Commercial Reference Sample Research Articles

Abstract 320: Development and automation of a streamlined targeted enrichment method for cancer mutation detection

Abstract Next Generation Sequencing (NGS) of DNA is a powerful tool for the detection of genetic variations, including single nucleotide polymorphisms, copy number variation, and small insertions/deletions. Target enrichment technologies enhance DNA sequencing by enabling users to analyze specific regions of interest only, which helps to effectively increase sequencing depth and sample throughput while minimizing cost. However, many targeted DNA library construction workflows are not optimal for routine genetic testing needs due to inconsistent, lengthy workflow. This poses significant challenge to application like cancer mutation profiling that requires detection sensitivity down to 1% or below due to heterogeneous nature of tumor tissue. In addition, high throughput testing with minimal hands on time is desirable with the rapid advance of precision medicine. Magnetic bead separations are commonly used between the individual reactions of targeted DNA library preparation workflows for cleanup and size selection. These bead clean up reactions are not only labor-intensive and tedious procedures but can also greatly contribute to sample-to sample variation especially when employing automated library preparation procedures. With the sophisticated QIAseq Targeted DNA Pro, we developed a novel streamlined targeted DNA workflow that greatly reduces handling variation by replacing the majority of bead clean up steps with enzymatic reactions, which now can be finished in as little as six hours. In combination with the newly developed QIAseq Normalizer kit, the protocol has been successfully implemented on the Hamilton NGS Star liquid handling platform resulting in up to 96 highly uniform, complex and ready-to-sequence libraries that can be effortless generated in one run. This complete automated solution saves researcher up to four hours of hands-on time. When using commercial reference samples, cancer mutations down to 1% were consistently detected with this automated workflow. The presented data demonstrate that this integrated and streamlined workflow does not only provide an automation friendly workflow but also allows to reliably identify low frequent cancer mutations. The applications presented here are for research use only. Not for use in diagnostic procedures. Citation Format: Zhong Wu, Michelle Baird, Cornelia Mechlen, Peter Hahn, Jonathan M. Shaffer. Development and automation of a streamlined targeted enrichment method for cancer mutation detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 320.

Exploring the morphological surface resistance and optical absorption of thin black carbon nanotube films for electronic and optoelectronic devices

This study investigates the optical and electrical properties of thin black films of carbon nanotubes (CNTs) fabricated under various conditions to explore their potential integration as either a perfect broadband absorber or enhanced counter electrode. The study involves SEM measurements, surface resistance measurements, and UV–Vis. spectrometer analysis. The results show that the CNT thin films exhibit high electrical conductivity and strong light absorption across various wavelengths. Optically, we investigated the impact of varying the growth temperature and catalyst temperature on the absorption profile of the thin films. The fabricated and deposited CNTs showed broadband absorption spectra, reaching 92.8% of the commercial reference sample, covering both visible and near-infrared spectra. Alternatively, the morphological surface resistance for the CNT thin films recorded agonist commercial CNT samples and FTO-coated glass. An average surface resistance of 20.5 Ω/Sq.

Longitudinal Analysis of Circulating Tumor DNA (ctDNA) in Diffuse Large B-Cell Lymphoma (DLBCL) Using KAPA HyperCap Design Share Non-Hodgkin Lymphoma (KAPA HyperCap DS NHL) Next-Generation Sequencing (NGS) Panel

