An introduction to low-level analysis methods of DNA microarray data

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of nucleic acid abundance in a set of tissues or cell populations for thousands of transcripts or loci simultaneously. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. This includes the design of probes, the experimental design, the image analysis of microarray scanned images, the normalization of fluorescence intensities, the assessment of the quality of microarray data and incorporation of quality information in subsequent analyses, the combination of information across arrays and across sets of experiments, the discovery and recognition of patterns in expression at the single gene and multiple gene levels, and the assessment of significance of these findings, considering the fact that there is a lot of noise and thus random features in the data. For all of these components, access to a flexible and efficient statistical computing environment is an essential aspect.

Virulence typing of Escherichia coli using microarrays

We describe a microarray based broad-range screening technique for Escherichia coli virulence typing. Gene probes were amplified by PCR from a plasmid bank of characterised E. coli virulence genes and were spotted onto a glass slide to form an array of capture probes. Genomic DNA from E. coli strains which were to be tested for the presence of these virulence gene sequences was labelled with fluorescent cyanine dyes by random amplification and then hybridised against the array of probes. The hybridisation, washing and data analysis conditions were optimised for glass slides, and the applicability of the method for identifying the presence of the virulence genes was determined using reference strains and clinical isolates. It was found to be a sensitive screening method for detecting virulence genes, and a powerful tool for determining the pathotype of E. coli. It will be possible to expand and automate this microarray technique to make it suitable for rapid and reliable diagnostic screening of bacterial isolates.

A DNA sequencing strategy that requires only five bases of known terminal sequence for priming.

We have previously reported an enhanced version of sequencing by hybridization (SBH), termed positional SBH (PSBH). PSBH uses partially duplex probes containing single-stranded 3' overhangs, instead of simple single-stranded probes. Stacking interactions between the duplex probe and a single-stranded target allow us to reduce the probe sizes required to 5-base single-stranded overhangs. Here we demonstrate the use of PSBH to capture relatively long single-stranded DNA targets and perform standard solid-state Sanger sequencing on these primer-template complexes without ligation. Our results indicate that only 5 bases of known terminal sequence are required for priming. In addition, the partially duplex probes have the ability to capture their specific target from a mixture of five single-stranded targets with different 3'-terminal sequences. This indicates the potential utility of the PSBH approach to sequence mixtures of DNA targets without prior purification.

Chromosomal insertion of foreign (adenovirus type 12, plasmid, or bacteriophage lambda) DNA is associated with enhanced methylation of cellular DNA segments.

Insertion of foreign DNA into an established mammalian genome can extensively alter the patterns of cellular DNA methylation. Adenovirus type 12 (Ad12)-transformed hamster cells, Ad12-induced hamster tumor cells, or hamster cells carrying integrated DNA of bacteriophage lambda were used as model systems. DNA methylation levels were examined by cleaving cellular DNA with Hpa II, Msp I, or Hha I, followed by Southern blot hybridization with 32P-labeled, randomly selected cellular DNA probes. For several, but not all, cellular DNA segments investigated, extensive increases in DNA methylation were found in comparison with the methylation patterns in BHK21 or primary Syrian hamster cells. In eight different Ad12-induced hamster tumors, moderate increases in DNA methylation were seen. Increased methylation of cellular genes was also documented in two hamster cell lines with integrated Ad12 DNA without the Ad12-transformed phenotype, in one cloned BHK21 cell line with integrated plasmid DNA, and in at least three cloned BHK21 cell lines with integrated lambda DNA. By fluorescent in situ hybridization, the cellular hybridization probes were located to different hamster chromosomes. The endogenous intracisternal A particle genomes showed a striking distribution on many hamster chromosomes, frequently on their short arms. When BHK21 hamster cells were abortively infected with Ad12, increases in cellular DNA methylation were not seen. Thus, Ad12 early gene products were not directly involved in increasing cellular DNA methylation. We attribute the alterations in cellular DNA methylation, at least in part, to the insertion of foreign DNA. Can alterations in the methylation profiles of hamster cellular DNA contribute to the generation of the oncogenic phenotype?

