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PubMed2026

Integrated Metabolomic and Transcriptomic Analysis Reveals Tissue-Specific Secondary Metabolic Differentiation and Indole Alkaloid Accumulation in Evodia rutaecarpa.

Evodia rutaecarpa is a valuable medicinal plant, yet its non-medicinal tissues remain largely underexplored. Here, we integrated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics and RNA sequencing (RNA-seq) transcriptomics to systematically profile the metabolic and transcriptional landscapes of roots, stems, leaves, and flowers of Evodia rutaecarpa (Juss.) Benth. Our aim was to characterize tissue-specific metabolic differentiation and its underlying transcriptional regulatory mechanisms. Metabolomic analysis, employing principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) with robust model parameters (R2Y > 0.9, Q2 > 0.5), identified 3090 differential metabolite features (variable importance in projection, VIP > 1.0; p < 0.05) across the four tissues, which exhibited distinct tissue-specific clustering patterns. Integrated Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and weighted gene co-expression network analysis (WGCNA) revealed that roots specifically accumulated quinolone alkaloids and flavonoid glycosides, accompanied by the coordinated upregulation of genes involved in flavonoid and phenylpropanoid biosynthetic pathways. In contrast, stems, leaves, and flowers were enriched in indole alkaloids (evodiamine and rutaecarpine) and volatile oil precursors, with concurrent upregulation of genes involved in tryptophan metabolism and indole alkaloid biosynthesis (e.g., tryptophan decarboxylase, TDC; s N-methyltransferase, NMT). Notably, leaves and flowers displayed particularly high accumulation levels of these bioactive alkaloids, suggesting their potential as alternative sources for industrial and pharmaceutical applications. WGCNA further identified multiple transcription factors and structural gene modules tightly correlated with evodiamine accumulation, offering promising candidate regulators for future biosynthetic pathway engineering. Collectively, this multi-omics integration study systematically elucidates the tissue-partitioned secondary metabolism of Evodia rutaecarpa (Juss.) Benth. and provides a solid scientific foundation for full-plant resource utilization, targeted development of non-medicinal tissues, and future metabolic engineering of indole alkaloid production.

Evodia rutaecarpa↗

PubMed1990

[Interpersonal anxiety and the self-others cognitive system: a study of the Self-identity System].

This study examined the self-others cognitive systems of anthropophobia in terms of the (an) object relationship disorder. The Self-identity Systems of 259 students were measured to clarify visually the relationship between self and others in terms of self and others cognition and interpersonal anxiety. Cluster analysis and principal components analysis of the Self-identity Systems led to the appearance of five Self-identity System types for each sex. Low anxiety level subjects tended more toward the "self convergence type" while high anxiety subjects tended more toward the "self alienation type". These results suggest that disorder in the self-others cognitive system and the problem of self-identity relate to anthropophobia.

Adult↗

PubMed2000

[Response of Capsicum frutescens metapopulation to simulated insect herbivorous behaviors].

Based on the theory of metapopulation, this paper studied the response of different leaf-cutting Capsicum frutescens metapopulation to simulated short-term insect pestes during high temperature period in July. Variance analysis (ANOVA), principal component analysis(PCA) and plant growth analysis were applied. The result shows that C. frutescens had a strong compensatory ability. The number, dry weight and leaf area of old leaves decreased with increasing leaf-cutting, but contrarily for new leaves. The total leaf number did not show any significant difference, but the total area and weight of leaves were significantly different, because of the influence of old leaves. The number, weight and lenght of branches were not significantly different with different treatments, and the number of fruits, flowers and flower buds also showed no significant difference. However, the difference of their dry weights was significant. It is practical to use number indexes, but not dry weight, leaf area and length for plant growth analysis in metapopulation, when the difference of dry weight between modulars is small. It is suggested that a certain degree of herbivory might be beneficial to the growth and fruit yield of C. frutescens during the high temperature period.

