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At least 271 records · Page 15Linked to original sources

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.

Animals↗

Hepatocyte transplantation and gene therapy.

Trials of liver-directed gene therapy are a clinical reality. Technology is rapidly developing for the isolation of large numbers of human hepatocytes. Recombinant DNA techniques are available to engineer recombinant retroviruses which express genes of clinical relevance. Familial hypercholesterolemia serves as the clinical paradigm for liver-directed gene therapy, and the clinical protocol is underway. Early results are promising. Techniques for hepatocyte delivery, optimization of gene transfer, and safety considerations are important considerations in designing a human trial. Other diseases which are likely to be among the first treated with this new approach are ornithine transcarbamylase deficiency, hemophilia B, and Crigler-Najjar syndrome.

Amino Acid Metabolism, Inborn Errors↗

Applications of ultrafast HPLC to process development of recombinant DNA-derived proteins.

The application of ultrafast HPLC to the development of recovery processes for proteins produced by recombinant DNA technology has been explored using wide-pore HPLC resins and instrumentation designed for rapid analysis. High-resolution analysis of complex samples was achieved with a total analysis time of less than 5 min from injection to injection. Fractions collected during preparative chromatography were analyzed by SDS gel electrophoresis and fast HPLC. Specific proteins in the fractions were detected and quantitated by fast HPLC providing real-time analysis for pooling. The technique was also applied to the formidable task of detecting and quantitating protein variants during the development of recovery processes. Several examples of post-translational variant detection are shown. Ultrafast HPLC is a new analytical tool that can be applied to the development of robust manufacturing processes producing therapeutic proteins essentially free of known impurities and variants.

Biotechnology↗

DNA hybridization to mismatched templates: a chip study.

High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the GeneChip system, the reconstruction of the sample mRNA concentrations depends upon the differential signal generated by hybridizing the RNA to two nearly identical templates: a perfect match probe (PM) containing the exact biological sequence; and a single mismatch (MM) differing from the PM by a single base substitution. It has been observed that a large fraction of MMs repetitively bind targets better than the PMs, against the obvious expectation of sequence specificity. We examine this problem via statistical analysis of a large set of microarray experiments. We classify the probes according to their signal to noise (S/N) ratio, defined as the eccentricity of a (PM,MM) pair's "trajectory" across many experiments. Of those probes having large S/N (>3) only a fraction behave consistently with the commonly assumed hybridization model. Our results imply that the physics of DNA hybridization in microarrays is more complex than expected, and suggest estimators for the target RNA concentration.

Animals↗

Biotechnology and medicine of the future.

The practice of biology and medicine has been revolutionized during the past ten years by the advent of three biotechnologies--recombinant DNA techniques, the monoclonal antibody technology, and the development of microchemical instrumentation, machines that permit the rapid and effective synthesis and sequence analysis of proteins and genes. In this article, these powerful biotechnologies will be discussed, with particular emphasis on microchemical instrumentation, a major focus of my efforts for the past 15 years. I will also discuss two fundamental problems in modern medicine that are being explored in my laboratory using these techniques--genetic engineering of the nervous system and the mapping and sequencing of the human genome.

Animals↗

Microarray technology--the future analyses tool in exercise physiology?

Microarray analysis offers a set of analytical platforms that provide rapid, affordable and substantial information at the DNA, RNA or protein level. It enables the analysis of thousands of genes simultaneously in a parallel manner across samples derived from various biological sources and treatment regimens. This development became possible as a result of the combination of three technological advances achieved at the beginning of the 1990's, namely parallelism, miniaturization and automation. In regular physical checkups the microarray technology could be used to supplement the current spectrum of tests and therefore enhance the quality of the data obtained. Arrays for analyses of RNA expression will allow gene expression profiling also in exercise physiology. DNA chips may also be used for genetic screening and diagnostics to analyze polymorphisms and mutations which may underlie genetic diseases or interindividual variations between subjects. Using microarrays in exercise physiology will provide new insights into the complex molecular mechanisms of the exercise-induced stress response, adaptation to training and modulation of immune function. Gene expression profiling and genetic screening will probably help to characterize and predict the individually variable response to and efficiency of training.

Exercise↗

Biochip sensors for the rapid and sensitive detection of viral disease.

Recent advances in DNA and protein microarray methodology and the emerging technology of cell-based sensors have massively increased the speed and sensitivity with which we can detect viral infections. The advantages of the multi-parameter microarray technologies could be combined with the speed and sensitivity of cell-based systems to give 'cell-omic' sensors.

Biosensing Techniques↗

Epigenomics: mapping the methylome.

