[Serum Proteomic Analysis and Construction of Protein-protein Interaction Networks about Ejaculation Praecox with Shen-yang Deficiency].

Objective To identify serum proteome of ejaculation praecox(EP) with Shen-yang de- ficiency, and to explore its pathogenesis of EP in the protein-protein interaction ( PPI) network. Methods The serum samples were respectively collected from 4 EP with Shen-yang deficiency patients and 4 healthy controls. After the serum proteome of EP with Shen-yang deficiency was obtained, the technology of isobaric tags for relative and absolute quantitation (iTRAQ) was adopted for identification. The STRING data- base was applied to construct the PPI network whose function was analyzed through bioinformatics meth- ods. Results A group of 238 serum proteins were identified in total, of which, 162 proteins reached the strict quantitative standard. Nine proteins were differently expressed, including 1 up-regulated and 8 down-regulated. The constructed PPI network was constituted by 72 protein nodes and 283 protein couples, and could be clustered to 16 clusters, in which 10 clusters were composed of 3 or more proteins. Each cluster could be found with a core protein correspondingly. The core protein of C3,C5,C1S and MASP2 were all main constituents of complement system, whose function involves in biological process of complement ac- tivation. Conclusions The protein models in PPI network of differently expressed serum proteome about EP with Shen-yang deficiency were functional enriched in the biological process of complement activa-, tion; which indicate that a immune dysfuction dominated by abnormal process of complent activation may' be one of the main mechanisms of EP with Shen-yang deficiency.

The Fourier transform infrared spectra of the key organs derived from Kidney (Shen)-yang deficiency syndrome mice.

OBJECTIVE: To explore an approach to rapidly and accurately identify the compounds as biomarkers of Chinese medicine (CM) syndromes. METHOD: The Fourier transform infrared (FT-IR) spectrometry was applied to investigate the characteristic components of a mice model of Kidney (Shen)-yang deficiency syndrome (KDS), and the remedial effect of a typical CM formula Shenqi Pill (). Thirty-six females and 18 males of Balb/c mice were randomly divided into KDS, Shenqi or control group. The females and males of the same group freely were mated for 96 h, and the males were taken out and only the female mice were raised. Females of the KDS group were threatened by a ferocious cat every other day for 14 d. After delivery, the KDS, or gestational threatened, offspring were raised at standard condition for 11 weeks. Then 10 male offspring were randomly selected, anaesthetized and their representative organs, i.e. testes, kidneys, lungs and feet were collected, for the FT-IR scan. Mice of the Shenqi group were intragastric administered Shenqi Pill; while mice in the KDS and control groups were given the same volume of saline. RESULTS: The attenuated birth outcomes of the KDS group were displayed. The remarkable FT-IR differences of all organs between KDS mice and healthy control were mainly at 1,735-1,745 cm(-1) (indicating the increased levels of lipids) and at 1,640-1,647 cm(-1) and 1,539-1,544 cm(-1) (displaying the decreased proteins). No statistic FT-IR difference between Shenqi and control mice was observed. CONCLUSION: In accordance with major traits of KDS, prenatal stress extensively impaired the building up of proteins and resulting in the excessive lipid storage, and FT-IR could effectively identify the biomarkers of KDS.

[The research course and the perspective of molecular regulation network and blood stasis syndrome].

Studying the literature of blood stasis syndrome (BSS), we reviewed the research course and the perspective of molecular regulation network and BSS. The essence study of BSS was firstly proposed by Chen Ke-ji and Wang Jie, and developed for more than thirty years. The course for BSS study mainly included the formulation of BSS diagnostic standard, the establishment of BSS animal model, pedigree methods, twins combined clinical epidemiological survey of BSS research, the four "zu" subjects combined molecular regulation network of BSS, signal transduction system network and BSS research, and so on. Along with a new sequencing approach in basic research, clinical diagnostics, and drug development, we are promising to see the whole gene network research of human diseases, such as metabolic disease, cancer, and etc. These achievements could provide a new way of thinking for further studying the essence of BSS.

Evaluation of diagnostic accuracy in detecting ordered symptom statuses without a gold standard.