Capsicum↗

PubMedDate not supplied

Spectrophotometric determination of caramel content in spirits aged in oak casks.

A new methodology was developed for determination of caramel in spirits aged in oak casks. The method is based on differences between the electronic spectra of oak aqueous alcoholic extracts and caramel solutions in the same solvent. The data were treated by 2 different approaches: the simplest one was based on the plot of caramel concentration versus the ratio of absorbance at 210 and 282 nm; the other was based on a partial least squares (PLS) calibration model using the first derivative of the spectral data. Both methodologies were applied to analysis of 159 aged spirit samples. The mean caramel content of several Brazilian sugar cane spirits (cachaça) and all United States whiskies was smaller than that of Scottish whiskies and other brandies from several countries. Correlation was good between caramel concentrations for the same sample calculated by the 2 methods. The uncertainties following PLS and the absorbance ratio method were 0.01 and 0.03 g/L, respectively, for a sample containing 0.45 g/L caramel. Treatment of UV-VIS spectra by pattern recognition using hierarchical clustering analysis and principal components analysis allowed discrimination of the samples as a function of their caramel content. It was possible to distinguish U.S. whiskies from other whiskies, but a clear differentiation among Brazilian cachaças as a function of their geographic origin was not feasible. Small caramel quantities as low as 0.08 g/L were clearly detected by these methodologies.

Alcoholic Beverages↗

PubMed2002

Polychlorinated biphenyl source attribution in Green Bay, Wisconsin, USA, using multivariate similarity among congener profiles in sediment samples.

Polychlorinated biphenyl (PCB) congener concentrations measured in 1,189 sediment samples from Green Bay (MI/WI, USA), Lake Michigan (MI/WI, USA), and the Fox River (WI, USA) were analyzed statistically to evaluate whether PCB congener profiles in outer Green Bay are more similar to those observed in inner Green Bay or Lake Michigan. Similarities among PCB profiles were assessed with complementary multivariate analysis techniques: Principal component analysis (PCA), cluster analysis, and classification trees. The PCA indicated that profiles in outer Green Bay are distinct from those of inner Green Bay or Lake Michigan but are more similar to those of inner Green Bay. The outer bay profiles are dissimilar to profiles that would result from a simple process of mixing contaminated sediments from the inner bay with Lake Michigan sediments and, therefore, support the conclusion that contaminants in outer Green Bay come from discharges of the Fox River. Several classification trees based on small sets of congener proportions defined simple rules that consistently distinguished the regional profiles. Application of these rules to classify the outer bay samples suggests that the profiles of less than 7% of outer bay samples are similar to Lake Michigan profiles. These results are interpreted with respect to physical transport and chemical weathering processes that may account for the observed differences.

Environmental Monitoring↗

PubMed1975

Pathogenicity to animals of fine dusts from Ruhr mines.

Twelve different groups of fine mine dusts were examined for their in vivo aggressivity by intraperitoneal injection. Twelve months after injection of the dust, quantitative morphometric analysis of the lymph nodes was carried out to determine (a) the extent of the typical quartz reaction, (b) the in vivo cytotoxicity, (c) the size of the lymph nodes. Different fine dusts showed significant variations in parameter (a) and (c). In the second part of the investigation, the results of the lymph node tests and of in vitro cytotoxicity tests, and also the quartz contents of the dusts were fed into a data matrix and subjected to correlation analysis and principal component analysis. The following hypotheses were arrived at to explain the effect of the fine dust in vivo: (1) The amount of fine dust which penetrates into the lymph nodes is dependent on its in vitro cytotoxicity (Factor A). This is not related to the quartz content of the dust and is not inhibited by PVNO. (2) The specific fibrogenic activity of the fine dust within the lymph node is primarily dependent on its quartz content (Factor B). It appears that this effect is inhibited by PVNO. (3) The total fibrogenic activity depends on a combination of Factor A and B.