Síntese, caracterização e aplicações de fluoróforos derivados do BODIPY

O desenvolvimento de técnicas analíticas, espectroscópicas e de imagem baseadas na detecção da fluorescência está associado com a necessidade por marcadores fluorescentes com variadas características e aplicabilidades. Dentre os diversos marcadores fluorescentes disponíveis, os derivados de borodipirrometenos (BODIPY), descobertos no final da década de 1960, passaram a ser amplamente utilizados desde o final da década de 1980. Esta tese de doutorado se trata de um estudo pioneiro no Brasil, envolvendo a síntese, modificação química e caracterização fotofísica de BODIPYs. Na primeira etapa do projeto métodos de obtenção de BODIPYs foram estabelecidos e aplicados na síntese de uma biblioteca de sondas fluorescentes. O estudo fotofísico dessa biblioteca de fluoróforos nos possibilitou identificar e estudar particularidades de alguns fluoróforos, como o solvatocromismo, halocromismo e ionocromismo. A segunda etapa do projeto envolveu o estabelecimento de métodos de modificação química de BODIPYs visando a diversificação fotofísica e estrutural da biblioteca de compostos. Foram sintetizados BODIPYs reativos que foram submetidos a reações de substituição nucleofílica, Suzuki, Sonogashira, Knoevenagel e arilação direta, levando à obtenção de compostos com propriedades ópticas diversas. Por fim, na terceira etapa do projeto, está descrito o desenvolvimento de novos métodos de modificação química de fluoróforos BODIPY. Foi desenvolvido um método simples de tiocianação direta dessa classe de compostos com bons rendimentos, baseado na utilização de tiocianato de amônio e oxone ®. O escopo e as limitações do novo método de tiocianação foi estudado em BODIPYs com propriedades eletrônicas diversas. Foi mostrada ainda a conversão de BODIPYs tiocianados a derivados tioalquilados com características ópticas particulares. Em conclusão, com esta tese de doutorado foi estabelecida uma linha de pesquisa inovadora envolvendo a síntese e modificação química de uma classe de compostos com ampla aplicação tecnológica.

Pencil it in: pencil drawn electrochemical sensing platforms

Inspired by recent reports concerning the utilisation of hand drawn pencil macroelectrodes (PDEs), we report the fabrication, characterisation (physicochemical and electrochemical) and implementation (electrochemical sensing) of various PDEs drawn upon a flexible polyester substrate. Electrochemical characterisation reveals that there are no quantifiable electrochemical responses upon utilising these PDEs with an electroactive analyte that requires an electrochemical oxidation step first, therefore the PDEs have been examined towards the electroactive redox probes hexaammineruthenium(III) chloride, potassium ferricyanide and ammonium iron(II) sulfate. For the first time, characterisation of the number of drawn pencil layers and the grade of pencil are examined; these parameters are commonly overlooked when utilising PDEs. It is demonstrated that a PDE drawn ten times with a 6B pencil presented the most advantageous electrochemical platform, in terms of electrochemical reversibility and peak height/analytical signal. In consideration of the aforementioned limitation, analytes requiring an electrochemical reduction as the first process were solely analysed. We demonstrate the beneficial electroanalytical capabilities of these PDEs towards p-benzoquinone and the simultaneous detection of heavy metals, namely lead(II) and cadmium(II), all of which are explored for the first time utilising PDEs. Initially, the detection limits of this system were higher than desired for electroanalytical platforms, however upon implementation of the PDEs in a back-to-back configuration (in which two PDEs are placed back-to-back sharing a single connection to the potentiostat), the detection limits for lead(II) and cadmium(II) correspond to 10 μg L−1 and 98 μg L−1 respectively within model aqueous (0.1 M HCl) solutions.

Design for Inspiration: Children, personal connections and educational technology

The project is working towards building an understanding of the personal interests and experiences of children with the aim of designing appropriate, usable and, most importantly, inspirational educational technology. kidprobe, an adaptation of the technology probe concept, has been used as a lightweight method of gaining contextual information about children's interactions with 'fun' technology. kidprobe has produced design inspiration which focuses primarily on the social and emotional connections children made. The use of kidprobe has generated some important ideas for improving the use of probes with children. It is an important first step in understanding how to effectively adapt probing techniques to inspire the design of technology for children.

Neuroendocrine control of a dynamic communication signal

Multiple physiological systems regulate the electric communication signal of the weakly electric gymnotiform fish, Brachyhypopomus pinnicaudatus. Fish were injected with neuroendocrine probes which identified pharmacologically relevant serotonin (5-HT) receptors similar to the mammalian 5-HT1AR and 5-HT2AR. Peptide hormones of the hypothalamic-pituitary-adrenal/interrenal axis also augment the electric waveform. These results indicate that the central serotonergic system interacts with the hypothalamic-pituitary-interrenal system to regulate communication signals in this species. The same neuroendocrine probes were tested in females before and after introducing androgens to examine the relationship between sex steroid hormones, the serotonergic system, melanocortin peptides, and EOD modulations. Androgens caused an increase in female B. pinnicaudatus responsiveness to other pharmacological challenges, particularly to the melanocortin peptide adrenocorticotropic hormone (ACTH). A forced social challenge paradigm was administered to determine if androgens are responsible for controlling the signal modulations these fish exhibit when they encounter conspecifics. Males and females responded similarly to this social challenge construct, however introducing androgens caused implanted females to produce more exaggerated responses. These results confirm that androgens enhance an individual's capacity to produce an exaggerated response to challenge, however another unidentified factor appears to regulate sex-specific behaviors in this species. These results suggest that the rapid electric waveform modulations B. pinnicaudatus produces in response to conspecifics are situation-specific and controlled by activation of different serotonin receptor types and the subsequent effect on release of pituitary hormones.