Our research is motivated by 2 methodological problems in assessing diagnostic accuracy of traditional Chinese medicine (TCM) doctors in detecting a particular symptom whose true status has an ordinal scale and is unknown-imperfect gold standard bias and ordinal scale symptom status. In this paper, we proposed a nonparametric maximum likelihood method for estimating and comparing the accuracy of different doctors in detecting a particular symptom without a gold standard when the true symptom status had an ordered multiple class. In addition, we extended the concept of the area under the receiver operating characteristic curve to a hyper-dimensional overall accuracy for diagnostic accuracy and alternative graphs for displaying a visual result. The simulation studies showed that the proposed method had good performance in terms of bias and mean squared error. Finally, we applied our method to our motivating example on assessing the diagnostic abilities of 5 TCM doctors in detecting symptoms related to Chills disease.

Preliminary correlation between warm needling treatment for knee osteoarthritis of deficiency-cold syndrome and metabolic functional genes and pathways.

The warm needling technique used in traditional Chinese medicine has been shown to be effective in the treatment and prevention of knee osteoarthritis (OA), but the biological mechanisms behind this action have not been well explored. This study investigated the molecular mechanisms behind warm needling using cDNA microarray technology, thus providing further scientific evidence for its efficacy. Ten patients with knee OA of deficiency-cold syndrome were selected for 2 weeks of warm needling treatment. This treatment involved stimulating the selected acupoints using needles with a burning moxa stick on their handle for 40 minutes per session. Pain intensity and accumulated clinical scores of deficiency-cold syndrome were assessed pretreatment and posttreatment using a 40-factor questionnaire of OA with deficiency-cold syndrome. Four patients with the best therapeutic efficacy were selected for cDNA microarray testing. Among the four patients, 41, 246, 57 and 70 differentially expressed genes were obtained, with more than 50% of these differentially expressed genes functionally linked to primary, cellular and energy metabolism pathways. This work demonstrates that the molecular mechanism behind warm needling treatment may be associated with the regulation of metabolism-related genes and pathways.

Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network.

Systems biology is a general trend of contemporary scientific development. When coupling the classical traditional Chinese medicine (TCM) Cold Syndrome and methodology of systems biology, we conformed to the genome, transcriptome, proteome, and metabolome that are supposed to run through the overall macro behavior, and explored the macro and micro framework of systems biology of TCM Syndrome. We introduced a new way to probe into the implicit stratification of Cold Syndrome, after surveying 4575 cases of Cold Syndrome patients and examining gene expression information of a typical Cold Syndrome pedigree by microarray. We underlined the genetic background of the Cold Syndrome family based on the molecular foundation to understand Syndrome, one of our earlier discoveries in which genes and chemical compounds in neuro-endocrine-immune (NEI) system are scored as Cold or Hot (or both) property. Results indicate that Cold Syndrome related genes play an essential role in energy metabolism, which are tightly correlated with the genes of neurotransmitters, hormones and cytokines in the NEI interaction network. Therefore, NEI interaction not only opens out mechanism of classical TCM theory on Syndrome but also enriches current research on complex diseases as well as systems biology.

Identification of Linkage Disequilibrium SNPs from a Kidney-Yang Deficiency Syndrome Pedigree.

In order to probe the genetic traits of Kidney-yang Deficiency Syndrome (KDS), we employed a national standard of KDS diagnosis for the collection of KDS subjects. Each candidate KDS subject from a typical family was diagnosed by 5 independent physicians of Traditional Chinese Medicine (TCM), and repeated for 3 years, all on the first Saturday of December. Fifteen samples of genomic DNA were isolated and genotyped by Affymetrix 100 K arrays of single nucleotide polymorphism (SNP). Then appropriate tools were used for the analysis of linkage disequilibrium (LD) and bioinformatic mining of LD SNPs. The results indicated that our procedure of TCM diagnosis can effectively collect KDS subjects and therefore provide substantial basis for the linkage analysis of KDS. Five SNPs (i.e. rs514207, rs1054020, rs7685923, rs10515889 and rs10516202) were identified as LD SNPs from this KDS family, representing an unprecedented set of LD SNPs derived from TCM syndrome. These SNPs demonstrate midrange linkage disequilibrium within the KDS family. Two genes with established functions were identified within 100 bp of these SNPs. One is Homo sapiens double cortin domain containing 5, which interacts selectively with mono-, di- or tri-saccharide carbohydrate and involves certain signaling cascades. Another one, leucyl-tRNA synthetase, is also a pleiotropic gene response to cysteinyl-tRNA aminoacylation and protein biosynthesis. In conclusion, KDS is involved in special SNP linkage disequilibrium in the intragenic level, and genes within the flanks of these SNPs suggest some essential symptoms of KDS. However, definitive evidence to confirm or exclude these loci and to establish their biological activities will be required.

