Screening insertion libraries for mutations in many genes simultaneously using DNA microarrays

We describe a method to screen pools of DNA from multiple transposon lines for insertions in many genes simultaneously. We use thermal asymmetric interlaced–PCR, a hemispecific PCR amplification protocol that combines nested, insertion-specific primers with degenerate primers, to amplify DNA flanking the transposons. In reconstruction experiments with previously characterized Arabidopsis lines carrying insertions of the maize Dissociation (Ds) transposon, we show that fluorescently labeled, transposon-flanking fragments overlapping ORFs hybridize to cognate expressed sequence tags (ESTs) on a DNA microarray. We further show that insertions can be detected in DNA pools from as many as 100 plants representing different transposon lines and that all of the tested, transposon-disrupted genes whose flanking fragments can be amplified individually also can be detected when amplified from the pool. The ability of a transposon-flanking fragment to hybridize declines rapidly with decreasing homology to the spotted DNA fragment, so that only ESTs with >90% homology to the transposon-disrupted gene exhibit significant cross-hybridization. Because thermal asymmetric interlaced–PCR fragments tend to be short, use of the present method favors recovery of insertions in and near genes. We apply the technique to screening pools of new Ds lines using cDNA microarrays containing ESTs for ≈1,000 stress-induced and -repressed Arabidopsis genes.

Análise de expressão gênica de Xylella fastidiosa cultivada em diferentes concentrações de glicose pela técnica de microarrays de DNA

Xylella fastidiosa (Xf) é o agente etiológico causador de doenças em uma grande variedade de cultivos de grande importância econômica, causando a c1orose variegada dos citros, uma das doenças mais danosas à indústria de citros no Brasil. Os genomas de algumas cepas deste fitopatógeno foram completamente seqüenciados promovendo assim estudos funcionais do genoma em larga escala. Neste trabalho nós nos propusemos a investigar o perfil de transcrição de Xf através da técnica microarranjos (no título da dissertação microarrays, mas a partir de agora usaremos microaarranjos) de DNA usando todo o genoma do fitopatógeno e cultivando-a sob meio definido variando a concentração de glicose. O objetivo inicial deste trabalho era observar se Xf comportava-se da mesma forma que Xac, que tem a expressão de goma aumentada devido ao aumento da concentração de glicose do meio. Nossas análises revelaram que enquanto os transcritos relacionados à goma não se mostraram afetados com a concentração de glicose, genes que codificam para análogos a Colicina-V e precursores de fimbria foram induzidos em alta concentração de glicose. Baseados nestes resultados, nós propusemos um modelo de mecanismo de produção e defesa contra a Colicina em Xf.

Searching oligo sets of human chromosome 12 using evolutionary strategies

DNA Microarray is a powerful tool to measure the level of a mixed population of nucleic acids at one time, which has great impact in many aspects of life sciences research. In order to distinguish nucleic acids with very similar composition by hybridization, it is necessary to design microarray probes with high specificities and sensitivities. Highly specific probes correspond to probes having unique DNA sequences; whereas highly sensitive probes correspond to those with melting temperature within a desired range and having no secondary structure. The selection of these probes from a set of functional DNA sequences (exons) constitutes a computationally expensive discrete non-linear search problem. We delegate the search task to a simple yet effective Evolution Strategy algorithm. The computational efficiency is also greatly improved by making use of an available bioinformatics tool.

The potential of microarrays to assist shrimp breeding and production: a review

The shrimp aquaculture industry is a relatively new livestock industry, having developed over the past 30 years. Thus, it is poised to take advantage of new technologies from the outset of selective breeding programs. This contrasts with long established livestock industries, where there are already highly specialised breeds. This review focuses specifically on the potential application of microarrays to shrimp breeding. Potential applications of microarrays in selective breeding programs are summarised. Microarrays can be used as a rapid means to generate molecular markers for genetic linkage mapping, and genetic maps have been constructed for yeast, Arabidopsis and barley using microarray technology. Microarrays can also be used in the hunt for candidate genes affecting particular traits, leading to development of perfect markers for these traits (i.e. causative mutations). However, this requires that microarray analysis be combined with genetic linkage mapping, and that substantial genomic information is available for the species in question. A novel application of microarrays is to treat gene expression as a quantitative trait in itself and to combine this with linkage mapping to identify quantitative trait loci controlling the levels of gene expression; this approach may identify higher level regulatory genes in specific pathways. Finally, patterns of gene expression observed using microarrays may themselves be treated as phenotypic traits in selection programs (e.g. a particular pattern of gene expression might be indicative of a disease tolerant individual). Microarrays are now being developed for a number of shrimp species in laboratories around the world, primarily with a focus on identifying genes involved in the immune response. However, at present, there is no central repository of shrimp genomic information, which limits the rate at which shrimp genomic research can be progressed. The application of microarrays to shrimp breeding will be extremely limited until there is a shared repository of genomic information for shrimp, and the collective will and resources to develop comprehensive genomic tools for shrimp.

