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Nature Methods Oct 2004MicroRNAs are short, noncoding RNA transcripts that post-transcriptionally regulate gene expression. Several hundred microRNA genes have been identified in...
MicroRNAs are short, noncoding RNA transcripts that post-transcriptionally regulate gene expression. Several hundred microRNA genes have been identified in Caenorhabditis elegans, Drosophila, plants and mammals. MicroRNAs have been linked to developmental processes in C. elegans, plants and humans and to cell growth and apoptosis in Drosophila. A major impediment in the study of microRNA function is the lack of quantitative expression profiling methods. To close this technological gap, we have designed dual-channel microarrays that monitor expression levels of 124 mammalian microRNAs. Using these tools, we observed distinct patterns of expression among adult mouse tissues and embryonic stem cells. Expression profiles of staged embryos demonstrate temporal regulation of a large class of microRNAs, including members of the let-7 family. This microarray technology enables comprehensive investigation of microRNA expression, and furthers our understanding of this class of recently discovered noncoding RNAs.
Topics: Animals; Cell Line; Equipment Design; Equipment Failure Analysis; Gene Expression Profiling; Mice; MicroRNAs; Microarray Analysis; Stem Cells
PubMed: 15782152
DOI: 10.1038/nmeth704 -
International Journal of Cardiology Jul 2016
Topics: Atherosclerosis; Biomedical Research; Cardiology; Coronary Artery Disease; Game Theory; Humans; Microarray Analysis
PubMed: 27111179
DOI: 10.1016/j.ijcard.2016.04.056 -
Biosensors & Bioelectronics Apr 2015Peptide nucleic acid (PNA) is a mimic of DNA that shows a high chemical stability and can survive the enzymatic degradation of nucleases and proteases. The superior... (Review)
Review
Peptide nucleic acid (PNA) is a mimic of DNA that shows a high chemical stability and can survive the enzymatic degradation of nucleases and proteases. The superior binding properties of PNA enable the formation of PNA/DNA or PNA/RNA duplex with excellent thermal stability and unique ionic strength effect. The introduction of microarray makes it possible to achieve accurate, high throughput parallel analysis of DNA or RNA with a highly integrated and low reagents consuming device. This powerful tool expands the applications of PNA in genotyping based on single nucleotide polymorphism (SNP) detection, the monitoring of disease-related miRNA expression and pathogen detection. This review paper discusses the fabrications of PNA microarrays through in situ synthesis strategy or spotting method by automatic devices, the various detection methods for the microarray-based hybridization and the current applications of PNA microarrays.
Topics: Bacteria; Biosensing Techniques; Fluorescent Dyes; Gene Expression; Genotype; Humans; Mass Spectrometry; Microarray Analysis; Molecular Mimicry; Nucleic Acid Hybridization; Peptide Nucleic Acids; Polymorphism, Single Nucleotide; Viruses
PubMed: 25499661
DOI: 10.1016/j.bios.2014.12.010 -
Annual Review of Analytical Chemistry... Jun 2017Advances in scientific instrumentation have allowed experimentalists to evaluate well-known systems in new ways and to gain insight into previously unexplored or poorly... (Review)
Review
Advances in scientific instrumentation have allowed experimentalists to evaluate well-known systems in new ways and to gain insight into previously unexplored or poorly understood phenomena. Within the growing field of multianalyte physiometry (MAP), microphysiometers are being developed that are capable of electrochemically measuring changes in the concentration of various metabolites in real time. By simultaneously quantifying multiple analytes, these devices have begun to unravel the complex pathways that govern biological responses to ischemia and oxidative stress while contributing to basic scientific discoveries in bioenergetics and neurology. Patients and clinicians have also benefited from the highly translational nature of MAP, and the continued expansion of the repertoire of analytes that can be measured with multianalyte microphysiometers will undoubtedly play a role in the automation and personalization of medicine. This is perhaps most evident with the recent advent of fully integrated noninvasive sensor arrays that can continuously monitor changes in analytes linked to specific disease states and deliver a therapeutic agent as required without the need for patient action.
