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Rapid Methods in Cosmetic Microbiology
Published in Philip A. Geis, Cosmetic Microbiology, 2020
Microarrays are collections of miniaturized test sites, arranged on solid substrates that permit many tests to be performed at the same time. They are composed of an orderly arrangement of protein or thousands of DNA or RNA fragments on glass, silicon or nylon substrates. This technology evolved from Southern Blot technology, in which fragmented DNA is attached to a substrate and then probed with a known gene or DNA fragment, using fluorescent tags to allow visual detection. Microarrays are usually fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography, inkjet printing or electrochemistry. Other methods may also be used, such as in situ synthesis, whereby the probes are synthesized directly on the chip instead of spotting them on the array. Applications for microarrays include nucleic acid sequence identification and measuring expression levels of genes. For example, the entire human genome (~50,000 known genes and gene variants) has been fit on a single chip and microarrays are currently being used to detect influenza A, Avian H5N1 (Bird Flu) and other clinically relevant viral strains.
Encephalitozoon
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
Alexandra Valencakova, Lenka Luptakova, Monika Halanova, Olga Danisova
The report about the implementation of methods of DNA chips (DNA “microarray”) for the parallel detection of several species of microsporidia (E. cuniculi, E. hellem, and E. intestinalis) in clinical samples75 is very interesting. The great advantage of a DNA “microarray” compared to the PCR method is the ability to diagnose a high number of unknown samples. Unlike PCR, DNA is not obtained through laborious processing of spores by preextraction steps, but by using FTA filters, which not only eliminates these labor-intensive procedures, but also helps avoid the significant loss of DNA and effectively removes inhibitors from fecal samples. Compared to the commercial DNA extraction kits, this method results in lower financial costs, requires less technical training, requires less equipment, and can process a larger number of samples simultaneously.76 The disadvantage of DNA “microarray” is not only expensive laboratory instrumentation, but also the synthesis of large amounts of primers. But once the preparation of the DNA microarray is completed, the actual execution of tests is considerably cheaper. The method of the DNA microarray, as described by Wang et al. (2005),75 represents a combination of the PCR method, which is followed by hybridization of the amplicons using more specific probes immobilized on a microchip. The fluorescence intensity correlates with the abundance of DNA in a sample.
Molecular biology
Published in Maxine Lintern, Laboratory Skills for Science and Medicine, 2018
The type of array used depends on the questions that you are trying to address and often, perhaps more importantly, the budget you have available to you. Microarrays are not cheap! In general there are two types: the spotted array and the photolithographically synthesised oligonucleotide arrays. Spotted arrays are generated by, not surprisingly, a spotter which uses glass needles to deliver a very small quantity of a particular DNA sequence, e.g. cDNA, oligonucleotides or plasmids. Most institutions using microarrays will have a ‘spotting machine’ allowing customised arrays to be generated to order. The advantage of the spotted array is that it is relatively cheap; however it can suffer from a potential reduction in spotting quality, such as inaccuracy in spot position and uniformity.
Gene expression for biodosimetry and effect prediction purposes: promises, pitfalls and future directions – key session ConRad 2021
Published in International Journal of Radiation Biology, 2022
Patrick Ostheim, Sally A. Amundson, Christophe Badie, Dimitry Bazyka, Angela C. Evans, Shanaz A. Ghandhi, Maria Gomolka, Milagrosa López Riego, Peter K. Rogan, Robert Terbrueggen, Gayle E. Woloschak, Frederic Zenhausern, Hanns L. Kaatsch, Simone Schüle, Reinhard Ullmann, Matthias Port, Michael Abend
Considering the causal pathway where biological processes in response to an exposure occur, the blood-based GE biomarkers can be used for upstream reconstruction of the exposure (Amundson et al. 2000, 2001). Examinations of the association of GE with dose represent the topic of the majority of molecular radiobiological publications. Herein, quantitative real-time PCR (qRT-PCR) is still the gold-standard methodology for providing robust and sensitive results. The technological developments in this field, especially microarray and RNA sequencing techniques have allowed an agnostic approach. This has resulted in the identification of complex responses comprising hundreds of genes for robustly discriminations, e.g. exposed from unexposed groups or different exposure levels (Abend et al. 2021; Amundson 2021).
Gut microbiota regulate tumor metastasis via circRNA/miRNA networks
Published in Gut Microbes, 2020
Zhuxian Zhu, Jianguo Huang, Xu Li, Jun Xing, Qiang Chen, Ruilin Liu, Feng Hua, Zhongmin Qiu, Yuanlin Song, Chunxue Bai, Yin-Yuan Mo, Ziqiang Zhang
In this study, we have used both microarray and next-generation sequencing (NGS) for gene profiling. While microarray technology was developed early days, NGS is a relatively new technology. Based on a comparative study,45 there is a high correlation between gene expression profiles generated by these two platforms. The advantages of microarray technology are high throughput, relatively quick, and sensitive at low cost. However, limitations for microarrays include a need for predesigned probes on the chip and thus it can only detect known genes. Other limitations associated with microarrays are cross-hybridization, nonspecific hybridization, and limited detection range of individual probes. On the other hand, NGS does not need predesigned probes, which would be able to identify new genes. In particular, NGS is better in detecting low abundance transcripts, differentiating biologically critical isoforms, and allowing the identification of genetic variants. Finally, NGS is capable of detecting a broader dynamic range than microarrays. Because of these features, NGS has become a predominant platform. That is why we adopted NGS for the experiments at the later stage of our study.
The development and clinical applications of proteomics: an Indian perspective
Published in Expert Review of Proteomics, 2020
Khushman Taunk, Bhargab Kalita, Vaikhari Kale, Venkatesh Chanukuppa, Tufan Naiya, Surekha M. Zingde, Srikanth Rapole
Clinical proteomics research has yielded several candidate biomarkers in diverse diseases. Nevertheless, the success of the transfer of this information from lab to clinics for the designing of potent drugs and/or management of these diseases is negligible. In this context, protein arrays are perfectly placed for the high-throughput screening of drug libraries to identify potential candidates that can specifically target these biomarkers. In India, the use of protein microarrays was started by Dr. Sanjeeva Srivastava in the proteomics lab at IIT-B, Mumbai where his team used protein microarrays for profiling autoantibodies in medulloblastoma and glioblastoma and biomarker identification in infectious diseases [22]. Tissue microarray, a variant of protein microarray that contains patient-specific tissue sections was used for profiling various cancers by a research group led by Dr. Sanjay Navani from Lab Surgpath, Mumbai. This technique was extended to validate biomarkers such as prosaposin, transgelin, and protein disulfide isomerase A 4 in gallbladder cancer and esophageal squamous cell carcinoma [71,72]. Therefore, microarrays hold tremendous potential for screening drugs and biomarker validation, the two important aspects of clinical research.