Home About us Contact
|
Home About us Contact | ||
|
|
||
Microarray Technique (microarray + technique)
Selected AbstractsBiomarkers for exposure to estrogenic compounds: Gene expression analysis in zebrafish (Danio rerio)ENVIRONMENTAL TOXICOLOGY, Issue 1 2008Ulf Kausch Abstract Gene expression analyses in male zebrafish (Danio rerio) were carried out using microarray technique and quantitative polymerase chain reaction. Genes responding to the exposure to 17,-estradiol, bisphenol A and genistein were identified, among them genes involved in metabolism, reproductional and developmental processes. Threshold levels of 17,-estradiol (200 ng/L), bisphenol A (2000 ,g/L), and genistein (5000 ,g/L) for the upregulation of the vtg1 gene in short-time exposures (11 days) were determined by qPCR. 14k microarrays were used to generate complete lists of genes regulated by these estrogenic compounds. For this purpose, liver samples from 10 exposed zebrafish and 10 controls were processed. In this case the expressions of 211 genes were significantly regulated by 17,-estradiol, 47 by bisphenol A and 231 by genistein. Furthermore, it is shown that fish exposed to 17,-estradiol and genistein have similarities in their gene expression patterns, whereas bisphenol A apparently affected gene expression in a different way. Only genes coding for egg-yolk precursor protein vitellogenin were found to be regulated by all three compounds, which shows that these genes are the only suitable markers for exposure to different estrogenic compounds. The regulated genes were assigned to gene ontology classes. All three estrogenic compounds regulated genes mainly involved in primary and cellular metabolism, but genistein regulated several genes involved in cell cycle-regulation and bisphenol A several genes involved in protein biosynthesis. Genistein also upregulated the expression of four eggshell proteins, which can be used as biomarkers for exposure to this chemical. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2008. [source] Direct detection of Kitasatospora species with a chaperone oligonucleotide microarray method lacking PCR amplificationJOURNAL OF BASIC MICROBIOLOGY, Issue 4 2008Sebastian Guenther Abstract Identification of members of the genus Kitasatospora from soil samples has been introduced to evaluate occurrence of potential natural compound producers in different habitats. The microarray hybridization usually involves PCR amplification of the target DNA. Since PCR might lead to biased amplification, a diagnostic Kitasatospora microarray technique was improved by a protocol lacking PCR amplification prior to hybridization. The described advanced hybridization method used chaperone oligonucleotides for direct co-hybridization with genomic DNA on an oligonuclotide microarray with optical readout. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] IgE to peanut allergen components: relation to peanut symptoms and pollen sensitization in 8-year-oldsALLERGY, Issue 9 2010A. Asarnoj To cite this article: Asarnoj A, Movérare R, Östblom E, Poorafshar M, Lilja G, Hedlin G, van Hage M, Ahlstedt S, Wickman M. IgE to peanut allergen components: relation to peanut symptoms and pollen sensitization in 8-year-olds. Allergy 2010; 65: 1189,1195. Abstract Background:, Allergen-specific IgE testing is often performed with crude peanut extract, but the results may be difficult to interpret because of cross-reactions between peanut and other plant allergens. The aim was to investigate IgE reactivity to peanut allergen components in children from a birch-rich region in relation to pollen sensitization and peanut symptoms. Methods:, From a birth cohort, clinical parameters were obtained through questionnaires and IgE antibody levels to peanut and birch pollen were measured. Different peanut/birch sensitization phenotypes were defined among 200 selected children. IgE reactivity to peanut and pollen allergen components was analysed using microarray technique. Results:, Peanut symptoms were reported in 87% of the children with IgE reactivity to any of the peanut allergens Ara h 1, 2 or 3 but not to Ara h 8 (n = 46) vs 17% of children with IgE reactivity to Ara h 8 but not to Ara h 1, 2 or 3 (n = 23), P < 0.001. Furthermore, symptoms were more severe in children with Ara h 1, 2 or 3 reactivity. Children with IgE reactivity both to Ara h 2 and to Ara h 1 or 3 more often reported peanut symptoms than children with IgE only to Ara h 2 (97%vs 70%, P = 0.016), particularly respiratory symptoms (50%vs 9%, P = 0.002). Conclusions:, IgE analysis to peanut allergen components may be used to distinguish between peanut-sensitized individuals at risk of severe symptoms and those likely to have milder or no symptoms to peanut if sensitized to pollen allergens and their peanut homologue allergens. [source] Amplification of Hot DNA segments in Escherichia coliMOLECULAR MICROBIOLOGY, Issue 6 2002Ken-ichi Kodama Summary In Escherichia coli, a replication fork blocking event at a DNA replication terminus (Ter) enhances homologous recombination at the nearby sister chromosomal region, converting the region into a recombination hotspot, Hot, site. Using a RNaseH negative (rnhA,) mutant, we identified eight kinds of Hot DNAs (HotA,H). Among these, enhanced recombination of three kinds of Hot DNAs (HotA,C) was dependent on fork blocking events at Ter sites. In the present study, we examined whether HotA DNAs are amplified when circular DNA (HotA plus a drug-resistance DNA) is inserted into the homologous region on the chromosome of a rnhA, mutant. The resulting HotA DNA transformants were analysed using pulsed-field gel electrophoresis, fluorescence in situ hybridization and DNA microarray technique. The following results were obtained: (i) HotA DNA is amplified by about 40-fold on average; (ii) whereas 90% of the cells contain about 6,10 copies of HotA DNA, the remaining 10% of cells have as many as several hundred HotA copies; and (iii) amplification is detected in all other Hot DNAs, among which HotB and HotG DNAs are amplified to the same level as HotA. Furthermore, HotL DNA, which is activated by blocking the clockwise oriC -starting