High-density microarrays for gene expression analysis

Digital DNA microarray generation on glass substrates

In this work we show how DNA microarrays can be produced batch wise on standard microscope slides in a fast, easy, reliable and cost-efficient way. Contrary to classical microarray generation, the microarrays are generated via digital solid phase PCR. We have developed a cavity-chip system made of a PDMS/aluminum composite which allows such a solid phase PCR in a scalable and easy to handle manner. For the proof of concept, a DNA pool composed of two different DNA species was used to show that digital PCR is possible in our chips. In addition, we demonstrate that DNA microarray generation can be realized with different laboratory equipment (slide cycler, manually in water baths and with an automated cartridge system). We generated multiple microarrays and analyzed over 13,000 different monoclonal DNA spots to show that there is no significant difference between the used equipment. To show the scalability of our system we also varied the size and number of the cavities located in the array region up to more than 30,000 cavities with a volume of less than 60 pL per cavity. With this method, we present a revolutionary tool for novel DNA microarrays. Together with new established label-free measurement systems, our technology has the potential to give DNA microarray applications a new boost.

Physiological and transcriptome analysis of heteromorphic leaves and hydrophilic roots in response to soil drying in desert Populus euphratica

Populus euphratica Olivier, which has been considered as a tree model for the study of higher plant response to abiotic stresses, survive in the desert ecosystem characterized by extreme drought stress. To survive in the harsh environmental condition the plant species have developed some plasticity such as the development of heteromorphic leaves and well-developed roots system. We investigated the physiological and molecular mechanisms enabling this species to cope with severe stress caused by drought. The heterophylly, evolved from linear to toothed-ovate shape, showed the significant difference in cuticle thickness, stomata densities, and sizes. Physiological parameters, SOD, POD, PPO, CAT activity, free proline, soluble protein and MDA contents fluctuated in response to soil drying. Gene expression profile of roots monitored at control and 4 moisture gradients regimes showed the up-regulation of 124, 130, 126 and 162 and down-regulation of 138, 251, 314, 168 DEGs, respectively. Xyloglucan endotransglucosylase/ hydrolase gene (XET) up-regulated at different moisture gradients, was cloned and expressed in tobacco. The XET promoter sequence harbors the drought signaling responsive cis-elements. The promoter expression activity varies in different organs. Over-expression and knocked down transgenic tobacco plant analysis confirmed the role of XET gene in roots growth and drought resistance.

Flow cytometry and sorting in Arabidopsis

Flow cytometry, and the accompanying technology of cell sorting, represents an established and valuable experimental platform for the analysis of cellular populations. Applications involving higher plants, which started to emerge around 30 years ago, are now widely employed both to provide unique information regarding fundamental questions in basic and applied bioscience and to advance agricultural productivity in practical ways. Further developments of this platform are being actively pursued, promising additional advances in our understanding of the interactions of cells within the complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types and second that their individual cells are generally larger than those of mammals. This chapter focuses on the use of flow cytometry and cell sorting with the model species Arabidopsis thaliana, in particular addressing (1) fluorescence in vivo labeling of specific cell types, (2) fluorescence-activated sorting of protoplasts and nuclei, and (3) transcriptome analyses using sorted protoplasts and nuclei.

Changes in mitochondrial DNA alter expression of nuclear encoded genes associated with tumorigenesis

We previously reported the presence of a mtDNA mutation hotspot in UV-induced premalignant and malignant skin tumors in hairless mice. We have modeled this change (9821insA) in murine cybrid cells and demonstrated that this alteration in mtDNA associated with mtBALB haplotype can alter the biochemical characteristics of cybrids and subsequently can contribute to significant changes in their behavioral capabilities. This study shows that changes in mtDNA can produce differences in expression levels of specific nuclear-encoded genes, which are capable of triggering the phenotypes such as seen in malignant cells. From a potential list of differentially expressed genes discovered by microarray analysis, we selected MMP-9 and Col1a1 for further studies. Real-time PCR confirmed up-regulation of MMP-9 and down-regulation of Col1a1 in cybrids harboring the mtDNA associated with the skin tumors. These cybrids also showed significantly increased migration and invasion abilities compared to wild type. The non-specific MMP inhibitor, GM6001, was able to inhibit migratory and invasive abilities of the 9821insA cybrids confirming a critical role of MMPs in cellular motility. Nuclear factor-κB (NF-κB) is a key transcription factor for production of MMPs. An inhibitor of NF-κB activation, Bay 11-7082, was able to inhibit the expression of MMP-9 and ultimately decrease migration and invasion of mutant cybrids containing 9821insA. These studies confirm a role of NF-κB in the regulation of MMP-9 expression and through this regulation modulates the migratory and invasive capabilities of cybrids with mutant mtDNA. Enhanced migration and invasion abilities caused by up-regulated MMP-9 may contribute to the tumorigenic phenotypic characteristics of mutant cybrids.

