Jiyang Dong

Identification of biochemical changes in lactovegetarian urine using 1H NMR spectroscopy and pattern recognition

A vegetarian diet has been demonstrated to have a profound influence on human metabolism as well as to aid the prevention of several chronic diseases relative to an omnivorous diet. However, there have been no systematic metabolomic studies on all of the biochemical changes induced in human subjects by long-term vegetarianism. In this study, 1H NMR spectroscopy in combination with multivariate statistical analysis was applied to explore the variability in the metabolic urinary profiles of healthy populations from four groups: lactovegetarian male (VEGMALE), lactovegetarian female (VEGFEMALE), omnivorous male (OMNMALE), and omnivorous female (OMNFEMALE). Differences in metabolic profiles were examined in relation to diet and gender by principal component analysis (PCA) and spectral integrals. It was found that the most influential low molecular weight metabolites responsible for the differences between the diet groups were N-acetyl glycoprotein (NAG), succinate, citrate, trimethylamine-N-oxide (TMAO), taurine, glycine, hippurate, phenylalanine, methylhistidine and formate, whereas for the differences in gender groups the most discriminatory metabolites were NAG, succinate, creatinine, arginine, TMAO, taurine, hippurate, mannitol, phenylalanine, and methylhistidine. The results from the PCA of all four groups indicated that diet plays a greater role in influencing metabolite differences than gender. As an exploration, this work shows the potential of metabolomics when applied to nutritional and physiological studies, and it will aid further studies.

An efficient de-convolution reconstruction method for spatiotemporal- encoding single-scan 2D MRI

Spatiotemporal-encoding single-scan MRI method is relatively insensitive to field inhomogeneity compared to EPI method. Conjugate gradient (CG) method has been used to reconstruct super-resolved images from the original blurred ones based on coarse magnitude-calculation. In this article, a new de-convolution reconstruction method is proposed. Through removing the quadratic phase modulation from the signal acquired with spatiotemporal-encoding MRI, the signal can be described as a convolution of desired super-resolved image and a point spread function. The de-convolution method proposed herein not only is simpler than the CG method, but also provides super-resolved images with better quality. This new reconstruction method may make the spatiotemporal-encoding 2D MRI technique more valuable for clinic applications.

Draining Algorithm for the Maximum Flow Problem

A new augmenting path based algorithm called draining algorithm is proposed for the maximum flow problem in this letter. Unlike other augmenting path based algorithms which augment gradually the flow from zero-flow to the maximum flow, the proposed algorithm drains the redundant capacities out of the network to achieve the maximum flow. Experimental results shown the high efficiency of the proposed algorithm in near saturated network, thought it has a same computational complex with the traditional augmenting path approach for regular flow networks.

Metabolomic Profilings of Urine and Serum from High Fat-Fed Rats via 1H NMR Spectroscopy and Pattern Recognition

Abstract1H NMR spectroscopy in combination with multivariate statistical analysis was applied to explore the metabolic variability in urine and serum of high fat-fed rats relative to normal chow-fed ones. Metabolites contributing to intergroup discrimination identified by partial least squares discriminant analysis include 3-hydroxybutyrate, glutamate, glutamine, citrate, choline, hippurate, alanine, lactate, creatinine, taurine, acetate, etc. The aging effect along with long-term feeding was delineated with metabolic trajectory in principal component analysis score plot and age-related differences on metabolic profiling under different dietary intervention were recognised. The identified metabolites responsible for obesity were all imported into a web tool for network-based interpretation of compound lists to interpret their functional context, molecular mechanisms and disturbed signalling pathway globally and systematically. The results are useful for interpreting the pathology of obesity and further probing into the relationship between dietary-induced obesity and type 2 diabetes mellitus.