Anthracosilicosis↗

PubMed2002

Environmetric approaches to estimate pollution impacts on a coastal area by sediment and river water studies.

This paper represents an effort to demonstrate the opportunities of some environmetric methods like regression analysis, cluster analysis and principal components analysis. Their role for data modeling is stressed and the basic theoretical principles are given. The application of the multivariate statistical methods is illustrated by two major examples: Assessment of metal pollution based on multivariate statistical modeling of "hot spot" sediments from the Black Sea; and a trend study of Kamchia River water quality. In the first part of the study the environmetric approach makes it possible to separate three zones of the marine environment with different levels of pollution (Bourgas gulf, Varna gulf and lake buffer zone). Further, the extraction of four latent factors offers a specific interpretation of the possible pollution sources and separates the natural factors from the anthropogenic ones, the latter originating from contamination by chemical and steel-works and an oil refinery. In the second part of the study nine sampling sites along Kamchia River were considered as sources for water quality monitoring data. Trends for all parameters are calculated by the use of linear regression analysis and special attention is paid to a specific coastal site. Then five latent factors were extracted from the monitoring data set in order to gain information about some structural characteristics of the set.

Cluster Analysis↗

PubMed2003

[Physiological value of pelvic and spinal parameters of sagital balance: analysis of 250 healthy volunteers].

PURPOSE OF THE STUDY: Sagital balance of the spine is a fundamental element necessary for understanding spinal disease and instituting proper treatment. The aim of this prospective work was to establish the physiological values of pelvic and spinal parameters of sagital balance of the spine and to investigate their interactions. MATERIAL AND METHOD: Pelvic and spinal parameters were measured on the standing radiographs of 250 healthy volunteers. The following parameters were measured on lateral views including the head, the spine and the pelvis: lumbar lordosis, thoracic kyphosis, sagital tilt at T9, sacral inclination, pelvic incidence, pelvic version, intervertebral angulation, and the vertebral cuneiformization from T9 to S1. These measurements were taken after digitalization of the radiographs. Two types of analysis were performed: a descriptive univariate analysis to characterize the angular parameters and multivariate analysis (correlation, principal component analysis) to detail the relative variations of these parameters. RESULTS AND DISCUSSION: Mean values were: maximal lumbar lordosis 61 +/- 12.7 degrees, maximal thoracic kyphosis 41.4 +/- 9.2 degrees, sacral inclination 44.2 +/- 8.5 degrees, pelvic version 13 +/- 6 degrees, pelvic incidence 55 +/- 11.2 degrees, sagital tilt at T9 10.5 +/- 3.1 degrees. There was a strong correlation between sacral inclination and pelvic incidence (r=0.86), pelvic version and pelvic incidence (r=0.66), lumbar lordosis pelvic incidence pelvic version and thoracic kyphosis (r=0.9) and finally between pelvic incidence and the following parameters: sagital tilt at T9, sacral inclination, pelvic version, lumbar lordosis, and thoracic kyphosis (r=0.98). The relations between the different parameters studied demonstrated that saggital tilt at T9, which reflects spinal balance, is determined by three independent factors. The first is a linear combination of pelvic incidence, lumbar lordosis, and sacral inclination. The second is pelvic version. The third is thoracic kyposis. CONCLUSION: This work provided a useful tool for analyzing and understanding anteroposterior imbalance in patients with spinal disease and also a means of calculating corrections to be made with treatment, established from the linear regression equations which were elaborated.

Adult↗

PubMed2003

[Spatial distribution of water quality in Xiangxi River, China].

