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microarray Analysis of mRNA and MicroRNA Expression Profile Reveals the Role of β-Sitosterol-D-glucoside in the Proliferation of Neural Stem Cell

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EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013年第1期2013卷 360302-360302页

作者： Jiang, Li-hua Yang, Nian-yun Yuan, Xiao-lin Zou, Yi-jie Jiang, Ze-qun Zhao, Feng-ming Chen, Jian-ping Wang, Ming-yan Lu, Da-xiang Jinan Univ Coll Med Guangzhou 510632 Guangdong Peoples R China Nanjing Univ Chinese Med Dept Pharmacognosy Nanjing 210038 Jiangsu Peoples R China Nanjing Univ Chinese Med Basic Med Coll Nanjing 210038 Jiangsu Peoples R China Jiangsu Prov Hosp Tradit Chinese Med Nanjing 210029 Jiangsu Peoples R China

Neural stem cells (NSCs) are self-regenerating cells, but their regenerative capacity is limited. The present study was conducted to investigate the effect of beta-sitosterol-D-glucoside (BSSG) on the proliferation of hippocampal NSCs and to determine the corresponding molecular mechanism. Results of CCK-8 assay showed that BSSG significantly increased NSC proliferation and the effectiveness of BSSG was similar to that of basic fibroblast growth factor and epidermal growth factor. mRNA expression profiling showed that 960 genes were differentially expressed after NSCs were treated with BSSG. Among the 960 genes, IGF1 is considered as a key regulatory gene that functionally promotes NSC proliferation. MicroRNA (miRNA) expression profiling indicated that 30 and 84 miRNAs were upregulated and downregulated, respectively. miRNA-mRNA relevance analysis revealed that numerous mRNAs including IGF1mRNA were negatively regulated by miRNAs with decreased expression, thereby increasing the corresponding mRNA expression. The increased expression of IGF1 protein was validated by ELISA. Picropodophyllin (PPP, an inhibitor of IGF-1R) inhibition test confirmed that the proliferation-enhancing effect depended on IGF1. This study provided information about BSSG as an efficient and inexpensive growth factor alternative, of which the effect is closely involved in IGF1.

关键词： ANALYSIS of variance ENZYME-linked immunosorbent assay NEURONS POLYMERASE chain reaction RESEARCH -- Finance STEM cells DATA analysis -- Software microarray technology GENE expression profiling

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Identification of Putative Ortholog Gene Blocks Involved in Gestant and Lactating Mammary Gland Development: A Rodent Cross- Species microarray Transcriptomics Approach

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INTERNATIONAL JOURNAL OF GENOMICS 2013年第1期2013卷 624681-624681页

作者： Rodriguez-Cruz, Maricela Coral-Vazquez, Ramon M. Hernandez-Stengele, Gabriel Sanchez, Raul Salazar, Emmanuel Sanchez-Munoz, Fausto Encarnacion-Guevara, Sergio Ramirez-Salcedo, Jorge Inst Mexicano Seguro Social Ctr Med Nacl Siglo 21 Hosp Pediat Unit Med Res Nutr Mexico City 06725 DF Mexico Inst Politecn Nacl Escuela Super Med Secc Estudios Posgrad & Invest Mexico City 11340 DF Mexico Inst Seguridad & Serv Sociales Trabajadores Estad Ctr Med Nacl Noviembre 20 Subdirecc Ensenanza & Invest Mexico City 03100 DF Mexico Univ Nacl Autonoma Mexico Genom Sci Ctr Cuernavaca 62210 Morelos Mexico Inst Nacl Cardiol Ignacio Chavez Dept Immunol Mexico City 140080 DF Mexico Univ Nacl Autonoma Mexico Microarray Unit Inst Fisiol Celular Mexico City 04510 DF Mexico