Urinary Metabolomics Reveals Alterations of Aromatic Amino Acid Metabolism of Alzheimer’s Disease in the Transgenic CRND8 Mice

Alzheimers disease (AD) is a progressive neurodegenerative disorder, with amyloid plaques accumulation as the key feature involved in its pathology. To date, however, the biochemical changes in AD have not been clearly characterized. Here, we present that urinary metabolomics based on high resolution mass spectrometry was employed for delineation of metabolic alterations in transgenic CRND8 mice. In this noninvasive approach, urinary metabolome reveals the biochemical changes in early onset of this AD mouse model. In virtue of comprehensive metabolite profiling and multivariate statistical analysis, a total of 73 differential metabolites of urine sample sets was identified in 12-week and 18-week transgenic mice compared to wild-type littermates, covering perturbations of aromatic amino acid metabolism, the Krebs cycle and one-carbon metabolism. Of particular interest is that divergent tryptophan metabolism, such as upregulation of serotonin pathway while downregulation of kynurenine pathway, was observed. Meanwhile, the accumulation of both N-acetylvanilalanine and 3-methoxytyrosine indicated aromatic L-amino acid decarboxylase deficiency. And the microbial metabolites derived from aromatic amino acid metabolism and drug-like phase II metabolic response via the glycine conjugation reactions were also highlighted, indicating that genetic modification in mouse brain not only alters genotype but also perturbs the gut microbiome. Together, our study demonstrated that the integrative approach employing mass spectrometry-based metabolomics and a transgenic mouse model for AD may provide new evidence for distinct metabolic signatures. The perturbations of metabolic pathways may have far-reaching implications for early diagnosis and intervention in AD.

Multi-focus image fusing based on non-negative matrix factorization

Multi-focus image fusion is a process of obtaining a new all in-focus merged image from two or more partially defocused images of the same scene and same imaging condition. The merged image includes the information of the original images and improves the reliability and intelligibility for object detection and target recognition. The most widespread methods for image fusion are wavelet transform based methods. However, the facts that the original pixel values of input images are not preserved in the fused image and different multi-scale image fusion schemes will lead to different results cause that the wavelet methods present a limited quality performance compared with a cut and pasted fusion reference model. In this paper, a new multi-focus image fusion approach is proposed based on non-negative matrix factorization (NAIF). The cut and pasted fusion scheme is adopted in the new fusion approach. Cut the source images into small-size blocks, factorize the corresponding image blocks using NAIF, pick out the sharpest blocks according the NAIF coefficient, and combine them as an in-focus image. The experiment results show that the proposed approach outperforms the wavelet based fusion methods, both in visual effect and objective evaluation criteria.

NMR-based metabolomics Reveals Alterations of Electro-acupuncture Stimulations on Chronic Atrophic Gastritis Rats

Chronic atrophic gastritis (CAG) is a common gastrointestinal disease which has been considered as precancerous lesions of gastric carcinoma. Previously, electro-acupuncture stimulation has been shown to be effective in ameliorating symptoms of CAG. However the underlying mechanism of this beneficial treatment is yet to be established. In the present study, an integrated histopathological examination along with molecular biological assay, as well as 1H NMR analysis of multiple biological samples (urine, serum, stomach, cortex and medulla) were employed to systematically assess the pathology of CAG and therapeutic effect of electro-acupuncture stimulation at Sibai (ST 2), Liangmen (ST 21), and Zusanli (ST 36) acupoints located in the stomach meridian using a rat model of CAG. The current results showed that CAG caused comprehensive metabolic alterations including the TCA cycle, glycolysis, membrane metabolism and catabolism, gut microbiota-related metabolism. On the other hand, electro-acupuncture treatment was found able to normalize a number of CAG-induced metabolomics changes by alleviating membrane catabolism, restoring function of neurotransmitter in brain and partially reverse the CAG-induced perturbation in gut microbiota metabolism. These findings provided new insights into the biochemistry of CAG and mechanism of the therapeutic effect of electro-acupuncture stimulations.

