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.     

Homoserine Lactones,Methyl Oligohydroxybutyrates,and Other Extracellular Metabolites of Macroalgae‐Associated Bacteria of the Roseobacter Clade: Identification and Functions

Twenty‐four strains of marine Roseobacter clade bacteria were isolated from macroalgae and investigated for the production of quorum‐sensing autoinducers, N‐acylhomoserine lactones (AHLs). GC/MS analysis of the extracellular metabolites allowed us to evaluate the release of other small molecules as well. Nineteen strains produced AHLs, ranging from 3‐OH‐C10:0‐HSL (homoserine lactone) to (2E,11Z)‐C18:2‐HSL, but no specific phylogenetic or ecological pattern of individual AHL occurrence was observed when cluster analysis was performed. Other identified compounds included indole, tropone, methyl esters of oligomers of 3‐hydroxybutyric acid, and various amides, such as N‐9‐hexadecenoylalanine methyl ester (9‐C16:1‐NAME), a structural analogue of AHLs. Several compounds were tested for their antibacterial and antialgal activity on marine isolates likely to occur in the habitat of the macroalgae. Both AHLs and 9‐C16:1‐NAME showed high antialgal activity against Skeletonema costatum, whereas their antibacterial activity was low.     

Factors affecting acceptability of dry-cured ham throughout extended maturation under "bodega" conditions

The evolution of biochemical, instrumental colour and texture, sensory parameters and consumer acceptability of 12-month dry-cured hams maintained up to 26 months under “bodega” conditions (18 °C, 75% relative humidity) was assessed, in order to investigate the influence of extended ripening on their sensory characteristics and acceptability. Results demonstrated that ham acceptability showed no significant differences (p > 0.05) from 12 to 22 months, while it decreased significantly (p < 0.05) until 26 months. Principal component analysis of all data brought about a comprehensive explanation of the biochemical, instrumental and sensory parameters involved in the acceptability decrease. In fact, high pastiness and adhesiveness values, as measured by both sensory and instrumental methods, appeared to be most related to decreasing acceptability. Those attributes were the result of an excessive proteolysis, as revealed by biochemical maturation indices.     

Untersuchungen zum System Holz-Zement

After it had been shown in a previous study that cements poor in alkali should be preferred when manufacturing wood-cement materials, this article outlines the investigations on the influence of wood (felling period, wood species, storage period) on the setting of cement. Detrimental impacts of the wood on the cement settings could be largely compensated by adding magnesium chloride or amorphous silicic acid (SiO₂-fume).     

Substrate constructed by an array of split ring resonators for a THz planar antenna

Metamaterials are artificial materials offering unique properties which render them useful for various applications. In the present paper, we examine whether it is possible to design a split ring resonators’ (SRRs) based metamaterial substrate for enhancing the performance of planar antennas operating at THz frequencies. Initially, the radiating characteristics of a simple rectangular patch antenna over two well-known SRR substrates are studied. The yielded results are then compared to those of two novel designs of metamaterial antenna substrate with SRRs of decreasing size which are proposed to improve the antenna’s performance.     

Use of High-Resolution X-Ray Micro-Computed Tomography for the Analysis of Internal Structural Changes in Maize Infected with <Emphasis Type="Italic">Fusarium verticillioides</Emphasis>

X-ray micro-computed tomography (X-ray micro-CT) is a non-destructive, three-dimensional (3D) imaging and analysis technique for the investigation of internal structure of a large variety of materials, including agricultural produce. As a relatively new method in the field of food science, X-ray micro-CT has been applied successfully to obtain micro-structural information of foods undergoing different physical and chemical changes. In this study, high-resolution X-ray micro-CT was used for non-destructive analysis of the internal structure of maize kernels infected with Fusarium verticillioides. The major anatomical features of the maize kernel were identified based on their differences in X-ray attenuation, i.e. the germ, scutellum, vitreous and floury endosperm. Fungal infection caused changes in the internal structure of the kernels over time, which included a decrease in total kernel volume and an increase in total volume of void space, with more voids observed in the germ and floury endosperm regions. No significant (P > 0.05) difference was observed between the control and the infected kernels; it was apparent that the changes observed in the infected kernels were not solely as a result of fungal growth. The grey level histograms of the control and infected kernels shifted to the lower grey value intensity range over time indicating an increase in void space within the kernels. In the 3D images, the increase in total volume of void space with fungal progression was clearer and the effect of fungal damage on the internal structure was evident.     

