     

Influence of Alkaline Additives and Buffers on Mineral Trapping of CO2 under Mild Conditions

Carbon dioxide (CO₂) gas is the main contributor to climate change. CO₂ storage in underground brines and oil‐field brines by mineral trapping has been considered as a promising alternative in order to reduce CO₂ emissions. However, permanent storage of CO₂ in stable carbonate minerals is greatly dependent on brine pH, being favored over an alkaline pH. The effect of alkaline additives (NaOH, KOH, CaO) and buffer solutions (NaHCO₃/NaOH, Na₂HPO₄/NaOH, NH₄Cl/NH₄OH) on the mineral trapping of CO₂ under mild conditions using a synthetic brine is investigated. The results indicate that both NaOH+NH₄Cl/NH₄OH and KOH+NH₄Cl/NH₄OH mixtures promote precipitation mainly of calcium carbonate (CaCO₃).     

On the Surface Nature of Bimetallic PdZn Particles Supported on a ZnO–CeO<Subscript>2</Subscript> Nanocomposite for the Methanol Steam Reforming Reaction

CO adsorption—as a molecular probe—was studied by transmission IR spectroscopy on pre-reduced Pd and bimetallic PdZn nanoparticles. Palladium was supported (2 wt% Pd) on pure CeO₂, ZnO and a ZnO–CeO₂ composite (atomic ratio Zn:Ce?=?1:2). The Pd 3d_5/2 binding energy shift, together with the formation of metallic zinc were consistent with the development of a PdZn alloy over the zinc-containing supports at increasing reduction temperature, as revealed by XPS. Following H₂ reduction at 623 K the bimetallic particles showed only linear CO adsorption (CO_L) at initial contact time (10 Torr CO, 298 K), giving rise to a convoluted IR band ascribed to different Pd sites, where it was assumed that the Pd–Pd distances were larger than for pure Pd crystallites, indicating the presence of a PdZn alloyed surface. However, for longer exposure time to CO and/or higher superimposed pressure, the appearance of bridge and hollow coordinated CO (CO_B and CO_H, respectively) on the Pd sites suggested the degradation of the PdZn surface alloy, most likely due to the segregation of Pd surface patches. The temperature-programmed, dynamic isobaric adsorption of CO (TPA-CO), under flowing CO(1%)/He on the catalysts pre-reduced at 623 K (that is, for similar conditions to those found in the methanol steam reforming—MSR-process) showed faster desorption of CO_L as compared to CO_B?+?CO_H species for supported Pd/CeO₂, as expected. However, the TPA-CO results on Pd/ZnO–CeO₂ were atypical: even under the superimposed, low CO partial pressure, and for a temperature range similar to those found at high methanol conversion in the MSR reaction, the PdZn bimetallic surface nature was recovered, which could be an explanation of the good selectivity to CO₂ of Pd/ZnO-based catalysts and—in particular—of the catalytically stable Pd/ZnO–CeO₂ materials.

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Color stability of denture shade tabs is affected by exposure to daylight and decontamination protocols

The purpose of this study was to investigate the effect of light exposure and decontamination protocols on the color stability of denture shade guide tabs. Fifty tabs for shades 62, 66, and 69 (Biotone IPN, Dentsply Sirona) were submitted to baseline L*a*b* measurements (EasyShade, Vita), separated into 5 experimental groups (n = 10), and subjected to one of the following conditions: G1–distilled water (DW‐H₂O)–control; G2 ?70% alcohol; G3–sodium hypochlorite 1% (NaClO); G4–no light exposure; G5–natural light exposure for 6 months. The experimental conditions were designed to simulate 6 months of clinical use. After the test period, final color measurements were recorded. The mean tristimulus coordinate difference (ΔL*,Δa*,Δb*) and total color difference values () were analyzed using 2‐way ANOVA and the Tukey test, α = .05. G2 (alcohol) produced less (P < .05) color change in shade 69 than G3 (NaClO). G5 (light exposure) affected the color stability for all shades, producing a statistical difference (P < .05) from G4 (no light exposure). It was concluded that natural light changes the color stability of the shade guides and that decontamination with 70% alcohol had the least impact on the color stability of the shade guide tabs.     

The role of tryptophan in protein fibrillogenesis: relevance of Trp7 and Trp14 to the amyloidogenic properties of myoglobin

In order to understand the role of tryptophan in the mechanisms of fibrils formation, the ability of a series of analogs of the residue 7-18 span of myoglobin to form amyloid-like fibrils was investigated. Alternatively one or both tryptophans were substituted with alanine and leucine, to determine the contribution of hydrophobicity and aromaticity. The scale of aggregation propensity of the peptides determined indicates that tryptophan is crucial for the amyloidogenic process. Since the rare tryptophan residue is generally engaged in structural roles in proteins, or when exposed serves as binding sites, we surmise that its exposure in the amyloidogenic fragments allows for intermolecular clustering with residues from other molecules leading to the formation of amyloid aggregates.     

Structure–Activity Relationships of Benzenesulfonamide‐Based Inhibitors towards Carbonic Anhydrase Isoform Specificity

Carbonic anhydrases (CAs) are implicated in a wide range of diseases, including the upregulation of isoforms CA IX and XII in many aggressive cancers. However, effective inhibition of disease‐implicated CAs should minimally affect the ubiquitously expressed isoforms, including CA I and II, to improve directed distribution of the inhibitors to the cancer‐associated isoforms and reduce side effects. Four benzenesulfonamide‐based inhibitors were synthesized by using the tail approach and displayed nanomolar affinities for several CA isoforms. The crystal structures of the inhibitors bound to a CA IX mimic and CA II are presented. Further in silico modeling was performed with the inhibitors docked into CA I and XII to identify residues that contributed to or hindered their binding interactions. These structural studies demonstrated that active‐site residues lining the hydrophobic pocket, especially positions 92 and 131, dictate the positional binding and affinity of inhibitors, whereas the tail groups modulate CA isoform specificity. Geometry optimizations were performed on each ligand in the crystal structures and showed that the energetic penalties of the inhibitor conformations were negligible compared to the gains from active‐site interactions. These studies further our understanding of obtaining isoform specificity when designing small molecule CA inhibitors.