[Effects of warming-needle therapy on gene expression pathways in the patient with knee osteoarthritis of deficiency-cold syndrome].

OBJECTIVE: To explore the mechanism of warming-needle therapy in treatment of knee osteoarthritis of deficiency-cold syndrome. METHODS: Eight cases of knee osteoarthritis of deficiency-cold syndrome were selected and treated with warming-needle therapy at Guanyuan (CV 4), Qihai (CV 6) , Zosanli (ST 36), etc.. The gene expression profiles before and after treatment in 4 cases who showed better therapeutic effect were compared. Taking ratio < 0.5 or ratio > 2.0 as differentially expression gene and obtaining differentially expression pathway (P < 0.5, n>3) by http://www. DAVID 2006. RESULTS: Two cases were clinically cured, 4 cases were markedly effective, 1 case was effective and 1 case was ineffective. With help of the microarray, 449 differentially expression genes, and 10 differentially expression pathways were obtained including 2 energy metabolism pathways (oxidative phosphorylation, ATP synthetase), 4 cell signal transduction pathways (insulin signal pathway, Toll-like receptor signal pathway, JAK-STAT signal pathway, and MAPK signal pathway) and cell apoptosis pathway. CONCLUSION: Warming-needle therapy is an effective therapy for knee osteoarthritis with deficiency-cold syndrome , which is possibly involved in the control and regulation of many gene expression by various signal transduction pathways.

Transcriptome analysis of cold syndrome using microarray.

Microarrays are widely used to study changes in gene expression in diseases. In this paper, we use this technology to discover gene expression patterns in the cold syndrome in Chinese medicine. We identify differentially expressed genes and extracted gene modules that are enriched with differentially expressed genes in the cold syndrome by analyzing cDNA samples, which are purified from blood taken from a pedigree. Our results suggest that the cold syndrome might be caused by the physiological imbalance and/or the disorder of metabolite processes. The study confirms the hypotheses about molecular pathways responsible to human metabolic-related diseases.

[Research on gene expression of warm-hot drug treating cold syndrome].

OBJECTIVE: To study the therapeutic molecular mechanism of the warm-hot drugs treating cold syndrome. METHOD: A brother and his sister with deficiency-cold syndrome were chosen and treated with appropriate Chinese formula consisted chiefly of warm-hot drugs for 45 days. Then microarray technique was applied for comparing the gene expression difference of sister who had significant effect, the data was dialed with multiple analysis method and the results were mined though gene function and pathway. RESULT: 276 differential genes were obtained, which were related to metabolism and 18 pathways. CONCLUSION: Warm-hot drugs work on the gene expression of metabolism. It may be exerting the curative action by gene network and there is distinct difference between gene expression of curative effect and syndrome.

Establishment of a discriminant mathematical model for diagnosis of deficiency-cold syndrome using gene expression profiling.

