Development of a multivariate statistical model to predict peroxisome proliferation in the rat,based on urinary 1H-NMR spectral patterns

A previous report of this work (Ringeissen et al. 2003) described the use of nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical data analysis (MVDA) to identify novel biomarkers of peroxisome proliferation (PP) in Wistar Han rats. Two potential biomarkers of peroxisome proliferation in the rat were described, N-methylnicotinamide (NMN) and N-methyl-4-pyridone-3-carboxamide (4PY). The inference from these results was that the tryptophan-nicotinamide adenine dinucleotide (NAD⁺) pathway was altered in correlation with peroxisome proliferation, a hypothesis subsequently confirmed by TaqMan® analysis of the relevant genes encoding two key enzymes in the pathway, aminocarboxymuconate-semialdehyde decarboxylase (EC 4.1.1.45) and quinolinate phosphoribosyltransferase (EC 2.4.2.19). The objective of the present study was to investigate these data further and identify other metabolites in the NMR spectrum correlating equally with PP. MVDA Partial Least Squares (PLS) models were constructed that provided a better prediction of PP in Wistar Han rats than levels of 4PY and NMN alone. The resulting Wistar Han rat predictive models were then used to predict PP in a test group of Sprague Dawley rats following administration of fenofibrate. The models predicted the presence or absence of PP (above on arbitrary threshold of >2-fold mean control) in all Sprague Dawley rats in the test group.     

Learning to predict cancer-associated skeletal muscle wasting from 1H-NMR profiles of urinary metabolites

Cancer-associated muscle wasting is associated with reduction in functional status, in response to treatment and in life expectancy. Methods currently used to assess muscle loss involve diagnostic imaging techniques such as computed tomography (CT), which are costly, inconvenient, invasive, time consuming and have limited ability to detect early or slowly evolving wasting. We present a novel approach using single time-point urinary metabolite profiles to determine whether a patient is experiencing muscle wasting. We analyzed 93 random urine samples from patients with cancer using ¹H-NMR. Using two successive CT images we assessed their lumbar skeletal muscle area (cm²) to estimate the rate of muscle change (% loss or gain over time) for each patient. The average muscle change over time was −4.71%/100 days in the muscle-losing group and +3.91%/100 days in the comparator group. Bivariate statistics identified metabolites related with muscle loss, including constituents and metabolites of muscle (creatine, creatinine, 3-OH-isovalerate), amino acids (Leu, Ile, Val, Ala, Thr, Tyr, Gln, Ser) and intermediary metabolites. We also applied machine-learning techniques to identify patterns of urinary metabolites that identify which patients are likely to lose muscle mass. We evaluated the predictive performance of 8 machine-learning approaches using fivefold cross validation and permutation testing, and found that SVM provided the best generalization accuracy (82.2%). These results suggest that ¹H-NMR analysis of a single random urine sample may be a fast, cheap, safe and inexpensive tool to screen and monitor muscle loss, and that useful classifiers for predicting related metabolic conditions are possible with the methodology presented.     

Suppression of clofibrate-induced peroxisome proliferation in rat liver by nicardipine, a calcium antagonist

In vivo administration of nicardipine, nifedipine and diltiazem, known as calcium antagonists, suppressed the clofibrate-evoked induction of activities of peroxisomal enzymes, such as the peroxisomal fatty acyl-CoA oxidizing system and carnitine acetyltransferase. The inhibition activity of nicardipine with respect to clofibrate induction of the two enzyme systems was 62 and 33%, respectively. Induction of the peroxisomal bifunctional protein, enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase, by clofibrate was suppressed about 60% by nicardipine on analysis of the hepatic protein composition by SDS-polyacrylamide gel electrophoresis. Other drugs also exhibited similar inhibitory activity. These results provide the first demonstration of calcium antagonists, e.g. nicardipine, nifedipine and diltiazem, acting as inhibitors of peroxisome proliferation in animals. Such drugs might become useful as tools for elucidating the mechanism of peroxisome proliferation and for determination of the pathological conditions under which peroxisomal function is impaired.     