Themammary gland (MG) undergoes functional and metabolic changes during the transition frompregnancy to lactation, possibly by regulation of conserved genes. The objective was to elucidate orthologous genes, chromosome clusters and putative conserved transcriptionalmodules duringMGdevelopment. We analyzed expression of 22,000 transcripts usingmurinemicroarrays and RNA samples of MG from virgin, pregnant, and lactating rats by cross-species hybridization. We identified 521 transcripts differentially expressed;upregulated in early (78%) and midpregnancy (89%) and early lactation (64%), but downregulated in mid-lactation (61%). Putative orthologous genes were identified. We mapped the altered genes to orthologous chromosomal locations in human and mouse. Eighteen sets of conserved genes associated with key cellular functions were revealed and conserved transcription factor binding site search entailed possible coregulation among all eight block sets of genes. This study demonstrates that the use of heterologous array hybridization for screening of orthologous gene expression from rat revealed sets of conserved genes arranged in chromosomal order implicated in signaling pathways and functional ontology. Results demonstrate the utilization power of comparative genomics and prove the feasibility of using rodent microarrays to identification of putative coexpressed orthologous genes involved in the control of human mammary gland development.

关键词： DEVELOPMENT of mammary glands MAMMARY gland physiology LACTATION GENETIC regulation in mammals DOWN-regulation (Biology) microarray technology RODENTS as laboratory animals

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microarray Analysis Reveals the Molecular Basis of Antiarthritic Activity of Huo-Luo-Xiao-Ling Dan

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EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013年第1期2013卷 524746-524746页

作者： Yu, Hua Lee, David Y. -W. Nanjundaiah, Siddaraju M. Venkatesha, Shivaprasad H. Berman, Brian M. Moudgil, Kamal D. Univ Maryland Sch Med Dept Microbiol & Immunol Baltimore MD 21201 USA Harvard Univ Sch Med McLean Hosp Mailman Res Ctr Belmont MA 02478 USA Univ Maryland Sch Med Ctr Integrat Med Baltimore MD 21201 USA Univ Maryland Sch Med Dept Med Div Rheumatol Baltimore MD 21201 USA

Rheumatoid arthritis (RA) is a chronic inflammatory disease of autoimmune origin. Huo-luo-xiao-ling dan (HLXL) is an herbal mixture that has been used in traditional Chinese medicine over several decades to treat chronic inflammatory diseases including RA. However, the mechanism of the anti-arthritic action of this herbal remedy is poorly understood at the molecular level. In this study, we determined by microarray analysis the effects of HLXL on the global gene expression profile of the draining lymph node cells (LNC) in the rat adjuvant arthritis (AA) model of human RA. In LNC restimulated in vitro with the disease-related antigen mycobacterial heat-shock protein 65 (Bhsp65), 84 differentially expressed genes (DEG) (64 upregulated and 20 downregulated) versus 120 DEG (94 upregulated and 26 downregulated) were identified in HLXL-treated versus vehicle (Water)-treated rats, respectively, and 62 DEG (45 upregulated and 17 downregulated) were shared between the two groups. The most affected pathways in response to HLXL treatment included immune response, inflammation, cellular proliferation and apoptosis, and metabolic processes, many of which are directly relevant to arthritis pathogenesis. These results would advance our understanding of the mechanisms underlying the anti-arthritic activity of HLXL.

关键词： ARTHRITIS -- Drug therapy ANTIRHEUMATIC agents ANIMAL experimentation CELL culture GENE expression HERBAL medicine MOLECULAR probes CHINESE medicine PROBABILITY theory RATS RESEARCH -- Finance microarray technology GENE expression profiling THERAPEUTICS THERAPEUTIC use

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microarray Analysis of Transcriptome of Medulla Identifies Potential Biomarkers for Parkinson's Disease

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INTERNATIONAL JOURNAL OF GENOMICS 2013年第1期2013卷 606919-606919页

作者： Liao, Xiao-Yang Wang, Wei-Wen Yang, Zheng-Hui Wang, Jun Lin, Hang Wang, Qing-Song Wu, Yu-Xian Liu, Yu Sichuan Univ West China Hosp Unit Gen Practice Chengdu 610041 Peoples R China Cheng Du Mil Gen Hosp Dept Neurol Chengdu 610083 Peoples R China