A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays

Motivation: An important problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. We provide a straightforward and easily implemented method for estimating the posterior probability that an individual gene is null. The problem can be expressed in a two-component mixture framework, using an empirical Bayes approach. Current methods of implementing this approach either have some limitations due to the minimal assumptions made or with more specific assumptions are computationally intensive. Results: By converting to a z-score the value of the test statistic used to test the significance of each gene, we propose a simple two-component normal mixture that models adequately the distribution of this score. The usefulness of our approach is demonstrated on three real datasets.

Mixture models for detecting differentially expressed genes in microarrays

An important and common problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. As this problem concerns the selection of significant genes from a large pool of candidate genes, it needs to be carried out within the framework of multiple hypothesis testing. In this paper, we focus on the use of mixture models to handle the multiplicity issue. With this approach, a measure of the local FDR (false discovery rate) is provided for each gene. An attractive feature of the mixture model approach is that it provides a framework for the estimation of the prior probability that a gene is not differentially expressed, and this probability can subsequently be used in forming a decision rule. The rule can also be formed to take the false negative rate into account. We apply this approach to a well-known publicly available data set on breast cancer, and discuss our findings with reference to other approaches.

Searching oligo sets of human chromosome 12 using evolutionary strategies

DNA microarray is a powerful tool to measure the level of a mixed population of nucleic acids at one time, which has great impact in many aspects of life sciences research. In order to distinguish nucleic acids with very similar composition by hybridization, it is necessary to design probes with high specificities, i.e. uniqueness, and also sensitivities, i.e., suitable melting temperature and no secondary structure. We make use of available biology tools to gain necessary sequence information of human chromosome 12, and combined with evolutionary strategy (ES) to find unique subsequences representing all predicted exons. The results are presented and discussed.

Gold nanoparticles decorated with oligo(ethylene glycol) thiols:enhanced Hofmeister effects in colloid−protein mixtures

Oligo(ethylene glycol) (OEG) thiol self-assembled monolayer (SAM) decorated gold nanoparticles (AuNPs) have potential applications in bionanotechnology due to their unique property of preventing the nonspecific absorption of protein on the colloidal surface. For colloid-protein mixtures, a previous study (Zhang et al. J. Phys. Chem. A 2007, 111, 12229) has shown that the OEG SAM-coated AuNPs become unstable upon addition of proteins (BSA) above a critical concentration, c*. This has been explained as a depletion effect in the two-component system. Adding salt (NaCl) can reduce the value of c*; that is, reduce the stability of the mixture. In the present work, we study the influence of the nature of the added salt on the stability of this two-component colloid-protein system. It is shown that the addition of various salts does not change the stability of either protein or colloid in solution in the experimental conditions of this work, except that sodium sulfate can destabilize the colloidal solutions. In the binary mixtures, however, the stability of colloid-protein mixtures shows significant dependence on the nature of the salt: chaotropic salts (NaSCN, NaClO4, NaNO3, MgCl2) stabilize the system with increasing salt concentration, while kosmotropic salts (NaCl, Na2SO4, NH4Cl) lead to the aggregation of colloids with increasing salt concentration. These observations indicate that the Hofmeister effect can be enhanced in two-component systems; that is, the modification of the colloidal interface by ions changes significantly the effective depletive interaction via proteins. Real time SAXS measurements confirm in all cases that the aggregates are in an amorphous state.

Generation of primary hepatocyte microarrays by piezoelectric printing

We demonstrate a single-step method for the generation of collagen and poly-l-Lysine (PLL) micropatterns on a poly(ethylene glycol) (PEG) functionalized glass surface for cell based assays. The method involves establishing a reliable silanization method to create an effective non-adhesive PEG layer on glass that inhibits cell attachment, followed by the spotting of collagen or PLL solutions using non-contact piezoelectric printing. We show for the first time that the spotted protein micropatterns remain stable on the PEG surface even after extensive washing, thus significantly simplifying protein pattern formation. We found that adherence and spreading of NIH-3T3 fibroblasts was confined to PLL and collagen areas of the micropatterns. In contrast, primary rat hepatocytes adhered and spread only on collagen micropatterns, where they formed uniform, well defined functionally active cell arrays. The differing affinity of hepatocytes and NIH-3T3 fibroblasts for collagen and PLL patterns was used to develop a simple technique for creating a co-culture of the two cell types. This has the potential to form structured arrays that mimic the in vivo hepatic environment and is easily integrated within a miniaturized analytical platform for developing high throughput toxicity analysis in vitro.

