Megavariate Analysis of Environmental QSAR Data. Part II – Investigating Very Complex Problem Formulations Using Hierarchical, Non-Linear and Batch-Wise Extensions of PCA and PLS

Emerging frontiers in microbe-mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment

The overuse of pesticides for augmenting agriculture productivity always comes at the cost of environment, biodiversity, and human health and has put the land, water, and environmental footprints under severe threat throughout the globe. Underpinning and maximizing the microbiome functions in pesticide-contaminated environments has become a prerequisite for a sustainable environment and resilient agriculture. It is imperative to elucidate the metabolic network of the microbial communities and environmental variables at the contaminated site to predict the best strategy for remediation and soil microbe-pesticide interactions. High throughput next-generation sequencing and in silico analysis allow us to identify and discern the members and characteristics of core microbiomes at the contaminated site. Integration of modern high throughput multi-omics investigations and informatics pipelines provide novel approaches and pathways to capitalize on the core microbiomes for enhancing environmental functioning and mitigation. The role of eco-genomics tools in visualising the microbial network, taxonomy, functional potential, and environmental variables in contaminated habitats is discussed in this review. The integrated role of the potential microbe identification as individual or consortia, mechanistic approach for pesticide degradation, identification of responsible enzymes/genes, and in silico approach is emphasized for the prospects of the area.

An integrated method for monitoring thermal processing temperature of pork based on Q-Exactive mass spectrometry and chemometrics

Meat heating endpoint temperature (EPT) is an important indicator to ensure the safety of cooked meat. Accurately determining the EPT of cooked meat and ready-to-eat meat products is an important strategy to ensure food safety. In this study, a comprehensive metabolic method based on UPLC-Q Exactive and chemometrics was developed to study the metabolites differences among pork roasted at different temperatures in order to select markers indicating EPT and discover new toxic heat-induced compounds. A two-step extraction method was applied to avoid the loss of metabolite information caused by sample preparation. Using chemometrics, the five compounds of creatine, creatinine, 2-amino-1-methyl-6-phenylimidazo (4,5-b) pyridine (PhIP), 2-methyl-6-amino-5-hydroxymethylpyrimidine (TMP) and compound with the m/z of 114.04316 were selected as markers, and four of them were further confirmed by chemical standards. It is worth noting that TMP was discovered in roasted pork for the first time. In addition, targeting studies aimed at quantifying the selected markers were conducted at different thermal processing temperatures. From the quantification results, it can be concluded that the heat temperature not exceed 180 °C is recommended to reduce the content of toxic compounds. This study has proved that the integration of UPLC-Q Exactive and chemometrics could provide an efficient method for the study of markers related to thermal process and new toxic heat-induced compounds.

Differentiation of skin biopsies by light scattering spectroscopy

Introduction

Spectroscopic systems are medical tools that are used for the detection of cancerous tissues ex vivo and in vivo.

Aim

To differentiate inflammatory and benign skin lesions of excised biopsy samples via a combination of multivariate statistical analysis.

Material and methods

Spectral data were obtained from a total of 22 inflammatory and ten benign skin biopsy samples from 30 patients in the visible wavelength (450–750 nm) regions. Spectral data were compared with the dermatopathology results. Spectral data analyses of biopsy samples were performed via principal component analysis (PCA), followed by linear discriminant analysis (LDA). The differentiation performance was calculated with the receiver operating characteristic (ROC) curve analysis.

Results

The classification based on the discriminant function score provided a sensitivity of 90.9% and a specificity of 80% in discriminating benign from inflammatory lesions with an accuracy of 87.5%.

Conclusions

Our study revealed that light scattering spectroscopy could discriminate between inflammatory and benign skin lesions of excised biopsy samples with high sensitivity by using multivariate statistical analysis. It can be concluded that the high diagnostic accuracy of the optical spectroscopy method has the potential to use as a supplementary system to distinguish inflammatory skin lesions from benign during the pathological examination.

Simultaneous authentication of species identity and geographical origin of shrimps: Untargeted metabolomics to recurrent biomarker ions

Mandatory disclosure of the species identity, production method, and geographical origin are embedded in the regulations and traceability systems, governing international seafood trade. A high-resolution mass spectrometry-based metabolomics approach could simultaneously authenticate the species identity and geographical origin of commercially important shrimps. The highly innovative approach spared the need for multiple testing methods which are in routine use currently. A robust chemometric model, developed using the metabolite fingerprint dataset, could accurately predict the species identity of the shrimp samples. Subsequently, species-specific biomarkers were discovered and a tandem mass spectrometry method for authentication of the species was developed. Two other chemometric models from the metabolomics experiment accurately predicted the geographical origin of king prawns and tiger prawns. The study has shown for the first time that food-metabolomics along with chemometrics can simultaneously check for multiple seafood fraud issues in the global seafood supply-chain.