Cluster analysis and principal component analysis were used to analyze the physical and chemical characteristics of water samples collected from 19 sampling sites along Xiangxi River. The result of cluster analysis showed that Xiangxi River could be divided into three reaches, which belonged to different sub-basins. The principle component analysis on each reach showed that the main information of water quality was different from each other. In the upper reach, the main information of river water quality was hardness and total alkalinity; in the middle reach, the main information was dissolved phosphorus, total phosphorus and Cl-, in the lower reach, the main information was pH, NO2(-)-N, total nitrogen and COD. Furthermore, considering the geographical and environmental backgrounds of the Xiangxi River basin, the reason that caused the different distribution pattern of water quality in Xiangxi River was discussed. Hence, a simple approach to analyze the spatial distribution of water quality was provided.

Cluster Analysis↗

PubMed2004

Identification of differentially expressed genes involved in colorectal carcinogenesis using a cDNA microarray.

To identify candidate genes involved in human colorectal carcinogenesis, we constructed the gene expression profiles of 50 colorectal cancers (CRCs) and 12 normal colorectal epithelia using a cDNA microarray specially constructed for CRC. Hierarchical clustering analysis and principal component analysis could clearly distinguish the gene profiles of cancer tissues from those of normal tissues. Our results confirm there are indeed differences in gene expression between cancer and normal mucosa. Our cDNA microarray identified 22 up-regulated genes and 32 down-regulated genes in CRC. Many of these genes have been previously identified in relation to human carcinogenesis, 68% and 78%, respectively. Subsequent validation of selected genes by serial analysis of gene expression and reverse transcription polymerase chain reaction, demonstrated expression patterns that were almost identical to our microarray analysis. Using a four-fold larger sample relative to that used in our previous study, candidate genes involved in human colorectal carcinogenesis were reproducibly identified. Further studies of comprehensive gene expression using our technique may elucidate the mechanism of CRC tumorigenesis.

Cell Line, Tumor↗

PubMed2004

[Numerical taxonomy of medicinal plants of Curcuma in China].

OBJECTIVE: To provide some new evidences for the classfication and identification of medicinal plants of Curcuma. METHOD: A numerical taxonomy by means of cluster analysis and principal Component analysis is used. Combined with RAPD analysis, computer image analysis and chemical analysis, the taxonomical relationships of the plants of Curcuma in China were characterized qualitatively and quantitatively. RESULT AND CONCLUSION: The plants of Curcuma is systematized into 9 species, 1 species complex, 3 cultivated varieties. A lot of taxonomic confusion and disputations were consequently expounded.

Cluster Analysis↗

PubMed2006

[Effects of Arbuscular Mycorrhizae on growth and essential oil of Atractylodes lancea].

OBJECTIVE: To study the effects of Arbuscular Mycorrhizae on cultivated Atractylodes lancea. METHOD: Pot experiment of A. lancea, with (code as AM) or without (code as CK) Glomus mosseae (GM) was conducted 5 times respectively, then the biomass, essential oil, and soil nutrition, soil organism, soil microbial were detected after A. lancea were harvested. RESULT: (1) Mycorrhizal dependency of A. lancea was 245%, and height of individuals, numbers of leaves, leaf area, biomass of A. lancea were all higher in AM than in CK (P < 0.05). (2) GC-MS analysis with cluster analysis and principal components analysis showed that there were no differences in essential oil of A. lancea between AM and CK. (T3) Total N, available N, available P and available K in AM soil were all lower than in CK soil. (4) GC-MS analysis showed organic matters changed differenly in AM soil and CK soil, components 5,6 in AM soil were higher than that in CK soil, but component 9, 10, 11 were lower in AM soil than that in CK soil. (5) Biolog detect showed AWCD of AM soil microbe were higher than that of CK soil throughout the incubation, and AWCD of the former was 0.66, and the later was 0.46 after 192 h incubation. and t-test showed, Shannon seven indices and McIntosh'seven indices were same both at 72 h and 192 h, and diversity indices of Shannon and McIntosh were also same at 72 h, but AM soil microbe were higher than CK soil microbe at 168 h (P < 0.05). CONCLUSION: AM could promote nutrition uptake, improve the function diversity and activity of microbe in rhizosphere of A. lancea, influence the composition of the organic matter, that lead the growth of A. lancea, but not to the quality.

