Identification and characterization of Bacillus anthracis by multiplex PCR on DNA chip

Bacillus anthracis can be identified by detecting virulence factor genes located on two plasmids, pXO1 and pXO2. Combining multiplex PCR with arrayed anchored primer PCR and biotin-avidin alkaline phosphatase indicator system, we developed a qualitative DNA chip method for characterization of B. anthracis, and simultaneous confirmation of the species identity independent of plasmid contents. The assay amplifies pag gene (in pXO1), cap gene (in pXO2) and Ba813 gene (a B. anthracis specific chromosomal marker), and the results were indicated by an easy-to-read profile based on the color reaction of alkaline phosphatase. About 1 pg of specific DNA fragments on the chip wells could be detected after PCR. With the proposed method, the avirulent (pXO1(+)/2(-), pXO1(-)/2(+) and pXO1(-)/2(-)) strains of B. anthracis and distinguished 'anthrax-like' strains from other B. cereus group bacteria were unambiguously identified, while the genera other than Bacillus gave no positive signal. (C) 2004 Elsevier B.V. All rights reserved.

Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism

An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates. (C) 2003 Elsevier B.V. All rights reserved.

DNA chip designed antisense oligodeoxynucleotides targeting EGFR MRNA for brain tumour therapy

Glioblastoma multiforme (GBM) is a malignant brain tumour for which there is currently no effective treatment regime. It is thought to develop due to the overexpression of a number of genes, including the epidermal growth factor receptor (EGFR), which is found in over 40% of GBM. Novel forms of treatment such as antisense therapy may allow for the specific inhibition of aberrant genes and thus they are optimistic therapies for future treatment of GBM. Oligodeoxynucleotides (ODNs) are small pieces of DNA that are often modified to increase their stability to nucleases and can be targeted to the aberrant gene in order to inhibit it and thus prevent its transcription into protein. By specifically binding to mRNA in an antisense manner, they can bring about its degradation by a variety of mechanisms including the activation of RNase H and thus have great potential as therapeutic agents. One of the main drawbacks to the utilisation of this therapy so far is the lack of techniques that can successfully predict accessible regions on the target mRNA that the ODNs can bind to. DNA chip technology has been utilised here to predict target sequences on the EGFR mRNA and these ODNs (AS 1 and AS2) have been tested in vitro for their stability, uptake into cells and their efficacy on cellular growth, EGFR protein and mRNA. Studies showed that phosphorothioate and 2'O-methyl ODNs were significantly more stable than phosphodiester ODNs both in serum and serum-free conditions and that the mechanism of uptake into A431 cells was temperature dependent and more efficient with the use of optimised lipofectin. Efficacy results show that AS 1 and AS2 phosphorothioate antisense ODNs were capable of inhibiting cell proliferation by 69% ±4% and 65% ±4.5% respectively at 500nM in conjunction with a non-toxic dose of lipofectinTM used to enhance cellular delivery. Furthermore, control ODN sequences, 2' O-methyl derivatives and a third ODN sequence, that was found not to be capable of binding efficiently to the EGFR mRNA by DNA chip technology, showed no significant effect on cell proliferation. AS 1 almost completely inhibited EGFR protein levels within 48 hours with two doses of 500nM AS 1 with no effect on other EGFR family member proteins or by control sequences. RNA analysis showed a decrease in mRNA levels of 32.4% ±0.8% but techniques require further optimisation to confirm this. As there are variations found between human glioblastoma in situ and those developed as xenografts, analysis of effect of AS 1 and AS2 was performed on primary tumour cell lines derived from glioma patients. ODN treatment showed a specific knockdown of cell growth compared to any of the controls used. Furthermore, combination therapies were tested on A431 cell growth to determine the advantage of combining different antisense approaches and that of conventional drugs. Results varied between the combination treatments but indicated that with optimisation of treatment regimes and delivery techniques that combination therapies utilising antisense therapies would be plausible.