Decomposing biodiversity data using the Latent Dirichlet Allocation model,a probabilistic multivariate statistical method

We propose a novel multivariate method to analyse biodiversity data based on the Latent Dirichlet Allocation (LDA) model. LDA, a probabilistic model, reduces assemblages to sets of distinct component communities. It produces easily interpretable results, can represent abrupt and gradual changes in composition, accommodates missing data and allows for coherent estimates of uncertainty. We illustrate our method using tree data for the eastern United States and from a tropical successional chronosequence. The model is able to detect pervasive declines in the oak community in Minnesota and Indiana, potentially due to fire suppression, increased growing season precipitation and herbivory. The chronosequence analysis is able to delineate clear successional trends in species composition, while also revealing that site‐specific factors significantly impact these successional trajectories. The proposed method provides a means to decompose and track the dynamics of species assemblages along temporal and spatial gradients, including effects of global change and forest disturbances.     

Effect of peroxisome proliferation on ether phospholipid biosynthesizing enzymes in rat liver

1. The effect of the peroxisome proliferators clofibrate and plasticizer on the activities of the first two enzymes involved in either phospholipid biosynthesis, i.e. dihydroxyacetone-phosphate acyltransferase (DHAP-AT) and alkyldihydroxyacetone-phosphate synthase, were studied in rat liver homogenates and purified peroxisomes. 2. DHAP-AT in homogenates increased by 2 to 3-fold both in total and specific activity. However, the specific activity in purified peroxisomes showed no significant increase demonstrating for the first time that there is no specific induction of this enzyme that exceeds the induction of total peroxisomal protein. 3. Alkyldihydroxyacetone-phosphate synthase showed no significant increase in total and specific activity in homogenates and a slight decrease of its specific activity in purified peroxisomes was observed. 4. The total amount of plasmalogens did not increase upon proliferation and a slight decrease in the percentage plasmalogens in total phospholipids was observed. 5. Proliferation did not influence the phospholipid composition of the peroxisomal membrane.     

Development of a salinity-secondary flow-approach model to predict mangrove spreading

This paper presents a new salinity-secondary flow-approach (SSA) model for identifying areas likely to be colonized by mangrove species based on two indices: water salinity concentration and river secondary flow intensity, R/W (the ratio of radius of curvature to river width). The mangrove Kandelia obovata is spreading rapidly in the Tanshui River system and therefore resulting in flooding impact to riparian wetlands; however, few studies have examined the dispersal characteristics of this species on the reach scale. According to the literature review and our observation, the salinity is the major factor in determining the spreading capabilities of mangroves. In addition, the effect of secondary flow can also facilitate mangrove invasion through the creation of bare mudflats.The case study of the Tanshui River system shows that the SSA model can be used for the determination of the habitat requirements and thus the dispersal capabilities of K. obovata. The results of the study show that the optimum conditions for the growth and dispersal of K. obovata exist in waters with mean annual salinity levels that are higher than 5 ppt (parts per thousand). Although K. obovata can survive in brackish wetlands with mean annual salinity levels lower than 5 ppt, its spreading capability is impaired. In tidal freshwater wetlands with mean annual salinity levels that are lower than 0.1 ppt, K. obovata cannot survive. The study also found that the R/W lower than 3 led to large mudflats, which provide an ideal environment for the growth of mangroves, due to the secondary flow.It shows that the SSA model can identify the potential habitat of mangrove in tidal region, so it might help with not only estuarine wetland management but also mangrove restoration project, especially for the sea level rise effect and its impact on potential mangrove invasion.     