CASCADING SVMS AS A TOOL FOR MEDICAL DIAGNOSIS USING MULTI-CLASS GENE EXPRESSION DATA

In this paper we propose a novel Support Vector Machines-based architecture for medical diagnosis using multi-class gene expression data. It consists of a pre-processing unit and N-1 sequentially ordered blocks capable of classifying N classes in a cascading manner. Each block embodies both a gene selection and a classification module. It offers the flexibility of constructing block-specific gene expression spaces and hypersurfaces for the discrimination of the different classes. The proposed architecture was applied for medical diagnostic tasks including prostate and lung cancer diagnosis. Its performance was evaluated by using a leave-one-out cross validation approach which avoids the bias introduced by the gene selection process. The results show that it provides high accuracy which in most cases exceeds the accuracy achieved by the popular one-vs-one and one-vs-all SVM combination schemes and Nearest-Neighbor classifiers. The cascading SVMs can be successfully applied as a medical diagnostic tool.

Global analysis of cell type-specific gene expression

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

Multiparametric analysis, sorting, and transcriptional profiling of plant protoplasts and nuclei according to cell type

Flow cytometry has been employed for the analysis of higher plants for approximately the last 30 years. For the angiosperms, ∼500,000 species, itself a daunting number, parametric measurements enabled through the use of flow cytometers started with basic descriptors of the individual cells and their contents, and have both inspired the development of novel cytometric methods that subsequently have been applied to organisms within other kingdoms of life, and adopted cytometric methods devised for other species, particularly mammals. Higher plants offer unique challenges in terms of flow cytometric analysis, notably the facts that their organs and tissues are complex three-dimensional assemblies of different cell types, and that their individual cells are, in general, larger than those of mammals.This chapter provides an overview of the general types of parametric measurement that have been applied to plants, and provides detailed methods for selected examples based on the plant model Arabidopsis thaliana. These illustrate the use of flow cytometry for the analysis of protoplasts and nuclear DNA contents (genome size and the cell cycle). These are further integrated with measurements focusing on specific cell types, based on transgenic expression of Fluorescent Proteins (FPs), and on analysis of the spectrum of transcripts found within protoplasts and nuclei. These measurements were chosen in particular to illustrate, respectively, the issues encountered in the flow analysis and sorting of large biological cells, typified by protoplasts; how to handle flow analyses under conditions that require processing of large numbers of samples in which the individual samples contain only a very small minority of objects of interest; and how to deal with exceptionally small amounts of RNA within the sorted samples.

A microarray analysis of early activated pathways in concanavalin A-induced hepatitis

OBJECTIVE

To explore the mechanisms of fulminant hepatitis (FH) in the early stages, and to determine the critical pathways in its initiation and progression.

METHODS

Twelve BALB/c mice were divided into four groups: one group left as negative control and sacrificed immediately after injection of phosphate-buffered saline (PBS), and another three groups with concanavalin A (Con A) administration sacrificed at 1, 3, and 6 h after injection. Affymetrix GeneChip(R) Mouse 430 2.0 Array was employed to evaluate the expression profile of each of the 12 samples. Further analysis was done on the microarray data to extract the genes that were differentially expressed. Enrichment analysis was carried out to determine relevant pathways within which regulated genes were significantly enriched.

RESULTS

A total of 393, 8354 and 11 344 differentially expressed genes were found, respectively, at three time points. During 0-1 h and 1-3 h, most of the pathways enriched with regulated genes were related to immune response and inflammation, among which Toll-like receptor (TLR) signaling and mitogen-activated protein kinase (MAPK) signaling appeared during both phases, while cytokine-cytokine receptor interaction, apoptosis, T cell receptor signaling, and natural killer (NK) cell-mediated cytotoxicity pathways emerged during the second phase. Pathways found to be significant during 3-6 h were mostly related to metabolic processes.