Introduction Studies have shown that dynamic changes in lymphoma ctDNA levels are associated with patient outcomes and that monitoring lymphoma ctDNA may help identify patients who are at risk of refractory disease or relapse. NGS panels can successfully identify patient-specific tumor reporter variants in plasma specimens using a tissue-naïve approach that avoids limitations of patient tissue availability. Recently, using the AVENIO Oncology Assay (AOA) NHL Test* validated by the Roche Molecular CAP/CLIA Laboratory, a pre-specified analysis plan using samples from ~800 DLBCL patients from the POLARIX study validated ctDNA as an early prognostic biomarker (Herrera et al., Blood 2022). To further support clinical research on early molecular response (EMR) to treatment and minimal residual disease (MRD) in NHL, we introduce a KAPA HyperCap DS NHL panel designed to cover 100% of the target regions in the AOA NHL Test used for the POLARIX study. We describe the NGS workflow and bioinformatics analysis suitable for identification and monitoring of ctDNA using a tissue-naïve approach. We further describe performance characterization studies and feasibility of ctDNA detection using plasma specimens from patients with DLBCL. Methods KAPA HyperCap DS NHL panel covers coding and/or untranslated regions of 383 genes, plus additional intergenic regions, for a total of 341 Kb. This panel is used in combination with KAPA HyperCap workflows and KAPA reagents on Illumina® platforms, to sequence plasma cfDNA and matched genomic (g)DNA to identify tumor-specific single-nucleotide variants (SNVs) and monitor the dynamics of ctDNA. ctDNA detection and monitoring are supported by open-source bioinformatics tools for a fully integrated MRD analysis solution. Contrived samples for workflow characterization were comprised of commercially available reference materials with known SNV allele frequencies (AF) mimicking cfDNA (SeraSeq® Complete Mutation Mix and Twist Pan-cancer Reference Standard), as well as pre-characterized healthy donor cfDNA. Clinically annotated DLBCL samples were characterized and serially diluted to demonstrate feasibility of longitudinal mutation analysis. Results Serially diluted cfDNA samples and high molecular weight gDNA samples were used to assess the performance of the plasma cfDNA and germline workflows. Library quality control metrics met the yield and size distribution criteria for sequencing. A median of 88 M raw reads were obtained across all libraries. De-duplication yielded a median coverage depth range from 5000-9100 across samples. Median on-target rate (% selected bases) was between 74% and 80%. Average error rate was between 0.00024 or 0.00031 mismatches/read depth. 9 and 3 variants were detected after germline and blocklist filtering in the two commercial reference samples. Variant calling sensitivity was 100% across replicates at 5, 1 and 0.5% AF. In the serial dilution analysis, ctDNA was detected in all replicates at 5, 0.1 and 0.05% mean AF. For samples at 0.01% mean AF, ctDNA detection sensitivity was 83%. Initial data demonstrate that 131 SNV reporters were detected at 23% mean AF in a plasma sample from a treatment-naïve DLBCL patient. 4 SNV reporters were detected at 1.9% mean AF in a plasma sample from an immunochemotherapy-treated DLBCL patient. After 10x and 500x dilution, ctDNA positivity was accurately called at 2.3% and 0.05% mean AF levels for the patient with 131 reporters, and at 0.19% mean AF level for the patient with 4 reporters (Monte Carlo p-value <0.0001). Conclusion The use of KAPA HyperCap DS NHL panel with KAPA HyperCap workflows and open-source bioinformatics tools enables the detection and monitoring of ctDNA for NHL research applications. In contrived samples, variants were detected with high reproducibility at AF as low as 0.05% and with good reproducibility at AF of 0.01%. For a DLBCL patient with 131 SNV reporters in plasma, ctDNA was detectable down to 0.05% mean AF levels, while for a DLBCL patient with 4 SNV reporters, ctDNA was detectable down to 0.19% mean AF levels, demonstrating that sensitivity of Monte Carlo-based ctDNA detection depends on the number of reporter variants. *AVENIO Oncology Assay (AOA) NHL Test and KAPA HyperCap Design Share panels are for Research Use Only, not for use in diagnostic procedures. AVENIO and KAPA are trademarks of Roche. All other product names and trademarks are the property of their respective owners.

Willow (Salix spp.) bark hot water extracts inhibit both enveloped and non-enveloped viruses: study on its anti-coronavirus and anti-enterovirus activities.