OBJECTIVE: To screen diagnostic markers of Deficiency-Cold syndrome by gene expression profile and to establish a discriminant mathematical milliliters model for the clinical diagnosis of this syndrome based on a support vector machine (SVM). METHODS: A family suffering from Deficiency-Cold syndrome is chosen for this study. This family has 5 patients with Deficiency-Cold syndrome and 10 normal members. The peripheral blood samples for these 5 patients and 5 normal members are tested by using cDNA microarray with 18,816 clones to get their differential expression genes. These genes are further explored to understand their biological functions and pathways through existing databases. A SVM model for clinical diagnosis is then developed based on these differential expression genes. RESULTS: A total of 83 differential expression genes were identified between patients and normal members, in which 21 genes were recorded in the FATIGO database and 16 genes were related to metabolism. Eight (8) pathways were sorted out in the KEGG database, and half pathways were associated with human metabolism. A discriminant mathematical model based on a support vector machine successfully predicted a normal person and a patient with heavy Deficiency-Cold syndrome based on their gene differential expression profiles. Thus, this model may classify the Deficiency-Cold syndrome. CONCLUSION: This work demonstrates that the differential expression genes can be used to identify normal persons and patients with Deficiency-Cold syndrome. Deficiency-Cold syndrome is mainly associated with the metabolism-related gene regulations. In addition, the discriminant mathematical model based on a support vector machine is applicable to the clinical diagnosis for Deficiency-Cold syndrome.

[The informatics of human genome and traditional Chinese medicine].

Guided by the theory and methodology of yin-yang set derived from Changing Book and Medicine Canon, and using genetics as a bridge, we have tried to bring together the ancient functional systematology and modern structural one as well as Eastern and Western medicine, thereby promoting the modernization of traditional Chinese medicine (TCM) in theory and in clinical practice. Herein, we used virtual technology to transform the genetic information in OMIM of NCBI (National Center for Biotechnology Information of USA, http://www.ncbi.nlm.nih.gov ) into a secondary database in the form of webpages. There are sixteen kinds of the database named gene morbidity ones as followings as: the nature of gene, the profile of common phenotype, a interaction of endogenous, the disease of a organ or a viscera pathogenesis phenomenon, TCM, the sign of diagnosis of western medicine, the gene response to environment, syndrome, disease, nerve and -endocrine, tumor and cancer, psychology and behavior, morbidity, endo-factor of molecular information, expression, the interaction between endogenous and exogenous in which there is 4 711 words, files. The advantages of the database are its aptness for using human fuzzy intelligence to recognize things, suitability to uncovering the noumenon (yinyang) nature of an object and applicability to clinical use.

[Application of metabonomics in complicated theory system research of traditional Chinese medicine].

Metabonomics, a new and rapid-developing technology, will be powerful means to the research of complexed theory system and modernization of traditional Chinese medicine (TCM). Discovery of biomarkers and analysis of common properties from the metabolome of a specific TCM syndrome will facilitate the modernized study of TCM system, promote the quantitative and scientific elucidation of TCM syndrome differentiation, provide an in-depth understanding of the TCM theory of Zang-xiang, help predict the disease on-set, and achieve a comprehensive evaluation of systemic clinical efficacy, safety and mechanism of action of the TCM combination formulas along with a better understanding of intestinal microflora ecology. The new approach with combined metabonomics and TCM methodologies will provide a new pathway and methodology for the study of complicated theory system of TCM and its modernization.

Clinical and molecular evaluation of warming and tonic herb treatment for sibling patients of a typical kidney-yang deficiency family.

It is essential to explore the molecular therapeutic effect of warm and tonic herb treatment for individuals with typical kidney-yang deficiency. In this report, we have identified members of a family with a history of suffering from cold and kidney-yang deficiency syndromes. First, we have employed the accumulated scores of the 40-items clinical scoring indicators for kidney-yang deficiency and cold syndromes to clinically assess the presence or absence of the deficiency for 15 family members. We then proceeded to compare the gene expression profiles of RNA isolated from blood samples, prior to and post-herbal treatment, of a sibling (brother and younger sister) that are suffering from the deficiency using cDNA microarrays with 18816 genes. Following treatments with the warming and tonic herb, the accumulated clinical scores obtained from the 40-items clinical scoring indicators were compared to those obtained pre-treatment. It was observed that the accumulated clinical scores were reduced by 1/3 for the brother and 2/3 for his younger sister following the treatments. Furthermore, we have demonstrated that the level of gene expression for a total of 33 genes at pre-treatment was modulated after treatments with the warming and tonic herb and correlated well with the clinical improvements of their syndromes. These results suggest that the combination of gene profiling and the accumulated clinical scores obtained from the 40-items clinical scoring indicators may provide an accurate clinical assessment and a way to monitor the therapeutic efficacy of the warming and tonic herb treatment.