CONCLUSION

The TLR signaling pathway dominates the early responses of Con A-induced FH in mice. It stimulates the production of type I cytokines, therefore recruiting and activating T/NK cells. Activated T/NK cells exert their cytotoxicity on hepatocytes through inducing death receptor-intermediated apoptosis, resulting in liver injury.

Enhanced Single-Molecule Detection using Porous Silver Membrane

We evaluated a commercial porous silver membrane as a support substrate for direct localization and visualization of single molecule events. We characterized the fluorescence behaviors of fluorescently labeled DNA oligonucleotides on the silver membranes. The fluorescence from the fluorescent probes that were immobilized on the porous silver is greatly enhanced. Additionally, correlated to reflectance contour image, it appears that enhanced fluorescence came from location close to the "valley" of the pore channels (or in the voids). These results are of great interest to increase the effectiveness of fluorescence-based single molecule DNA analysis.

Transcriptomic responses to aluminum stress in roots of Arabidopsis thaliana

To help characterize the cellular mechanisms underlying the toxicity of Al to plants, we present the first large-scale, transcriptomic analysis of root responses to Al, using a microarray representing approximately 93% of the predicted genes in the genome of Arabidopsis. More transcripts were responsive to Al (25 microM) during long (48 h, 1,114 genes), as compared to short (6 h, 401 genes) exposures, which contrasts with previous microarray analyses of plant responses to other types of abiotic stress. Exposure to Al triggered changes in the transcript levels for several genes related to oxidative stress pathway, membrane transporters, cell wall, energy, and polysaccharide metabolism. Interestingly, lack of abundance of transcripts encoding TCA cycle enzymes, except for malate dehydrogenase, suggested that synthesis of organic anions in response to Al may not be transcriptionally regulated. Al exposures induced differential abundance of transcripts for several ribosomal proteins, peptidases and protein phosphatases mostly after 48 h. We also detected increased abundance of transcripts for several membrane receptor kinases and non-membrane calcium response kinases, which could play a role in transmission of Al-stress signals. Among Al responsive transcription factors, the most predominant families identified were AP2/EREBP, MYB and bHLH. Further, we studied the kinetics of Al stress responses for class III peroxidases using Q-RT-PCR. Our results indicated that Al triggered dynamic changes in transcript abundance of various peroxidases within 1 h. The results of this screen contribute to the identification of candidate genes for the generation of Al-tolerant transgenic plants.

High-throughput, high-sensitivity analysis of gene expression in Arabidopsis

High-throughput gene expression analysis of genes expressed during salt stress was performed using a novel multiplexed quantitative nuclease protection assay that involves customized DNA microarrays printed within the individual wells of 96-well plates. The levels of expression of the transcripts from 16 different genes were quantified within crude homogenates prepared from Arabidopsis (Arabidopsis thaliana) plants also grown in a 96-well plate format. Examples are provided of the high degree of reproducibility of quantitative dose-response data and of the sensitivity of detection of changes in gene expression within limiting amounts of tissue. The lack of requirement for RNA purification renders the assay particularly suited for high-throughput gene expression analysis and for the discovery of novel chemical compounds that specifically modulate the expression of endogenous target genes.

Enhanced fluorescence of Cy5-labeled oligonucleotides near silver island films: a distance effect study using single molecule spectroscopy

We investigated fluorescence enhancements and lifetime reductions of Cy5 probe molecules at various distances from the deposited silver island film surface using single molecule spectroscopic methods. The proximity of fluorophore molecules to the surface was controlled by alternating layers of biotinylated bovine serum albumin (BSA-biotin) and avidin, followed by binding of Cy5-labeled oligonucleotides to the top of a BSA-biotin layer structure. We observed dramatically varied brightness of fluorophores with distances from metal structures as well with reduced blinking in the presence of silver island films. In addition, distributions of fluorescence lifetimes and apparent emission intensities from individual molecules indicate an inhomogeneous nature of local matrix surface near metallic nanostructures. These studies illustrate the exclusive information that is otherwise hidden in ensemble measurements.

