Dynamic chromatin conformation and accessibility changes mediate the spatial-specific gene regulatory network in Bombyx mori.

Silk gland genes of Bombyx mori can have strict spatial expression patterns, which impact their functions and silk quality. However, our understanding of their regulation mechanisms is currently insufficient. To address this, the middle silk gland (MSG) and posterior silk gland (PSG) of the silkworm were investigated. Gene ontology annotation showed that spatially specific expressed genes were involved in the formation of H3k9me and chromatin topology. Chromatin conformation data generated by Hi-C showed that the topologically associated domain boundaries around FibL and Sericin1 genes were significantly different between MSG and PSG. Changes in chromatin conformation led to changes in chromatin activity, which significantly affected the expression of nearby genes in silkworm. Chromatin accessibility regions of MSG and PSG were analyzed using FAIRE-seq, and 1006 transcription factor motifs were identified in open chromatin regions. Furthermore, the spatial-specific expression patterns of silk gland genes were mainly associated with homeobox-contained transcription factors, such as POU-M2, which was specifically bound and relatively highly expressed in the MSG. The regulatory network mediated by POU-M2 regulated most of the spatial-specific expressed genes in MSG, such as ADH1. These results can aid in improving silk performance, optimizing silkworm breeding, and improving the gene spatial regulatory model research for insects.

Role of microRNA-19b-3p on osteoporosis after experimental spinal cord injury in rats.

Osteoporosis is a common complication accompanied by spinal cord injury (SCI) occurrence. MicroRNAs (miRNAs) have been proved to play a crucial role in the progression of osteoporosis, but their regulating mechanism is unclear. The present study investigated miRNA-19b-3p level in SCI rats induced by modified Allen method, as well as the role of miRNA-19b-3p in osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs). MiRNA-19b-3p expression and bone mineral density (BMD) of femurs were measured at day 21 and day 60 after SCI in rats. Obvious miRNA-19b-3p up-regulation and aggravated bone loss were observed. MiRNA-19b-3p overexpression suppressed BMSC-derived osteoblast differentiation, which was confirmed by the decrease in alkaline phosphatase (ALP) activity, EBF2 expression, osteoprotegrin (OPG) to receptor activator of nuclear factor kappa-B ligand (RANKL) ratio and cell mineralization degree. Besides, MiRNA-19b-3p knockdown could reverse this phenomenon. Dual-luciferase reporter assays verified the targeting relationship between miRNA-19b-3p and EBF2. The in vivo experiments confirmed miRNA-19b-3p down-regulation could significantly attenuate osteoporosis after SCI, which was verified by increased BMD, collagen content, femur mineralization degree, EBF2 protein, and OPG-to-RANKL ratio. The results show that miRNA-19b-3p plays an important role in the osteoporosis process after SCI through regulating EBF2 expression.

WITHDRAWN: Role of microRNA-19b-3p on osteoporosis after experimental spinal cord injury in rats.

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Chemometrics-based approach to modeling quantitative composition-activity relationships for Radix Tinosporae.

Quantitative composition-activity relationship (QCAR) study makes it possible to discover active components in traditional Chinese medicine (TCM) and to predict the integral bioactivity by its chemical composition. In the study, 28 samples of Radix Tinosporae were quantitatively analyzed by high performance liquid chromatography, and their analgesic activities were investigated via abdominal writhing tests on mice. Three genetic algorithms (GA) based approaches including partial least square regression, radial basis function neural network, and support vector regression (SVR) were established to construct QCAR models of R. Tinosporae. The result shows that GA-SVR has the best model performance in the bioactivity prediction of R. Tinosporae; seven major components thereof were discovered to have analgesic activities, and the analgesic activities of these components were partly confirmed by subsequent abdominal writhing test. The proposed approach allows discovering active components in TCM and predicting bioactivity by its chemical composition, and is expected to be utilized as a supplementary tool for the quality control and drug discovery of TCM.

Metabonomic characterization of aging and investigation on the anti-aging effects of total flavones of Epimedium.

