Deciphering composition and connectivity of a natural product with the assistance of MS and 2D NMR

A complementary application of three analytical techniques, viz. multidimensional nuclear magnetic resonance spectroscopy (NMR), mass spectrometry (MS), and single‐crystal X‐ray diffractometry was required to identify and refine two natural products isolated from Millettia versicolor and solvent of crystallization. The two compounds, namely 3‐(2H‐1,3‐benzodioxol‐5‐yl)‐6‐methoxy‐8,8‐dimethyl‐4H ,8H‐pyrano[2,3‐h ]chromen‐4‐one, or durmillone, (I), and (2E )‐1‐(4‐{[(2E )‐3,7‐dimethylocta‐2,6‐dien‐1‐yl]oxy}‐2‐hydroxyphenyl)‐3‐(4‐hydroxyphenyl)prop‐2‐en‐1‐one, (II), could not be separated by routine column chromatography and cocrystallized in a 2:1 ratio with 0.13 molecules of ethanol solvent. Compound (II) and ethanol could not be initially identified by single‐crystal X‐ray analysis due to complex disorder in the aliphatic chain region of (II). Mass spectrometry ensured that (II) represented only one species disordered over several positions in the solid state, rather than several species cohabitating on the same crystallographic site. The atomic identification and connectivity in (II) were established by several 2D (two‐dimensional) NMR techniques, which in turn relied on a knowledge of its exact mass. The derived connectivity was then used in the single‐crystal analysis to model the disorder of the aliphatic chain in (II) over three positions and allowed identification of a partially occupied ethanol solvent molecule that was disordered over an inversion center. The disordered moieties were refined with restraints and constraints.     

Utilizing Paper-Based Devices for Antimicrobial-Resistant Bacteria Detection

Antimicrobial resistance (AMR), the ability of a bacterial species to resist the action of an antimicrobial drug, has been on the rise due to the widespread use of antimicrobial agents. Per the World Health Organization, AMR has an estimated annual cost of USD 34 billion in the US and is predicted to be the number one cause of death worldwide by 2050. One way AMR bacteria can spread, and by which individuals can contract AMR infections, is through contaminated water. Monitoring AMR bacteria in the environment currently requires that samples be transported to a central laboratory for slow and labor intensive tests. We have developed an inexpensive assay using paper-based analytical devices (PADs) that can test for the presence of β-lactamase-mediated resistance. To demonstrate viability, the PAD was used to detect β-lactam resistance in wastewater and sewage and identified resistance in individual bacterial species isolated from environmental water sources.     

Bipartite network analysis reveals metabolic gene expression profiles that are highly associated with the clinical outcomes of acute myeloid leukemia

Dysregulated and reprogrammed metabolism are one of the most important characteristics of cancer, and exploiting cancer cell metabolism can aid in understanding the diverse clinical outcomes for patients. To investigate the differences in metabolic pathways among patients with acute myeloid leukemia (AML) and differential survival outcomes, we systematically conducted microarray data analysis of the metabolic gene expression profiles from 384 patients available from the Gene Expression Omnibus and Cancer Genome Atlas databases. Pathway enrichment analysis of differentially expressed genes (DEGs) showed that the metabolic differences between low-risk and high-risk patients mainly existed in two pathways: biosynthesis of unsaturated fatty acids and oxidative phosphorylation. Using the gene-pathway bipartite network, 62 metabolic genes were identified from 272 DEGs involved in 88 metabolic pathways. Based on the expression patterns of the 62 genes, patients with shorter overall survival (OS) durations in the training set (hazard ratio (HR) = 1.58, p = 0.038) and in two test sets (HR = 1.69 and 1.56 and p = 0.089 and 0.029, respectively) were well discriminated by hierarchical clustering analysis. Notably, the expression profiles of ALAS2, BCAT1, BLVRB, and HK3 showed distinct differences between the low-risk and high-risk patients. In addition, models for predicting the OS outcome of AML from the 62 gene signatures achieved improved performance compared with previous studies. In conclusion, our findings reveal significant differences in metabolic processes of patients with AML with diverse survival durations and provide valuable information for clinical translation.     

A novel feature selection for RNA-seq analysis

RNA-seq data are challenging existing omics data analytics for its volume and complexity. Although quite a few computational models were proposed from different standing points to conduct differential expression (D.E.) analysis, almost all these methods do not provide a rigorous feature selection for high-dimensional RNA-seq count data. Instead, most or even all genes are invited into differential calls no matter they have real contributions to data variations or not. Thus, it would inevitably affect the robustness of D.E. analysis and lead to the increase of false positive ratios.In this study, we presented a novel feature selection method: nonnegative singular value approximation (NSVA) to enhance RNA-seq differential expression analysis by taking advantage of RNA-seq count data's non-negativity. As a variance-based feature selection method, it selects genes according to its contribution to the first singular value direction of input data in a data-driven approach. It demonstrates robustness to depth bias and gene length bias in feature selection in comparison with its five peer methods. Combining with state-of-the-art RNA-seq differential expression analysis, it contributes to enhancing differential expression analysis by lowering false discovery rates caused by the biases. Furthermore, we demonstrated the effectiveness of the proposed feature selection by proposing a data-driven differential expression analysis: NSVA-seq, besides conducting network marker discovery.     