Atractylodes↗

PubMed1989

Method for the classification of countries according to health-related indicators.

A taxonomic approach using cluster analysis and principal component analysis has grouped the countries of the world in eight clusters, in an initial attempt to propose a worldwide spatial classification based on the following health-related indicators: (a) those directly related to the health status of the population; (b) those measuring the provision of health care; (c) those linked to population characteristics; and (d) those reflecting economic parameters. The cartographic representation was based on demographic maps which display the area of each country in proportion to its population size.

Classification↗

PubMed1989

Psychoacoustic abilities of subjects with unilateral and bilateral cochlear hearing impairments and their relationship to the ability to understand speech.

This paper is concerned with deficits in the ability to distinguish sounds, which accompany hearing loss of cochlear origin, and with the relationship of those deficits to the ability to understand speech in quiet and in background noise. Nine subjects with moderate unilateral cochlear hearing loss and 6 with moderate bilateral cochlear hearing loss took part in a series of psychoacoustic and speech perception tests. The impaired ears showed deficits in several of the psychoacoustic tests, including: detection of temporal gaps in bands of noise; frequency discrimination of pure tones; frequency discrimination of complex tones; and frequency selectivity as measured by the masking of tones by notched noise. The impaired ears showed near-normal performance in the detection of changes in intensity and for detecting temporal gaps in sinusoidal signals. Speech reception thresholds (SRTs--defined as the level of speech required for 50% intelligibility) were measured both in quiet and in speech-shaped noise, and were invariably higher for the impaired than for the normal ears. Correlational analysis, principal-components analysis and multiple-regression analysis were used to explore the relationships between the psychoacoustic measures and the SRTs. The results suggest that SRTs in quiet are determined primarily by absolute thresholds as measured by the pure-tone audiogram. SRTs in noise are related more to supra-threshold discrimination abilities, such as the detection of temporal gaps in noise and the frequency discrimination of pure and complex tones, and to age. Possible clinical applications of the results are briefly discussed.

Adult↗

PubMed1987

[Comparative analysis of serum levels of CA-50, CA-125, CA-19.9, enolase and CEA in bronchopulmonary cancer].

A serum assay of CA-50, CA-125, CA-19.9, ENOLASE (NSE) and CEA was performed in 65 patients with primary lung cancer, 63% of whom had visceral metastases, with the following histological distribution: squamous carcinoma (40), adenocarcinoma (9), large cell carcinoma (4), oat cell carcinoma (12). A raised CEA level was detected in 37% of cases, compared with 40.6% for CA-50, 44.6% for CA-19.9 and 40.6% for CA-125 and only 26.6% for NSE. Overall, at least one marker was positive in 83% of cases. Statistical analysis of the different markers (correlation analysis and principal component analysis) demonstrated the existence of a strict correlation between the levels of CA-50, CEA and CA-19.9 (p less than 0.01). ENOLASE was more frequently elevated in oat cell carcinomas (42%) than in non-oat cell carcinomas (30%), but the difference was not significant. In contrast, CA-125 appears to be a good marker for non-oat cell carcinomas (51%) (p less than 0.05). The authors also found a correlation between the presence of a raised level of CA-50 (p less than 0.05), CA-125 (p less than 0.02) and especially CEA (p less than 0.001) and the presence of visceral metastases. The initial survey of disseminated lung cancers should include the assay of at least 4 of these markers in order to obtain a reliable serum tracer in more than 2/3 of cases.

Adenocarcinoma↗

PubMed1981

Suitability of control materials for determination of alpha-amylase activity.