Recurring viral outbreaks have a significant negative impact on society. This creates a need to develop novel strategies to complement the existing antiviral approaches. There is a need for safe and sustainable antiviral solutions derived from nature. This study aimed to investigate the antiviral potential of willow (Salix spp.) bark hot water extracts against coronaviruses and enteroviruses. Willow bark has long been recognized for its medicinal properties and has been used in traditional medicines. However, its potential as a broad-spectrum antiviral agent remains relatively unexplored. Cytopathic effect inhibition assay and virucidal and qPCR-based assays were used to evaluate the antiviral potential of the bark extracts. The mechanism of action was investigated using time-of-addition assay, confocal microscopy, TEM, thermal, and binding assays. Extracts were fractionated and screened for their chemical composition using high-resolution LC-MS. The native Salix samples demonstrated their excellent antiviral potential against the non-enveloped enteroviruses even at room temperature and after 45 s. They were equally effective against the seasonal and pandemic coronaviruses. Confocal microscopy verified the loss of infection capacity by negligible staining of the newly synthesized capsid or spike proteins. Time-of-addition studies demonstrated that Salix bark extract had a direct effect on the virus particles but not through cellular targets. Negative stain TEM and thermal assay showed that antiviral action on enteroviruses was based on the added stability of the virions. In contrast, Salix bark extract caused visible changes in the coronavirus structure, which was demonstrated by the negative stain TEM. However, the binding to the cells was not affected, as verified by the qPCR study. Furthermore, coronavirus accumulated in the cellular endosomes and did not proceed after this stage, based on the confocal studies. None of the tested commercial reference samples, such as salicin, salicylic acid, picein, and triandrin, had any antiviral activity. Fractionation of the extract and subsequent MS analysis revealed that most of the separated fractions were very effective against enteroviruses and contained several different chemical groups such as hydroxycinnamic acid derivatives, flavonoids, and procyanidins. Salix spp. bark extracts contain several virucidal agents that are likely to act synergistically and directly on the viruses.

Bendable transparent films from cellulose nanocrystals–Study of surface and microstructure-property relationship

The presented work focuses on preparing transparent bendable films from nanocellulose. In comparison to cellulose nanofibrils and bacterial cellulose, nanocrystalline cellulose are shorter and have higher crystallinity (CI<95 %). Sulfated CNC (CNCIH-OSO3H) were prepared, and by changing their counter ions from H+ to Na+ and Et4N+ (Tetraethyl ammonium) flexible films were prepared with a strength of 70.5 MPa and 2.6 % elongation at break. The CNC suspensions showed excellent dispersibility in DI water with Zeta-potential (ζ) values > -35 mV. In the preparation of films, pre-sonication was key in improving the tensile strength and improved elongation (>30 % increase compared to films prepared without sonication) and hydrophobicity. The change of counter ion, H+ to Na+ or Et4N+, improved the thermal and mechanical properties of CNC films. The films were investigated with UV–Vis spectroscopy and optical polarized spectroscopy to explain the arrangement of nanocellulose crystals in correlation with the mechanical properties. The wettability of CNC samples was also studied and explained in detail. CNC from CelluForce was also studied as commercial reference samples. The modified CNC films have adequate properties for application in flexible electronics, energy storage, and biodegradable smart packaging.

Personalized Cancer Monitoring Assay for the Detection of ctDNA in Patients with Solid Tumors.

Highly sensitive molecular assays have been developed to detect plasma-based circulating tumor DNA (ctDNA), and emerging evidence suggests their clinical utility for monitoring minimal residual disease and recurrent disease, providing prognostic information, and monitoring therapy responses in patients with solid tumors. The Invitae Personalized Cancer Monitoring™ assay uses a patient-specific, tumor-informed variant signature identified through whole exome sequencing to detect ctDNA in peripheral blood of patients with solid tumors. The assay's tumor whole exome sequencing and ctDNA detection components were analytically validated using 250 unique human specimens and nine commercial reference samples that generated 1349 whole exome sequencing and cell-free DNA (cfDNA)-derived libraries. A comparison of tumor and germline whole exome sequencing was used to identify patient-specific tumor variant signatures and generate patient-specific panels, followed by targeted next-generation sequencing of plasma-derived cfDNA using the patient-specific panels with anchored multiplex polymerase chain reaction chemistry leveraging unique molecular identifiers. Whole exome sequencing resulted in overall sensitivity of 99.8% and specificity of >99.9%. Patient-specific panels were successfully designed for all 63 samples (100%) with ≥20% tumor content and 24 (80%) of 30 samples with ≥10% tumor content. Limit of blank studies using 30 histologically normal, formalin-fixed paraffin-embedded specimens resulted in 100% expected panel design failure. The ctDNA detection component demonstrated specificity of >99.9% and sensitivity of 96.3% for a combination of 10 ng of cfDNA input, 0.008% allele frequency, 50 variants on the patient-specific panels, and a baseline threshold. Limit of detection ranged from 0.008% allele frequency when utilizing 60 ng of cfDNA input with 18-50 variants in the patient-specific panels (>99.9% sensitivity) with a baseline threshold, to 0.05% allele frequency when using 10 ng of cfDNA input with an 18-variant panel with a monitoring threshold (>99.9% sensitivity). The Invitae Personalized Cancer Monitoring assay, featuring a flexible patient-specific panel design with 18-50 variants, demonstrated high sensitivity and specificity for detecting ctDNA at variant allele frequencies as low as 0.008%. This assay may support patient prognostic stratification, provide real-time data on therapy responses, and enable early detection of residual/recurrent disease.