Development of a surrogate model based on patient weight,bone mass and geometry to predict femoral neck strains and fracture loads

Osteoporosis and related bone fractures are an increasing global burden in our ageing society. Areal bone mineral density assessed through dual energy X-ray absorptiometry (DEXA), the clinically accepted and most used method, is not sufficient to assess fracture risk individually. Finite element (FE) modelling has shown improvements in prediction of fracture risk, better than aBMD from DEXA, but is not practical for widespread clinical use. The aim of this study was to develop an adaptive neural network (ANN)-based surrogate model to predict femoral neck strains and fracture loads obtained from a previously developed population-based FE model. The surrogate model performance was assessed in simulating two loading conditions: the stance phase of gait and a fall.The surrogate model successfully predicted strains estimated by FE (r² = 0.90–0.98 for level gait load case, r² = 0.92–0.96 for the fall load case). Moreover, an ANN model based on three measurements obtainable in clinics (femoral neck length (level gait) or maximum femoral neck diameter (fall), femoral neck bone mass, body weight) was able to give reasonable predictions (r² = 0.84–0.94) for all of the strain metrics and the estimated femoral neck fracture load. Overall, the surrogate model has potential for clinical applications as they are based on simple measures of geometry and bone mass which can be derived from DEXA images, accurately predicting FE model outcomes, with advantages over FE models as they are quicker and easier to perform.     

基于多元统计分析的不同诃子属药材多指标成分研究

建立了诃子属药材的多指标成分含量测定方法,为诃子属药材的质量评价提供依据.测定44批不同诃子属药材中7个鞣质类成分含量,并结合方差分析、聚类分析(HCA)、主成分分析(PCA)和正交偏最小二乘法-判别分析(OPLS-DA)评价诃子属3种不同药材的鞣质类成分差异.可见诃子属3种药材中7个成分含量存在明显差异,方差分析结果...     

Oscillations in the perception of ambiguous patterns a model based on synergetics

An algorithm which can be realized by synergetic systems and which was introduced by one of us (Haken 1987) for the recognition of patterns is extended so that the perception of ambiguous patterns can be modelled. In this approach so-called attention parameters are subjected to a damping mechanism mimicking the effect of saturation of attention. In this way oscillations of perception arise quite naturally. Our approach takes also ambiguous patterns with bias into account which leads to different periods of the attention paid to the one or the other interpretation of the pattern. Our results are in good agreement with previous psycho-physical studies by other authors. Finally we show how hysteresis of perception can be modelled.     

Conformations of a model cyclic hexapeptide,CYIQNC: 1H-NMR and molecular dynamics studies

Solution conformation of the cyclic hexapeptide sequence, [cyclo-S-Cys-Tyr-Ile-Gln-Asn-Cys-S] (CYIQNC) – a disulfide-linked fragment of a neurohypophyseal peptide hormone oxytocin (OT) – has been investigated by high-field one-dimensional (1D) and two-dimensional (2D) NMR spectroscopic methods and compared with the results obtained from computer simulation studies. ¹H-NMR results based on temperature dependence of amide proton chemical shifts and nuclear Overhauser effect indicate that peptide in solution populates different conformations, characterized by two fused β-turns. The segment Ile³-Gln⁴-Asn⁵-Cys⁶ yields a preferred type-III β-turn at residues 4, 5 (HB, 3HN → 6CO), while the segment Cys⁶, Cys¹-Tyr²-Ile³ exhibits inherently weaker, flexible β-turn either of type I/II’/III/half-turn at residues 1, 2 (HB, 6HN → 3CO). The computer simulation studies using a mixed protocol of distance geometry-simulated annealing followed by constrained minimization, restrained molecular dynamics, and energy minimization showed the possibility of existence of additional conformations with the hydrogen bonds, (a) 5HN → 3CO and (b) 2HN → 6CO. These results, therefore, indicate that the additional conformations obtained from both NMR and simulation studies can also be possible to the peptide. These additional conformations might have very small population in the solution and did not show their signatures in these conditions. These findings will be helpful in designing more analogs with modifications in the cyclic moiety of OT.     

1H-NMR study on the chitotrisaccharide binding to hen egg white lysozyme.