Modern automated microextraction procedures for bioanalytical,environmental, and food analyses

Sample preparation frequently is considered the most critical stage of the analytical workflow. It affects the analytical throughput and costs; moreover, it is the primary source of error and possible sample contamination. To increase efficiency, productivity, and reliability, while minimizing costs and environmental impacts, miniaturization and automation of sample preparation are necessary. Nowadays, several types of liquid-phase and solid-phase microextractions are available, as well as different automatization strategies. Thus, this review summarizes recent developments in automated microextractions coupled with liquid chromatography, from 2016 to 2022. Therefore, outstanding technologies and their main outcomes, as well as miniaturization and automation of sample preparation, are critically analyzed. Focus is given to main microextraction automation strategies, such as flow techniques, robotic systems, and column-switching approaches, reviewing their applications to the determination of small organic molecules in biological, environmental, and food/beverage samples.     

Comparison of a single-use pH test strip and a glass electrode for potentiometric titration

The potentiometric titration of a carbonate mixture or an acetate solution is a common experiment in analytical laboratories. Typically, a glass electrode combined with a calomel or Ag/AgCl reference electrode is used to locate the equivalence points in neutralization titrations. The dissociation constants of weak acids and bases can be calculated from the pH at the half-neutralization point. Recently, a new commercial product for measuring pH has been developed. This novel acid–base detection strip is a single-use sensor that requires neither storage in a preservation liquid nor calibration prior to use. This study examined its suitability for the continuous monitoring of pH changes in potentiometric titrations of carbonate mixtures, acetate solutions, or ammonia solutions. There were no significant differences in the concentrations of solutions tested using a glass electrode and a pH test strip. The pK_a, pK_b, and pH values determined using the two systems differed by less than 5%. The results confirmed that the pH strips are suitable for continuously monitoring pH changes during neutralization titrations. However, the strips can only be used once.     

Cloud-Enabled Handheld NIR Spectroscopy: A Transformative Approach for Real-Time Forensic Analysis of Cannabis Specimens

In the past few years, there has been significant interest within the forensic community regarding the deployment of portable solutions that provide real-time results. This article introduces an innovative technology or technology architecture that enables the integration of a handheld device, specifically, Viavi MicroNIR, with a cloud-based system. This cloud system encompasses a server responsible for data processing and a mobile application acting as a user interface. To demonstrate the transformative impact of this technology on field operators, the analysis of cannabis specimens has been utilized. System's capacity to distinguish between CBD-type and THC-type cannabis has been particularly highlighted, along with the remarkable congruence observed between the near-infrared (NIR) spectra and the reference analytical method involving ultra-high-performance liquid chromatography (UHPLC) The article will present the advantages of this application primarily focusing on its potential to alleviate the burden on laboratories by expediting routine illicit drug analysis. Viavi MicroNIR technology provides laboratory personnel with additional time to handle more complex cases, thereby enhancing overall efficiency.     

Method development for quantitative monitoring of monoclonal antibodies in upstream cell-culture process samples with limited sample preparation – An evaluation of various capillary coatings

Monoclonal antibodies (mAbs) have become an important class of biopharmaceuticals used for the treatment of various diseases. Their quantification during the manufacturing process is important. In this work, a capillary zone electrophoresis (CZE) method was developed for the monitoring of the mAb concentration during cell-culture processes. CZE method development rules are outlined, particularly discussing various capillary coatings, such as a neutral covalent polyvinyl alcohol coating, a dynamic successive multiple ionic-polymer coating, and dynamic coatings using background electrolyte additives such as triethanolamine (T-EthA) and triethylamine. The dynamic T-EthA coating resulted in most stable electro-osmotic flows and most efficient peak shapes. The method is validated over the range 0.1–10 mg/ml, with a linear range of 0.08–1.3 mg/ml and an extended range of 1–10 mg/ml by diluting samples in the latter concentration range 10-fold in water. The intraday precision and accuracy were 2%–12% and 88%–107%, respectively, and inter-day precision and accuracy were 4%–9% and 93%–104%, respectively. The precision and accuracy of the lowest concentration level (0.08 mg/ml) were slightly worse and still well in scope for monitoring purposes. The presented method proved applicable for analysing in-process cell-culture samples from different cell-culture processes and is possibly well suited as platform method.     

Analytical Methods for Determination of Phytic Acid and Other Inositol Phosphates: A Review

From the early precipitation-based techniques, introduced more than a century ago, to the latest development of enzymatic bio- and nano-sensor applications, the analysis of phytic acid and/or other inositol phosphates has never been a straightforward analytical task. Due to the biomedical importance, such as antinutritional, antioxidant and anticancer effects, several types of methodologies were investigated over the years to develop a reliable determination of these intriguing analytes in many types of biological samples; from various foodstuffs to living cell organisms. The main aim of the present work was to critically overview the development of the most relevant analytical principles, separation and detection methods that have been applied in order to overcome the difficulties with specific chemical properties of inositol phosphates, their interferences, absence of characteristic signal (e.g., absorbance), and strong binding interactions with (multivalent) metals and other biological molecules present in the sample matrix. A systematical and chronological review of the applied methodology and the detection system is given, ranging from the very beginnings of the classical gravimetric and titrimetric analysis, through the potentiometric titrations, chromatographic and electrophoretic separation techniques, to the use of spectroscopic methods and of the recently reported fluorescence and voltammetric bio- and nano-sensors.