Range Of Sample Types Research Articles

Phage based biosensors: Enhancing early detection of emerging pathogens in diagnostics

Global health is seriously threatened by an increase in antibiotic resistance among ESKAPE pathogens- E- E. faecium, S- S.aureus, K- K.pneumoniae, A-A.baumannii, P- P.aeruginosa, and E-Enterobacter. The resistance of many bacteria to traditional antibiotics is increasing, making the search for novel approaches critical. In order to minimize the effect of these diseases, early detection, diagnosis, and treatment are important. However, there are drawbacks to traditional detection techniques such molecular-based, biochemical, and microbiological assays. These include the inability to detect on-site, as well as their time-consuming, expensive, and labour-intensive nature. Viral agents that target bacteria exclusively, known as bacteriophages, have shown promise in combating over infections resistant to antibiotics. Bacteriophage-based biosensors are adaptable to many environmental conditions and offer special features such as host specificity and ability to identify active infections. They're very accurate, very specific, and have quick assay times, which makes them beneficial tools for detection. Also, phages are more easily produced than antibodies and can withstand high pH, temperature, and chemical solvents. The potential of bacteriophage-based biosensors in the fight against ESKAPE pathogens is highlighted by this review. Bacteriophage-based biosensors provide simplified detection processes in contrast to conventional approaches, which makes them invaluable in environmental and clinical situations. Numerous platforms, including electrochemical, magnetoelastic, quartz crystal microbalance, and surface plasmon resonance sensors, being investigated for their potential use to detect pathogenic bacteria in a range of sample types.

One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes

Mass spectrometry (MS)-based proteomics workflows typically involve complex, multi-step processes, presenting challenges with sample losses, reproducibility, requiring substantial time and financial investments, and specialized skills. Here we introduce One-Tip, a proteomics methodology that seamlessly integrates efficient, one-pot sample preparation with precise, narrow-window data-independent acquisition (nDIA) analysis. One-Tip substantially simplifies sample processing, enabling the reproducible identification of >9000 proteins from ~1000 HeLa cells. The versatility of One-Tip is highlighted by nDIA identification of ~6000 proteins in single cells from early mouse embryos. Additionally, the study incorporates the Uno Single Cell Dispenser™, demonstrating the capability of One-Tip in single-cell proteomics with >3000 proteins identified per HeLa cell. We also extend One-Tip workflow to analysis of extracellular vesicles (EVs) extracted from blood plasma, demonstrating its high sensitivity by identifying >3000 proteins from 16 ng EV preparation. One-Tip expands capabilities of proteomics, offering greater depth and throughput across a range of sample types.

Development of an amplicon-based sequencing approach in response to the global emergence of mpox.

The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.

Validation of the InnoXtract™ DNA extraction method for bone, teeth, and rootless hair

Forensic casework samples often include human hairs, teeth, and bones. Hairs with roots are routinely processed for DNA analysis, while rootless hairs are either not tested or processed using mitochondrial DNA. Bones and teeth are submitted for human remains identifications for missing persons and mass disaster cases. DNA extraction from these low templates and degraded samples is challenging. The new InnoXtract DNA extraction method utilizes magnetic beads that are optimized to bind small DNA fragments, as small as 100 base pairs, to purify high-yield DNA from compromised samples. This validation study evaluates InnoXtract's ability to obtain amplifiable DNA from samples such as rootless hairs and skeletal remains. Studies performed include sensitivity, stability, repeatability, reproducibility, non-probative samples, and comparison to standard organic extractions. Sensitivity studies demonstrate average yield recoveries ranging from 53% to 100% and 73% to 85% for the InnoXtract hair and bone methods, respectively. Studies demonstrate consistent results across a range of sample types, such as insulted and un-insulted bone and teeth, as well as hair shafts from donors of various ages, gender, race, and hair characteristics. The InnoXtract bone method outperformed organic extraction. The method was successfully automated on a MagMAX™ Express-96, with recoveries over 70% relative to the manual version. InnoXtract has the potential as an automated high-throughput, high-yield bone extraction method with 6h of total extraction time for up to 96 samples. The validation study results demonstrate that the InnoXtract kits produce high-yield and high-quality DNA from compromised bone, teeth, and hair shaft samples.

Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem

Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Currently available protocols for metataxonomy assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. It has been suggested that the addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases during processing and support direct comparisons of microbiota composition, but the impact of MC on diversity estimates of samples is unknown. Here, large and small aliquots of pulverized bovine fecal samples were extracted with no, low or high doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We demonstrated that sample diversity estimates were distorted only if MC dose was high compared to sample mass (i.e. when MC > 10% of sample reads). We also showed that MC was an informative in situ positive control, permitting an estimation of the sample 16S copy number, and detecting sample outliers. We tested this approach on a range of sample types from a terrestrial ecosystem, including rhizosphere soil, whole invertebrates, and wild vertebrate fecal samples, and discuss possible clinical applications.

A Modified Ultra-Sensitive ELISA for Measurement of LH in Mice.

A major obstacle to monitoring pulsatile luteinizing hormone (LH) secretion in mice has been an assay with sufficient sensitivity in small blood volumes. In 2013, Steyn and colleagues published a highly sensitive enzyme-linked immunosorbent assay (ELISA) that overcame this barrier by coupling a duo of LH antibodies effective in accurately measuring LH in 4-µL whole-blood aliquots. To address the unavailability of the original detection antibody, AFP240580Rb, we validated a replacement detection antibody, biotinylated-5303 SPRN-5, to be used within the established ELISA. This modified LH ELISA demonstrated a minimum detection limit of 0.0028 ng/mL and a limit of quantification of 0.0333 ng/mL or 0.0666 ng/mL in diluted whole-blood samples of volume 6.4 µL (1:10) or 3.2 µL (1:20), respectively. Detection antibody 5303 SPRN-5 demonstrated parallelism, high precision, and accuracy across the standard curve. LH concentrations in comparison assays, using either 5303 SPRN-5 or AFP240580Rb, were highly correlated (R2 = 0.9829) and demonstrated LH pulse profiles from gonadectomized mice that were nearly superimposable. Pulsatile LH secretion was demonstrated in gonad-intact males and diestrous females and basal LH levels measured with 5303 SPRN-5 were approximately 5-fold higher than the limit of quantification. In addition, we document utility of this new LH ELISA to accurately measure LH in whole blood or serum across multiple sampling sites, as well as in pituitary extracts, LβT2 cells, or media. In summary, the modified LH ELISA described here is highly effective in measuring LH across a range of sample types and small volumes in mice.

Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation

Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.

New Methods for the Chemical Isolation and Stable Isotope Measurement of Multiple Transition Metals, with Application to the Earth Sciences

Rapid advances in multi‐collector inductively coupled plasma‐mass spectrometry have made the routine, precise and accurate measurement of metal stable isotope ratios feasible, providing an opportunity to investigate past and present geochemical processes using transition metal abundances, abundance ratios and stable isotope compositions. Many studies have stressed the matrix of different controls on different metals and highlight the potential utility of studies of multiple metals on the same samples. Here we describe a new, multi‐step chemical separation procedure that allows robust, and with blank contamination‐free, measurements of the isotope systems of the transition metals Mo, Cu, Fe, Zn and Ni at high precision from a single sample aliquot and from a range of sample types. We test the approach via the isotopic analysis of four USGS rock reference materials: two basalts (BCR‐2, BHVO‐2) and two Fe‐Mn nodules (Nod‐A1 and Nod‐P1) as well as a shale (SGR‐1). The good ‘reproducibility’, and the agreement between measured values and reference values where available, demonstrates the validity and efficacy of our multi‐step protocol. We also discuss in detail the key requirements of the approach, and the potential pitfalls that are encountered.

A Meta-Analytic Review of Emotion Regulation Focused Psychosocial Interventions for Adolescents.