Brewing a Craft Belgian-Style Pale Ale Using Pichia kudriavzevii 4A as a Starter Culture.

There is an expanding market for beer of different flavors. This study aimed to prepare a craft Belgian-style pale ale with a non-Saccharomyces yeast. Pichia kudriavzevii 4A was used as a sole starter culture, and malted barley as the only substrate. The ingredients and brewing process were carefully monitored to ensure the quality and innocuousness of the beverage. During fermentation, the yeast consumed 89.7% of total sugars and produced 13.8% v/v of ethanol. The product was fermented and then aged for 8 days, adjusted to 5% v/v alcohol, and analyzed. There were no traces of mycotoxins, lead, arsenic, methanol, or microbiological contamination that would compromise consumer health. According to the physicochemical analysis, the final ethanol concentration (5.2% v/v) and other characteristics complied with national and international guidelines. The ethyl acetate and isoamyl alcohol present are known to confer sweet and fruity flavors. The sensory test defined the beverage as refreshing and as having an apple and pear flavor, a banana aroma, and a good level of bitterness. The judges preferred it over a commercial reference sample of Belgian-style pale ale made from S. cerevisiae. Hence, P. kudriavzevii 4A has the potential for use in the beer industry.

Preparation of Activated Carbon from Hawthorn Core Stones by Chemical Activation

The objective of this study is the characterization of activated carbon prepared from hawthorn core natural residue which is a vegetation waste. By using zinc chloride (ZnCl2) as a chemical agent 40 % for 25 hours at (25 °C) as a raw material in this work. The best conditions were determined to be a carbonization temperature of 400 °C for 1 hour and a maximum yield is 82 % Different operational factors such as carbonization time and temperature were used to prepare activated carbon from hawthorn core stones, pH, ash content, density, humidity content, conductivity, iodine number, and methylene blue dye absorption were all investigated in the generated activated carbon. Characterization of the activated carbon obtained was performed by using scanning electron microscopy (SEM), X-ray diffraction (XRD) and energy dispersive X-ray (EDX). Finally, the activated carbon synthesized in this study has acquired good properties that enable it to play an important function in a variety of environmental applications, including eco-protection, water treatment, and wastewater treatment and it was compared to a commercial reference sample from the B. D. H Company in industrial applications.

Next-Generation DNA Sequencing-Based Gene Panel for Diagnosis and Genetic Risk Stratification in Onco-Hematology.

Simple SummaryThe present work comes up after detecting stakeholders’ need to test for manifold molecular biomarkers in each sample from an individual diagnosed with myeloid neoplasm or acute leukemia. The development of gene panels based on NGS technology is considered a potentially effective testing alternative with less human effort, compared to that required by other conventional techniques (PCR, FISH, conventional karyotype, etc.). The validation of this panel aims to propose a new solution for hospitals to face the challenges posed by the molecular study of this group of onco-hematological diseases.A suitable diagnostic classification of myeloid neoplasms and acute leukemias requires testing for a large number of molecular biomarkers. Next-generation sequencing is a technology able to integrate identification of the vast majority of them in a single test. This manuscript includes the design, analytical validation and clinical feasibility evaluation of a molecular diagnostic kit for onco-hematological diseases. It is based on sequencing of the coding regions of 76 genes (seeking single-nucleotide variants, small insertions or deletions and CNVs), as well as the search for fusions in 27 target genes. The kit has also been designed to detect large CNVs throughout the genome by including specific probes and employing a custom bioinformatics approach. The analytical and clinical feasibility validation of the Haematology OncoKitDx panel has been carried out from the sequencing of 170 patient samples from 6 hospitals (in addition to the use of commercial reference samples). The analytical validation showed sensitivity and specificity close to 100% for all the parameters evaluated, with a detection limit of 2% for SNVs and SVs, and 20% for CNVs. Clinically relevant mutations were detected in 94% of all patients. An analysis of the correlation between the genetic risk classification of AML (according to ELN 2017) established by the hospitals and that obtained by the Haematology OncoKitDx panel showed an almost perfect correlation (K = 0.94). Among the AML samples with a molecular diagnosis, established by the centers according to the WHO, the Haematology OncoKitDx analysis showed the same result in 97% of them. The panel was able to adequately differentiate between MPN subtypes and also detected alterations that modified the diagnosis (FIP1L1-PDGFRA). Likewise, the cytogenetic risk derived from the CNV plot generated by the NGS panel correlated substantially with the results of the conventional karyotype (K = 0.71) among MDS samples. In addition, the panel detected the main biomarkers of prognostic value among patients with ALL. This validated solution enables a reliable analysis of a large number of molecular biomarkers from a DNA sample in a single assay.