Metabolic profiling study on potential toxicity in male mice treated with Dechlorane 602 using UHPLC-ESI-IT-TOF-MS

Dechlorane 602 (Dec 602), a chlorinated flame retardant, has been widely detected in different environmental matrices and biota. However, toxicity data for Dec 602 seldom have been reported. A metabolomics study based on ultra-high performance liquid chromatography coupled with ion trap time-of-flight mass spectrometry was employed to study the urine and sera metabolic profiles of mice administered with Dec 602 (0, 0.001, 0.1, and 10 mg/kg body weight per day) for 7 days. A significant difference in metabolic profiling was observed between the Dec 602 treated group and the control group by multivariate analysis, which directly reflected the metabolic perturbations caused by Dec 602. The metabolomics analyses of urine from Dec 602-exposed animals exhibited an increase in the levels of thymidine and tryptophan as well as a decrease in the levels of tyrosine, 12,13-dihydroxy-9Z-octadecenoic acid, 2-hydroxyhexadecanoic acid and cuminaldehyde. The metabolomics analyses of sera showed a decrease in the levels of kynurenic acid, daidzein, adenosine, xanthurenic acid and hypoxanthine from Dec 602-exposed animals. These findings indicated Dec 602 induced disturbance in phenylalanine, tyrosine and tryptophan biosynthesis, tryptophan metabolism, tyrosine metabolism, pyrimidine metabolism, purine metabolism, ubiquinone and other terpenoid-quinone biosynthesis; phenylalanine metabolism and aminoacyl-tRNA biosynthesis. Significant alterations of immune and neurotransmitter-related metabolites (tyrosine, tryptophan, kynurenic acid, and xanthurenic acid) suggest that the toxic effects of Dec 602 may contribute to its interactions with the immune and neuronal systems. This study demonstrated that the UHPLC-ESI-IT-TOF-MS-based metabolomic approach can obtain more specific insights into the potential toxic effects of Dec 602 at molecular level.

Chemometric-assisted method development in hydrophilic interaction liquid chromatography: A review

With an enormous growth in the application of hydrophilic interaction liquid chromatography (HILIC), there has also been significant progress in HILIC method development. HILIC is a chromatographic method that utilises hydro-organic mobile phases with a high organic content, and a hydrophilic stationary phase. It has been applied predominantly in the determination of small polar compounds. Theoretical studies in computer-aided modelling tools, most importantly the predictive, quantitative structure retention relationship (QSRR) modelling methods, have attracted the attention of researchers and these approaches greatly assist the method development process. This review focuses on the application of computer-aided modelling tools in understanding the retention mechanism, the classification of HILIC stationary phases, prediction of retention times in HILIC systems, optimisation of chromatographic conditions, and description of the interaction effects of the chromatographic factors in HILIC separations. Additionally, what has been achieved in the potential application of QSRR methodology in combination with experimental design philosophy in the optimisation of chromatographic separation conditions in the HILIC method development process is communicated. Developing robust predictive QSRR models will undoubtedly facilitate more application of this chromatographic mode in a broader variety of research areas, significantly minimising cost and time of the experimental work.

Integrated omics analysis of specialized metabolism in medicinal plants

Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.

Unravelling the metabolic impact of SBS-associated microbial dysbiosis: Insights from the piglet short bowel syndrome model

Liver disease is a major source of morbidity and mortality in children with short bowel syndrome (SBS). SBS-associated microbial dysbiosis has recently been implicated in the development of SBS-associated liver disease (SBS-ALD), however the pathological implications of this association have not been explored. In this study high-throughput sequencing of colonic content from the well-validated piglet SBS-ALD model was examined to determine alterations in microbial communities, and concurrent metabolic alterations identified in urine samples via targeted mass spectrometry approaches (GC-MS, LC-MS, FIA-MS) further uncovered impacts of microbial disturbance on metabolic outcomes in SBS-ALD. Multi-variate analyses were performed to elucidate contributing SBS-ALD microbe and metabolite panels and to identify microbe-metabolite interactions. A unique SBS-ALD microbe panel was clearest at the genus level, with discriminating bacteria predominantly from the Firmicutes and Bacteroidetes phyla. The SBS-ALD metabolome included important alterations in the microbial metabolism of amino acids and the mitochondrial metabolism of branched chain amino acids. Correlation analysis defined microbe-metabolite clustering patterns unique to SBS-ALD and identified a metabolite panel that correlates with dysbiosis of the gut microbiome in SBS.

