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Effect of controlled ovarian hyperstimulation in IVF on endometrial gene expression profiles

MOLECULAR HUMAN REPRODUCTION 2005年第3期11卷 195-205页

作者： Horcajadas, JA Riesewijk, A Polman, J van Os, R Pellicer, A Mosselman, S Simón, C Univ Valencia Inst Valenciano Infertilidad Fdn FIVI E-46003 Valencia Spain NV Organon Dept Pharmacol NL-5340 BH Oss Netherlands

Controlled ovarian hyperstimulation (COH) used in IVF produces lower implantation rates per embryo transferred compared to natural cycles utilized in ovum donation, suggesting a suboptimal endometrial development. Endometrial receptivity has recently been investigated in natural menstrual cycles with the aid of microarray technology. The aim of this study is to investigate the impact of COH using urinary gonadotrophins with a long protocol with GnRH agonists without progesterone supplementation (similar to the natural cycle) on endometrial gene expression profiles during the window of implantation by comparing the profiles at day hCG+7 of COH versus LH+7 of a previous natural cycle in the same women. For this purpose we have used microarray technology by Affymetrix (GeneChip HG_U133A), which allows more than 22 000 genes to be tested simultaneously. Results were validated by semi-quantitative PCR and quantitative PCR experiments. We found that more than 200 genes showed a differential expression of more than 3-fold when COH and normal cycles were compared at hCG+7 versus LH+7. We simultaneously re-analysed the LH+2 versus LH+7 endometrial gene expression profiles in previous natural cycles in the same subject using this specific GeneChip, the results obtained were consistent with our own published results. This is the first time that gene expression profiles of the endometrium during COH are reported. The large degree of gene expression disturbance is surprising and highlights the need for further efforts to optimize COH protocols.

关键词： microarray technology ovum donation COEFFICIENT OF HAZE Assisted Reproductive Technologies Luteinizing Hormone Gene Expression Profiles Fertilization in Vitro

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Detection of encephalic and hemorrhagic viruses: Integration of micro- and nano-fabrication with computational tools

Detection of encephalic and hemorrhagic viruses: Integration...

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International Conference on MEMS, NANO and Smart Systems

作者： Valdivia-Granda, W Keating, CD Kann, M Beresford, R Kelley, SO Orion Integrated Biosciences Inc. United States Pennsilvania State University United States NLM National Institutes of Health United States Brown University United States Boston College United States

ISBN: (纸本)0769523986

This document present an overview or the use of microarray technology, quantum dots, nanowires and carbon nanotubes to detect pathogens, in particular encephalic and hemorrhagic viruses. The relevance and challenges in the development of detection nanosystems and their integration with computational analysis tools and viral evolutionary genomics techniques are highlighted.

关键词： biological techniques genetics microorganisms nanotechnology carbon nanotubes computational analysis tools encephalic viruses hemorrhagic viruses micro-fabrication microarray technology nano-fabrication nanowires pathogens quantum dots viral evolutionary microarray technology Biological techniques Nanofabrication Quantum dots Nanowire Nanotechnologies Infectious Agent computational analysis Carbon Nanotubes Genetics Microbes Hemorrhagic Change

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Comorbid alcohol and nicotine dependence:: From the Biomolecular basis to clinical consequences

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ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH 2005年第8期29卷 1541-1549页

作者： Ait-Daoud, N Wiesbeck, GA Bienkowski, P Li, MD Pfützer, RH Singer, MV Lesch, OM Johnson, BA Univ Virginia Dept Psychiat Med Charlottesville VA 22908 USA Univ Basel Dept Psychiat Basel Switzerland Inst Psychiat & Neurol Dept Pharmacol Warsaw Poland Univ Texas Hlth Sci Ctr Dept Psychiat San Antonio TX 78284 USA Univ Hosp Mannheim Dept Med 2 Mannheim Germany Med Univ Vienna Dept Psychiat Vienna Austria

This article represents the proceedings of a symposium presented at the 12th Congress of the International Society for Biomedical Research on Alcoholism held in Heidelberg/Mannheim, Germany, on October 1, 2004. The organizers and cochairs were Nassima Ait-Daoud, MD, and Gerhard A. Wiesbeck, MD. The presentations included the following: (1) The Role of Nicotinic Acetylcholine Receptors in Alcohol-Seeking Behavior, by Przemyslaw Bienkowski, MD, PhD;(2) Utilization of Linkage Analysis Combined with microarray technology to Identify Genes and Mechanisms Underlying Nicotine and Alcohol Use and Abuse in Humans and Rodents, by Ming D. Li, PhD;(3) Smoking and Alcoholic Chronic Pancreatitis: The Underestimated Risk?, by Roland H. Pfutzer, MD;(4) Anticraving Medication in Alcohol and Nicotine Dependence, by Otto M. Lesch, MD, PhD;and (5) Pharmacotherapy for Promotion of Abstinence from Nicotine Among Alcohol-Dependent Individuals, by Bankole A. Johnson, DSc, MD, PhD.