Charged aerosol detector HPLC as a characterization and quantification application of biopharmaceutically relevant polysialic acid from E. coli K1

Polysialic acid (polySia) is widely investigated in various biopharmaceutical applications (e.g. treatment of inflammatory neurodegenerative diseases), whereby a certain polySia chain length with an average degree of polymerization 20 (polySia avDP20) shows most promising effects.In this study, a rapid analytical method using a HPLC and charged aerosol detector (CAD) for the direct chain length characterization of biopharmaceutically relevant polySia was developed. It was evaluated as a fast alternative to the commonly used 1,2-diamino-4,5-methylenedioxybenzene (DMB) HPLC application. In contrast to HPLC-FLD, the CAD-application provides the actual chain length of polySia within ∼3 h. The reliability of the HPLC-CAD was evaluated with a commercial reference sample of known chain length and biotechnologically produced LC polySia (long chain polySia with a DP ∼130). Moreover, HPLC-CAD was successfully applied in the direct detection of oligo- and polySia until DP ∼65 and can be used to monitor the thermal hydrolysis and subsequent chromatographic isolation of polySia avDP20 (average degree of polymerization 20) without DMB sample derivatization.In addition, CAD was successfully applied for polySia quantification using a modified elution gradient. It was tested as a fast alternative to commonly used thiobarbituric acid (TBA) assay. A differentiation between LC polySia and smaller, hydrolysed polySia chains was intended and possible. For LC polySia and polySia avDP20, a quadratic relation between polySia mass-concentration and CAD signal was observed. In case of LC polySia, a quadratic dependency with a determination coefficient of R2 = 0.99 in a broad concentration range between 0.025 and 15 mg mL−1 was determined. Quantification of polySia avDP20 was found to have quadratic dependency with a determination coefficient of R2 = 0.99 in a concentration range between 0.02 and 0.25 mg mL−1. The HPLC-CAD was tested for quantification with polySia references of known concentration and showed high accordance with a concentration deviation ≤6.7%. The CAD quantification method was also applied in the polySia avDP20 production process and was compared to the TBA assay. Results of a correlation plot showed a high determination coefficient of R2 = 0.98. Overall, HPLC-CAD analysis was successfully tested as a suitable characterization and quantification application in the biopharmaceutical production of polySia.

NiWS/Al2O3 Diesel Fraction Deep Hydrotreating Catalyst Synthesized Using Mesostructured Aluminum Hydroxide

On the basis of alumina synthesized via addition of mesostructured aluminum hydroxide gel, which is prepared by the hydrolysis of secondary aluminum butoxide in the presence of triblock copolymer Pluronic P123 to the AlOOH commercial powder, and the commercial reference sample, NiWS/Al2O3 catalysts are prepared using H3PW12O40 heteropolyacid and nickel citrate. The physicochemical properties of the supports and catalysts are studied by low-temperature nitrogen adsorption, temperature-programmed desorption of ammonia, and high-resolution transmission electron microscopy. The catalytic properties are investigated in the process of straight-run diesel fraction hydrotreating in a flow unit. It is shown that the use of the synthesized alumina as a catalyst support leads to an increase in the dispersity of nanosized particles of the NiWS active phase. The catalytic activity in targeted reactions also grows appreciably. The causes of these phenomena are discussed.