Screening and expression analysis of Phytophthora infestans induced genes in potato leaves with horizontal resistance

Horizontal resistance to late blight with quantitative and durable characteristics is a major objective for potato breeding programs. With the aim of investigating the molecular aspects of horizontal resistance, a cDNA microarray was used to identify Phytophthora infestans-induced genes from 100 expressed sequence tags (ESTs) selected from a subtractive cDNA library. Of the 100 cDNA clones represented on the array, 76 were differentially expressed in infected plants as compared with mock-inoculated control plants. Four groups of genes could be identified according to their expression patterns at three time points, 24, 48 and 72 h postinoculation (hpi). Group A appeared to be strongly induced (>10-fold) at 72 hpi. Group B demonstrated up-regulated expression patterns at all the three time points. The transcripts of group C peaked at 48 hpi, while genes of group D were up-regulated at 24 hpi and decreased slightly thereafter. Blast algorithm searches revealed that the largest set of up-regulated genes (about 35%) was assigned to the primary/secondary metabolism. Other genes with known or putative functions included disease defense or cell rescue (about 18%), transcription, signal transduction, cellular transporter/transport facilitation, development, protein synthesis/destination, as well as those playing roles in cellular organization. Furthermore, 15 genes encoding unknown function proteins were also identified. The results indicated that multiple defense mechanisms are involved in horizontal potato resistance to late blight and alteration in metabolic pathways is one of the most important defense responses.

Enhanced fluorescence of Cy5-labeled DNA tethered to silver island films: fluorescence images and time-resolved studies using single-molecule spectroscopy

Methods that increase the total emission per fluorophore would provide increased sensitivity and a wider dynamic range for chemical analysis, medical diagnostics, and in vivo molecular imaging. The use of fluorophore-metal interactions has the potential to dramatically increase the detectability of single fluorophores for bioanalytical monitoring. The fabrication and single-molecule analysis of fluorophore-labeled DNA molecules tethered to silver island films are described in this article. The single-molecule spectroscopic method reveals some insightful information on the behaviors of single molecules, rather than an ensemble of molecules. Analysis of fluorescence images, intensity profiles, total emitted photons, and lifetime distributions reveals some of sample heterogeneities. Investigations of time-dependent emission characteristics of single molecules indicate that the total number of emitted photons on the silvered surface is more than 10 times greater than on free labeled DNA molecules on a glass substrate. In addition, time-correlated single-photon counting results reveal the reduced lifetimes of single molecules tethered to silver island films.

Gene-expression changes induced by Feline immunodeficiency virus infection differ in epithelial cells and lymphocytes

Infection of cats with Feline immunodeficiency virus (FIV) is an important model for understanding comparative lentivirus biology. In vivo, FIV infects lymphocytes and monocyte/macrophages, but in vitro infection is commonly investigated in epithelial Crandell-Reese Feline Kidney (CRFK) cells. In this study, the transcriptional responses of CRFK cells and primary lymphocytes to infection with FIV 34TF, a cloned subtype A virus, and FIV USgaB01, a biological subtype B isolate, were determined. Reverse-transcribed mRNA from both cell types was hybridized to microarrays containing 1700 human expressed sequence tags in duplicate and data were analysed with Significance Analysis of Microarrays (sam) software. Results from six experiments assessing homeostatic cross-species hybridization excluded 3.48 % inconsistently detected transcripts. Analysis of data from five time points over 48 h after infection identified 132 and 24 differentially expressed genes in epithelial cells and lymphocytes, respectively. Genes involved in protein synthesis, the cell cycle, structure and metabolism were affected. The magnitude of gene-expression changes ranged from 0.62 to 1.62 and early gene induction was followed by downregulation after 4 h. Transcriptional changes in CRFK cells were distinct from those in lymphocytes, except for heat-shock cognate protein 71, which was induced at multiple time points in both cell types. These findings indicate that FIV infection induces transcriptional changes of a modest magnitude in a wide range of genes, which is probably reflective of the relatively non-cytopathic nature of virus infection.

Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression

Immunoaffinity purification of polyribosomes (polysomes) from crude leaf extracts of Arabidopsis (Arabidopsis thaliana) was achieved with transgenic genotypes that overexpress a translational fusion of a ribosomal protein (RP) with a His(6)-FLAG dual epitope tag. In plants with a cauliflower mosaic virus 35S:HF-RPL18 transgene immunopurification with anti-FLAG agarose beads yielded 60-Svedberg ribosomal subunits, intact 80-Svedberg monosomes and polysomes. Sucrose density gradient fractionation of the purified complexes demonstrated that the distribution of polysome size was similar in crude cell extracts and the purified complexes. The immunopurified complexes included putative cytosolic RPs of Arabidopsis and ribosome-associated proteins, as well as full-length transcripts of high and low abundance. Whole-genome profiling using long DNA oligonucleotide-based microarrays provided a high level of reproducibility between polysomal mRNA samples immunopurified from two independent biological replicates (r approximately 0.90). Comparison of immunopurified and total cellular RNA samples revealed that for most of the genes, the mRNAs were associated with the epitope-tagged polysomal complexes, with an average relative level of association of 62.06% +/- 4.39%. The results demonstrate that the immunopurification of polysomes can be a valuable tool for the quantification of mRNAs present in translation complexes in plant cells. This technology can be extended to evaluation of mRNA populations at the cell- or tissue-specific level by regulation of the tagged RP with distinct promoters.

Two-photon induced fluorescence of Cy5-DNA in buffer solution and on silver island films

We report the observation of a strong two-photon induced fluorescence emission of Cy5-DNA within the tunable range of a Ti:Sapphire laser. The estimated two-photon cross-section for Cy5-DNA of 400GM is about 3.5-fold higher than it was reported for rhodamine B. The fundamental anisotropies of Cy5-DNA are close to the theoretical limits of 2/5 and 4/7 for one- and two-photon excitation, respectively. We also observed an enhanced two-photon induced fluorescence (TPIF) of Cy5-DNA deposited on silver island films (SIFs). In the presence of SIFs, the TPIF is about 100-fold brighter. The brightness increase of Cy5-DNA TPIF near SIFs is mostly due to enhanced local field.

Application of microarray technology in pulmonary diseases

Microarrays are a powerful tool that have multiple applications both in clinical and cell biology arenas of common lung diseases. To exemplify how this tool can be useful, in this review, we will provide an overview of the application of microarray technology in research relevant to common lung diseases and present some of the future perspectives.

Fluorescence spectral properties of labeled thiolated oligonucleotides bound to silver particles

We examined the fluorescent spectral properties of fluorescein-labeled DNA oligomers when directly bound to metallic silver particles via a terminal sulfhydryl group. We found a 12-fold increase in fluorescence intensity and 25-fold decrease in lifetime for a fluorescein residue positioned 23 nucleotides from the silver surface compared to labeled oligomers in free solution. Similar results were found for a 23-mer labeled with five fluorescein residues. The absence of long lifetime components in the intensity decays suggests that all labeled oligomers are bound to silver and affected similarly by the metallic surfaces. These results provide the basic knowledge needed to begin use of metal-enhanced fluorescence for the detection of target sequences in simple formats potentially without a washing separation step. The use of metal-enhanced fluorescence provides a generic approach to obtaining a hybridization-dependent increase in fluorescence with most, if not all, commonly used fluorophores.

Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles

Salt cress (Thellungiella halophila) is a small winter annual crucifer with a short life cycle. It has a small genome (about 2 x Arabidopsis) with high sequence identity (average 92%) with Arabidopsis, and can be genetically transformed by the simple floral dip procedure. It is capable of copious seed production. Salt cress is an extremophile native to harsh environments and can reproduce after exposure to extreme salinity (500 mm NaCl) or cold to -15 degrees C. It is a typical halophyte that accumulates NaCl at controlled rates and also dramatic levels of Pro (>150 mm) during exposure to high salinity. Stomata of salt cress are distributed on the leaf surface at higher density, but are less open than the stomata of Arabidopsis and respond to salt stress by closing more tightly. Leaves of salt cress are more succulent-like, have a second layer of palisade mesophyll cells, and are frequently shed during extreme salt stress. Roots of salt cress develop both an extra endodermis and cortex cell layer compared to Arabidopsis. Salt cress, although salt and cold tolerant, is not exceptionally tolerant of soil desiccation. We have isolated several ethyl methanesulfonate mutants of salt cress that have reduced salinity tolerance, which provide evidence that salt tolerance in this halophyte can be significantly affected by individual genetic loci. Analysis of salt cress expressed sequence tags provides evidence for the presence of paralogs, missing in the Arabidopsis genome, and for genes with abiotic stress-relevant functions. Hybridizations of salt cress RNA targets to an Arabidopsis whole-genome oligonucleotide array indicate that commonly stress-associated transcripts are expressed at a noticeably higher level in unstressed salt cress plants and are induced rapidly under stress. Efficient transformation of salt cress allows for simple gene exchange between Arabidopsis and salt cress. In addition, the generation of T-DNA-tagged mutant collections of salt cress, already in progress, will open the door to a new era of forward and reverse genetic studies of extremophile plant biology.

Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction

BACKGROUND

High throughput gene expression data from spotted cDNA microarrays are collected by scanning the signal intensities of the corresponding spots by dedicated fluorescence scanners. The major scanner settings for increasing the spot intensities are the laser power and the voltage of the photomultiplier tube (PMT). It is required that the expression ratios are independent of these settings. We have investigated the relationships between PMT voltage, spot intensities, and expression ratios for different scanners, in order to define an optimal scanning procedure.

RESULTS

All scanners showed a limited intensity range from 200 to 50 000 (mean spot intensity), for which the expression ratios were independent of PMT voltage. This usable intensity range was considerably less than the maximum detection range of the PMTs. The use of spot and background intensities outside this range led to errors in the ratios. The errors at high intensities were caused by saturation of pixel intensities within the spots. An algorithm was developed to correct the intensities of these spots, and, hence, extend the upper limit of the usable intensity range.

CONCLUSIONS

It is suggested that the PMT voltage should be increased to avoid intensities of the weakest spots below the usable range, allowing the brightest spots to reach the level of saturation. Subsequently, a second set of images should be acquired with a lower PMT setting such that no pixels are in saturation. Reliable data for spots with saturation in the first set of images can easily be extracted from the second set of images by the use of our algorithm. This procedure would lead to an increase in the accuracy of the data and in the number of data points achieved in each experiment compared to traditional procedures.

Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses

To identify cold-, drought-, high-salinity-, and/or abscisic acid (ABA)-inducible genes in rice (Oryza sativa), we prepared a rice cDNA microarray including about 1700 independent cDNAs derived from cDNA libraries prepared from drought-, cold-, and high-salinity-treated rice plants. We confirmed stress-inducible expression of the candidate genes selected by microarray analysis using RNA gel-blot analysis and finally identified a total of 73 genes as stress inducible including 58 novel unreported genes in rice. Among them, 36, 62, 57, and 43 genes were induced by cold, drought, high salinity, and ABA, respectively. We observed a strong association in the expression of stress-responsive genes and found 15 genes that responded to all four treatments. Venn diagram analysis revealed greater cross talk between signaling pathways for drought, ABA, and high-salinity stresses than between signaling pathways for cold and ABA stresses or cold and high-salinity stresses in rice. The rice genome database search enabled us not only to identify possible known cis-acting elements in the promoter regions of several stress-inducible genes but also to expect the existence of novel cis-acting elements involved in stress-responsive gene expression in rice stress-inducible promoters. Comparative analysis of Arabidopsis and rice showed that among the 73 stress-inducible rice genes, 51 already have been reported in Arabidopsis with similar function or gene name. Transcriptome analysis revealed novel stress-inducible genes, suggesting some differences between Arabidopsis and rice in their response to stress.

Enhanced emission of highly labeled DNA oligomers near silver metallic surfaces

Fluorescein is a widely used fluorescent probe in DNA analysis. One difficulty with fluorescein is its self-quenching due to resonance energy transfer between the residues, which results in decreased intensities with increasing labeling density. We examined the emission spectral properties of DNA oligomers labeled with one or five fluorescein residues. The emission intensity of the more highly labeled oligomer was decreased due to self-quenching. The self-quenching was mostly eliminated when this oligomer was held approximately 90 A from the surface of metallic silver particles. The intensities increased 7- and 19-fold for the oligomers with one or five fluoresceins, respectively. The increased intensity did not result in increased photobleaching. These results suggest the use of substrates coated with silver particles for increased sensitivity on DNA arrays or for DNA analysis.