Interaction between hen egg white lysozyme and chitotrisaccharide was investigated by 1H-NMR spectroscopy using partially acetylated chitotrisaccharides and chemically modified lysozyme. Monoacetyl (GlcN-GlcN-GlcNAc), diacetyl (GlcN-GlcNAc-GlcNAc), or triacetyl chitotrisaccharide [(GlcNAc)3] was added to the lysozyme solution, and the changes in the 1H-NMR signals of the lysozyme were analyzed. Although many of the resonances were affected by addition of the saccharide, the most remarkable effect was seen on the signal of Trp28 C5H which is in a hydrophobic box adjacent to the saccharide-binding site. The signal shifted upfield by 0.2 ppm upon (GlcNAc)3 binding, whereas the chemical shift change of the signal resulting from binding of GlcN-GlcNAc-GlcNAc or GlcN-GlcN-GlcNAc was smaller than that resulting from (GlcNAc)3 binding. When the Asp101-modified lysozyme was used instead of the native lysozyme, the chemical shift change of the Trp28 C5H signal resulting from (GlcNAc)3 binding was also smaller than that for the native lysozyme. The chemical shift change of the signal reflects the conformational change of the hydrophobic box region which should synchronize with the movement of the binding site resulting from the saccharide binding. Therefore, the conformational change resulting from the saccharide binding might be reduced when the sugar residues located at binding subsites A and B of the lysozyme are deacetylated, as well as when Asp101 interacting with the sugar residues at the same subsites is modified.     

Potential urinary and plasma biomarkers of peroxisome proliferation in the rat: identification of N-methylnicotinamide and N-methyl-4-pyridone-3-carboxamide by 1H nuclear magnetic resonance and high performance liquid chromatography.

This study identified two potential novel biomarkers of peroxisome proliferation in the rat. Three peroxisome proliferator-activated receptor (PPAR) ligands, chosen for their high selectivity towards the PPARalpha, -delta and -gamma subtypes, were given to rats twice daily for 7 days at doses known to cause a pharmacological effect or peroxisome proliferation. Fenofibrate was used as a positive control. Daily treatment with the PPARalpha and -delta agonists produced peroxisome proliferation and liver hypertrophy. 1H nuclear magnetic resonance spectroscopy and multivariate statistical data analysis of urinary spectra from animals given the PPARalpha and -delta agonists identified two new potential biomarkers of peroxisome proliferation--N-methylnicotinamide (NMN) and N-methyl-4-pyridone-3-carboxamide (4PY)--both endproducts of the tryptophan-nicotinamide adenine dinucleotide (NAD+) pathway. After 7 days, excretion of NMN and 4PY increased 24- and three-fold, respectively, following high doses of fenofibrate. The correlation between total NMN excretion over 7 days and the peroxisome count was r=0.87 (r2=0.76). Plasma NMN, measured using a sensitive high performance liquid chromatography method, was increased up to 61-fold after 7 days' treatment with high doses of fenofibrate. Hepatic gene expression of aminocarboxymuconate-semialdehyde decarboxylase (EC 4.1.1.45) was downregulated following treatment with the PPARalpha and -delta agonists. The decrease was up to 11-fold compared with controls in the groups treated with high doses of fenofibrate. This supports the link between increased NMN and 4PY excretion and regulation of the tryptophan-NAD+ pathway in the liver. In conclusion, NMN, and possibly other metabolites in the pathway, are potential non-invasive surrogate biomarkers of peroxisome proliferation in the rat.     