Emotion regulation (ER) is the ability to monitor, evaluate, and modify one's emotional responses to be appropriate for environmental demands. Poor ER has been considered a transdiagnostic risk factor for a range of internalizing and externalizing disorders and overall decreased well-being in adolescents. A range of evidence-based interventions exist which may improve ER. However, much of the intervention research to date does not include a measure of ER to assess change pre and post treatment, with limited information about the efficacy of these interventions in youth across a range of sample types. There is a clear need for a comprehensive review of the literature examining ER-focused interventions in adolescents with a wide range of presenting disorders. A literature search was originally conducted in January 2020 and an updated search was conducted in February 2021 which elicited 1245 articles, of which 605 were duplicates and were removed. Abstracts of the remaining 640 articles were screened with 121 articles being reviewed in full. Of note, 16 additional articles were identified through references and other sources during this process and were also included in the full review. Of the 137 articles reviewed in full, 41 studies were ultimately included in the present review. The present paper provides a descriptive review of intervention approaches and findings from community prevention programs, programs for war-affected youth, programs for clinical populations, and programs for incarcerated and delinquent adolescents. The overall pooled effect was significantly different from zero based on the pre/post effects [Hedge's g = 0.29, 95% CI (0.22, 0.36)] and the intervention/control effects [Hedge's g = 0.19, 95% CI (0.06-0.32)]. Although neither sex nor age significantly accounted for heterogeneity in effect sizes, there were significant findings for population type (clinical vs. community), with community samples having significantly lower effect sizes on average. Impacts of the different ER measures used and significant methodological variability (e.g., use of control groups, length of intervention) across included studies are discussed. Implications and suggestions for future research are reviewed, specifically, that additional understanding of moderators of effects are needed and that measures used to assess change in ER, both dysregulation and adaptive skill use, may need to more directly align with the intervention's focus and the strategies taught as part of the intervention.

Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA

Background: Abnormal CpG methylation in cancer is ubiquitous and generally detected in tumour specimens using a variety of techniques at a resolution encompassing single CpG loci to genome wide coverage. Analysis of samples with very low DNA inputs, such as formalin fixed (FFPE) biopsy specimens from clinical trials or circulating tumour DNA is challenging at the genome-wide level because of lack of available input. We present the results of low input experiments into the Illumina Infinium HD methylation assay on FFPE specimens and ctDNA samples. Methods: For all experiments, the Infinium HD assay for methylation was used. In total, forty-eight FFPE specimens were used at varying concentrations (lowest input 50 ng); eighteen blood derived specimens (lowest input 10 ng) and six matched ctDNA input (lowest input 10 ng)/fresh tumour specimens (lowest input 250 ng) were processed. Downstream analysis was performed in R/Bioconductor for quality control metrics and differential methylation analysis as well as copy number calls. Results: Correlation coefficients for CpG methylation were high at the probe level averaged R2 = 0.99 for blood derived samples and R2 > 0.96 for the FFPE samples. When matched ctDNA/fresh tumour samples were compared, R2 > 0.91 between the two. Results of differential methylation analysis did not vary significantly by DNA input in either the blood or FFPE groups. There were differences seen in the ctDNA group as compared to their paired tumour sample, possibly because of enrichment for tumour material without contaminating normal. Copy number variants observed in the tumour were generally also seen in the paired ctDNA sample with good concordance via DQ plot. Conclusions: The Illumina Infinium HD methylation assay can robustly detect methylation across a range of sample types, including ctDNA, down to an input of 10 ng. It can also reliably detect oncogenic methylation changes and copy number variants in ctDNA. These findings demonstrate that these samples can now be accessed by methylation array technology, allowing analysis of these important sample types.

Sampling and Analysis of Animal Scent Signals.

We have developed an effective methodology for sampling and analysis of odor signals, by using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry, to understand how they may be used in animal communication. This technique allows the semi-quantitative analysis of the volatile components of odor secretions by enabling the separation and tentative identification of the components in the sample, followed by the analysis of peak area ratios to look for trends that could signify compounds that may be involved in signaling. The key strengths of this current approach are the range of sample types that can be analyzed; the lack of need for any complex sample preparation or extractions; the ability to separate and analyze the components of a mixture; the identification of the components detected; and the capability to provide semi-quantitative and potentially quantitative information on the components detected. The main limitation to the methodology relates to the samples themselves. Since the components of specific interest are volatile, and these could easily be lost, or their concentrations altered, it is important that the samples are stored and transported appropriately after their collection. This also means that sample storage and transport conditions are relatively costly. This method can be applied to a variety of samples (including urine, feces, hair and scent-gland odor secretions). These odors consist of complex mixtures, occurring in a range of matrices, and thus necessitate the use of techniques to separate the individual components and extract the compounds of biological interest.

Gene Expression Analysis by Reverse Transcription Quantitative PCR.

The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a rapid detection technology that allows the amplification and quantification of specific RNA transcripts. RT-qPCR has increasingly been adopted for the detection and quantification of H. pylori across a range of sample types and applications. In addition, it is widely used to monitor host gene expression in cells and tissues in response to H. pylori infection . Outlined here is a two-step protocol that can be employed to analyze gene expression in H. pylori or H. pylori-infected samples.