1H NMR-based metabolomics investigation of copper-laden rat: a model of Wilson's disease

Background and Purpose Wilson’s disease (WD), also known as hepatoleticular degeneration (HLD), is a rare autosomal recessive genetic disorder of copper metabolism, which causes copper to accumulate in body tissues. In this study, rats fed with copper-laden diet are used to render the clinical manifestations of WD, and their copper toxicity-induced organ lesions are studied. To investigate metabolic behaviors of ‘decoppering’ process, penicillamine (PA) was used for treating copper-laden rats as this chelating agent could eliminate excess copper through the urine. To date, there has been limited metabolomics study on WD, while metabolic impacts of copper accumulation and PA administration have yet to be established. Materials and Methods A combination of 1HNMR spectroscopy and multivariate statistical analysis was applied to examine the metabolic profiles of the urine and blood serum samples collected from the copper-laden rat model of WD with PA treatment. Results Copper accumulation in the copper-laden rats is associated with increased lactate, creatinine, valine and leucine, as well as decreased levels of glucose and taurine in the blood serum. There were also significant changes in p-hydroxyphenylacetate (p-HPA), creatinine, alpha-ketoglutarate (α-KG), dimethylamine, N-acetylglutamate (NAG), N-acetylglycoprotein (NAC) in the urine of these rats. Notably, the changes in p-HPA, glucose, lactate, taurine, valine, leucine, and NAG were found reversed following PA treatment. Nevertheless, there were no changes for dimethylamine, α-KG, and NAC as a result of the treatment. Compared with the controls, the concentrations of hippurate, formate, alanine, and lactate were changed when PA was applied and this is probably due to its side effect. A tool named SMPDB (Small Molecule Pathway Database) is introduced to identify the metabolic pathway influenced by the copper-laden diet. Conclusion The study has shown the potential application of NMR-based metabolomic analysis in providing further insights into the molecular mechanism underlying disorder due to WD.

Metabolic Effect of Dietary Taurine Supplementation on Nile Tilapia (Oreochromis nilotictus) Evaluated by NMR-Based Metabolomics

Taurine is indispensable in aquatic diets that are based solely on plant protein, and it promotes growth of many fish species. However, the physiological and metabolome effects of taurine on fish have not been well described. In this study, 1H NMR-based metabolomics approaches were applied to investigate the metabolite variations in Nile tilapia (Oreochromis nilotictus) muscle in order to visualize the metabolic trajectory and reveal the possible mechanisms of metabolic effects of dietary taurine supplementation on tilapia growth. After extraction using aqueous and organic solvents, 19 taurine-induced metabolic changes were evaluated in our study. The metabolic changes were characterized by differences in carbohydrate, amino acid, lipid, and nucleotide contents. The results indicate that taurine supplementation could significantly regulate the physiological state of fish and promote growth and development. These results provide a basis for understanding the mechanism of dietary taurine supplementation in fish feeding. 1H NMR spectroscopy, coupled with multivariate pattern recognition technologies, is an efficient and useful tool to map the fish metabolome and identify metabolic responses to different dietary nutrients in aquaculture.

Geographical Origin Discrimination of Oolong Tea (TieGuanYin, Camellia sinensis (L.) O. Kuntze) Using Proton Nuclear Magnetic Resonance Spectroscopy and Near-Infrared Spectroscopy

A total of 90 oolong tea samples were collected from three different growing places in the Fujian province of China. Both proton nuclear magnetic resonance (1H NMR) and near-infrared spectroscopy (NIR) were used to analyze the collected tea samples. With the aid of chemometric methods, differential components in 1H NMR data and characteristic wavenumbers from NIR spectra were identified. Since NMR and NIR provide complementary information for tea samples, data fusion was carried out by combining 1H NMR and NIR spectra of the collected tea sample. Experimental results showed that a better discrimination accuracy of geographical origins of oolong tea could be achieved by combining NMR and NIR data (86.2–95.8%), as compared to using NMR data (68.2–78.7%) or NIR data (80.0–89.3%) alone. The current data suggested that a combination of NMR and NIR methods could serve as an efficient way for geographical origin discrimination and qualitative control of oolong tea.