[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 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.

Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family.

Objective. To explore the genetic traits of Kidney-yang deficiency syndrome (KDS). Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibrium (LD) SNPs were generated using GeneChip DNA analysis software (GDAS, Affymetrix). Genes located within 100 bp of the flanks of LD SNPs were mined via GeneView. 29 exons of the doublecortin domain containing 5 (DCDC5), a representative gene within the flank of an LD SNP, were resequenced. Results. Five LD SNPs display midrange linkage with KDS. Two genes with established functions, DCDC5 and Leucyl-tRNA synthetase, were mined in the flanks of LD SNPs. Resequencing of DCDC5 revealed a nonsynonymous variation, in which 3764T/A was replaced by C/G. Accordingly, the Ser(1172) was substituted by Pro(1172). The S1172P substitution effect was evaluated as "possibly damaging" by PolyPhen. Conclusion. We have identified a genomic variation of DCDC5 based on the LD SNPs derived from a KDS family. DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.

Observations on Copy Number Variations in a Kidney-yang Deficiency Syndrome Family.

We have performed an analysis of a family with kidney-yang deficiency syndrome (KDS) in order to determine the structural genomic variations through a novel approach designated as "copy number variants" (CNVs). Twelve KDS subjects and three healthy spouses from this family were included in this study. Genomic DNA samples were genotyped utilizing an Affymetrix 100 K single nucleotide polymorphism array, and CNVs were identified by Copy Number Algorithm (CNAT4.0, Affymetrix). Our results demonstrate that 447 deleted and 476 duplicated CNVs are shared among KDS subjects within the family. The homologus ratio of deleted CNVs was as high as 99.78%. One-copy-duplicated CNVs display mid-range homology. For two copies of duplicated CNVs (CNV(4)), a markedly heterologous ratio was observed. Therefore, with the important exception of CNV(4), our data shows that CNVs shared among KDS subjects display typical Mendelian inheritance. A total of 113 genes with established functions were identified from the CNV flanks; significantly enriched genes surrounding CNVs may contribute to certain adaptive benefit. These genes could be classified into categories including: binding and transporter, cell cycle, signal transduction, biogenesis, nerve development, metabolism regulation and immune response. They can also be included into three pathways, that is, signal transduction, metabolic processes and immunological networks. Particularly, the results reported here are consistent with the extensive impairments observed in KDS patients, involving the mass-energy-information-carrying network. In conclusion, this article provides the first set of CNVs from KDS patients that will facilitate our further understanding of the genetic basis of KDS and will allow novel strategies for a rational therapy of this disease.

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.

[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.

[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.

[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.

Genes underlying positive influence of prenatal environmental enrichment and negative influence of prenatal earthquake simulation and corrective influence of Chinese herbal medicine on rat offspring: Irf7 and Ninj2.

BACKGROUND: Prenatal environmental enrichment (EE) has been proven to positively affect but prenatal stress negatively influence the physiological and psychological processes in animals, whose trans-generational genetic mechanism remains unclearly defined. We aimed to investigate and find out key genes underlying the positive-negative effects derived from prenatal interventions. MATERIALS AND METHODS: Pregnant rats were randomized into EE group (EEG), earthquake simulation group (ESG), herbal group (HG) received herbal supplements in feed after earthquake simulation, and control group (CG). RESULTS: Light Box Defecation Test (LBDT) showed EEG offspring presented less fecal pellets than CG offspring, ESG's more than CG's, and HG's less than ESG (p's<0.05). Open-field Test (OFT) score of EEG was higher than CG offspring, of ESG's was lower than CG's, and HG's higher than ESG's. Irf7 and Ninj were screened, which were up-regulated in EEG, down-regulated in ESG (FC<0.5), and were neutralized in HG. Prenatal EE could positively promote the nervous system development, prenatal earthquake simulation could retard the nervous system development and Chinese herbal remedy (JKSQW) which could correct the retardation. CONCLUSION: The negative-positive prenatal effect could contribute to altered gene expression of Irf7 and Ninj2 which also could play a key role in the improving function of JKSQW for the kidneys.

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 impact of the Wenchuan earthquake on birth outcomes.

BACKGROUND: Earthquakes and other catastrophic events frequently occurring worldwide can be considered as outliers and cause a growing and urgent need to improve our understanding of the negative effects imposed by such disasters. Earthquakes can intensively impact the birth outcomes upon psychological and morphological development of the unborn children, albeit detailed characteristics remain obscure. METHODS AND FINDINGS: We utilized the birth records at Du Jiang Yan and Peng Zhou counties to investigate the birth outcomes as a consequence of a major earthquake occurred in Wenchuan, China on May 12, 2008. Totally 13,003 of neonates were recorded, with 6638 and 6365 for pre- and post- earthquake, respectively. Significant low birthweight, high ratio of low birthweight, and low Apgar scores of post-earthquake group were observed. In contrast, the sex ratio at birth, birth length and length of gestation did not show statistical differences. The overall ratio of birth-defect in the post-earthquake (1.18%) is statistically high than that of pre-earthquake (0.99%), especially for those in the first trimester on earthquake day (1.47%). The birth-defect spectrum was dramatically altered after earthquake, with the markedly increased occurrences of ear malformations. The ratio of preterm birth post-earthquake (7.41%) is significant increased than that of pre-earthquake (5.63%). For the birth outcomes of twins, significant differences of the ratio of twins, birth weight, ratio of low birthweight and birth-defect rate were observed after earthquake. CONCLUSION: A hospital-based study of birth outcomes impacted by the Wenchuan earthquake shows that the earthquake was associated with significant effects on birth outcomes, indicating it is a major monitor for long-term pregnant outcomes.

[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.