To complement the molecular pathways contributing to Parkinson's disease (PD) and identify potential biomarkers, gene expression profiles of two regions of the medulla were compared between PD patients and control. GSE19587 containing two groups of gene expression profiles [6 dorsal motor nucleus of the vagus (DMNV) samples from PD patients and 5 from controls, 6 inferior olivary nucleus (ION) samples from PD patients and 5 from controls] was downloaded from Gene Expression Omnibus. As a result, a total of 1569 and 1647 differentially expressed genes (DEGs) were, respectively, screened in DMNV and ION with limma package of R. The functional enrichment analysis by DAVID server (the Database for Annotation, Visualization and Integrated Discovery) indicated that the above DEGs may be involved in the following processes, such as regulation of cell proliferation, positive regulation of macromolecule metabolic process, and regulation of apoptosis. Further analysis showed that there were 365 common DEGs presented in both regions (DMNV and ION), which may be further regulated by eight clusters of microRNAs retrieved with WebGestalt. The genes in the common DEGs-miRNAs regulatory network were enriched in regulation of apoptosis process via DAVID analysis. These findings could not only advance the understandings about the pathogenesis of PD, but also suggest potential biomarkers for this disease.

关键词： PARKINSON'S disease diagnosis microarray technology MEDULLA oblongata BIOCHEMICAL markers PREVENTIVE medicine GENE expression

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The Phytochemical Shikonin Stimulates Epithelial-Mesenchymal Transition (EMT) in Skin Wound Healing

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EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013年第1期2013卷 262796-262796页

作者： Yin, Shu-Yi Peng, An-Ping Huang, Li-Ting Wang, Ya-Ting Lan, Chun-Wen Yang, Ning-Sun Acad Sinica Agr Biotechnol Res Ctr Taipei 115 Taiwan

Although various pharmacological activities of the shikonins have been documented, understanding the hierarchical regulation of these diverse bioactivities at the genome level is unsubstantiated. In this study, through cross examination between transcriptome and microRNA array analyses, we predicted that topical treatment of shikonin in vivo affects epithelial-mesenchymal transition (EMT) and the expression of related microRNAs, including 200a, 200b, 200c, 141, 205, and 429 microRNAs, in mouse skin tissues. In situ immunohistological analyses further demonstrated that specific EMT regulatory molecules are enhanced in shikonin-treated epidermal tissues. RT-PCR analyses subsequently confirmed that shikonin treatment downregulated expression of microRNA-205 and other members of the 200 family microRNAs. Further, expression of two RNA targets of the 200 family microRNAs in EMT regulation, Sip1 (Zeb2) and Tcf8 (Zeb1), was consistently upregulated by shikonin treatment. Enhancement of these EMT activities was also detected in shikonin-treated wounds, which repaired faster than controls. These results suggest that topical treatment with shikonin can confer a potent stimulatory effect on EMT and suppress the expression of the associated microRNAs in skin wound healing. Collectively, these cellular and molecular data provide further evidence in support of our previous findings on the specific pharmacological effects of shikonin in wound healing and immune modulation.

关键词： ANALYSIS of variance ANIMAL experimentation BIOLOGICAL models BIOPHYSICS EPITHELIUM RESEARCH -- Methodology MICE POLYMERASE chain reaction RESEARCH -- Finance RNA SKIN WOUND healing PHYTOCHEMICALS REVERSE transcriptase polymerase chain reaction microarray technology

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Immunomodulatory Role of an Ayurvedic Formulation on Imbalanced Immunometabolics during Inflammatory Responses of Obesity and Prediabetic Disease

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EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013年第1期2013卷 795072-795072页

作者： Tikoo, Kamiya Misra, Shashank Rao, Kanury V. S. Tripathi, Parul Sharma, Sachin Int Ctr Genet Engn & Biotechnol Immunol Grp New Delhi 110067 India