Abstract 4651: Development of a targeted NGS panel for solid tumor actionable gene targets using multiplex PCR-based enrichment in an integrated fluidic circuit

Abstract Introduction: Next-generation sequencing (NGS) has been being rapidly adopted in clinical research to align actionable variants in tumors to targeted therapies or clinical trials. Comprehensive NGS-based tumor profiling assays are an efficient and effective method to characterize a variety of clinically relevant somatic mutations. We have developed a targeted NGS cancer gene panel that focuses on actionable gene mutations and employs a NGS library preparation method based on multiplex PCR enrichment in an integrated fluidic circuit (IFC) and the automated JunoTM System. Methods: 53 actionable cancer genes were selected based on both clinical and research knowledge that covers 15 solid tumor types. Assays for the selected regions of the 53 genes were designed by an internal assay design pipeline. Multiplex PCR using target-specific primers is conducted in an LP—48.48 IFC on the Fluidigm Juno™ system, where up to 48 DNA samples can be processed simultaneously. A unique barcode is incorporated in one of the PCR primers to distinguish individual samples. To evaluate the assay performance, three sets of cell line gDNA samples were identified from commercial sources: set 1: 22 commercial reference samples, set 2: 12 samples for single nucleotide variants (SNVs) and indels, and set 3: 12 samples for copy number variations (CNVs). Each sample was tested on the IFC in 4 replicates. PCR products harvested from the IFC were pooled and purified with Agencourt® AMPure® XP magnetic beads. A second PCR step using a universal primer pair was performed to add sequencing adapters. After a second purification, the DNA library was sequenced on a NextSeq™ 500 system. The data analysis was performed by a service provider partner (GenomOncology). Results: A total of 1,508 primer pairs with an average insert size of 155 bp were selected to cover SNVs, indels, and CNVs. The assays were separated into 44 pools to minimize the interaction between assay primers and improve performance. The percentage of reads mapped to the genome was 98.9%, and the percentage of reads that mapped to amplicons was 96.8%. Mutation detection sensitivity was 4% variant allele frequency (VAF.) In 47 selected samples, the total SNVs, CNVs and indels represented are 182, 154 and 28, respectively. For SNVs, the positive percent agreement (PPA) is 1.0 and positive predictive value (PPV) is 0.974. For CNVs, the PPA is 1.0 and PPV is 0.969 and for indels, the PPA and PPV are 1.0 and 0.966, respectively. Overall concordance is 0.99. Conclusions: A targeted NGS cancer panel employing PCR-based enrichment on an IFC has been developed and yielded high quality of libraries generated on the JunoTM system for detecting SNVs, indels and CNV in solid tumor samples. This panel covers actionable targets in 53 cancer genes and utilizes a microfluidic device to provide a simple streamlined workflow for library preparation of up to 48 DNA samples per IFC. Citation Format: Peilin Chen, Jaibiao Gong, David Wang, Devin Do, Lianne McLean, Tom Goralski. Development of a targeted NGS panel for solid tumor actionable gene targets using multiplex PCR-based enrichment in an integrated fluidic circuit [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4651.

New life of recycled rare earth-oxides powders for lighting applications.

In this work we analysed the optical and structural properties of Ce:YAG regenerated phosphors. The concentrate resulted as the final product of an industrial recycling process of waste electrical and electronic equipment (WEEE), and in particular fluorescent powders coming from spent lamps treatment plant. The waste pristine materials were re-utilized without any further purification and or separation process as starting materials to obtain a YAG matrix (Y2Al5O12) doped with Cerium ions. We tested out the recovered concentrate against commercial Ce:YAG phosphors comparing their structural and optical properties by means of XRD measurements and steady time and time resolved luminescence. The analysis reveals that the new phosphors obtained by scrap powder have the same crystal structure as the commercial reference sample and comparable optical properties. In particular, the Ce-related emission efficiency has a quantum yield of about 0.75 when excited at 450 nm, in good agreement with our reference sample and with the one of commercial powder presently exploited in white LED. This achievement strongly suggests the possibility of a new life for the exhausted phosphors and a possible step forward to a complete circular process for lighting equipment.

Effect of hot air assisted infrared drying on drying characteristics and quality of rice bran pellets

The objective of this study was to determine drying characteristics and quality of rice bran pellet subjected to hot air assisted infrared (HA-IR) drying at different levels of infrared (IR) intensity (750 – 3750 W/m2) and air temperature (40 – 80°C). The rice bran pellets were dried from 0.18 to 0.08 g water/g dry matter. The maximum drying rate (DR) and drying time were in the ranges of 0.0030 – 0.0165 g water/g dry matter·min and 8 – 54 min, respectively. Higher IR intensity and air temperature resulted in greater maximum DR and shorter drying time. The same trend was also observed for the effective moisture diffusivity (Deff) values which were between 0.3103×10-7 and 2.7603×10-7 m2/s. As compared to the commercial reference sample of dried rice bran pellets, the products of this study had higher oil content and lower FFA content. The oil content was affected by IR intensity only while the FFA content was affected both by IR intensity and air temperature. HA-IR drying could improve drying characteristics of the rice bran pellets and produce better quality of the dried products.