Preprocess and data analysis techniques for affymetrix DNA microarrays using bioconductor: a case study in Alzheimer disease

DNA microarray, or DNA chip, is a technology that allows us to obtain the expression level of many genes in a single experiment. The fact that numerical expression values can be easily obtained gives us the possibility to use multiple statistical techniques of data analysis. In this project microarray data is obtained from Gene Expression Omnibus, the repository of National Center for Biotechnology Information (NCBI). Then, the noise is removed and data is normalized, also we use hypothesis tests to find the most relevant genes that may be involved in a disease and use machine learning methods like KNN, Random Forest or Kmeans. For performing the analysis we use Bioconductor, packages in R for the analysis of biological data, and we conduct a case study in Alzheimer disease. The complete code can be found in https://github.com/alberto-poncelas/ bioc-alzheimer

Multiplex detection of mutations in clinical isolates of rifampin-resistant Mycobacterium tuberculosis by short oligonucleotide Ligation assay on DNA chips

A new approach, short-oligonucleotide-ligation assay on DNA chip (SOLAC), is developed to detect mutations in rifampin-resistant Mycobacterium tuberculosis. The method needs only four common probes to detect 15 mutational variants of the rpoB gene within 12 h. Fifty-five rifampin-resistant M. tuberculosis isolates were analyzed, resulting in 87.3% accuracy and 83.6% concordance relative to DNA sequencing.

Impacto do lodo de esgoto na comunidade bacteriana do solo: avaliação por microarranjo de DNA

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides.

The challenge of the Human Genome Project is to increase the rate of DNA sequence acquisition by two orders of magnitude to complete sequencing of the human genome by the year 2000. The present work describes a rapid detection method using a two-dimensional optical wave guide that allows measurement of real-time binding or melting of a light-scattering label on a DNA array. A particulate label on the target DNA acts as a light-scattering source when illuminated by the evanescent wave of the wave guide and only the label bound to the surface generates a signal. Imaging/visual examination of the scattered light permits interrogation of the entire array simultaneously. Hybridization specificity is equivalent to that obtained with a conventional system using autoradiography. Wave guide melting curves are consistent with those obtained in the liquid phase and single-base discrimination is facile. Dilution experiments showed an apparent lower limit of detection at 0.4 nM oligonucleotide. This performance is comparable to the best currently known fluorescence-based systems. In addition, wave guide detection allows manipulation of hybridization stringency during detection and thereby reduces DNA chip complexity. It is anticipated that this methodology will provide a powerful tool for diagnostic applications that require rapid cost-effective detection of variations from known sequences.

Evolution and detection of cyanobacterial hepatotoxin synthetase genes

Mass occurrences (blooms) of cyanobacteria are common in aquatic environments worldwide. These blooms are often toxic, due to the presence of hepatotoxins or neurotoxins. The most common cyanobacterial toxins are hepatotoxins: microcystins and nodularins. In freshwaters, the main producers of microcystins are Microcystis, Anabaena, and Planktothrix. Nodularins are produced by strains of Nodularia spumigena in brackish waters. Toxic and nontoxic strains of cyanobacteria co-occur and cannot be differentiated by conventional microscopy. Molecular biological methods based on microcystin and nodularin synthetase genes enable detection of potentially hepatotoxic cyanobacteria. In the present study, molecular detection methods for hepatotoxin-producing cyanobacteria were developed, based on microcystin synthetase gene E (mcyE) and the orthologous nodularin synthetase gene F (ndaF) sequences. General primers were designed to amplify the mcyE/ndaF gene region from microcystin-producing Anabaena, Microcystis, Planktothrix, and Nostoc, and nodularin-producing Nodularia strains. The sequences were used for phylogenetic analyses to study how cyanobacterial mcy genes have evolved. The results showed that mcy genes and microcystin are very old and were already present in the ancestor of many modern cyanobacterial genera. The results also suggested that the sporadic distribution of biosynthetic genes in modern cyanobacteria is caused by repeated gene losses in the more derived lineages of cyanobacteria and not by horizontal gene transfer. Phylogenetic analysis also proposed that nda genes evolved from mcy genes. The frequency and composition of the microcystin producers in 70 lakes in Finland were studied by conventional polymerase chain reaction (PCR). Potential microcystin producers were detected in 84% of the lakes, using general mcyE primers, and in 91% of the lakes with the three genus-specific mcyE primers. Potential microcystin-producing Microcystis were detected in 70%, Planktothrix in 63%, and Anabaena in 37% of the lakes. The presence and co-occurrence of potential microcystin producers were more frequent in eutrophic lakes, where the total phosphorus concentration was high. The PCR results could also be associated with various environmental factors by correlation and regression analyses. In these analyses, the total nitrogen concentration and pH were both associated with the presence of multiple microcystin-producing genera and partly explained the probability of occurrence of mcyE genes. In general, the results showed that higher nutrient concentrations increased the occurrence of potential microcystin producers and the risk for toxic bloom formation. Genus-specific probe pairs for microcystin-producing Anabaena, Microcystis, Planktothrix, and Nostoc, and nodularin-producing Nodularia were designed to be used in a DNA-chip assay. The DNA-chip can be used to simultaneously detect all these potential microcystin/nodularin producers in environmental water samples. The probe pairs detected the mcyE/ndaF genes specifically and sensitively when tested with cyanobacterial strains. In addition, potential microcystin/nodularin producers were identified in lake and Baltic Sea samples by the DNA-chip almost as sensitively as by quantitative real-time PCR (qPCR), which was used to validate the DNA-chip results. Further improvement of the DNA-chip assay was achieved by optimization of the PCR, the first step in the assay. Analysis of the mcy and nda gene clusters from various hepatotoxin-producing cyanobacteria was rewarding; it revealed that the genes were ancient. In addition, new methods detecting all the main producers of hepatotoxins could be developed. Interestingly, potential microcystin-producing cyanobacterial strains of Microcystis, Planktothrix, and Anabaena, co-occurred especially in eutrophic and hypertrophic lakes. Protecting waters from eutrophication and restoration of lakes may thus decrease the prevalence of toxic cyanobacteria and the frequency of toxic blooms.