Metabolomics Reveals that Aryl Hydrocarbon Receptor Activation by Environmental Chemicals Induces Systemic Metabolic Dysfunction in Mice

Environmental exposure to dioxins and dioxin-like compounds poses a significant health risk for human health. Developing a better understanding of the mechanisms of toxicity through activation of the aryl hydrocarbon receptor (AHR) is likely to improve the reliability of risk assessment. In this study, the AHR-dependent metabolic response of mice exposed to 2,3,7,8-tetrachlorodibenzofuran (TCDF) was assessed using global (1)H nuclear magnetic resonance (NMR)-based metabolomics and targeted metabolite profiling of extracts obtained from serum and liver. (1)H NMR analyses revealed that TCDF exposure suppressed gluconeogenesis and glycogenolysis, stimulated lipogenesis, and triggered inflammatory gene expression in an Ahr-dependent manner. Targeted analyses using gas chromatography coupled with mass spectrometry showed TCDF treatment altered the ratio of unsaturated/saturated fatty acids. Consistent with this observation, an increase in hepatic expression of stearoyl coenzyme A desaturase 1 was observed. In addition, TCDF exposure resulted in inhibition of de novo fatty acid biosynthesis manifested by down-regulation of acetyl-CoA, malonyl-CoA, and palmitoyl-CoA metabolites and related mRNA levels. In contrast, no significant changes in the levels of glucose and lipid were observed in serum and liver obtained from Ahr-null mice following TCDF treatment, thus strongly supporting the important role of the AHR in mediating the metabolic effects seen following TCDF exposure.

OPLS in batch monitoring - Opens up new opportunities

In batch statistical process control (BSPC), data from a number of "good" batches are used to model the evolution (trajectory) of the process and they also define model control limits, against which new batches may be compared. The benchmark methods used in BSPC include partial least squares (PLS) and principal component analysis (PCA). In this paper, we have used orthogonal projections to latent structures (OPLS) in BSPC and compared the results with PLS and PCA. The experimental study used was a batch hydrogenation reaction of nitrobenzene to aniline characterized by both UV spectroscopy and process data. The key idea is that OPLS is able to separate the variation in data that is correlated to the process evolution (also known as 'batch maturity index') from the variation that is uncorrelated to process evolution. This separation of different types of variations can generate different batch trajectories and hence lead to different established model control limits to detect process deviations. The results demonstrate that OPLS was able to detect all process deviations and provided a good process understanding of the root causes for these deviations. PCA and PLS on the other hand were shown to provide different interpretations for several of these process deviations, or in some cases they were unable to detect actual process deviations. Hence, the use of OPLS in BSPC can lead to better fault detection and root cause analysis as compared to existing benchmark methods and may therefore be used to complement the existing toolbox.

ProAlgaZyme subfraction improves the lipoprotein profile of hypercholesterolemic hamsters, while inhibiting production of betaine, carnitine, and choline metabolites

Background

Previously, we reported that ProAlgaZyme (PAZ) and its biologically active fraction improved plasma lipids in hypercholesterolemic hamsters, by significantly increasing the high density lipoprotein cholesterol (HDL-C) while reducing non-HDL cholesterol and the ratio of total cholesterol/HDL-C. Moreover, hepatic mRNA expression of genes involved in HDL/reverse cholesterol transport were significantly increased, while cholesteryl ester transfer protein (CETP) expression was partially inhibited. In the current study, we investigated the therapeutic efficacy of the biologically active fraction of PAZ (BaP) on the plasma lipid and plasma metabolomic profiles in diet induced hypercholesterolemic hamsters.

Methods

Fifty male Golden Syrian hamsters were fed a high fat diet for 4 weeks prior to randomization into 6 groups, based on the number of days they received subsequent treatment. Thus animals in T0, T3, T7, T10, T14, and T21 groups received BaP for 0, 3, 7, 10, 14, and 21 days, respectively, as their drinking fluid. Plasma lipids were assayed enzymatically, while real-time reverse transcriptase polymerase chain reaction (RT-PCR) provided the transcription levels of the Apolipoprotein (Apo) A1 gene. The plasma metabolomic profile was determined using ¹H nuclear magnetic resonance (NMR) spectroscopy in conjunction with multivariate analysis.

Results

Plasma HDL-C was significantly increased in T3 (P < 0.05) and T21 (P < 0.001), while non-HDL cholesterol was significantly reduced in T3, T7, T10 (P < 0.001) and T14, T21 (P < 0.01). Moreover, the ratio of total cholesterol/HDL-C was significantly lower in all BaP treated groups (P < 0.001) as compared with T0. Quantitative RT-PCR showed an increase in Apo A1 expression in T10 (3-fold) and T21 (6-fold) groups. NMR data followed by multivariate analysis showed a clear separation between T0 and T21 groups, indicating a difference in their metabolomic profiles. Plasma concentrations of metabolites associated with a risk for atherosclerosis and cardiovascular disease, including choline, phosphocholine, glycerol-phosphocholine, betaine and carnitine metabolites were significantly lower in the T21 group.