A Helicobacter pylori Vacuolating Cytotoxin A: Mouse DHFR Fusion Protein Triggers Dye Release from Liposomes

The membrane perturbing action of the VacA toxin from Helicobacter pylori is responsible for vacuole formation in intracellular compartments and the induction of apoptosis. The VacA toxin contains 2 major domains, p33 and p55, which are involved in receptor binding and membrane pore formation, respectively. Improved methodologies for VacA purification and assays are urgently needed for further detailed investigations on the mechanism of action of this significant virulence factor. We found that by fusing mouse DHFR with the N-terminus of the full-length (p88) VacA toxin, expression levels in recombinant E. coli were substantially increased when compared to the conventional (His)6-tagged protein. The DHFR-VacA fusion protein was active in sulforhodamine dye-release assays using liposomes at acidic pH in a concentration-dependent manner. Enzymatic activity of DHFR in the fusion protein was comparable to a commercial reference sample of purified DHFR; however, activity was insensitive to inhibition by methotrexate. Our findings suggest that the VacA p88 toxin with a modified N-terminus still maintains its capability for membrane insertion and that pH-dependent conformational changes occur during interaction of VacA with membranes.

Comparison of genomic and gene expression profile between cancer and healthy samples.

e13001 Background: A variety of chromosomal aberrations underlie developmental abnormalities and cancer. Use of techniques such as microarrays provides an opportunity to perform gene expression analysis. A recent approach is the use of array based comparative genomic hybridization (aCGH) to detect genomic abnormalities in human tumors. The aim of this study is to compare genomic and gene expression profile between cancer patients and healthy individuals. Methods: DNA and RNA were isolated from peripheral blood mononuclear cells from 9 patients, with different types of cancer and 4 normal donors. aCGH (Agilent-60K) and gene expression microarrays (Microarrays Inc.-whole genome platform) were performed using commercial reference samples. Data were analyzed with Array-Pro analyzer and Cytogenomics software. Results: The aCGH data demonstrated the majority of gains and amplifications were observed in cancer samples, while the deletions and losses were higher in normal individuals. Among aberrations, common genes in both types of samples were detected. These genes included ACAD8, ACP1, B3GAT1, IDI1, IDI2, IGSF9B, IRX1, IRX2, JAM3, MYT1L, NTM, OPCML, PXDN, THYN1, TPO. However, there were abnormalities that included genes, which appeared only in cancer samples, like cadherins ( CDH11, CDH8 and CDH5) and EPHA5, while genes such as ACOX1, PTPRN2, TYMS and genes of zinc-finger proteins were observed only in normal samples. No statistical significant difference in gene expression, between cancer and normal samples, was observed. On the contrary, overexpression was observed in genes that were not detected in aCGH. Conclusions: Whereas it is acceptable that great achievements have been carried out in cancer field, the mechanism of tumorigenesis is not clear understood. The present study demonstrated that even though genomic aberrations exist, these are not always representative at gene expression level. However, the combination of both techniques could be used for more accurate and reliable data. This requires study in more samples including different cancer types so to be used at clinical level.

Soot and hydrocarbon oxidation over vanadia-based SCR catalysts

The selective catalytic reduction (SCR) of NOx with NH3 and the oxidation of propylene and soot have been investigated on a series of V-W-TiO2 SCR catalysts prepared by incipient wetness impregnation, flame spray pyrolysis and a commercial reference sample. Depending on the preparation method, monomeric vanadly, polymeric vanadia and also two-dimensional vanadyl structures with vanadium in the +5 oxidation state on the catalyst surface were identified using Raman and X-ray photoelectron spectroscopy. The amount of acidic sites was highest if SiO2 was added to the catalyst. The SCR-performance of the catalysts prepared by incipient wetness impregnation was similar to those reported in literature and to that shown by the commercial catalyst. The catalysts were also very attractive for propylene and soot oxidation. The synthesis method had a strong effect on the SCR of NOx and on both the propylene and soot oxidation activity. In all cases, CO and CO2 were detected as oxidation products from propylene. Catalytic soot oxidation led predominantly to CO2 formation. The presence of propylene has a strong impact on the SCR activity particularly in the temperature range where C3H6 oxidation occurs.