Phosphorylation du CTD de l'ARN polymérase II et impact de l'histone H2A.Z sur le positionnement des nucléosomes chez S. cerevisiae

La phosphorylation du domaine C-terminal de l’ARN polymérase II permet à ce complexe protéique d’exécuter la transcription des gènes, en plus de coupler à la transcription des événements moléculaires comme la maturation des ARNm. Mes résultats montrent que même si cette phosphorylation suit un patron similaire à l’ensemble des gènes, il existe des exceptions pouvant être dues à des mécanismes alternatifs de phosphorylation du CTD. Le présent ouvrage s’intéresse également au rôle qu’occupe la variante d’histone H2A.Z dans l’organisation de la chromatine. Des études précédentes on montré que le positionnement de certains nucléosomes le long de l’ADN serait influencé par H2A.Z et aurait une influence sur la capacité de transcrire les gènes. Par une approche génomique utilisant les puces à ADN, j’ai cartographié l’impact de la délétion de H2A.Z sur la structure des nucléosomes. Enfin, des résultats intéressants sur la dynamique d’incorporation de H2A.Z à la chromatine ont été obtenus.

Étude de l’expression de « Bcl-2 modifying factor » (Bmf) et son implication dans la néphropathie diabétique

Objectif : Étudier les mécanismes apoptotiques impliqués dans la néphropathie diabétique en identifiant les gènes responsables de l’apoptose et activés par les espèces réactives de l’oxygène (ROS) dans les cellules de tubules proximaux rénaux (RPTC) de différents modèles diabétiques. Méthodes : Une hybridation par puce à AND a été réalisée sur les ARN extraits à partir de RPTC de souris heterozygotes db/m+, db/db and db/db catalase (CAT)-transgénique (Tg) de 20 semaines. Des expériences de PCR en temps réel et d’immunohistochimie réalisées sur ces modèles et sur le modèle ou le diabète avait été induit par traitement au streptozotocin (STZ) ont permis de valider les gènes apoptotiques identifiés par puce à ADN. Des RPTC immortalisées de rat ont été utilisées pour montrer l’activité de ces gènes apoptotique et la régulation de leur expression. De plus, une étude additionnelle réalisée sur des sections rénales provenant de patients diabétiques et non diabétiques a démontré également une surexpression de ces gènes apoptotiques dans les IRPTC. Résultats: L’expression de Bcl-2-modifying factor (Bmf), une protéine apoptotique, semble augmentée dans les RPTC de souris db/db comparé aux souris contrôles db/m+, ou aux souris db/db CAT-tg. La surexpression de Bmf a également été identifiée dans les RPTC du modèle diabétique STZ. La normalisation de l’hyperglycémie chez ces souris par traitement à l’insuline semble normaliser également l’expression de Bmf. In vitro, la surexpression du cDNA de Bmf dans les RPTC promouvoit l’apoptose et augmente l’activité de caspase 3. La stimulation de RPTC de Rat avec le glucose élevé (25mM de D-glucose) semble augmenter l’expression de Bmf et le traitement de ces cellules avec la roténone, les Diphénylène iodonium, la catalase et l’apocynine semble renverser cette stimulation. L’inhibition de Bmf avec un siRNA semble réduire l’apoptose induite par le glucose élevé. L’expression de Bmf a également été démontrée dans les RPTC de patients diabétiques. Conclusion: Ces résultats ont démontré une surexpression de Bmf dans les RPTC de différents modèles diabétiques et suggèrent son potentiel rôle dans la régulation de l’apoptose et de l’atrophie tubulaire chez les diabétiques.