Species differences in hepatic peroxisome proliferation, cell replication and transforming growth factor-beta1 gene expression in the rat, Syrian hamster and guinea pig

The objective of this study was to evaluate species differences in the hepatic effects of three potent rodent peroxisome proliferators, namely methylclofenapate (MCP), ciprofibrate (CIP) and Wy-14,643 (WY), particularly with respect to effects on replicative DNA synthesis and transforming growth factor-beta1 (TGF-beta1) gene expression. Male Sprague-Dawley rats, Syrian hamsters and Dunkin-Hartley guinea pigs were given daily oral doses of 0 (corn oil) and 75 mg/kg MCP for periods of 6 and 21 days. Syrian hamsters and guinea pigs were also treated with 25 mg/kg CIP and 25 mg/kg WY. Relative liver weights were significantly increased in peroxisome proliferator-treated rats and Syrian hamsters, but not in guinea pigs. Hepatic peroxisomal (palmitoyl-CoA oxidation) and microsomal (lauric acid 12-hydroxylase) fatty acid oxidising enzyme activities and CYP4A isoform mRNA levels were significantly increased in rats and Syrian hamsters, whereas only minor effects were observed in the guinea pig. Replicative DNA synthesis was studied by implanting 7-day osmotic pumps containing 5-bromo-2'-deoxyuridine during study days -1 to 6 and 14 to 21. Hepatocyte labelling index values were increased by MCP in the rat, but neither MCP, CIP nor WY produced any significant effect on replicative DNA synthesis in the Syrian hamster and guinea pig. MCP treatment increased TGF-beta1 and insulin-like growth factor II/mannose-6-phosphate (IGFII/Man6P) receptor gene expression in the rat. In the Syrian hamster, effects on TGF-beta1 and IGFII/Man6P receptor gene expression were also observed in some instances, whereas TGF-beta1 mRNA levels were essentially unchanged in the guinea pig. These results provide further evidence for marked species differences in response to rodent peroxisome proliferators. While peroxisome proliferators produce a wide spectrum of effects in rat liver, other species such as the Syrian hamster and guinea pig are less responsive and in the case of some endpoints (e.g., cell replication) may be refractory.     

细菌性脑膜炎大鼠模型的尿液蛋白质组学变化

与脑脊液和血液不同,尿液不受到稳态机制的调节,更倾向于积累和反应机体生理和病理状态下的变化。生物标志物的本质特征是变化,因此尿液是寻找疾病早期标志物的更好来源。在世界范围内,细菌性脑膜炎依然是引起新生儿和儿童疾病的主要原因。为了降低死亡率和致残率,需要用无创的方法寻找细菌性脑膜炎的相关线索。本研究中,使用大鼠脑室内注射大肠杆菌模型模拟细菌性脑膜炎,在第1天和第3天的大鼠尿液中寻找尿液蛋白谱的差异变化,为进一步寻找大肠杆菌性脑膜炎的早期生物标记物研究进行初步的探索。通过膜上酶切和胶内酶切将尿蛋白切成肽段并通过液相色谱串联质谱技术(LC-MS/MS)分析肽段信息。第1天的尿液通过胶内酶切方法鉴定到17个差异蛋白,通过膜上酶切鉴定到20个差异蛋白;第3天的尿液通过膜上酶切方法鉴定到5个差异蛋白。这些差异蛋白为寻找细菌性脑膜炎早期生物标志物的初步探索奠定了基础。     

Lack of stereoselectivity of the peroxisome proliferation induced by 2-phenylpropionic acid: Evidence against a role for lipid disturbance in peroxisome proliferation

The significance of disturbances of lipid metabolism caused by xenobiotic acyl-CoAs as possible causes of peroxisomal proliferation has been studied with the enantiomers of 2-phenylpropionic acid (2-PPA), the (R)-enantiomer of which is converted to the acyl-CoA in rats while its (S)-antipode is not. rac-2-PPA (250 mg/kg/day ip × 3) was shown to be an hepatic peroxisomal proliferator in male Sprague–Dawley rats on the basis of increases in microsomal cytochrome P-450 content and lauric acid hydroxylation and hepatic CN^?-insensitive palmitoyl-CoA oxidation, a peroxisomal marker activity, while electron microscopy revealed a rise in the peroxisome/mitochondria ratio in hepatocytes. Further studies established the dose–response relationships for these biochemical changes. The (R)- and (S)-enantiomers were administered at a dose of 50 mg/kg/day ip × 3 and both were peroxisome proliferators of very similar potency. The effects of 100 mg/kg/day ip × 3 of the racemate, a dose giving ca. 75% of maximal response, were essentially additive of those of 50 mg/kg/day ip × 3 of its two component isomers. The stereoselectivity of acyl-CoA formation from the enantiomers of 2-PPA was confirmed by their differential inhibition of microsomal palmitoyl-CoA synthesis. Taken together, these data indicate that it is very unlikely that the acyl-CoA of 2-PPA plays any role in the peroxisomal proliferation which this compound causes in the rat. © 1994 Wiley-Liss, Inc.     