Antimicrobial properties of highly efficient photocatalytic TiO2 nanotubes

A rapid chlorine-based electrochemical anodization method resulted in the production of free-standing bundles of titania (TiO2) nanotubes with high-aspect ratio (up to 100μm long and about 20nm in diameter). XRD and Raman spectroscopy revealed the presence of partially crystalline amorphous titania nanostructures modified with surface hydroxyl groups. Photocatalytic antimicrobial properties of these nanotubes have been investigated using Escherichia coli and Staphylococcus aureus and compared with a commercial reference sample, Evonic-Degussa P25. Titania nanotubes were found to be highly efficient in inactivating both E. coli (97.53%) and S. aureus (99.94%) in under 24h of UV irradiation. On the other hand, commercial Evonik Degussa P-25 titania nanoparticles and control samples did not reveal antimicrobial properties for the same amount of time under either light or dark conditions. These results indicate that along with material properties, the high-aspect ratio nanotube architecture, surface hydroxyls, physicochemical properties of TiO2 nanotubes as well as experimental conditions of the biological investigations play a significant role in the antibacterial activity.

Random amplified polymorphic DNA (RAPD) fingerprint and antioxidants profile as markers for Tropea red onion (Allium cepa L.) authenticity

Random amplified polymorphic DNA (RAPD) and chemotype analyses were applied to characterise Tropea red onion (Allium cepa L.), a typical Italian variety that is cultivated in specific areas of Calabria. Seven Tropea red onion samples and three commercial cultivars of different coloured onions were evaluated. Amplification of genomic DNA using random primers highlighted a good clustering differentiating Tropea red onion cultivar from commercial reference samples used in this study. The total antioxidant activity and the content of quercetin-3,4′-O-diglucoside (3,4′Qdg) and quercetin-4′-O-monoglucoside (4′Qmg) were measured using photochemiluminescence method (Photochem®) and capillary electrophoresis, both very interesting because of their very short measuring times. The difference in antioxidant activity and quercetin contents between Tropea red onion and commercial sample and also the difference within Tropea cultivar suggested that the nutrient composition did not depend only on particular genetic characters but was probably connected to the intrinsic pedological soil and climate features.

Characterization and surface reactivity of natural and synthetic magnetites

Magnetite is an Fe (II/III) oxide mineral that occurs naturally and potentially as small particles with significant surface reactivity, and although much work is reported on synthetic material, little work exists for natural samples. The goal of the present work was to carefully characterize four natural magnetite samples from an iron ore deposit and two synthetic commercial reference samples, and to compare their surface characteristics and reactivity with the aim of evaluating their geochemical behavior towards adsorption of environmentally relevant ions, as well as their potential for use as environmental remediation sorbents. The techniques used were wet chemistry, X-ray diffraction, Raman spectroscopy, magnetic measurements (hysteresis curves), dynamic light scattering, scanning electron microscopy, low and high resolution transmission electron microscopy, BET Nitrogen adsorption, and electrophoresis. In addition, their As(V) adsorption behavior was measured at pH6, and was analyzed as related to the surface characteristics and particle aggregation behavior determined. The analyses revealed high magnetite purity in the natural samples, and specific surface areas (SSA) ranging from 1 to 8m2/g. Small alumino-silicate impurities were found in natural magnetites, apparently occurring at the particle surfaces and thus significantly lowering their isoelectric points as compared to the pure synthetic materials. All samples are composed of aggregates of 39–52nm magnetite particle units, but highly aggregated with very large size dispersions. The synthetic sample with the smallest particle size (30nm in average — 39m2/g) showed its entire surface area available for adsorption, despite its highly aggregated state observed, suggesting an open and highly dynamic aggregate framework. The other larger samples showed more complex aggregation behavior, which produced: (1) a widely variable As(V) adsorption behavior with no clear predictable pattern among samples; and (2) a large decrease of the As(V) adsorption maxima with increasing solids concentration imposed in the experimental set-up for any one particular sample. Therefore, we recommend high caution in using the BET-SSA and solids concentration parameters when performing experimental adsorption work with microsized magnetite, especially when extrapolating laboratory results to field geochemical or engineered conditions for evaluating contaminant adsorption.