DNA methylation is integral to normal development and disease processes. However, the genomic distribution of methylated sequences--the methylome--is poorly understood. We have recently developed a platform technology for rapid assessment of methylation status throughout the human genome in a high-resolution, high-throughput manner. This is achieved by coupling a methylated DNA immunoprecipitation (MeDIP) method for isolating methyl cytosine rich fragments with array-based comparative genomic hybridization (array CGH). Using a combination of whole genome tiling path BAC arrays and CpG island microarrays, DNA methylation profiles are obtained simultaneously at both genome-wide and locus-specific levels. A comparison between male and female DNA using MeDIP-array CGH revealed unexpected hypomethylation of the inactive x-chromosome in gene-poor regions. Furthermore, comparisons between cancer and noncancer cell types yielded differential methylation patterns that link genetic and epigenetic instability offering a new approach to decipher misregulation in cancer. Finally, we provide new data showing epigenomic instability in lung cancer cells with concurrent regions of genetic and epigenetic alterations harboring known oncogenes.

Chromatin Immunoprecipitation↗

Integration of genomic technologies for accelerated cancer drug development.

New technologies have greatly increased the scientist's ability to investigate complex molecular interactions that occur in cancer development and to identify genetic alterations and drug targets. However, these new capabilities have not accelerated drug development efforts; rather, they may be contributing to increased research and development costs because the large number of new drug targets discovered through genomics need to be investigated in great detail to characterize their putative functional involvement in the disease process. One solution to this bottleneck in functional analysis is the use of high-throughput technologies to produce efficient processes that can rapidly handle the large flood of information at every stage of disease. This review examines the use of new and emerging DNA, tissue, and live-cell transfection microarray technologies that can be used to discover, validate, and translate information resulting from the completion of the Human Genome Project.

Biotechnology↗

Antibody arrays: an embryonic but rapidly growing technology.

Protein arrays are now an attractive proposition as they can measure a diverse range of protein interactions not possible with traditional DNA arrays. Antibody arrays are a specific subset of this technology. Originally conceived as multi-analyte detectors, antibody arrays are now used in a wide variety of applications. For instance, the potential of this technology to diagnose human diseases, such as leukemia, breast cancer and, potentially, heart failure, has stimulated much interest. Furthermore, identification of new protein targets in particular disease states will prove to be an invaluable tool in drug discovery and development. Patient prognosis and treatment are also potential applications of the technology. Antibody arrays have proved to be dynamic in response to these broad range of possibilities. This review examines variations in antibody array design and discusses current and potential applications of this novel and interesting technology.

Animals↗

Development of DNA-based microsatellite marker technology for studies of genetic diversity in stressor impacted populations.

In recent years microsatellite marker applications in various disciplines increased rapidly. Microsatellites are characterized as independent and highly variable markers most noted for their usefulness and popularity among researchers. Microsatellites can be constructed in-house from a partial genomic library, ordered from a vendor, or "borrowed" from a species that is closely related to the target species. Microsatellite application in natural populations can reveal present as well as historical impacts of stressors to particular population.

Animals↗

Prenatal diagnosis by chorionic villus sampling.

Chorionic villus sampling (CVS) retains its great advantage over mid-trimester amniocentesis by producing early results. Moreover, rapid analytical techniques reduce significantly the waiting time between sampling and diagnosis, while recombinant DNA technology and human gene mapping progress amplify enormously the spectrum of the indications. The recent inclusion in the prenatal diagnosis package of screening tests based on DNA analysis for the major genetic diseases (i.e. cystic fibrosis, fragile-X mental retardation syndrome) may efficiently contribute to prevent the genetic disease. The role of CVS in twin pregnancy has been investigated and compared to amniocentesis. Although these techniques are equally safe, CVS should be considered the approach of choice for a number of technical advantage and in relation to selective fetal reduction in discordant twins. Recent reports have substantially contributed on the hypothetical relationship between limb reduction defects (LRDs) and chorion biopsy. The analysis of LRDs among more than 130,000 CVS reported to WHO CVS-Registry has been unable to find out any relationship between sampling and fetal malformations, including LRDs. In conclusion, first trimester CVS should be considered the gold standard procedure for prenatal diagnosis of genetic diseases.

Amniocentesis↗

Characterization and applications of CataCleave probe in real-time detection assays.

Cycling probe technology (CPT), which utilizes a chimeric DNA-RNA-DNA probe and RNase H, is a rapid, isothermal probe amplification system for the detection of target DNA. Upon hybridization of the probe to its target DNA, RNase H cleaves the RNA portion of the DNA/RNA hybrid. Utilizing CPT, we designed a catalytically cleavable fluorescence probe (CataCleave probe) containing two internal fluorophores. Fluorescence intensity of the probe itself was weak due to Förster resonance energy transfer. Cleavage of the probe by RNase H in the presence of its target DNA caused enhancement of donor fluorescence, but this was not observed with nonspecific target DNA. Further, RNase H reactions with CataCleave probe exhibit a catalytic dose-dependent response to target DNA. This confirms the capability for the direct detection of specific target DNA through a signal amplification process. Moreover, CataCleave probe is also ideal for detecting DNA amplification processes, such as polymerase chain reaction (PCR) and isothermal rolling circle amplification (RCA). In fact, we observed signal enhancement proportional to the amount of RCA product formed. We were also able to monitor real-time PCR by measuring enhancement of donor fluorescence. Hence, CataCleave probe is useful for real-time monitoring of both isothermal and temperature-cycling nucleic acid amplification methods.