Gold nanoparticles decorated with oligo(ethylene glycol) thiols:kinetics of colloid aggregation driven by depletion forces

We have studied the kinetics of the phase-separation process of mixtures of colloid and protein in solutions by real-time UV-vis spectroscopy. Complementary small-angle X-ray scattering (SAXS) was employed to determine the structures involved. The colloids used are gold nanoparticles functionalized with protein resistant oligo(ethylene glycol) (OEG) thiol, HS(CH(2))(11)(OCH(2)CH(2))(6)OMe (EG6OMe). After mixing with protein solution above a critical concentration, c*, SAXS measurements show that a scattering maximum appears after a short induction time at q = 0.0322 angstrom(-1) stop, which increases its intensity with time but the peak position does not change with time, protein concentration and salt addition. The peak corresponds to the distance of the nearest neighbor in the aggregates. The upturn of scattering intensities in the low q-range developed with time indicating the formation of aggregates. No Bragg peaks corresponding to the formation of colloidal crystallites could be observed before the clusters dropped out from the solution. The growth kinetics of aggregates is followed in detail by real-time UV-vis spectroscopy, using the flocculation parameter defined as the integral of the absorption in the range of 600-800 nm wavelengths. At low salt addition (<0.5 M), a kinetic crossover from reaction-limited cluster aggregation (RLCA) to diffusion-limited cluster aggregation (DLCA) growth model is observed, and interpreted as being due to the effective repulsive interaction barrier between colloids within the depletion potential. Above 0.5 M NaCl, the surface charge of proteins is screened significantly, and the repulsive potential barrier disappeared, thus the growth kinetics can be described by a DLCA model only.

Gold nanoparticles decorated with oligo(ethylene glycol) thiols:protein resistance and colloidal stability

The interactions between proteins and gold colloids functionalized with protein-resistant oligo(ethylene glycol) (OEG) thiol, HS(CH(2))(11) (OCH(2)CH(2))(6)OMe (EG(6)OMe), in aqueous solution have been studied by small-angle X-ray scattering (SAXS) and UV-vis spectroscopy. The mean size, 2R, and the size distribution of the decorated gold colloids have been characterized by SAXS. The monolayer-protected gold colloids have no correlations due to the low volume fraction in solution and are stable in a wide range of temperatures (5-70 degrees C, pH (1.3-12.4), and ionic strength (0-1.0 M). In contrast, protein (bovine serum albumin) solutions with concentrations in the range of 60-200 mg/mL (4.6-14.5 vol show a pronounced correlation peak in SAXS, which results from the repulsive electrostatic interaction between charged proteins. These protein interactions show significant dependence on ionic strength, as would be expected for an electrostatic interaction (Zhang et al. J. Phys. Chem. B 2007, 111, 251). For a mixture of proteins and gold colloids, the protein-protein interaction changes little upon mixing with OEG-decorated gold colloids. In contrast, the colloid-colloid interaction is found to be strongly dependent on the protein concentration and the size of the colloid itself. Adding protein to a colloidal solution results in an attractive depletion interaction between functionalized gold colloids, and above a critical protein concentration, c*, the colloids form aggregates and flocculate. Adding salt to such mixtures enhances the depletion effect and decreases the critical protein concentration. The aggregation is a reversible process (i.e., diluting the solution leads to dissolution of aggregates). The results also indicate that the charge of the OEG self-assembled monolayer at a curved interface has a rather limited effect on the colloidal stabilization and the repulsive interaction with proteins.

The application of fixed hydrophobic patterns for confinement of aqueous solutions in proteomic microarrays

A protein microarray hybridisation system has been implemented by employing patterned hydrophobic thin films on hydrophilic substrates as a means of confinement for aqueous samples. This approach has the ability to handle, and keep separate, small sample volumes of just a few microlitres. In addition, the system is more straightforward to use than the existing multi-well gasket solution. The paper describes the fabrication method and the system is demonstrated for a model protein microarray assay. © 2011 American Institute of Physics.