Clinical translation of a hand-held optical imager for breast cancer diagnostics: In vitro and in vivo tomography studies

Optical imaging is an emerging technology towards non-invasive breast cancer diagnostics. In recent years, portable and patient comfortable hand-held optical imagers are developed towards two-dimensional (2D) tumor detections. However, these imagers are not capable of three-dimensional (3D) tomography because they cannot register the positional information of the hand-held probe onto the imaged tissue. A hand-held optical imager has been developed in our Optical Imaging Laboratory with 3D tomography capabilities, as demonstrated from tissue phantom studies. The overall goal of my dissertation is towards the translation of our imager to the clinical setting for 3D tomographic imaging in human breast tissues. A systematic experimental approach was designed and executed as follows: (i) fast 2D imaging, (ii) coregistered imaging, and (iii) 3D tomographic imaging studies. (i) Fast 2D imaging was initially demonstrated in tissue phantoms (1% Liposyn solution) and in vitro (minced chicken breast and 1% Liposyn). A 0.45 cm3 fluorescent target at 1:0 contrast ratio was detectable up to 2.5 cm deep. Fast 2D imaging experiments performed in vivo with healthy female subjects also detected a 0.45 cm3 fluorescent target superficially placed ∼2.5 cm under the breast tissue. (ii) Coregistered imaging was automated and validated in phantoms with ∼0.19 cm error in the probe’s positional information. Coregistration also improved the target depth detection to 3.5 cm, from multi-location imaging approach. Coregistered imaging was further validated in-vivo , although the error in probe’s positional information increased to ∼0.9 cm (subject to soft tissue deformation and movement). (iii) Three-dimensional tomography studies were successfully demonstrated in vitro using 0.45 cm3 fluorescence targets. The feasibility of 3D tomography was demonstrated for the first time in breast tissues using the hand-held optical imager, wherein a 0.45 cm3 fluorescent target (superficially placed) was recovered along with artifacts. Diffuse optical imaging studies were performed in two breast cancer patients with invasive ductal carcinoma. The images showed greater absorption at the tumor cites (as observed from x-ray mammography, ultrasound, and/or MRI). In summary, my dissertation demonstrated the potential of a hand-held optical imager towards 2D breast tumor detection and 3D breast tomography, holding a promise for extensive clinical translational efforts.

A heuristic algorithm to generate test program sequences for moving probe electronic test equipment

The electronics industry, is experiencing two trends one of which is the drive towards miniaturization of electronic products. The in-circuit testing predominantly used for continuity testing of printed circuit boards (PCB) can no longer meet the demands of smaller size circuits. This has lead to the development of moving probe testing equipment. Moving Probe Test opens up the opportunity to test PCBs where the test points are on a small pitch (distance between points). However, since the test uses probes that move sequentially to perform the test, the total test time is much greater than traditional in-circuit test. While significant effort has concentrated on the equipment design and development, little work has examined algorithms for efficient test sequencing. The test sequence has the greatest impact on total test time, which will determine the production cycle time of the product. Minimizing total test time is a NP-hard problem similar to the traveling salesman problem, except with two traveling salesmen that must coordinate their movements. The main goal of this thesis was to develop a heuristic algorithm to minimize the Flying Probe test time and evaluate the algorithm against a "Nearest Neighbor" algorithm. The algorithm was implemented with Visual Basic and MS Access database. The algorithm was evaluated with actual PCB test data taken from Industry. A statistical analysis with 95% C.C. was performed to test the hypothesis that the proposed algorithm finds a sequence which has a total test time less than the total test time found by the "Nearest Neighbor" approach. Findings demonstrated that the proposed heuristic algorithm reduces the total test time of the test and, therefore, production cycle time can be reduced through proper sequencing.