Biomimese biologischer Membranen: Konzeptionierung, Synthese und biophysikalische Charakterisierung einer Hierarchie festkörpergestützter Mimikry biologischer Membranen

Im Rahmen dieser Arbeit wurden drei neue Modelle zur funktionellen Mimiese biologischer Membranen im Bereich der Bionanotechnologie entwickelt. Um den Rahmen der notwendigen Faktoren und Komponenten für biomimetische Membranmodelle abzustecken, wurde das biologische Vorbild im Bezug auf Zusammensetzung, Organisation und Funktion analysiert. Die daraus abgeleiteten Erkenntnisse erlauben das Erreichen von biologisch relevanten Membranwiderständen im Bereich von mehreren MOhm cm2 und eine gute lokale Fluidität. Ein weiteres Ziel dieser Arbeit war die Entwicklung einer Hierachie unterschiedlich stark von der Festkörperoberfläche entkoppelter Membranen zur Vergrößerung des submembranen Raumes. Diese Ziele konnten realisiert werden. Das auf archaealen Etherlipiden basierende DPTL-System wurde analog dem biologischen Vorbild stereoselektiv synthetisiert und ist in der Lage die Membran bei maximaler Elongation des TEG-Spacers mit mehr als 2 nm von der Oberfläche zu entkoppeln. Die erzielten Wiederstände liegen im hohen ein- bis zweistelligen MOhm-Bereich, die Kapazität entspricht mit 0,5 µF cm-2 ebenfalls dem Wert biologischer Membranen. Die Membraneigenschaften wurden mit Hilfe von SPS, EIS, IR-Spektroskopie, QCM, AFM und Kontaktwinkelmessungen charakterisiert. Die Funktionalität und lokale Fluidität der DPTL-Membran konnte anhand des Valinomycin vermittelten K+-Transports über die Membran gezeigt werden. Fluide Elektroden oder laterale Verdünnung mit TEGL erlauben den Einbau größerer Ionenkanäle. Lipo-Glycopolymere (LGP) mit unterschiedlichen Kettenlängen wurden mit Hilfe der kontrollierten radikalischen Polymerisation mit einer PD < 1.2 synthetisiert. Es zeigte sich, daß die Vororientierung der LGPs auf dem LB-Trog, gefolgt von einem LB-Übertrag auf einen funktionalisierten Träger mit photoreaktivem SAM, nach Belichten des Systems zu einer verlässlichen kovalenten Anbindung der supramolekularen LGP-Architektur führt. Da die Lipo-Glycopolymerketten am Glycopolymerterminus nur mit oberflächennahen Repetiereinheiten an die photoaktivierte Oberfläche binden, sind sie in der Lage Oberflächenrauhigkeiten des Festkörpersubstrates auszugleichen. Die photochemische Immobilisierung von funktionell orientierten supramolekularen LGP-Architekturen auf Goldoberflächen resultiert in tBLMs mit großen vertikalen Enkopplungen der Membran von der Festkörperoberfläche (>8 nm). Der funktionelle Ionentransport von Kaliumionen durch Valinomycin zeigt eine ausreichende lokale Fluidität der Membran die mit einem guten Membranwiderstand (mehrere MOhm) kombiniert ist. Große Membran-Oberflächenentkopplungen konnten mit Hilfe plasmapolymerisierter elektrophiler Polymere erreicht werden. Filmdicken von 50 nm sind mit homogener Oberfläche und Rauhigkeiten im Bereich von Nanometern möglich. Das System zeigt interessante fluide Eigenschaften mit guten Erholungsraten bei FRAP-Experimenten (Diffusionskonstanten von etwa 17 mikro m2 s-1). Die elektrischen Eigenschaften liegen mit Widerständen von wenigen kOhm unterhalb der für gute Membranmimikrie notwendigen Werte. Erstmalig konnte gezeigt werden, daß mit Hilfe dieser Methode inerte Polymere/Plastikträger (zum Beispiel Polypropylen und TOPAS) in effizienter Weise kovalent mit reaktiven Polymeroberflächen modifiziert werden können (Anwendung als DNA-Chip ist beschrieben).