Weight loss and metabolic profiles in obese individuals using two different approaches

Intentional weight loss with a reduction in adipose tissue is associated with an improvement in medical complications linked to obesity. The aim of this study was to compare the effect of two different weight loss diets on obese individuals (BMI 30-40 kg m(-2)) for improvements in anthropometric measurements and blood biomarkers. Study 1 comprised a low energy diet (LED) of 5000-6000 kJ d(-1) for a slow but steady weight loss over 12 weeks. Study 2 comprised a very low energy diet (VLED) of 3000 kJ d(-1) using meal replacements for rapid weight loss over a shorter period of 4 weeks followed by 10 weeks of weight stabilisation to prevent rebound after rapid weight loss. Nutrition information sessions were given to both groups. Fasting blood samples, anthropometric measurements and 3-day food diaries were collected at baseline and again at completion of weight loss, at 12 weeks for LED group and 4 weeks for VLED group. Mean weight loss in the LED group (n = 18) was -3.17 kg (-3.7%) compared to a -6.54 kg (-7%) loss in the VLED group (n = 14) (p < 0.001). The VLED group experienced significantly greater reductions in fat mass, -13.9% compared to -8.9% for the LED group (p < 0.05). Significantly greater reductions in blood glucose (p < 0.05), cholesterol and LDL-C (p < 0.01 for both), and waist circumference (p≤ 0.05) were noted in VLED compared to those for LED diet. Short-term, rapid weight loss produced the desired ≥5% weight loss suggested to substantially reduce metabolic abnormalities associated with obesity, and to reduce health risks.     

Exposure to fine and ultrafine particles from secondhand smoke in public places before and after the smoking ban, Italy 2005

Background

A smoking ban in all indoor public places was enforced in Italy on 10 January 2005.

Methods

We compared indoor air quality before and after the smoking ban by monitoring the indoor concentrations of fine (<2.5 μm diameter, PM_2.5) and ultrafine particulate matter (<0.1 μm diameter, UFP). PM_2.5 and ultrafine particles were measured in 40 public places (14 bars, six fast food restaurants, eight restaurants, six game rooms, six pubs) in Rome, before and after the introduction of the law banning smoking (after 3 and 12 months). Measurements were taken using real time particle monitors (DustTRAK Mod. 8520 TSI; Ultra‐fine Particles Counter‐TRAK Model 8525 TSI). The PM_2.5 data were scaled using a correction equation derived from a comparison with the reference method (gravimetric measurement). The study was completed by measuring urinary cotinine, and pre‐law and post‐law enforcement among non‐smoking employees at these establishments

Results

In the post‐law period, PM_2.5 decreased significantly from a mean concentration of 119.3 μg/m³ to 38.2 μg/m³ after 3 months (p<0.005), and then to 43.3 μg/m³ a year later (p<0.01). The UFP concentrations also decreased significantly from 76 956 particles/cm³ to 38 079 particles/cm³ (p<0.0001) and then to 51 692 particles/cm³ (p<0.01). Similarly, the concentration of urinary cotinine among non‐smoking workers decreased from 17.8 ng/ml to 5.5 ng/ml (p<0.0001) and then to 3.7 ng/ml (p<0.0001).

Conclusion

The application of the smoking ban led to a considerable reduction in the exposure to indoor fine and ultrafine particles in hospitality venues, confirmed by a contemporaneous reduction of urinary cotinine.     

Effect of Capsicum annuum (Red Sweet and Cayenne) and Piper nigrum (Black and White) Pepper Powders on the Shelf Life of Fresh Pork Sausages Packaged in Modified Atmosphere

ABSTRACT Capsicum annuum (red sweet and hot cayenne) and Piper nigrum (black and white) pepper powders were evaluated for inhibition of oxidative reactions and extension of the shelf life of fresh pork sausages packaged in a modified atmosphere. Sausages containing either red sweet pepper or cayenne pepper (0.1%, 0.5%, or 2%) or black or white pepper (0.1%, 0.5%, or 1%) were packaged in a modified atmosphere of 80% O₂+ 20% CO₂, stored for 16 d in the dark at 2 °C, and analyzed each 4 d for pH, CIE L*, a*, and b*, 2‐thiobarbituric acid‐reactive substances (TBARS), psychrotrophic aerobes, sensory discoloration, and off‐odor. Results demonstrated that Capsicum peppers (sweet red and hot cayenne) enhanced red color but failed to prevent discoloration, whereas they were very effective in inhibiting lipid oxidation, chiefly at the highest concentration used (2%), which resulted in a delay of off‐odor formation. Piper peppers (black and white) significantly delayed discoloration with small modification of sausage color; furthermore, they also inhibited lipid oxidation, which led to a delay of off‐odor formation, particularly in the form of black pepper. Besides this, all those spices inhibited microbial growth when added at the highest concentration (1%Piper and 2%Capsicum).