Conclusion

Treatment with BaP significantly improved the plasma lipid profile by increasing HDL-C and lowering non-HDL cholesterol. In addition, BaP potentially improved the plasma metabolomic profile by reducing the concentration of key metabolites associated with risk for atherosclerosis and cardiovascular disease.

Traumatic axonal injury in the mouse is accompanied by a dynamic inflammatory response, astroglial reactivity and complex behavioral changes

BACKGROUND

Diffuse traumatic axonal injury (TAI), a common consequence of traumatic brain injury, is associated with high morbidity and mortality. Inflammatory processes may play an important role in the pathophysiology of TAI. In the central fluid percussion injury (cFPI) TAI model in mice, the neuroinflammatory and astroglial response and behavioral changes are unknown.

METHODS

Twenty cFPI-injured and nine sham-injured mice were used, and the neuroinflammatory and astroglial response was evaluated by immunohistochemistry at 1, 3 and 7 days post-injury. The multivariate concentric square field test (MCSF) was used to compare complex behavioral changes in mice subjected to cFPI (n = 16) or sham injury (n = 10). Data was analyzed using non-parametric statistics and principal component analysis (MCSF data).

RESULTS

At all post-injury time points, β-amyloid precursor protein (β-APP) immunoreactivity revealed widespread bilateral axonal injury and IgG immunostaining showed increased blood-brain barrier permeability. Using vimentin and glial fibrillary acidic protein (GFAP) immunohistochemistry, glial cell reactivity was observed in cortical regions and important white matter tracts peaking at three days post-injury. Only vimentin was increased post-injury in the internal capsule and only GFAP in the thalamus. Compared to sham-injured controls, an increased number of activated microglia (MAC-2), infiltrating neutrophils (GR-1) and T-cells (CD3) appearing one day after TAI (P<0.05 for all cell types) was observed in subcortical white matter. In the MCSF, the behavioral patterns including general activity and exploratory behavior differed between cFPI mice and sham-injured controls.

CONCLUSIONS

Traumatic axonal injury TAI resulted in marked bilateral astroglial and neuroinflammatory responses and complex behavioral changes. The cFPI model in mice appears suitable for the study of injury mechanisms, including neuroinflammation, and the development of treatments targeting TAI.

Estimating persistence of brominated and chlorinated organic pollutants in air, water, soil, and sediments with the QSPR-based classification scheme

We have estimated degradation half-lives of both brominated and chlorinated dibenzo-p-dioxins (PBDDs and PCDDs), furans (PBDFs and PCDFs), biphenyls (PBBs and PCBs), naphthalenes (PBNs and PCNs), diphenyl ethers (PBDEs and PCDEs) as well as selected unsubstituted polycyclic aromatic hydrocarbons (PAHs) in air, surface water, surface soil, and sediments (in total of 1,431 compounds in four compartments). Next, we compared the persistence between chloro- (relatively well-studied) and bromo- (less studied) analogs. The predictions have been performed based on the quantitative structure-property relationship (QSPR) scheme with use of k-nearest neighbors (kNN) classifier and the semi-quantitative system of persistence classes. The classification models utilized principal components derived from the principal component analysis of a set of 24 constitutional and quantum mechanical descriptors as input variables. Accuracies of classification (based on an external validation) were 86, 85, 87, and 75% for air, surface water, surface soil, and sediments, respectively. The persistence of all chlorinated species increased with increasing halogenation degree. In the case of brominated organic pollutants (Br-OPs), the trend was the same for air and sediments. However, we noticed that the opposite trend for persistence in surface water and soil. The results suggest that, due to high photoreactivity of C-Br chemical bonds, photolytic processes occurring in surface water and soil are able to play significant role in transforming and removing Br-OPs from these compartments. This contribution is the first attempt of classifying together Br-OPs and Cl-OPs according to their persistence, in particular, environmental compartments.

Technology insight: metabonomics in gastroenterology-basic principles and potential clinical applications

Metabonomics-the study of metabolic changes in an integrated biologic system-is an emerging field. This discipline joins the other 'omics' (genomics, transcriptomics and proteomics) to give rise to a comprehensive, systems-biology approach to the evaluation of holistic in vivo function. Metabonomics, especially when based on nuclear magnetic resonance spectroscopy, has the potential to identify biomarkers and prognostic factors, enhance clinical diagnosis, and expand hypothesis generation. As a consequence, the use of metabonomics has been extensively explored in the past decade, and applied successfully to the study of human diseases, toxicology, microbes, nutrition, and plant biology. This Review introduces the basic principles of nuclear magnetic resonance spectroscopy and commonly used tools for multivariate data analysis, before considering the applications and future potential of metabonomics in basic and clinical research, with emphasis on applications in the field of gastroenterology.