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Microarrays, Volume 1, Issue 1 (June 2012), Pages 1-63

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Editorial

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Open AccessEditorial The Journal Microarrays
Microarrays 2012, 1(1), 1-2; doi:10.3390/microarrays1010001
Received: 6 October 2011 / Accepted: 13 October 2011 / Published: 14 October 2011
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Abstract
Our publishing company MDPI AG has its headquarters in Basel, Switzerland where there are thousands of scientists working in the laboratories of pharmaceutical companies and institutes including Novartis [1], F. Hoffmann-La Roche [2] and institutes affiliated with University of Basel [3]. In 1996,
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Our publishing company MDPI AG has its headquarters in Basel, Switzerland where there are thousands of scientists working in the laboratories of pharmaceutical companies and institutes including Novartis [1], F. Hoffmann-La Roche [2] and institutes affiliated with University of Basel [3]. In 1996, the first annual microplate conference MipTec was held in Basel, and the MipTec 2011 was held a few days ago in Basel [4]. I published a paper on microplate standardization presented at MipTec 1996 in MDPI’s longest-running journal Molecules [5-7]. [....] Full article
Open AccessEditorial Microarrays—Current and Future Applications in Biomedical Research
Microarrays 2012, 1(1), 42-43; doi:10.3390/microarrays1010042
Received: 16 November 2011 / Accepted: 22 November 2011 / Published: 22 November 2011
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Abstract
Microarrays covers research where microarrays are applied to address complex biological questions. This new open access journal publishes articles where novel applications or state-of-the art technology developments in the field are reported. In addition, novel methods or data analysis algorithms are under the
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Microarrays covers research where microarrays are applied to address complex biological questions. This new open access journal publishes articles where novel applications or state-of-the art technology developments in the field are reported. In addition, novel methods or data analysis algorithms are under the scope of Microarrays. This journal will serve as a platform for fast and efficient sharing of data within this large user community. As one of the first microarray users in Europe back in 1996, I am proud to serve as Editor-in-Chief and I believe we have assembled a highly proficient Editorial Board, responsible for a fair and fast peer-review of articles. [...] Full article

Research

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Open AccessArticle A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity
Microarrays 2012, 1(1), 25-41; doi:10.3390/microarrays1010025
Received: 1 September 2011 / Revised: 14 October 2011 / Accepted: 17 October 2011 / Published: 31 October 2011
Cited by 7 | PDF Full-text (252 KB) | HTML Full-text | XML Full-text
Abstract
A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation)
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A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. Deviating from the concept of GeoChip-type microarrays, the presented EcoChip microarray phylogenetic information was obtained using a dedicated set of barcoding microarray probes, whereas functional gene expression was analyzed by conserved domain-specific probes. By unlinking these two target groups, the shortage of broad sequence information of functional enzyme-coding genes in environmental communities became less important. The novel EcoChip microarray could be successfully applied to identify specific degradation activities in environmental samples at considerably high phylogenetic resolution. Reproducible and unbiased microarray signals could be obtained with chemically labeled total RNA preparations, thus avoiding the use of enzymatic labeling steps. ITS precursor rRNA was detected for the first time in a microarray experiment, which confirms the applicability of the EcoChip concept to selectively quantify the transcriptionally active part of fungal communities at high phylogenetic resolution. In addition, the chosen microarray platform facilitates the conducting of experiments with high sample throughput in almost any molecular biology laboratory. Full article
Open AccessArticle In Silico Analysis of Microarray-Based Gene Expression Profiles Predicts Tumor Cell Response to Withanolides
Microarrays 2012, 1(1), 44-63; doi:10.3390/microarrays1010044
Received: 19 April 2012 / Revised: 9 May 2012 / Accepted: 15 May 2012 / Published: 22 May 2012
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Abstract
Withania somnifera (L.) Dunal (Indian ginseng, winter cherry, Solanaceae) is widely used in traditional medicine. Roots are either chewed or used to prepare beverages (aqueous decocts). The major secondary metabolites of Withania somnifera are the withanolides, which are C-28-steroidal lactone triterpenoids. Withania somnifera
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Withania somnifera (L.) Dunal (Indian ginseng, winter cherry, Solanaceae) is widely used in traditional medicine. Roots are either chewed or used to prepare beverages (aqueous decocts). The major secondary metabolites of Withania somnifera are the withanolides, which are C-28-steroidal lactone triterpenoids. Withania somnifera extracts exert chemopreventive and anticancer activities in vitro and in vivo. The aims of the present in silico study were, firstly, to investigate whether tumor cells develop cross-resistance between standard anticancer drugs and withanolides and, secondly, to elucidate the molecular determinants of sensitivity and resistance of tumor cells towards withanolides. Using IC50 concentrations of eight different withanolides (withaferin A, withaferin A diacetate, 3-azerininylwithaferin A, withafastuosin D diacetate, 4-B-hydroxy-withanolide E, isowithanololide E, withafastuosin E, and withaperuvin) and 19 established anticancer drugs, we analyzed the cross-resistance profile of 60 tumor cell lines. The cell lines revealed cross-resistance between the eight withanolides. Consistent cross-resistance between withanolides and nitrosoureas (carmustin, lomustin, and semimustin) was also observed. Then, we performed transcriptomic microarray-based COMPARE and hierarchical cluster analyses of mRNA expression to identify mRNA expression profiles predicting sensitivity or resistance towards withanolides. Genes from diverse functional groups were significantly associated with response of tumor cells to withaferin A diacetate, e.g. genes functioning in DNA damage and repair, stress response, cell growth regulation, extracellular matrix components, cell adhesion and cell migration, constituents of the ribosome, cytoskeletal organization and regulation, signal transduction, transcription factors, and others. Full article

Review

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Open AccessReview Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens
Microarrays 2012, 1(1), 3-24; doi:10.3390/microarrays1010003
Received: 17 August 2011 / Revised: 5 October 2011 / Accepted: 7 October 2011 / Published: 14 October 2011
Cited by 1 | PDF Full-text (433 KB) | HTML Full-text | XML Full-text
Abstract
Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity;
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Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples. Full article

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