Quantitative Sub-Cellular Acyl-Coa Analysis Reveals Distinct Nuclear Regulation

Quantitative sub-cellular metabolomic measurements can yield crucial insights into the roles of metabolites in cellular processes, but are subject to multiple confounding factors. We developed Stable Isotope Labeling of Essential nutrients in cell Culture - Sub-cellular Fractionation (SILEC-SF), which uses isotope labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-Coenzyme A thioesters in sub-cellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing we identified the branched chain amino acid (BCAA) isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.

Abstract LB-315: Oncology research applications on an electrical impedance based, high accuracy sequencing platform

Abstract Next Generation Sequencing (NGS) technologies have revolutionized basic biological and clinical research, especially in oncology. NGS cancer assays are used to determine cancer predisposition, identify tumor mutations, monitor treatment response and develop personalized therapies. Here, GenapSys presents a scalable, low cost, and high accuracy sequencing platform based on electrical impedance detection. We demonstrate that a single run with a 16M sensor chip generates up to 2 Gb of data, with greater than 99% raw accuracy and an average read length of about 150 bp. We highlight its applications for oncology research, using diverse cancer panels on reference and clinical samples. We tested hybrid-capture and multiplex PCR-based cancer panels on a range of DNA sources, including oncology reference standards derived from cell line DNA, cfDNA standards, as well as clinical samples: FFPE, fresh frozen tumor tissue, and blood. For hybrid-capture libraries, we used the IDT xGen Pan Cancer 1.5 and Exome Research panels. We detected low frequency mutations in the range of 1%-24.5% across multiple reference standards with the cancer panel, and observed high correlation in allele frequency with expected values (R2 > 0.99). Similar results were obtained with an amplicon panel, the Ion AmpliSeq Cancer Hotspot Panel v2. Whole exome sequencing and pan cancer sequencing of clinical FFPE, fresh frozen and blood samples showed high concordance (F1-score > 95%) of SNV mutation calling with commonly used NGS technology. Thus, we demonstrate that the GenapSys Sequencing Platform is an accurate, scalable, and low cost solution for oncology research on a wide range of sample types and NGS assays. Citation Format: Saurabh Paliwal, Mohammad Fallahi, Ali Nabi, Tyson A. Clark, Bin Dong, Srijeeta Bagchi, Maryam Jouzi, Hannah Ritchie, Lydia Bonar, Anthony Thomas, Narin Tangprasertchai, Meysam R. Barmi, Xavier Gomes, Subra Sankar, Hesaam Esfandyarpour. Oncology research applications on an electrical impedance based, high accuracy sequencing platform [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-315.

Articles of Significant Interest in This Issue

Approaches targeting the DNA of microorganisms found within a range of sample types are being investigated with growing frequency for their suitability as tools for forensic science. Allwood et al. (e01504-19) discuss the status of such work. They focus on the potential to use DNA-based approaches targeting microorganism DNA to link samples to place of origin and to link people to places and objects.

Abstract 3528: Novel enzymatic DNA fragmentation integrated into library construction

Abstract Next Generation Sequencing (NGS) is rapidly becoming a powerful tool, by providing a high resolution and global view of the cancer genome mainly through whole genome, whole exome and transcriptome sequencing. This knowledge is important to support drug development targeted towards precision medicine. Obtaining high quality sequencing data begins with optimal sample preparation. DNA fragmentation is one of the critical first steps in the construction of high quality libraries for NGS, but current fragmentation methods create a bottleneck on library preparation throughput. We have developed an efficient, one tube fragmentation system that integrates enzyme-based DNA fragmentation with end-repair and dA-tailing in a single step, followed by adaptor ligation in the same tube. This streamlined method is compatible with a wide range of DNA samples and input amounts, resulting in reproducible and reliable fragment sizes. Genomic DNA (100pg to 500ng) with various GC content, was used in the construction of libraries, that were sequenced on an Illumina platform. For low input samples, PCR amplification was performed prior to sequencing. Libraries constructed using intact genomic DNA and this novel library preparation method produced substantially higher yields than standard methods and mechanically-fragmented DNA. Enzyme-based shearing increases library yield by reducing DNA damage and sample loss. High library yields also enable PCR-free workflows from as little as 50ng starting material. This method can be used for DNA extraction and library preparation from whole blood and dried blood samples.Sequencing quality of libraries generated with inputs ranging from 100pg to 500ng DNA show similar coverage uniformity and fragment size distribution, with minimal GC bias. We have developed an enzymatic DNA fragmentation kit that enables the construction of high quality libraries from a range of sample types and inputs with minimal sequence bias, high yields and low duplication rates. This method eliminates the need for expensive equipment to fragment DNA as well as numerous cleanup and liquid transfer steps thereby reducing the time, cost and errors associated with library construction. These advances in NGS technologies, supported by powerful bioinformatics tools, promises to revolutionize cancer research, diagnosis and therapy. Citation Format: Vaishnavi Panchapakesa, Lynne Apone, Karen Duggan, Bradley Langhorst, Chen Song, Pingfang Liu, Timur Shtatland, Christine Rozzi, Christine Sumner, Fiona Stewart, Eileen Dimalanta, Theodore Davis. Novel enzymatic DNA fragmentation integrated into library construction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3528.

