Application Of DNA Microarray Technology Research Articles

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BioTechniquesVol. 50, No. 3 BioSpotlightOpen AccessBioSpotlightPatrick C.H. Lo & Kristie NyboPatrick C.H. LoSearch for more papers by this author & Kristie NyboSearch for more papers by this authorPublished Online:3 Apr 2018https://doi.org/10.2144/000113620AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInReddit Diving BAC into the Pool with MicroarraysSecond-generation sequencing with its short read lengths is not practicable when determining whole-genome sequences from species possessing large genomes with a high content of repetitive DNA. Realistically, reference sequences for these species can only be obtained using physical map–based sequencing of BAC clones. A key step to this genome sequencing methodology is the ordering and orientation of BAC clones through their anchoring to a genetic map. This approach typically requires screening BAC libraries for clones with specific gene sequences using DNA hybridization or PCR, rendering it low-throughput and labor-intensive. In this issue, P. Hedley and colleagues at the Scottish Crop Research Institute (Dundee, Scotland) describe a new strategy for the high-throughput addressing of thousands of genes to thousands of BACs in parallel using a novel application of DNA microarray technology developed for the unsequenced 5.3-Gb genome of barley. Whole genome–amplified DNA derived from multidimensional pools of barley BAC clones was screened on a custom microarray of 42,000 expressed barley genes. The BACs were pooled using a previously developed “matrix” pooling strategy whereby the location of a clone along a particular dimension (plate, row, or column of 384-well plates) of a Super Pool (SP) of seven 384-well plates could be determined by the presence of positive signals in two separate matrix pools in that dimension. As a proof of principle, the authors tested 2 SPs out of the 55 SPs from a barley BAC library with ~148,000 clones. All matrix pools from the first SP were labeled with Cy3 while those of the second SP were labeled with Cy5. Pairs of labeled matrix pools, one from each SP, were then cohybridized to a microarray. Signals extracted from the scanned images of the hybridized microarrays were analyzed using customized scripts to first identify those probes with a high signal in only two matrix pools in a particular dimension, and then to combine the information from all three dimensions for deconvolution and identification of specific BAC clones containing the microarray probe sequence. This cost-effective, high-throughput, and accurate method for anchoring BACs should be applicable to any species where a whole-genome sequence is lacking.(See “Highly parallel gene-to-BAC addressing using microarrays”)Magnetic AttractionDiscovering the molecular mechanisms governing the differentiation of neural stem cells (NSCs) is essential before these cells can be used to develop therapies for neurodegenerative diseases. For those researchers wishing study specific genes that could induce or suppress differentiation of NSCs, an obstacle has been the difficulty in transfecting NSCs using conventional methods. Nucleofection and lipofection are commonly used for delivering genes to cells, but when applied to NSCs, they exhibit extensive toxicity soon after transfection and may interfere with studies of differentiation. While nucleofection does result in a reasonable percentage of transfected cells, it is costly and most cells die during electroporation. Writing in this issue of BioTechniques, Sapet et al. from OZ Biosciences (Marseille, France) along with colleagues from the National Center for Scientific Research in Paris demonstrate that magnetofection is a viable alternative method for efficiently delivering DNA to NSCs that minimizes undesired toxic effects and does not appear to affect differentiation. Magnetofection is accomplished by associating nucleic acid vectors carrying the desired sequences with super-paramagnetic nanoparticles, which are added to a cell culture. When a magnetic field is then applied to the culture particles rapidly accumulate around the cells, leading to uptake of the DNA. The authors present an optimized protocol for transfecting NSCs using magnetofection, and show that the magnetofection method can be used to identify genes involved in the neuronal differentiation of NSCs. Because of the simplicity, low cost, reduced toxicity, and reliability of this method, the approach has the potential to be valuable for both small scale and high throughput projects seeking to identify new regulators of neuronal differentiation facilitating understanding of the differentiation of these cells and adding further insight into their potential for therapeutic development.Neural stem cell differentiation.Images of neural stem cells acquired 4 days after NeuroMag transfection of a mix between a GFP vector together with either an empty vector (A) or a NeuroD1 expressing vector (B).(See “High transfection efficiency of neural stem cells with magnetofection”)FiguresReferencesRelatedDetails Vol. 50, No. 3 Follow us on social media for the latest updates Metrics History Published online 3 April 2018 Published in print March 2011 Information© 2011 Author(s)PDF download

Application of DNA microarray technology in Bos taurus genomic analysis: preliminary results

The most common type of genetic variation is the SNP (Single Nucleotide Polymorphism), a position in the genome at which two alternative bases occur in the population. Although individual SNPs are less informative than the currently used genetic markers, they are more abundant and have greater potential for automation (Conner et al., 1983; Cronin et al., 1996). For this reason genotyping of SNPs will likely be a major part of every genetic investigation, not only in Human but also in livestock specie genetics. Microarray (or “chip”)-based hybridation analysis.......

Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress

The application of DNA microarray technology to investigate multiple-species microbial communities presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri, and Methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community in response to oxidative stress. In order to minimize the possibility of cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. This study showed that S. fumaroxidans and M. hungatei responded to the oxidative stress with up-regulation of several genes known to be involved in reactive oxygen species (ROS) detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. However, D. vulgaris seemed to be less sensitive to the oxidative stress as a member of a four-species community, since no gene involved in ROS detoxification was up-regulated. Our work demonstrated the successful application of microarrays to a multiple-species microbial community, and our preliminary results indicated that this approach could provide novel insights on the metabolism within microbial communities.

Antibody therapy (IVIG): evaluation of the use of genomics and proteomics for the study of immunomodulation therapeutics

Intravenous immunoglobulin (IVIG) is used for an increasingly diverse number of therapeutic applications as an immunomodulation drug. Although it has demonstrated therapeutic effectiveness, the mechanism of action of IVIG in these disorders is poorly understood; this lack of understanding complicates rational clinical application and reimbursement for 'off-label' use. Selected literature on the clinical use of IVIG as an immunomodulation drug is reviewed. We present a brief description of DNA microarray and protein microarray technology and the application of such technologies to the study of immune system cells. The several studies on the application of DNA microarray technology to study gene expression in response to IVIG are presented. There is increasing data on the use of DNA microarray and protein microarray technology to study gene expression in immune system cells including T cells, B cells, macrophages, and leucocytes. There is less information on the effect of IVIG on gene expression in immune system cells. However, there is sufficient information available to suggest that this is a practical approach with the caveat that such work will require careful experimental design and clear definition of the normal population. DNA and protein microarray assays can be used to (i) provide rational indications for the clinical use of IVIG, (ii) provide for specific analysis of raw material and end product IVIG in screening for content related to immunomodulation, and (iii) accelerate the development of next generation products which would be more focused and/or targeted therapeutics.

Effects of Target Length on the Hybridization Efficiency and Specificity of rRNA-Based Oligonucleotide Microarrays

The effect of target size on microarray hybridization efficiencies and specificity was investigated using a set of 166 oligonucleotide probes targeting the 16S rRNA gene of Escherichia coli. The targets included unfragmented native rRNA, fragmented rRNA ( approximately 20 to 100 bp), PCR amplicons (93 to 1,480 bp), and three synthetic single-stranded DNA oligonucleotides (45 to 56 bp). Fluorescence intensities of probes hybridized with targets were categorized into classes I (81 to 100% relative to the control probe), II (61 to 80%), III (41 to 60%), IV (21 to 40%), V (6 to 20%), and VI (0 to 5%). Good hybridization efficiency was defined for those probes conferring intensities in classes I to IV; those in classes V and VI were regarded as weak and false-negative signals, respectively. Using unfragmented native rRNA, 13.9% of the probes had fluorescence intensities in classes I to IV, whereas the majority (57.8%) exhibited false-negative signals. Similar trends were observed for the 1,480-bp PCR amplicon (6.6% of the probes were in classes I to IV). In contrast, after hybridization of fragmented rRNA, the percentage of probes in classes I to IV rose to 83.1%. Likewise, when DNA target sizes were reduced from 1,480 bp to 45 bp, this percentage increased approximately 14-fold. Overall, microarray hybridization efficiencies and specificity were improved with fragmented rRNA (20 to 100 bp), short PCR amplicons (<150 bp), and synthetic targets (45 to 56 bp). Such an understanding is important to the application of DNA microarray technology in microbial community studies.

Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions

BackgroundDNA microarrays, which have been increasingly used to monitor mRNA transcripts at a global level, can provide detailed insight into cellular processes involved in response to drugs and toxins. This is leading to new understandings of signaling networks that operate in the cell, and the molecular basis of diseases. Custom printed oligonucleotide arrays have proven to be an effective way to facilitate the applications of DNA microarray technology. A successful microarray experiment, however, involves many steps: well-designed oligonucleotide probes, printing, RNA extraction and labeling, hybridization, and imaging. Optimization is essential to generate reliable microarray data.ResultsHybridization and washing steps are crucial for a successful microarray experiment. By following the hybridization and washing conditions recommended by an oligonucleotide provider, it was found that the expression ratios were compressed greater than expected and data analysis revealed a high degree of non-specific binding. A series of experiments was conducted using rat mixed tissue RNA reference material (MTRRM) and other RNA samples to optimize the hybridization and washing conditions. The optimized hybridization and washing conditions greatly reduced the non-specific binding and improved the accuracy of spot intensity measurements.ConclusionThe results from the optimized hybridization and washing conditions greatly improved the reproducibility and accuracy of expression ratios. These experiments also suggested the importance of probe designs using better bioinformatics approaches and the need for common reference RNA samples for platform performance evaluation in order to fulfill the potential of DNA microarray technology.

The QscR Quorum-Sensing Regulon of Pseudomonas aeruginosa : an Orphan Claims Its Identity

Quorum sensing is a process by which bacteria release and subsequently respond to signal molecules, as a mechanism for sensing population density (4). Acylated homoserine lactones (AHLs) are well-studied quorum-sensing signals among proteobacteria and are most commonly synthesized by enzymes of the LuxI family (3). AHLs are usually recognized by members of the LuxR family of transcription factors, often encoded adjacent to their corresponding LuxI-type AHL synthases. Proteobacterial genome sequencing has revealed the existence of many more LuxR homologues than were known or suspected to exist, frequently in significant excess over the number of recognized AHL synthases in the genome. Many of these regulatory genes are orphans, retaining key attributes of better-studied luxR homologues but not linked to or associated with an AHL synthase gene. Some of these orphans are substantially different in size from characterized LuxR homologues, with large truncations or additional sequences. Of those typically sized LuxR-type proteins with end-to-end similarity, many lack one or more conserved amino acid residues known to be critical to the function of most LuxR-type proteins (3). These imperfect LuxR homologues might function to recognize AHLs by an alternate mechanism, provide ligand-independent activity, act as dominant-negative inhibitors, or even detect alternate small molecules. In other cases, all or most of the critical residues are present. These more highly conserved LuxR-type orphans may respond to endogenously synthesized AHL(s), generated by an otherwise unassociated AHL synthase of the same microbe or possibly signals from different microbes. A study from Lequette et al., published in this issue of the Journal of Bacteriology, establishes the role of an intriguing orphan LuxR homologue called QscR (quorum-sensing control repressor) in a previously unrecognized regulatory pathway within the larger AHL quorum-sensing network of the opportunistic human pathogen Pseudomonas aeruginosa (12). This work provides important new insights into the activity of the orphan QscR protein within this complex control system and also illustrates an impressive application of DNA microarray technology to address specific hypotheses at a genomic scale.

CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks

BackgroundThe application of DNA microarray technology in post-genomic analysis of bacterial genome sequences has allowed the generation of huge amounts of data related to regulatory networks. This data along with literature-derived knowledge on regulation of gene expression has opened the way for genome-wide reconstruction of transcriptional regulatory networks. These large-scale reconstructions can be converted into in silico models of bacterial cells that allow a systematic analysis of network behavior in response to changing environmental conditions.DescriptionCoryneRegNet was designed to facilitate the genome-wide reconstruction of transcriptional regulatory networks of corynebacteria relevant in biotechnology and human medicine. During the import and integration process of data derived from experimental studies or literature knowledge CoryneRegNet generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure. Reconstructed regulatory networks can be visualized by using the yFiles JAVA graph library. As an application example of CoryneRegNet, we have reconstructed the global transcriptional regulation of a cellular module involved in SOS and stress response of corynebacteria.ConclusionCoryneRegNet is an ontology-based data warehouse that allows a pertinent data management of regulatory interactions along with the genome-scale reconstruction of transcriptional regulatory networks. These models can further be combined with metabolic networks to build integrated models of cellular function including both metabolism and its transcriptional regulation.