Detection of a nafenopin-binding protein in rat liver cytosol associated with the induction of peroxisome proliferation by hypolipidemic compounds

[3H]nafenopin, a known inducer of liver peroxisomal enzymes, was shown to bind to a specific, saturable pool of binding sites in cytosols from rat liver and kidney cortex. Tissue levels of this binding protein (liver greater than kidney cortex; not detectable in myocardium, skeletal muscle) were seen to correlate with the ability of nafenopin to induce peroxisomal enzymes in these organs. Clofibrate and ciprofibrate, which are structurally similar to nafenopin, competitively blocked the specific binding of [3H]nafenopin. Phenobarbital, a non-inducer of peroxisomes, and [4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio]acetic acid and 4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio(N-beta-hydroxyethyl)acetamide, which are structurally unrelated peroxisome proliferators, did not complete for the specific [3H]nafenopin binding sites. The [3H]nafenopin binding protein is proposed as a mediator of the drug-induced increase in peroxisomes and associated peroxisomal enzymes.     

Enantioselectivity in the induction of peroxisome proliferation by 2-ethylhexanoic acid.

The stereoselectivity of the peroxisome proliferation potency of 2-ethylhexanoic acid (2-EHA), a metabolite of the plasticizer di-(2-ethylhexyl) adipate, was investigated in vitro. The enantiomers of 2-EHA were prepared via the semipreparative HPLC resolution of their diastereoisomeric (+)-(R)-1-phenylethylamine derivatives and the subsequent hydrolytic cleavage. Monolayers of hepatocytes were incubated 3 days with solution of (-)-(R), (+)-(S), and (+/-)-2-EHA. The peroxisome proliferation potency was measured by means of determination of the peroxisomal palmitoyl coenzyme A oxidation. The theoretical induction component due to each enantiomer were calculated from the experimental data considering the enantiomeric purities of the acids. The (+)-(S)-enantiomer was found to be the most potent inducer e.g., the eutomer, while the (-)-(R) was the distomer. The eudismic ratio was about 1.6 and the racemic mixture exhibited an intermediary potency. These results, obtained in vitro in conditions avoiding confounding factors such as pharmacokinetics, suggest that the peroxisome proliferation induced by 2-ethylhexanoic acid is a stereoselective phenomenon.     

Use of a multivariate model using allele frequency distributions to analyse patterns of genetic differentiation among populations

Very few studies have attempted to relate the properties of some ordination techniques to classical tools of population genetics as F -statistics. A multivariate model to analyse population genetics data based on the properties of 'joint scaling' of populations and loci is developed. The design of population genetics data means that this model deals with a modified version of the classical Multiple Correspondence Analysis which is called Constant Row Total-Multiple Correspondence Analysis (CRT-MCA) and is an original tool in population genetics. Such a model allows estimates of the degree of population differentiation by studying the variability of the distribution of allele frequencies in different samples. Some clear relationships exist between some model parameters and the classical F_st statistics. The CRT-MCA also allows all the studied loci to be considered simultaneously and the role of each locus in patterns of population differentiation to be expressed. Such a multivariate approach prevents the use of any pooling strategy as is classically used in studies of hierarchical F -statistics. The relevance of the CRT-MCA model is illustrated by the analysis of population structure of 15 dogwhelk ( Nucella lapillus ) populations in south-west England. The advantages and limitations of CRT-MCA are presented.