Abstract 4348: DNA-based fusion detection using a pan-cancer tumor profiling 532-oncogene panel

Abstract Large-scale cancer profiling using next generation sequencing (NGS) has become instrumental to the discovery and identification of new, targetable cancer alterations. A comprehensive set of 532 oncogene targets were combined to create the new xGen® Pan-Cancer Panel V2 for hybrid capture sequencing. This xGen panel covers 2.2 Mb of the human genome, and allows for the simultaneous detection of copy number variations (CNVs), insertions and deletions (indels), gene rearrangements, and microsatellite instability across a wide range of sample types, inputs, and quality. Using a new library prep workflow optimized for low quality samples and low input, panel performance was first evaluated with 30 ng of input DNA using libraries built from matched samples [formalin-fixed paraffin-embedded (FFPE) tumor gDNA, frozen adjacent normal tissue gDNA, and cell-free DNA (cfDNA)] from five lung cancer donors (n = 15). Sample quality ranged from a mean DIN of 4.4 ±1.1 to 8.3 ±0.9 for FFPE tumor gDNA and frozen normal gDNA, respectively. After subsampling to 200X mean target coverage, 96% of target bases had at least 40X coverage for all libraries. Comparative hierarchal clustering analysis was then used to identify lung cancer mutations shared in all tumor samples. NGS gDNA reference standards from Horizon Discovery (HD753, HD798, HD799, and HD803) with verified CNVs, single nucleotide variations (SNVs), amplifications, and fusions, and were used to evaluate detection rates at different library input masses down to 1 ng. cDNA libraries were also prepared from RNA extracted from FFPE 5-Fusion RNA Multiplex Reference Standards (HD796, HD783). We identified all possible gene fusion events in the positive control using the structural variant caller, LUMPY (https://github.com/arq5x/lumpy-sv). The xGen Pan-Cancer Panel V2 enables a cost-efficient and time-saving approach for the detection of multiple oncogene targets. Citation Format: Katharine Dilger, Yongming Sun, Kevin Lai, Ushati Das Chakravarty, Nicole Sponer, Kristina Giorda, Patrick Lau, Yu Wang. DNA-based fusion detection using a pan-cancer tumor profiling 532-oncogene panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4348.

Method development and validation for total haloxyfop analysis in infant formulas and related ingredient matrices using liquid chromatography-tandem mass spectrometry.

According to the European Commission directive 2006/141/EC, haloxyfop residue levels should not exceed 0.003mg/kg in ready-to-feed infant formula, and the residue definition includes sum of haloxyfop, its esters, salts, and conjugates expressed as haloxyfop. A simple method for total haloxyfop analysis in infant formula and related ingredient matrices was developed and validated using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The sample preparation consisted of an alkaline hydrolysis with methanolic sodium hydroxide to release haloxyfop (parent acid) from its bound forms prior to the extraction with acetonitrile. A mixture of magnesium sulfate (MgSO4) and sodium chloride (NaCl) (4:1, w/w) was added to the extract to induce phase separation and force the analyte into the upper acetonitrile-methanol layer and then a 1-mL aliquot was subsequently cleaned up by dispersive solid phase extraction with 150mg of MgSO4 and 50mg of octadecyl (C18) sorbent. The analytical procedure was developed and carefully optimized to enable low-level, total haloxyfop analysis in a variety of challenging matrices, including infant formulas and their important high-carbohydrate, high-protein, high-fat, and emulsifier ingredients. The final method was validated in two different laboratories by fortifying samples with haloxyfop and haloxyfop-methyl, which was used as a model compound simulating bound forms of the analyte. Mean recoveries of haloxyfop across all fortification levels and evaluated matrices ranged between 92.2 and 114% with repeatability, within-lab reproducibility, and reproducibility RSDs ≤14%. Based on the validation results, this method was capable to convert the haloxyfop ester into the parent acid in a wide range of sample types and to reliably identify and quantify total haloxyfop at the target 0.003mg/kg level in infant formulas (both powdered and ready-to-feed liquid forms). Graphical abstract LC-MS/MS-based workflow for the determination of the total haloxyfop in infant formula and related ingredients.