Immobilization of oligodeoxyribonucleotides with multiple anchors to microchips

Facile modification of oligodeoxyribonucleotides is required for efficient immobilization to a pre-activated glass surface. This report presents an oligodeoxyribonucleotide which contains a hairpin stem–loop structure with multiple phosphorothioate moieties in the loop. These moieties are used to anchor the oligo to glass slides that are pre-activated with bromoacetamidopropylsilane. The efficiency of the attachment reaction was improved by increasing the number of phosphorothioates in the loop, as shown in the remarkable enhancement of template hybridization and single base extension through catalysis by DNA polymerase. The loop and stem presumably serve as lateral spacers between neighboring oligodeoxyribonucleotides and as a linker arm between the glass surface and the single-stranded sequence of interest. The oligodeoxyribonucleotides of this hairpin stem–loop architecture with multiple phosphorothioate moieties have broad application in DNA chip-based gene analysis.

Mapping protein-DNA interactions using ChIP-sequencing

Chromatin immunoprecipitation (ChIP) allows enrichment of genomic regions which are associated with specific transcription factors, histone modifications, and indeed any other epitopes which are present on chromatin. The original ChIP methods used site-specific PCR and Southern blotting to confirm which regions of the genome were enriched, on a candidate basis. The combination of ChIP with genomic tiling arrays (ChIP-chip) allowed a more unbiased approach to map ChIP-enriched sites. However, limitations of microarray probe design and probe number have a detrimental impact on the coverage, resolution, sensitivity, and cost of whole-genome tiling microarray sets for higher eukaryotes with large genomes. The combination of ChIP with high-throughput sequencing technology has allowed more comprehensive surveys of genome occupancy, greater resolution, and lower cost for whole genome coverage. Herein, we provide a comparison of high-throughput sequencing platforms and a survey of ChIP-seq analysis tools, discuss experimental design, and describe a detailed ChIP-seq method.Chromatin immunoprecipitation (ChIP) allows enrichment of genomic regions which are associated with specific transcription factors, histone modifications, and indeed any other epitopes which are present on chromatin. The original ChIP methods used site-specific PCR and Southern blotting to confirm which regions of the genome were enriched, on a candidate basis. The combination of ChIP with genomic tiling arrays (ChIP-chip) allowed a more unbiased approach to map ChIP-enriched sites. However, limitations of microarray probe design and probe number have a detrimental impact on the coverage, resolution, sensitivity, and cost of whole-genome tiling microarray sets for higher eukaryotes with large genomes. The combination of ChIP with high-throughput sequencing technology has allowed more comprehensive surveys of genome occupancy, greater resolution, and lower cost for whole genome coverage. Herein, we provide a comparison of high-throughput sequencing platforms and a survey of ChIP-seq analysis tools, discuss experimental design, and describe a detailed ChIP-seq method.

Development of an automated DNA purification module using a micro-fabricated pillar chip

We present a fully automated DNA purification module comprised of a micro-fabricated chip and sequential injection analysis system that is designed for use within autonomous instruments that continuously monitor the environment for the presence of biological threat agents. The chip has an elliptical flow channel containing a bed (3.5 × 3.5 mm) of silica-coated pillars with height, width and center-to-center spacing of 200, 15, and 30 µm, respectively, which provides a relatively large surface area (ca. 3 cm²) for DNA capture in the presence of chaotropic agents. We have characterized the effect of various fluidic parameters on extraction performance, including sample input volume, capture flow rate, and elution volume. The flow-through design made the pillar chip completely reusable; carryover was eliminated by flushing lines with sodium hypochlorite and deionized water between assays. A mass balance was conducted to determine the fate of input DNA not recovered in the eluent. The device was capable of purifying and recovering Bacillus anthracis genomic DNA (input masses from 0.32 to 320 pg) from spiked environmental aerosol samples, for subsequent analysis using polymerase chain reaction-based assays.