Kal-1 is a polyherbal decoction of seven different natural ingredients, traditionally used in controlling sugar levels, inflammatory conditions particularly regulating metabolic and immunoinflammatory balance which are the major factors involved in obesity and related diseases. In the present study, we aimed to investigate the effect of Kal-1 (an abbreviation derived from the procuring source) on diet-induced obesity and type II diabetes using C57BL/6J mice as a model. The present study was performed with two experimental groups involving obese and prediabetic mice as study animals. In one, the mice were fed on high-fat with increased sucrose diet, and different amounts (5, 20, and 75 mu L) of Kal-1 were administered with monitoring of disease progression over a period of 21 weeks whereas in the second group the mice were first put on the same diet for 21 weeks and then treated with the same amounts of Kal-1. A significant reduction in body weight, fat pads, fasting blood glucose levels, insulin levels, biochemical parameters, immunological parameters, and an array of pro-and anticytokines was observed in obese and diabetic mice plus Kal-1 than control (lean) mice fed on normal diet. In conclusion, Kal-1 has immunomodulatory potential for diet-induced obesity and associated metabolic disorders.

关键词： MEDICINAL plants -- Therapeutic use ANALYSIS of variance ANIMAL experimentation BLOOD analysis CYTOKINES IMMUNOLOGICAL adjuvants AYURVEDIC medicine MICE OBESITY PREDIABETIC state RESEARCH -- Finance T-test (Statistics) DATA analysis -- Software microarray technology

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Sharp variation in coercivity and magnetic interactions in patterned Co_xNi_1-x nanoarrays

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JOURNAL OF APPLIED PHYSICS 2013年第6期114卷 063902-063902页

作者： Yang, Chao-Yao Wang, Liang-Wei Chen, Po-An Lin, Hong-Ji Lai, Chih-Huang Tseng, Yuan-Chieh Natl Chiao Tung Univ Dept Mat Sci & Engn Hsinchu 30010 Taiwan Natl Tsing Hua Univ Dept Mat Sci & Engn Hsinchu 30043 Taiwan Natl Synchrotron Radiat Res Ctr Hsinchu 30076 Taiwan

We present a study concerning the unexpectedly large coercivity increase and associated magneto-structural properties of CoxNi1-x patterned arrays. An increase in x led to an face-center-cubic (FCC)-> hexagonal-close-packed (HCP) transition in CoxNi1-x arrays, accompanied by a 6-fold increase in coercivity and strong 3d exchange interactions probed by x-ray magnetic circular dichroism. Sum-rule analysis revealed that orbital moment involved very little in the variable coercivity and magnetic anisotropy;this is distinct from other nanostructures displaying variable coercivity. The sharp rise in coercivity can be attributed to the geometrical confinement of the arrays, causing the microstructure of the nano-clusters to switch magnetization reversal mechanism from fanning to coherent with increasing x, based on the chain-of-spheres model. First-order-reversal curves revealed that the FCC and HCP arrays comprised both soft and hard ferromagnetic components;however, the soft component of the FCC was much more pronounced, leading to differences in reversibility. This type of nanostructure provides a sharp control of magnetic hardness that could be tailored in related technologies. (C) 2013 AIP Publishing LLC.

关键词： RESEARCH Magnetization reversal Coercive fields (Electronics) microarray technology Ferromagnetic materials Magnetic anisotropy

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A Robust Rerank Approach for Feature Selection and Its Application to Pooling-Based GWA Studies

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COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013年第1期2013卷 860673-860673页

作者： Liu, Jia-Rou Kuo, Po-Hsiu Hung, Hung Acad Sinica Inst Stat Sci Taipei 11529 Taiwan Natl Taiwan Univ Inst Epidemiol & Prevent Med Taipei 10055 Taiwan Natl Taiwan Univ Res Ctr Genes Environm & Human Hlth Taipei 10055 Taiwan