Comparison of chemical procedures for Re-isotopic measurements by N-TIMS

Precise and accurate measurements of the isotopic composition of rhenium (Re) in geologic samples are of paramount importance for the successful application of the Re-Os geochronometer. Two methods for chemical isolation of Re are used in the geochronology community – column chemistry using anion exchange resin and solvent-solvent extraction using a sodium hydroxide-acetone mixture. Despite their ubiquitous application, a systematic comparison of these two methods is missing. Here we compare Re-isotopic data on a variety of samples (sulfides, hydrocarbons, shales, and in-house standard solutions) that were processed by both chemical methods. Measured 185Re/187Re ratios for both methods have similar precision and overlap within the propagated long-term analytical reproducibility of ~1‰ for samples that yield moderate to strong intensities (>50 mV on the weaker Re mass). In contrast, measured 185Re/187Re ratios for most samples that yield less intense Re signals (<50 mV on the weaker Re mass) disagree by ~3–6‰ between the two methods, exceeding the propagated analytical uncertainty of ~3‰ for low-intensity measurements. A systematic investigation of samples with natural Re isotopic composition (shale, molybdenite, and standard solutions) shows that use of anion exchange resin (column chemistry) may cause elevated 185Re/187Re ratios. This effect is more pronounced for low-Re shales (<1 ng total Re processed) and becomes nearly or completely insignificant for high-Re samples measured over a wide range of signal intensities. Standard solutions processed through column chemistry, however, preserve their natural Re isotopic composition. Together, these data suggest that complex sample matrices leading to sample-derived impurities passed through column chemistry may cause isobaric interferences that deviate measured 185Re/187Re ratios in geologic samples. In contrast, the acetone-NaOH method produces more consistent Re isotopic results across the same range of sample types, Re loads and signal intensities. Thus, we recommend use of the acetone-NaOH solvent-solvent extraction procedure for low-Re samples, and provide a practical way to lower the typically higher Re blank supplied by NaOH.

From Multistep Enzyme Monitoring to Whole-Cell Biotransformations: Development of Real-Time Ultraviolet Resonance Raman Spectroscopy.

Process analytical technologies (PAT) are used within industry to give real-time measurements of critical quality parameters, ultimately improving the quality by design (QbD) of the final product and reducing manufacturing costs. Spectroscopic and spectrophotometric methods are readily employed within PAT due to their ease of use, compatibility toward a range of sample types, robustness, and multiplexing capabilities. We have developed a UV resonance Raman (UVRR) spectroscopy approach to quantify industrially relevant biotransformations accurately, focusing on nitrile metabolizing enzymes: nitrile hydratase (NHase) and amidase versus nitrilase activity. Sensitive detection of the amide intermediate by UVRR spectroscopy enabled discrimination between the two nitrile-hydrolyzing pathways. Development of a flow-cell apparatus further exemplifies its suitability toward PAT measurements, incorporating in situ analysis within a closed system. Multivariate curve resolution-alternating least-squares (MCR-ALS) was applied to the UVRR spectra, as well as off-line HPLC measurements, to enable absolute quantification of substrate, intermediate, and product. Further application of hard modeling to MCR-ALS deconvolved concentration profiles enabled accurate kinetic determinations, thus removing the requirement for comparative off-line HPLC. Finally, successful quantitative measurements of in vivo activity using whole-cell biotransformations, where two Escherichia coli strains expressing either NHase (transforming benzonitrile to benzamide) or amidase (further conversion of benzamide to benzoic acid), illustrate the power, practicality, and sensitivity of this novel approach of multistep and, with further refinement, we believe, multiple micro-organism biotransformations.