Application of DNA microarray technology for detection, identification, and characterization of food-borne pathogens

DNA microarrays represent the latest advance in molecular technology. In combination with bioinformatics, they provide unparalleled opportunities for simultaneous detection of thousands of genes or target DNA sequences and offer tremendous potential for studying food-borne microorganisms. This review provides an up-to-date look at the application of DNA microarray technology to detect food-borne pathogenic bacteria, viruses, and parasites. In addition, it covers the advantages of using microarray technology to further characterize microorganisms by providing information for specific identification of isolates, to understand the pathogenesis based on the presence of virulence genes, and to indicate how new pathogenic strains evolved epidemiologically and phylogenetically.

Recent applications of DNA microarray technology to toxicology and ecotoxicology.

Gene expression is a unique way of characterizing how cells and organisms adapt to changes in the external environment. The measurements of gene expression levels upon exposure to a chemical can be used both to provide information about the mechanism of action of the toxicant and to form a sort of “genetic signature” for the identification of toxic products. The development of high-quality, commercially available gene arrays has allowed this technology to become a standard tool in molecular toxicology. Several national and international initiatives have provided the proof-of-principle tests for the application of gene expression for the study of the toxicity of new and existing chemical compounds. In the last few years the field has progressed from evaluating the potential of the technology to illustrating the practical use of gene expression profiling in toxicology. The application of gene expression profiling to ecotoxicology is at an earlier stage, mainly because of the the many variables involved in analyzing the status of natural populations. Nevertheless, significant studies have been carried out on the response to environmental stressors both in model and in nonmodel organisms. It can be easily predicted that the development of stressor-specific signatures in gene expression profiling in ecotoxicology will have a major impact on the ecotoxicology field in the near future. International collaborations could play an important role in accelerating the application of genomic approaches in ecotoxicology.

Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response

There are > 1.15 million cases of breast cancer diagnosed worldwide annually, and it is the second leading cause of cancer death in the European Union. The optimum management of patients with breast cancer requires accurate prognostic and predictive factors. At present, only a small number of such factors are used clinically. DNA microarrays have the potential to measure the expression of tens of thousands of genes simultaneously. Recent preliminary findings suggest that DNA microarray-based gene expression profiling can provide powerful and independent prognostic information in patients with newly diagnosed breast cancer. As well as providing prognostic information, emerging results suggest that DNA microarrays can also be used for predicting response or resistance to treatment, especially to neoadjuvant chemotherapy. Prior to clinical application, these preliminary findings must be validated using large-scale prospective studies. This article reviews these advances and also examines the role of DNA microarrays in reducing the number of patients who receive inappropriate chemotherapy. The most recent data supporting the integration of various publicly available data sets is also reviewed in detail.

Influence of Royal Jelly on Mouse Hepatic Gene Expression and Safety Assessment with a DNA Microarray

We used a DNA microarray to compare the gene expression profiles in liver among three groups of mice fed a diet containing 5% royal jelly (RJ), a diet containing 5% RJ stored at 40 degrees C for 7 d (40-7d RJ) or a control diet which provides the same total energy as RJ. Expression of 267 genes was increased or decreased by 1.8-fold or more in animals given the RJ diet for 14 d as compared with control diet, though serum total cholesterol, triglyceride, phospholipid, glucose, insulin and leptin levels were unaffected. Many genes involved in cell growth, signal transduction, energy metabolism and transcription regulation were responsive to the RJ diet. Among the 267 genes whose expression was altered by RJ, 60% showed no change or a reduced change in response to 40-7d RJ diet. The 40-7d RJ diet contained little 57-kDa protein, identified as a possible freshness marker of RJ. Furthermore, the RJ diet did not influence the gene expression of cytochrome P450 enzymes and detoxifying enzymes, whereas the 40-7d RJ diet increased the gene expression of glutathione S-transferase and glutathione peroxidase. Indeed, the RJ diet decreased the gene expression of cytochrome P450 4A14 (CYP4A14), which catalyzes peroxidation of endogenous lipids that is associated with nonalcoholic steatohepatitis and alcoholic liver disease, while the 40-7d RJ diet was not effective to decrease the gene expression of CYP4A14. The results indicate that the efficacy of RJ decreased and the toxicity of RJ increased during storage at high temperature. We suggest that application of DNA microarray technology to the biochemical evaluation of food safety may be effective for rapid and precise quality control.