Topics: Biomarkers; Biosensing Techniques; Electrochemical Techniques; Electrophoresis; Humans; Microarray Analysis; Pharmaceutical Preparations; Point-of-Care Systems
PubMed: 28605606
DOI: 10.1146/annurev-anchem-061516-045334 -
Current Opinion in Biotechnology Feb 2008
Topics: Biotechnology; Microarray Analysis
PubMed: 18207732
DOI: 10.1016/j.copbio.2007.12.001 -
BMC Bioinformatics Oct 2004The imputation of missing values is necessary for the efficient use of DNA microarray data, because many clustering algorithms and some statistical analysis require a...
BACKGROUND
The imputation of missing values is necessary for the efficient use of DNA microarray data, because many clustering algorithms and some statistical analysis require a complete data set. A few imputation methods for DNA microarray data have been introduced, but the efficiency of the methods was low and the validity of imputed values in these methods had not been fully checked.
RESULTS
We developed a new cluster-based imputation method called sequential K-nearest neighbor (SKNN) method. This imputes the missing values sequentially from the gene having least missing values, and uses the imputed values for the later imputation. Although it uses the imputed values, the efficiency of this new method is greatly improved in its accuracy and computational complexity over the conventional KNN-based method and other methods based on maximum likelihood estimation. The performance of SKNN was in particular higher than other imputation methods for the data with high missing rates and large number of experiments. Application of Expectation Maximization (EM) to the SKNN method improved the accuracy, but increased computational time proportional to the number of iterations. The Multiple Imputation (MI) method, which is well known but not applied previously to microarray data, showed a similarly high accuracy as the SKNN method, with slightly higher dependency on the types of data sets.
CONCLUSIONS
Sequential reuse of imputed data in KNN-based imputation greatly increases the efficiency of imputation. The SKNN method should be practically useful to save the data of some microarray experiments which have high amounts of missing entries. The SKNN method generates reliable imputed values which can be used for further cluster-based analysis of microarray data.
Topics: Efficiency, Organizational; Microarray Analysis
PubMed: 15504240
DOI: 10.1186/1471-2105-5-160 -
Nanomedicine : Nanotechnology, Biology,... Mar 2005The early genesis of the concept of nanomedicine sprang from the visionary idea that tiny nanorobots and related machines could be designed, manufactured, and introduced... (Review)
Review
The early genesis of the concept of nanomedicine sprang from the visionary idea that tiny nanorobots and related machines could be designed, manufactured, and introduced into the human body to perform cellular repairs at the molecular level. Nanomedicine today has branched out in hundreds of different directions, each of them embodying the key insight that the ability to structure materials and devices at the molecular scale can bring enormous immediate benefits in the research and practice of medicine.
Topics: Biosensing Techniques; Microarray Analysis; Nanomedicine; Nanostructures; Robotics; Technology Assessment, Biomedical
PubMed: 17292052
DOI: 10.1016/j.nano.2004.11.003 -
BMC Bioinformatics Jul 2010Calibration of a microarray scanner is critical for accurate interpretation of microarray results. Shi et al. (BMC Bioinformatics, 2005, 6, Art. No. S11 Suppl. 2.)...
BACKGROUND
Calibration of a microarray scanner is critical for accurate interpretation of microarray results. Shi et al. (BMC Bioinformatics, 2005, 6, Art. No. S11 Suppl. 2.) reported usage of a Full Moon BioSystems slide for calibration. Inspired by the Shi et al. work, we have calibrated microarray scanners in our previous research. We were puzzled however, that most of the signal intensities from a biological sample fell below the sensitivity threshold level determined by the calibration slide. This conundrum led us to re-investigate the quality of calibration provided by the Full Moon BioSystems slide as well as the accuracy of the analysis performed by Shi et al.