Bacillus anthracis↗

A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors.

The DNA-binding specificities of transcription factors can be used to computationally predict cis-regulatory modules (CRMs) that regulate gene expression. However, the absence of specificity data for the majority of transcription factors limits the widespread implementation of this approach. We have developed a bacterial one-hybrid system that provides a simple and rapid method to determine the DNA-binding specificity of a transcription factor. Using this technology, we successfully determined the DNA-binding specificity of seven previously characterized transcription factors and one novel transcription factor, the Drosophila melanogaster factor Odd-skipped. Regulatory targets of Odd-skipped were successfully predicted using this information, demonstrating that the data produced by the bacterial one-hybrid system are relevant to in vivo function.

Animals↗

Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins.

We describe a new method for the assay of sequence-specific DNA-binding proteins in this paper. In this method, the sensitive fluorescence resonance energy transfer (FRET) technology is combined with the common DNA footprinting assay in order to develop a simple, rapid and high-throughput approach for quantitatively detecting the sequence-specific DNA-binding proteins. We named this method as exonuclease III (ExoIII) protection assay with FRET probe. The FRET probe used in this assay was a duplex DNA which was designed to contain one FRET pair in the center and two flanking protein-binding sites. During protein detection, if a target protein exists, it will bind to the two protein-binding sites of the FRET probe and thus protect the FRET pair from ExoIII digestion, resulting in high FRET. However, if the target protein does not exist, the FRET pair on the naked FRET probe will be degraded by ExoIII, resulting in low FRET. Three kinds of recombinant transcription factors including NF-kappaB, SP1 and p50, and the target protein of NF-kappaB in HeLa cell nuclear extracts, were successfully detected by the assay. This assay can be extensively used in biomedical research targeted at DNA-binding proteins.

Cell Nucleus↗

Microarray-based identification of thermophilic Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis.

DNA microarrays are an excellent potential tool for clinical microbiology, since this technology allows relatively rapid identification and characterization of microbial and viral pathogens. In the present study, an oligonucleotide microarray was developed and used for the analysis of thermophilic Campylobacter spp., the primary food-borne pathogen in the United States. We analyzed four Campylobacter species: Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis. Our assay relies on the PCR amplification of specific regions in five target genes (fur, glyA, cdtABC, ceuB-C, and fliY) as a first step, followed by microarray-based analysis of amplified DNAs. Alleles of two genes, fur and glyA, which are found in all tested thermophilic Campylobacter spp., were used for identification and discrimination among four bacterial species, the ceuB-C gene was used for discrimination between C. jejuni and C. coli, and the fliY and cdt genes were used as additional genetic markers specific either for C. upsaliensis and C. lari or for C. jejuni. The array was developed and validated by using 51 previously characterized Campylobacter isolates. All isolates were unambiguously identified on the basis of hybridization patterns with 72 individual species-specific oligoprobes. Microarray identification of C. jejuni and C. coli was confirmed by PCR amplification of other genes used for identification (hipO and ask). Our results demonstrate that oligonucleotide microarrays are suitable for rapid and accurate simultaneous differentiation among C. jejuni, C. coli, C. lari, and C. upsaliensis.

Base Sequence↗

Innovative techniques for harmful algal toxin analysis.

The global increase in frequency and intensity of harmful algal blooms (HABs) has led to more frequent incidence of seafood-borne illnesses and adverse impacts on natural resources. In response, public health agencies worldwide have mobilized to initiate HAB monitoring programs. To meet this demand, innovative analytical techniques are being developed that provide rapid and reliable detection of the causative organisms and the toxins produced. Modifications to conventional chromatography and mass spectrometry have greatly improved sensitivity and selectivity of these methods toward naturally occurring phycotoxins. Bioassay techniques using live organisms are giving way to molecular and cellular methods that measure the toxicologically significant activity of the toxin molecules. Molecular probes are being applied to distinguish species-specific RNA and DNA sequences for rapid identification of HAB-causing organisms. The direction of this new technology is to develop rapid and reliable screening methods for phycotoxins and the causative organisms to provide protection for public health, aquaculture, and natural resources. New methods also are being developed for detecting minute amounts of toxin molecules in microenvironments, leading to understanding the toxicokinetics and toxicological functions of the toxins.

Animals↗

Gene expression profiles in the brain from phencyclidine-treated mouse by using DNA microarray.

Recently DNA microarray technology has been introduced into analyses of comprehensive biological functions. This DNA microarray is a new technology for simultaneous analysis to examine expression patterns of thousands of genes. It was thought that this technique should be very useful for examination of cellular and molecular mechanisms of drugs of abuse: cocaine, amphetamine, and others. This technology was therefore applied for the rapid analysis of gene expression in the brain from phencyclidine-treated mice. Mainly mouse DNA microarray was examined by using labeled cDNAs produced from a control mouse brain mRNA and from brain mRNA of mouse exposed to drugs as probes. Some changes in a probe from brain mRNA of drug-treated mouse could be observed, but it was necessary to examine another DNA microarray, including more samples from the brain.

Animals↗