A liquid chromatography coupled with mass spectrometry (LC/MS) based metabonomics approach was applied to characterize the aging of rats, and the anti-aging effect of total flavones of Epimedium (TFE), a traditional Chinese medicine, has also been investigated. Serum samples collected from 4, 10, 18 and 24 month-old rats and TFE-administered rats have been profiled by LC/MS. Thirty age-related endogenous metabolites were discovered by partial least squares (PLS) and Hotelling's T(2) control chart, among which 25 metabolites were structurally identified by MS(n) analysis and ten of them were further confirmed via authentic chemicals. All important age-related metabolites, such as unsaturated fatty acids, saturated fatty acids, nucleotides, carnosine, ergothioneine and amino acids, displayed age-related changes, and most of them were reset to a younger level after TFE administration. This study indicated that aging could be characterized by changes of lipid metabolisms and accumulation of free radicals. The anti-aging effects of TFE might due to the intervention on lipid metabolism and its property of anti-oxidation.

A metabonomic approach to early prognostic evaluation of experimental sepsis by (1)H NMR and pattern recognition.

This study proposes an NMR-based metabonomic approach to early prognostic evaluation of sepsis. Forty septic rats receiving cecal ligation and puncture (CLP) were divided into the surviving group and nonsurviving group on day 6, while 20 sham-operated rats served as the control group. Serum samples were collected from septic and sham-operated rats at 12 h after surgery and analyzed using (1)H NMR spectroscopy. Orthogonal partial least squares (OPLS) were applied and showed clustering according to predefined groups, indicating that NMR-based metabolic profiling could reveal pathologic characteristics in the serum of sham-operated, surviving, and nonsurviving septic rats. In addition, six characteristic metabolites including lactate, alanine, acetate, acetoacetate, hydroxybutyrate, and formate, which are mainly involved in energy metabolism, changed markedly in septic rats, especially in the nonsurvivors. Using these metabolites, a predictive model for prognostic evaluation of sepsis was constructed using a radial basis function neural network (RBFNN) with a prediction accuracy of about 87% by test samples. The results indicated that the NMR-based metabonomic approach is a potential technique for the early prognostic evaluation of sepsis.

Metabonomic study on ageing: NMR-based investigation into rat urinary metabolites and the effect of the total flavone of Epimedium.

The aim of this work was to investigate the effects of ageing on rat urinary metabolites and to evaluate the anti-ageing effects of the total flavone of Epimedium (TFE). Proton nuclear magnetic resonance based metabonomic analyses was performed on urine from rats aged 4, 10, 18 and 24 months, and rats administered with TFE. By multivariate analysis, 26 characteristic resonances were found to be highly related with the age of rats, and ten of them were structurally postulated as creatinine, lactate, alanine, acetate, acetone, succinate, allantoin, methylamine, dimethylamine and trimethylamine-N-oxide; these metabolites involve creatinine metabolites, aliphatic amines metabolites and some important intermediates or end products of energy metabolism. Principal components analysis revealed that the metabolic profiles of 24-month-old rats treated with TFE closely resembled those of rats aged 18 months. In addition, most of these characteristic resonances were reset to younger levels by TFE intervention. The result suggests that TFE administration can markedly influence the ageing process and shows anti-ageing effects, which might due to the melioration of pyruyate metabolism and oxidative phosphorylation.

A metabonomic approach to early prognostic evaluation of experimental sepsis.

OBJECTIVES: Early prognostic evaluation of sepsis is an attractive strategy to decrease the mortality of septic patients, but presently there are no satisfactory approaches. Our goal is to establish an early, rapid and efficient approach for prognostic evaluation of sepsis. METHODS: Forty-five septic rats, induced by cecal ligation and puncture, were divided into surviving (n=23) and nonsurviving group (n=22) on day 6. Serum samples were obtained from septic and sham-operated rats (n=25) at 12h after surgery. HPLC/MS assays were performed to acquire serum metabolic profiles, and radial basis function neural network (RBFNN) was employed to build predictive model for prognostic evaluation of sepsis. RESULTS: Principle component analysis allows a clear discrimination of the pathologic characteristics among rats from surviving, nonsurviving and sham-operated groups. Six metabolites related to the outcome of septic rats were then structurally identified, which included linolenic acid, linoleic acid, oleic acid, stearic acid, docosahexaenoic acid and docosapentaenoic acid. A RBFNN model was built upon the metabolic profile data from rat serum, and a high predictive accuracy over 94% was achieved. CONCLUSIONS: HPLC/MS-based metabonomic approach combined with pattern recognition permits accurate outcome prediction of septic rats in the early stage. The proposed approach has advantages of rapid, low-cost and efficiency, and is expected to be applied in clinical prognostic evaluation of septic patients.