关键词： alcohol dependence nicotine dependence nicotinic acetylcholine receptors microarray technology alcoholic chronic pancreatitis pharmacotherapy

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Using worms to better understand how Bacillus thuringiensis kills insects

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TRENDS IN MICROBIOLOGY 2005年第8期13卷 347-350页

作者： Crickmore, N Univ Sussex Sch Life Sci Brighton BN1 9QG E Sussex England

Bacillus thuringiensis is widely used as a biological pesticide to control insects that either cause damage to crops or transmit disease. That it can also target the model organism Caenorhabditis elegans has not only provided exciting new insights into how the toxins produced by the bacterium target their victims but also how target insects counter the attack. Modern approaches such as reverse genetics and microarray technology have revealed novel receptors for the toxins and possible signal transduction pathways induced within the host following intoxication. This article will discuss how these findings fit in with current models and how they might influence future studies.

关键词： Signal Transduction Pathways Victims cause of damage Biopesticides bacteria microarray technology Biological Toxins Insecta Reverse Genetics Bacillus thuringiensis

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Protein microarray technology

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DRUG DISCOVERY TODAY 2002年第15期7卷 815-822页

作者： Templin, MF Stoll, D Schrenk, M Traub, PC Vöhringer, CF Joos, TO Univ Tubingen NMI Natl & Med Sci Inst D-72770 Reutlingen Germany

microarray technology allows the simultaneous analysis of thousands of parameters within a single experiment. Microspots of capture molecules are immobilised in rows and columns onto a solid support and exposed to samples containing the corresponding binding molecules. Readout systems based on fluorescence, chemiluminescence, mass spectrometry, radioactivity or electrochemistry can be used to detect complex formation within each microspot. Such miniaturised and parallelised binding assays can be highly sensitive, and the extraordinary power of the method is exemplified by array-based gene expression analysis. In these systems, arrays containing immobilised DNA pro zies are exposed to complementary targets and the degree of hybridisation is measured. Recent developments in the field of protein microarrays show applications for enzyme-substrate, DNA-protein and different types of protein-protein interactions. This article discusses theoretical advantages and limitations of any miniaturised capture-molecule-ligand assay system and discusses how the use of protein microarrays will change diagnostic methods and genome and proteome research.

关键词： Drug Industry Molecular Probe Techniques Proteins 制药工业分子探针技术蛋白质类 microarray technology Molecular Probe Techniques Chromosomal Probes non-sinking support Protein microarray technology hybridisation Pharmaceutical Industry Protein microarrays

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Dermal fibroblast-associated gene induction by asiaticoside shown in vitro by DNA microarray analysis

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BRITISH JOURNAL OF DERMATOLOGY 2004年第3期151卷 571-578页

作者： Lu, L Ying, K Wei, S Liu, Y Lin, H Mao, Y Fudan Univ Sch Life Sci Inst Genet State Key Lab Genet Engn Shanghai 200433 Peoples R China Shanghai Jahwa Co Ltd Dept Res & Dev Shanghai 200082 Peoples R China

Background Asiaticoside, isolated from Centella asiatica, promotes fibroblast proliferation and extracellular matrix (ECM) synthesis in wound healing. The precise mechanism, however, in molecular and gene expression levels is still unclear. Objective Using cDNA microarray technology, the alteration of gene expression profiles was determined for human dermal fibroblasts in vitro in the presence of asiaticoside (30 mug mL(-1)). Fifty-four genes, with known functions for cell proliferation, cell cycle progression and synthesis of ECM, were significantly upregulated in our 'genome-nest' expression profile at various time points. Furthermore, the mRNA levels and protein production of certain genes responsible for ECM synthesis (e.g. encoding type I and type III collagen proteins) were evaluated by Northern blot and radioimmunoassay, respectively. Results We found that there is a close correlation between the gene profile, mRNA and protein production in the response of the cells to asiaticoside stimulation. Conclusions This information could be used for exploring the response of the target genes to asiaticoside in fibroblasts.

关键词： asiaticoside cluster analysis fibroblast gene microarray technology Northern blot radioimmunoassay

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Cluster analysis for gene expression data: A survey

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IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2004年第11期16卷 1370-1386页

作者： Jiang, DX Tang, C Zhang, AD SUNY Buffalo Dept Comp Sci & Engn Buffalo NY 14260 USA

DNA microarray technology has now made it possible to simultaneously monitor the expression levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increases the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. A first step toward addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. Cluster analysis seeks to partition a given data set into groups based on specified features so that the data points within a group are more similar to each other than the points in different groups. A very rich literature on cluster analysis has developed over the past three decades. Many conventional clustering algorithms have been adapted or directly applied to gene expression data, and also new algorithms have recently been proposed specifically aiming at gene expression data. These clustering algorithms have been proven useful for identifying biologically relevant groups of genes and samples. In this paper, we first briefly introduce the concepts of microarray technology and discuss the basic elements of clustering on gene expression data. In particular, we divide cluster analysis for gene expression data into three categories. Then, we present specific challenges pertinent to each clustering category and introduce several representative approaches. We also discuss the problem of cluster validation in three aspects and review various methods to assess the quality and reliability of clustering results. Finally, we conclude this paper and suggest the promising trends in this field.