Large-p-small-n datasets are commonly encountered in modern biomedical studies. To detect the difference between two groups, conventional methods would fail to apply due to the instability in estimating variances in t-test and a high proportion of tied values in AUC (area under the receiver operating characteristic curve) estimates. The significance analysis of microarrays (SAM) may also not be satisfactory, since its performance is sensitive to the tuning parameter, and its selection is not straightforward. In this work, we propose a robust rerank approach to overcome the above-mentioned diffculties. In particular, we obtain a rank-based statistic for each feature based on the concept of "rank-over-variable." Techniques of "random subset" and "rerank" are then iteratively applied to rank features, and the leading features will be selected for further studies. The proposed re-rank approach is especially applicable for large-p-small-n datasets. Moreover, it is insensitive to the selection of tuning parameters, which is an appealing property for practical implementation. Simulation studies and real data analysis of pooling-based genome wide association (GWA) studies demonstrate the usefulness of our method.

关键词： FEATURE selection (Machine learning) GENOMES microarray technology MEDICAL sciences ROBUST control SIMULATION methods & models

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Combining bulk segregation analysis and microarrays for mapping of the pH trait in melon

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THEORETICAL AND APPLIED GENETICS 2013年第2期126卷 349-358页

作者： Sherman, Amir Eshed, Ravit Harel-Beja, Rotem Tzuri, Galil Portnoy, Vitaly Cohen, Shahar Rubinstein, Mor Schaffer, Arthur A. Burger, Joseph Katzir, Nurit Ophir, Ron Agr Res Org Volcani Res Ctr Inst Plant Sci Genom Unit IL-50250 Bet Dagan Israel Agr Res Org Newe Yaar Res Ctr Inst Plant Sci IL-30095 Ramat Yishay Israel

The availability of sequence information for many plants has opened the way to advanced genetic analysis in many non-model plants. Nevertheless, exploration of genetic variation on a large scale and its use as a tool for the identification of traits of interest are still rare. In this study, we combined a bulk segregation approach with our own-designed microarrays to map the pH locus that influences fruit pH in melon. Using these technologies, we identified a set of markers that are genetically linked to the pH trait. Further analysis using a set of melon cultivars demonstrated that some of these markers are tightly linked to the pH trait throughout our germplasm collection. These results validate the utility of combining microarray technology with a bulk segregation approach in mapping traits of interest in non-model plants.

关键词： MELONS -- Varieties MELONS -- Genetics CHROMOSOME segregation PLANT gene mapping microarray technology HYDROGEN-ion concentration in plants LOCUS in plant genetics PLANTS -- Identification

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An Empirical Bayes Optimal Discovery Procedure Based on Semiparametric Hierarchical Mixture Models

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COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013年第1期2013卷 568480-568480页

作者： Noma, Hisashi Matsui, Shigeyuki Inst Stat Math Dept Data Sci Tachikawa Tokyo 1908562 Japan

Multiple testing has been widely adopted for genome-wide studies such as microarray experiments. For effective gene selection in these genome-wide studies, the optimal discovery procedure (ODP), which maximizes the number of expected true positives for each fixed number of expected false positives, was developed as a multiple testing extension of the most powerful test for a single hypothesis by Storey (Journal of the Royal Statistical Society, Series B, vol. 69, no. 3, pp. 347-368, 2007). In this paper, we develop an empirical Bayes method for implementing the ODP based on a semiparametric hierarchical mixture model using the "smoothing-by-roughening" approach. Under the semiparametric hierarchical mixture model, (i) the prior distribution can be modeled flexibly, (ii) the ODP test statistic and the posterior distribution are analytically tractable, and (iii) computations are easy to implement. In addition, we provide a significance rule based on the false discovery rate (FDR) in the empirical Bayes framework. Applications to two clinical studies are presented.

关键词： GENOMES microarray technology EMPIRICAL Bayes methods PARAMETER estimation BIOLOGY experiments

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