A metabonomic approach to the diagnosis of oral squamous cell carcinoma, oral lichen planus and oral leukoplakia.

Early diagnosis of oral squamous cell carcinoma (OSCC) and precursor lesions is an attractive strategy to decrease patient morbidity and mortality, but presently there are no satisfied diagnostic approaches. This study proposed a metabonomics-based diagnostic approach for OSCC and its precancerous lesions, including oral lichen planus (OLP) and oral leukoplakia (OLK). Saliva samples were collected from patients and healthy donors, and HPLC/MS analysis was performed to acquire metabolic profiles. Diagnostic model was then constructed with hierarchical principal component analysis (HPCA) and discriminate analysis algorithms. The results indicate that metabolic profiling can properly describe the pathologic characteristics of OSCC, OLP and OLK. HPCA combined with kernel fisher discriminant analysis achieved 100% accuracy in diagnosis of test samples, which is superior to direct principal component analysis and other modeling algorithms. The metabonomic approach based on the integral investigation of oral metabolites enables the detection of OSCC and precancerous lesions on noninvasive saliva samples. The proposed approach is noninvasive, efficient and low-cost, and it can be developed as a promising method for population-based screening of cancers and precancers in the oral cavity.

Expression of hepatitis B virus proteins in transgenic mice alters lipid metabolism and induces oxidative stress in the liver.

BACKGROUND/AIMS: Hepatitis B virus transgenic mice (HBV-Tg mice) have been widely used as animal models in the study of pathogenesis and control of hepatitis B. It is important for the evaluation of such animal models to define the physiological differences between HBV-Tg and wild-type mice. The aim of this research was to investigate whether the integrated system biology approach that combines proteomics and metabonomics describes the physiological changes and provides new insights into the pathogenesis of the early stages of HBV infection. METHODS: In this study the protein and metabolite profiles of the liver were established based on two-dimensional electrophoresis and HPLC/MS analysis. RESULTS: Several protein molecules, whose expression was altered in HBV-Tg mouse liver, were identified including protective enzymes against oxidative stress and regulatory proteins related to lipid metabolism. Metabonomics confirmed the potential derangement of lipid metabolism by discovering the intermediate and the final products of lipid metabolism that were markedly changed in transgenic mice. CONCLUSIONS: This study demonstrated that HBV antigens could impair host cell lipid metabolism and induce modest oxidative stress in vivo.

[Applications of metabonomics in clinical diagnosis].

Metabonomics, as a newly developed technique, is expected to be a powerful technique in clinical diagnosis. Metabonomics-based diagnosis involves the global metabolic analysis of body-fluids, determination of biomarkers by multivariate statistic analysis, and establishemen of mathematic models for clinical diagnosis with the aid of pattern recognition. This article reviews the adoption of various analytical and computational strategies, application of metabonomics in clinical diagnosis, and potential challenges and development trends.

Quantitative analysis and chromatographic fingerprinting for the quality evaluation of Scutellaria baicalensis Georgi using capillary electrophoresis.

Quantitative analysis and chromatographic fingerprinting for the quality evaluation of a Chinese herb Scutellaria baicalensis Georgi using capillary electrophoresis (CE) technique was developed. The separation was performed with a 50.0cm (42.0cm to the detector window)x75mum i.d. fused-silica capillary, and the CE fingerprint condition was optimized using the combination of central composite design and multivariate analysis. The optimized buffer system containing 15mM borate, 40mM phosphate, 15mM SDS, 15% (v/v) acetonitrile and 7.5% (v/v) 2-propanol was employed for the method development, and the baseline separation was achieved within 15min. The determination of the major active components (Baicalin, Baicalein and Wogonin) was carried out using the optimized CE condition. Good linear relationships were provided over the investigated concentration ranges (the values of R(2): 0.9997 for Baicalin, 0.9992 for Baicalein, and 0.9983 for Wogonin, respectively). The average recoveries of these target components ranged between 96.1-105.6%, 98.6-105.2%, and 96.3-105.0%, respectively. CE fingerprints combined with the quantitative analysis can be used for the quality evaluation of S. baicalensis.