关键词： microarray technology gene expression data clustering

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DNA-directed protein immobilization on mixed self-assembled monolayers via a Streptavidin bridge

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LANGMUIR 2004年第19期20卷 8090-8095页

作者： Ladd, J Boozer, C Yu, QM Chen, SF Homola, J Jiang, S Univ Washington Dept Chem Engn Seattle WA 98195 USA Acad Sci Czech Republ Inst Radio Engn & Elect CR-18251 Prague Czech Republic

The simultaneous detection of multiple analytes is an important consideration for the advancement of biosensor technology. Currently, few sensor systems possess the capability to accurately and precisely detect multiple antigens. This work presents a simple approach for the functionalization of sensor surfaces suitable for multichannel detection. This approach utilizes self-assembled monolayer (SAM) chemistry to create a nonfouling, functional sensor platform based on biotinylated single-stranded DNA immobilized via a streptavidin bridge to a mixed SAM of biotinylated alkanethiol and oligo(ethylene glycol). Nonspecific binding is minimized with the nonfouling background of the sensor surface. A usable protein chip is generated by applying protein-DNA conjugates which are directed to specific sites on the sensor chip surface by utilizing the specificity of DNA hybridization. The described platform is demonstrated in a custom-built surface plasmon resonance biosensor. The detection capabilities of a sensor using this protein array have been characterized using human chorionic gonadotropin (hCG). The platform shows a higher sensitivity in detection of hCG than that observed using biotinylated antibodies. Results also show excellent specificity in protein immobilization to the proper locations in the array. The vast number of possible DNA sequences combine with the selectivity of base-pairing makes this platform an excellent candidate for a sensor capable of multichannel protein detection.

关键词： OLIGO(ETHYLENE GLYCOL) OLIGONUCLEOTIDE ARRAYS microarray technology CHIPtechnology ANTIBODY ARRAYS SOLID SUPPORTS HYBRIDIZATION DISCOVERY MOLECULES SURFACES

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Gene expression signatures in lymphoid tumours

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IMMUNOLOGY AND CELL BIOLOGY 2004年第2期82卷 154-160页

作者： Kees, UR Telethon Inst Child Hlth Res Div Childrens Leukaemia & Canc Res Perth WA 6872 Australia Univ Western Australia Ctr Child Hlth Res Perth WA 6009 Australia

Lymphoid tumours comprise the acute and chronic leukaemias, the broad spectrum of lymphomas, including Hodgkin's disease, and multiple myeloma. The subdivision of the acute leukaemias according to the proliferating type of white blood cells has had a major impact on the care of these patients. More recently, specific chromosomal translocations have been used to identify patients who may benefit from more intensive therapies. The novel high-throughput genomic technologies, such as microarrays, provide new avenues for the molecular diagnosis of the haematological malignancies. Rapid advances in genome sequencing and gene expression profiling provide unprecedented opportunities to identify specific genes involved in complex biological processes, including tumorigenesis. The features of microarray technology and the variety of experimental approaches to elucidate lymphoid malignancies are discussed. microarray technology has the potential to lead to more accurate prognostic assessment for patients and is expected to ultimately allow the clinician to select therapies optimally suited to each patient.

关键词： classification gene expression profiles lymphoid malignancies microarray technology resistance to therapy

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Caffeine suppresses the expression of the Bcl-2 mRNA in BeWo cell culture and rat placenta

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JOURNAL OF NUTRITIONAL BIOCHEMISTRY 2004年第6期15卷 342-349页

作者： Nomura, K Saito, S Ide, K Kamino, Y Sasahara, H Nakamoto, T Abiko, Y Nihon Univ Sch Dent Dept Biochem Matsudo Chiba 2718587 Japan Nihon Univ Sch Dent Dept Oral Diag Matsudo Chiba 2718587 Japan Nihon Univ Sch Dent Res Inst Oral Sci Matsudo Chiba 2718587 Japan Louisiana State Univ Hlth Sci Ctr Dept Physiol New Orleans LA 70119 USA Louisiana State Univ Hlth Sci Ctr Dept Pediat New Orleans LA 70119 USA

Chronic caffeine exposure during pregnancy has an effect on fetal growth;however, the adverse effects of caffeine on embryogenesis are not well understood and controversial. We used cDNA microarray technology to determine whether caffeine alters gene expressions in a human cytotrophoblast-like cell line, BeWo. We found that the expression of the B-cell CLL/lymphoma 2 (Bcl-2) gene in BeWo cells was down-regulated by caffeine, suggesting that chronic exposure during the gestational period could exert an influence on embryogenesis. We then focused on the Bcl-2- and Bcl-2-associated X protein gene, Bax, to study the responsive gene expression in BeWo cells as well as placentas of pregnant rats fed a diet supplemented with caffeine (2 mg/100 g body weight) during gestation, and analyzed the gene expressions using LightCycler-based quantitative real-time polymerase chain reaction assays. We found a significantly decreased level of Bcl-2 mRNA expression, which demonstrated the influence of caffeine on placental function. (C) 2004 Elsevier Inc. All rights reserved.

关键词： caffeine low birth weight fetal growth retardation Bcl-2 microarray technology lightcycler system

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