DNA Chip Technology in Brain Banks: Confronting a Degrading World

DNA microarray technology is based on the principle of hybridization between 2 complementary strands of nucleic acids, one being fixed into a solid membrane, the other being the sample to analyze. This has resulted in a very powerful method to examine differential gene expression between samples, and has been widely used in the study of tumors. The application of DNA microarray technology to the study of the nervous system has to consider several properties of the nervous tissue: composition of various neuronal types, as well as astrocytes, oligodendrocytes, and microglia; regional and area differences; developmental and age-dependent variations; and functional and pathological status. Moreover, human samples are usually obtained postmortem following variable agonal periods and postmortem delays between death and tissue preservation, which are accompanied by variable RNA degradation. Yet human postmortem nervous tissue stored in brain banks offers a unique opportunity to facilitate material for the study of diseases of the nervous system and to gain direct understanding on the mechanisms of disease. This review analyzes the application of DNA microarray technology to current practice using brain-banked tissues in order to recognize and minimize sub-optimal processing of brain samples and to correct pitfalls due to inadequate procedures. Also discussed are RNA preservation and RNA degradation effects on expression pattern assessments, analysis of individual versus pooled samples, array normalization, types of DNA chip platforms, whole genomic analysis versus specialized chips, and microgenomics. Minimizing RNA degradation and improving detection of resistant RNA in postmortem brain has been considered in detail in order to improve the efficiency and reliability of DNA microarray technology employed in the study of human postmortem nervous tissue.

Applications and challenges of DNA microarray technology in military medical research.

This review discusses the challenges and applications of DNA microarray technology as it is being used in each of the four major research areas of the U.S. Army Medical Research and Materiel Command: military infectious diseases, combat casualty care, military operational medicine, and medical chemical and biological defense. The overall objective of this review is two-fold. First, the objective is to increase awareness in senior military leadership of the challenges and opportunities presented by DNA microarray technology and the emerging and rapidly changing field of bioinformatics. Second, the aim is to publicize to the civilian research community the additional challenges associated with the use of microarray technology in military medical research. This discussion contains material that would be useful for making programmatic recommendations that team strategic research investments and emerging technologies with U.S. Army Medical Research and Materiel Command resources.

Application of DNA microarray technology in immunological research and its inspiration to researches on traditional Chinese medicine

DNA microarray technology is a high throughout method that can analyze the expression of thousands of genes at the same time to form a complete cellular gene expression profile. It has been applied in immunological researches such as the development, maturation, activation and differentiation of immune cells, the regulation of immune responses, the molecular mechanism of allergy, the relation between phenotype and gene expression, and immunological pharmacology, etc. It has deepened our perception of the immune system. It will as well be helpful in the research of the regulative mechanism of traditional Chinese medicine (TCM) toward immune cells and immune responses, the therapeutic mechanisms of TCM toward allergy, the standardization of differentiation of syndrome and herbal pharmacology, etc. The data analysis of the results of DNA microarray experiments is aimed to compare the difference of gene expression levels of different samples and obtain diagnostic gene expression profiles. But there are controversies about the number of samples and choices of statistical methods. Researchers are striving in setting standards of DNA microarray experiments.

Microarray gene analysis of the liver in a rat model of chronic, voluntary alcohol intake

The mechanisms underlying alcoholic liver disease are not fully understood. It has been established that alcohol interferes with transcriptional and translational regulatory steps of cell function. To understand such an effect, assessment of alcohol-induced changes in the simultaneous expression of a large number of genes may prove very useful. The purpose of the current study was to test a large number of genes (∼8,700) for possible changes in expression induced by alcohol alone or in addition to treatment with lipopolysaccharide (LPS), a putative mediator of alcohol effects on the liver. Male rats were fed an alcohol-containing liquid diet (Lieber–DeCarli) for 14–15 weeks, injected with Escherichia coli LPS (0.8 mg·kg −1), and killed 24 h later. Blood samples were taken for determination of plasma liver enzyme activity, and liver samples were obtained for histologic evaluation and total RNA extraction. Total RNA was analyzed for gene expression (Rat Toxicology U34 Array; Affymetrix, Santa Clara, CA). Of 8,740 genes on the microchip, 2,259 were expressed in the liver. Seven hundred ninety-eight genes underwent significant changes induced by either alcohol or LPS, but listed in this article are only those that significantly increased or decreased expression twofold or more. The genes were assigned to functional groups and reviewed. Gene changes were discussed from two viewpoints: relevance to established hypotheses of alcohol and LPS mechanisms of action and revealing of novel mechanisms of alcohol-induced liver injury. Application of DNA microarray technology to the study of alcohol-induced liver injury generated novel theoretical and experimental approaches to alcohol-induced liver injury.

Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays.

DNA microarray technology has become an important research tool for biotechnology and microbiology. It is now possible to characterize genetic diversity and gene expression in a genomewide manner. DNA microarrays have been applied extensively to study the biology of many bacteria including Escherichia coli, but only recently have they been developed for the Gram-positive Corynebacterium glutamicum. Both bacteria are widely used for biotechnological amino acid production. In this article, in addition to the design and generation of microarrays as well as their use in hybridization experiments and subsequent data analysis, we describe recent applications of DNA microarray technology regarding amino acid production in C. glutamicum and E. coli. We also discuss the impact of functional genomics studies on fundamental as well as applied aspects of amino acid production with C. glutamicum and E. coli.

DNA microarrays for detecting endocrine-disrupting compounds

It has recently been discovered that a number of synthetic chemicals and naturally occurring compounds released into the environment can influence endocrine activity. These endocrine-disrupting compounds (EDCs) are highly varied in structure, provenance, and mode of action (MOA). Many EDCs are anthropogenic, products of the chemical industry. Others are natural compounds. Although natural hormones exist at low levels in the environment, industrial sites such as pulp and paper mills and municipal sewage treatment plants can gather large amounts of natural EDCs and release them into the environment as part of their daily operations, thus increasing background environmental concentrations. The potential consequences of endocrine disruption are serious; however, comparatively little is known about the phenomenon. There is considerable debate over the true concentrations, sources, identity, and effects of potential EDCs. Investigation of the problem is hampered by the diversity of potential EDCs, which may have synergistic as well as individual effects, and the complexity of the endocrine system itself. Effective and standardized tests to accurately detect the presence of such chemicals in the environment are not available. While many tests have been proposed, they are unsatisfactory because they have only one limited endpoint (e.g., they can detect only one of many potential hormonal responses) and do not provide any mechanistic information. In addition, results from rapid screening tests are difficult to correlate with whole organism response, while larger whole organism bioassays are very costly and time consuming to perform. There is tremendous potential in the application of DNA microarray technology to screen for EDCs. DNA microarrays provide a “snapshot” of transcriptional activity in tissue samples showing which genes were actively expressed within the cells at one point in time. By combining this technology with human cell lines grown in vitro, it should be possible to conduct relatively rapid and straightforward assays to identify EDCs by observing the changes in gene expression patterns in response to exposure.

Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays

DNA microarray technology has become an important research tool for microbiology and biotechnology as it allows for comprehensive DNA and RNA analyses to characterize genetic diversity and gene expression in a genome-wide manner. DNA microarrays have been applied extensively to study the biology of many bacteria including Mycobacterium tuberculosis, but only recently have they been used for the related high-GC Gram-positive Corynebacterium glutamicum, which is widely used for biotechnological amino acid production. Besides the design and generation of microarrays as well as their use in hybridization experiments and subsequent data analysis, recent applications of DNA microarray technology in C. glutamicum including the characterization of ribose-specific gene expression and the valine stress response will be described. Emerging perspectives of functional genomics to enlarge our insight into fundamental biology of C. glutamicum and their impact on applied biotechnology will be discussed.

Effect of thyroid hormone on gene expression

Thyroid hormones are key regulators of development and metabolism that modulate transcription via nuclear receptors. Although the molecular actions of thyroid hormones have been thoroughly studied, their pleiotropic effects are mediated by complex changes in expression of numerous, but still largely unknown, target genes. This review summarizes the recent advances in the characterization of target genes in different organs. New patterns of gene expression regulation have been described in tissues with known physiological actions of thyroid hormone, that is brain, liver, skeletal and cardiac muscles, and brown and white adipose tissues. The studies have benefited from the numerous transgenic models with altered thyroid hormone receptor expression and the application of DNA microarray technology to mouse and human tissues. Data on thyroid hormone-mediated control of gene expression and on the roles of the different thyroid hormone receptor isoforms bring new clues to our understanding of the molecular mechanisms of thyroid hormone action in physiological situations and, most importantly, in diseases associated with alterations of the thyroid status.