The suitability of control materials for determination of alpha-amylase activity was assessed in comparison with reference groups of authentic human serum specimens containing alpha-amylase of either pancreatic or salivary origin, specimens from patients with no pancreatic pathology, and normal specimens to which porcine pancreatic alpha-amylase was added. After determination of alpha-amylase activity by 11 commonly used techniques (five different principles), the results were processed by both classical (linear representation, regression) and multivariate (correspondence analysis, principal-components analysis) statistical techniques. Specimens containing porcine pancreatic alpha-amylase did not behave like any of the other groups. We conclude that porcine enzyme should not be used for interlaboratory quality-control surveys or intermethod comparison studies. Determination of human salivary and pancreatic alpha-amylase showed intermethod biases similar to those for authentic patients' specimens. Human salivary alpha-amylase, both because of its behavior and its commercial availability, is a satisfactory source for alpha-amylase activity of quality-control specimens. The nature of the matrix (polyvinylpyrrolidone, albumin, delipidated serum, bovine serum, or human serum) little influenced the behavior of the specimens for any of the methods studied.

Amylases↗

PubMed1994

Diversity of ethnic and racial VNTR RFLP fixed-bin frequency distributions.

To examine the impact that intra- and interracial genetic diversities have on VNTR RFLP-fragment-size distributions, a multiracial (East Asian, African American, U.S. Southwest Hispanic, and European Caucasian) and multiethnic (Chinese, Japanese, Korean, and Vietnamese) database has been constructed for the following loci: D1S7, D2S44, D4S139, and D10S28. Homogeneity between samples was examined using the Komologorov-Smirnov two-sample test for RFLP fragment sizes and a log-likelihood test for fixed-bin frequencies with theoretical and Monte Carlo empirical significance levels. Small but significant differences between theoretical and empirical significance-level distributions were observed with both procedures, particularly with the latter. The significance levels of the two types of tests were poorly correlated. Statistically significant differences in fragment-size and fixed-bin distributions were found within and between races, with greater differences occurring between races. Cluster analysis and principal components analysis, using different similarity measures, did not support the hypothesis of greater intra- than interracial diversity, which suggests that ethnic variation can be conservatively estimated by racial variation.

Cluster Analysis↗

PubMed1995

Stereotactic biopsies from astrocytic tumors. Diagnostic information contributed by the quantitative chromatin pattern description.

OBJECTIVE: To reduce the problem of heterogeneity in astrocytic tumors by means of computer-assisted microscope analysis of Feulgen-stained nuclei. STUDY DESIGN: Thirty-eight glial tumors for which we obtained 227 stereotactic biopsies were subjected to digital cell image analysis of Feulgen-stained nuclei. This series of 38 glial tumors included 36 supratentorial astrocytic tumors (13 astrocytomas, 7 anaplastic astrocytomas and 16 glioblastoma multiformes) and 2 grade 3 astrocytic tumors of the cerebellum. RESULTS: The results suggest a new methodology, enabling the biologic characteristics of the brain parenchymal area surrounding a given glial tumor to be characterized. This methodology relies on the performance of three successive steps. The first is quantitative characterization of nuclear morphology and its chromatin pattern by means of 15 morphonuclear variables. This characterization is carried out by means of the computer-assisted microscope analysis of Feulgen-stained nuclei. The second step consists of setting up morphonuclear data banks, with each process giving the precise portrait of a given cell nuclear population. This process is carried out by means of multivariate analysis, taking into account the 15 variables mentioned above. Multivariate analysis includes principal components analysis followed by the canonical transformation of the data. The third step consists of testing unknown cases against these morphonuclear data banks. This is carried out by means of linear discriminant analysis, which enables the various cell nuclear types in the stereotactic biopsy to be quantified. CONCLUSION: The present methodology makes it possible to investigate whether infiltrating tumor cells are present in or absent from the parenchymal brain area surrounding a glial tumor. It can therefore contribute additional information to that contributed by computed tomography and/or magnetic resonance imaging with respect to the precise delineation of the volume of a brain tumor. This delineation must be as precise as possible to allow total surgical resection of the tumor and prevention of its recurrence.

Astrocytoma↗