Fluorescence spectral properties of cyanine dye-labeled DNA oligomers on surfaces coated with silver particles

We examined the fluorescence spectral properties of DNA oligomers, labeled with Cy3 or Cy5, when bound to quartz surfaces coated with metallic silver particles. Prior to binding of labeled DNA the surfaces were treated with polylysine or 3-aminopropyl triethoxysilane or were coated with avidin for binding of biotinylated oligomers. The fluorescence intensities were increased an average of 8-fold on these surfaces. Despite the increased emission intensity, the photostability of the labeled DNA was the same or higher on the silver-coated surfaces than on the uncoated slides. The time-integrated intensities, that is the area under the intensity plots with continuous illumination, increased an average of 6-fold. In all cases the lifetimes were dramatically shortened on the silver particles, indicating an over 100-fold increase in the radiative decay rates. These results suggest the use of substrates containing silver particles for increased sensitivity of DNA detection on DNA arrays.

Fluorescence spectral properties of cyanine dye labeled DNA near metallic silver particles

Recent studies have demonstrated that silver metallic particles can increase the quantum yield and decrease the lifetimes of nearby fluorophores. These studies are extended to double stranded DNA oligomers labeled with N,N'-(dipropyl)-tetramethylindocarbocyanine (Cy3) or N,N-(dipropyl)-tetramethylindodicarbocyanine (Cy5). The proximity to silver particles increases the apparent quantum yields and decreases the lifetimes of the double helical DNA 23-mer labeled individually with Cy3 or Cy5. The decreased lifetimes are accompanied by apparently increased photostability of the labeled oligomers near silver particles. Because of spatial averaging across the sample these results are likely to significantly underestimate the effects of silver particles on labeled DNA localized at an optimal distance from the metallic surface. These results suggest that DNA arrays fabricated on substrates with silver particles can display increased sensitivity and photostability in the analysis of gene expression.

A 3800 gene microarray for cattle functional genomics: comparison of gene expression in spleen, placenta, and brain

A cDNA microarray representing approximately 3800 cattle genes was created for functional genomic studies. The array elements were selected from > 7000 cDNA clones identified in a large-scale expressed sequence tag (EST) project that utilized spleen and normalized and subtracted placenta cDNA libraries. Sequence similarity searches of the 3820 ESTs represented on the array using BLASTN identified 3290 (86.1%) as putative human orthologs, with the remainder consisting of "novel" genes or highly divergent orthologs. Experiments were conducted with a prototype 768 gene microarray created from spleen cDNAs and with the 3800 gene array that included genes from spleen and placenta. The 768 gene array was used to profile RNA transcripts expressed by adult and fetal spleen. The 3800 gene array was used to profile transcripts expressed by adult brain and placenta. Microarray analysis of RNA extracted from fetal and adult spleen identified 29 genes that were differentially expressed two-fold or more. Transcriptional differences of two of these genes, IGJ and CTSS, were confirmed using TaqMan technology. The comparison of brain and placenta revealed 400 genes expressed at higher levels in brain and 72 genes expressed at higher levels in placenta. These results demonstrate the potential power of microarrays for understanding the molecular mechanisms of cattle development, disease resistance, nutrition, fertility and production traits.

Chapter 16 Production and gene expression of brush border disaccharidases and peptidases during development in pigs and calves

This chapter reviews the expression of intestinal brush-border disaccharidases (maltase-glucoamylase, sucrase-isomaltase, lactase, and trehalase) and peptidases (aminopeptidases A and N and dipeptidyl peptidase IV) during development in growing animals. It describes the roles of intestinal enzymes, focussing on complementarity with salivary, gastric, and pancreatic digestive enzymes and their hydrolytic function in the process of absorption. Gene expression of the enzymes and nutritional regulation of their expression appear during postnatal development up to maturity. After translation of the specific mRNA, a single precursor of maltaseglucoamylase (pro-MG), rich in mannose, is produced in the rough endoplasmic reticulum (RER). In contrast to the relatively small number of carbohydrases, the number of peptidases found in enterocytes in the small intestine is large, because of the large number of different peptide bonds in oligopeptides produced by the action of pancreatic proteases. The digestive function (disaccharidase and peptidase activities) of the enterocytes and their microvilli begins when structural differentiation is complete, that is, during the period of migration over the cryptvillus junction. Modern techniques and investigations are expected to yield relevant data for elaborating feeding strategies that take into account the complex interactions between the diet, the microflora, the luminal milieu and the physiology of the small intestine, including the optimal functioning of the immunological and endocrine systems.