METHODS
Signal intensities were recorded on three different microarray scanners at various photomultiplier gain levels using the same calibration slide from Full Moon BioSystems. Data analysis was conducted on raw signal intensities without normalization or transformation of any kind. Weighted least-squares method was used to fit the data.
RESULTS
We found that initial analysis performed by Shi et al. did not take into account autofluorescence of the Full Moon BioSystems slide, which led to a grossly distorted microarray scanner response. Our analysis revealed that a power-law function, which is explicitly accounting for the slide autofluorescence, perfectly described a relationship between signal intensities and fluorophore quantities.
CONCLUSIONS
Microarray scanners respond in a much less distorted fashion than was reported by Shi et al. Full Moon BioSystems calibration slides are inadequate for performing calibration. We recommend against using these slides.
Topics: Calibration; Fluorescence; Microarray Analysis; Sensitivity and Specificity
PubMed: 20594322
DOI: 10.1186/1471-2105-11-361 -
Analytical and Bioanalytical Chemistry Jun 2013Bacterial contamination of indoor air is a serious threat to human health. Pathogenic germs can be transferred from the liquid to the aerosol phase, for instance, when...
Bacterial contamination of indoor air is a serious threat to human health. Pathogenic germs can be transferred from the liquid to the aerosol phase, for instance, when water is sprayed in the air, such as in shower rooms, air conditioners, or fountains. Existing analytical methods for biological indoor air-quality assessment and contamination monitoring are mostly time consuming as they generally require a cultivation step. The need for a rapid, sensitive, and selective detection method for bioaerosols is evident. Our approach is based on the combination of a commercial wet particle sampler (Coriolis μ, Bertin Technologies, France) and a label-free microarray readout based on surface-enhanced Raman scattering (SERS) for detection, which was established in our laboratories. Heat-inactivated Escherichia coli bacteria were used as test microorganisms. An E. coli suspension was sprayed into the chamber by a jet air nebulizer. The resulting bioaerosol was dried, neutralized, and then collected by a Coriolis μ sampler. The bacteria collected were detected by a recently developed microarray readout system, based on label-free SERS detection. A special data evaluation procedure was applied in order to fully exploit the selectivity of the detection scheme, resulting in a detection limit of 144 particles per cubic centimeter.
Topics: Aerosols; Air Microbiology; Air Pollution, Indoor; Escherichia coli; Microarray Analysis; Microbial Viability; Spectrum Analysis, Raman
PubMed: 23657450
DOI: 10.1007/s00216-013-6984-0 -
Molecular Nutrition & Food Research Oct 2005Microarrays have become standard tools for gene expression profiling as the mRNA levels of a large number of genes can be measured in a single assay. Many technical... (Review)
Review
Microarrays have become standard tools for gene expression profiling as the mRNA levels of a large number of genes can be measured in a single assay. Many technical aspects concerning microarray production and laboratory usage have been addressed in great detail, but it remains still crucial to establish this technology in new research fields such as human nutrition and food-related areas. The correlation between diet and inter-individual variation in gene expression is an important and relatively unexplored issue in human nutrition. Therefore, nutritionists changed their research field dramatically from epidemiology and physiology towards the "omics" sciences. Nutrigenomics as a field of research is based on the complete knowledge of the human genome and refers to the entire spectrum of human genes that determine the interactions of nutrition with the organism. Nutrigenetics is based on the inter-individual, genetically determined differences in metabolism. Nutrigenomics and nutrigenetics carry the hope that individualized diet can improve human health and prevent nutrition-related diseases. In this article we give an overview of current DNA and protein microarray techniques (including fabrication, experimental procedure and data analysis), we describe their applications to nutrition and food research and point out the limitations, problems and pitfalls of microarray experiments.
Topics: Confidentiality; Food Microbiology; Food Technology; Humans; Microarray Analysis; Nucleic Acid Hybridization; Nutrition Disorders; Nutritional Physiological Phenomena; Oligonucleotide Array Sequence Analysis; Protein Array Analysis
PubMed: 16189797
DOI: 10.1002/mnfr.200500033