replication fork at the artificially inserted TerL site in the fork-blocked strain with a rnhA+ background, is also amplified, but is not amplified in the non-blocked strain. From these data, we propose a model that can explain production of three distinct forms of Hot DNA molecules by the following three recombination pathways: (i) unequal intersister recombination; (ii) intrasister recombination, followed by rolling-circle replication; and (iii) intrasister recombination, producing circular DNA molecules. [source] Immunohistopathological re-evaluation of adenocarcinoma of the lung with mixed subtypes using a tissue microarray technique and hierarchical clustering analysisPATHOLOGY INTERNATIONAL, Issue 12 2007Gehan Gamal To re-evaluate adenocarcinoma, mixed subtypes (ADMIX) of the lung, a total of 201 cases were classified into three main subgroups according to the most differentiated histological growth pattern; namely bronchioloalveolar carcinoma (BAC)-mixed, which was the most predominant (73.1%), papillary (PAP)-mixed (21.9%), and acinar-mixed (5%). The PAP-mixed was significantly male predominant and had more progressed clinicopathological features. A significant cytological difference was observed among the three subgroups. A tissue microarray was constructed and immunohistochemistry was undertaken using 15 biomarkers. Hierarchical clustering analysis was separately applied to the immunohistochemical results of ADMIX and ADMIX subgroups, and it was found that most acinar-mixed cases were placed in a separate cluster, while the BAC-mixed and PAP-mixed failed to form significant independent clusters. The antibody clustering profile for the acinar-mixed was clearly different from that for the BAC-mixed or PAP-mixed, but the PAP-mixed shared a dendrogram profile with the other two subgroups. Statistically, approximately half of the 15 biomarkers were significant for differentiating between ADMIX subgroups and between different histological growth patterns. In conclusion, ADMIX can be classified into three histopathological subgroups according to the most differentiated growth pattern, of which a PAP growth pattern might indicate more aggressive behavior than that of a BAC growth pattern. [source] Recent Progress in Biomolecular EngineeringBIOTECHNOLOGY PROGRESS, Issue 1 2000Dewey D. Y. Ryu During the next decade or so, there will be significant and impressive advances in biomolecular engineering, especially in our understanding of the biological roles of various biomolecules inside the cell. The advances in high throughput screening technology for discovery of target molecules and the accumulation of functional genomics and proteomics data at accelerating rates will enable us to design and discover novel biomolecules and proteins on a rational basis in diverse areas of pharmaceutical, agricultural, industrial, and environmental applications. As an applied molecular evolution technology, DNA shuffling will play a key role in biomolecular engineering. In contrast to the point mutation techniques, DNA shuffling exchanges large functional domains of sequences to search for the best candidate molecule, thus mimicking and accelerating the process of sexual recombination in the evolution of life. The phage-display system of combinatorial peptide libraries will be extensively exploited to design and create many novel proteins, as a result of the relative ease of screening and identifying desirable proteins. Even though this system has so far been employed mainly in screening the combinatorial antibody libraries, its application will be extended further into the science of protein-receptor or protein-ligand interactions. The bioinformatics for genome and proteome analyses will contribute substantially toward ever more accelerated advances in the pharmaceutical industry. Biomolecular engineering will no doubt become one of the most important scientific disciplines, because it will enable systematic and comprehensive analyses of gene expression patterns in both normal and diseased cells, as well as the discovery of many new high-value molecules. When the functional genomics database, EST and SAGE techniques, microarray technique, and proteome analysis by 2-dimensional gel electrophoresis or capillary electrophoresis in combination with mass spectrometer are all put to good use, biomolecular engineering research will yield new drug discoveries, improved therapies, and significantly improved or new bioprocess technology. With the advances in biomolecular engineering, the rate of finding new high-value peptides or proteins, including antibodies, vaccines, enzymes, and therapeutic peptides, will continue to accelerate. The targets for the rational design of biomolecules will be broad, diverse, and complex, but many application goals can be achieved through the expansion of knowledge based on biomolecules and their roles and functions in cells and tissues. Some engineered biomolecules, including humanized Mab's, have already entered the clinical trials for therapeutic uses. Early results of the trials and their efficacy are positive and encouraging. Among them, Herceptin, a humanized Mab for breast cancer treatment, became the first drug designed by a biomolecular engineering approach and was approved by the FDA. Soon, new therapeutic drugs and high-value biomolecules will be designed and produced by biomolecular engineering for the treatment or prevention of not-so-easily cured diseases such as cancers, genetic diseases, age-related diseases, and other metabolic diseases. Many more industrial enzymes, which will be engineered to confer desirable properties for the process improvement and manufacturing of high-value biomolecular products at a lower production cost, are also anticipated. New metabolites, including novel antibiotics that are active against resistant strains, will also be produced soon by recombinant organisms having de novo engineered biosynthetic pathway enzyme systems. The biomolecular engineering era is here, and many of benefits will be derived from this field of scientific research for years to come if we are willing to put it to good use. [source] | |||||||||||||