Neuroendocrine control of a dynamic communication signal

Multiple physiological systems regulate the electric communication signal of the weakly electric gymnotiform fish, Brachyhypopomuspinnicaudatus. Fish were injected with neuroendocrine probes which identified pharmacologically relevant serotonin (5-HT) receptors similar to the mammalian 5-HT1AR and 5-HT2AR. Peptide hormones of the hypothalamic-pituitary-adrenal/interrenal axis also augment the electric waveform. These results indicate that the central serotonergic system interacts with the hypothalamic-pituitaryinterrenal system to regulate communication signals in this species. The same neuroendocrine probes were tested in females before and after introducing androgens to examine the relationship between sex steroid hormones, the serotonergic system, melanocortin peptides, and EOD modulations. Androgens caused an increase in female B. pinnicaudatus responsiveness to other pharmacological challenges, particularly to the melanocortin peptide adrenocorticotropic hormone (ACTH). A forced social challenge paradigm was administered to determine if androgens are responsible for controlling the signal modulations these fish exhibit when they encounter conspecifics. Males and females responded similarly to this social challenge construct, however introducing androgens caused implanted females to produce more exaggerated responses. These results confirm that androgens enhance an individual's capacity to produce an exaggerated response to challenge, however another unidentified factor appears to regulate sex-specific behaviors in this species. These results suggest that the rapid electric waveform modulations B. pinnicaudatus produces in response to conspecifics are situation-specific and controlled by activation of different serotonin receptor types and the subsequent effect on release of pituitary hormones.

Obtenção e conservação de espermatozoides de cutia (Dasyprocta leporina Linneaus, 1753) do semiárido brasileiro

The general objective of this thesis was to stablish protocols to obtain and conserve agouti (Dasyprocta leporina) sperm bred in captivity in the Brazilian semi-arid, aiming its sustainable production. The thesis was divided in three experiments. In the first one, we studied the influence of the interaction between two probes (quadratics and sine waves) and two stimulation protocols (continuous and in series) on the agouti sperm collection by electroejaculation efficiency. The most efficient interaction on this obtainment was the one with probes with rings associated with stimuli in series (4/7; 57%, P<0.05). In the second experiment we compared the cryoprotectant effects of different substances (glycerol, ethyleneglycol, dimethylsulfoxide, dimethylformamide) on epididymis sperm cryopreservation. The highest values on motility (39.5±4.6%), vigor (2.9±0.2) and membrane integrity (30.6±4.5%) were observed on the samples cryopreserved using glycerol when compared to those with ethyleneglycol and dimethylformamide, but there was no difference (P>0.05) when compared to the samples cryopreserved with dimethylsulfoxide. At last, we studied the effects of the methods to obtain sperm (electroejaculation vs epididymal collection) on post thawing sperm quality. The samples obtained by epididymal retrograde flushing showed values for motility of 25.0±10.9% and vigor 2.4±0.8, and those obtained by electroejaculation had 31.2±14.2% of motility and vigor of 2.2±0.7, however, without statistical difference (P>0.05), which shows the possibility to successfully use the epididymal sperm cryopreservation protocol on agouti ejaculated sperm. In conclusion, significant advances on obtainment and processing of agouti sperm were made, allowing the establishment of germplasm banks from sperm samples obtained from the epididymis or by electroejaculation.

Development of tumour imaging and therapy strategies utilising unengineered bacteria

The ability of systemically administered bacteria to target and replicate to high numbers within solid tumours is well established. Tumour localising bacteria can be exploited as biological vehicles for the delivery of nucleic acid, protein or therapeutic payloads to tumour sites and present researchers with a highly targeted and safe vehicle for tumour imaging and cancer therapy. This work aimed to utilise bacteria to activate imaging probes or prodrugs specifically within target tissue in order to facilitate the development of novel imaging and therapeutic strategies. The vast majority of existing bacterial-mediated cancer therapy strategies rely on the use of bacteria that have been genetically modified (GM) to express genes of interest. While these approaches have been shown to be effective in a preclinical setting, GM presents extra regulatory hurdles in a clinical context. Also, many strains of bacteria are not genetically tractably and hence cannot currently be engineered to express genes of interest. For this reason, the development of imaging and therapeutic systems that utilise unengineered bacteria for the activation of probes or drugs represents a significant improvement on the current gold standard. Endogenously expressed bacterial enzymes that are not found in mammalian cells can be used for the targeted activation of imaging probes or prodrugs whose activation is only achieved in the presence of these enzymes. Exploitation of the intrinsic enzymatic activity of bacteria allows the use of a wider range of bacteria and presents a more clinically relevant system than those that are currently in use. The nitroreductase (NTR) enzymes, found only in bacteria, represent one such option. Chapter 2 introduces the novel concept of utilising native bacterial NTRs for the targeted activation of the fluorophore CytoCy5S. Bacterial-mediated probe activation allowed for non-invasive fluorescence imaging of in vivo bacteria in models of infection and cancer. Chapter 3 extends the concept of using native bacterial enzymes to activate a novel luminescent, NTR activated probe. The use of luminescence based imaging improved the sensitivity of the system and provides researchers with a more accessible modality for preclinical imaging. It also represents an improvement over existing caged luciferin probe systems described to date. Chapter 4 focuses on the employment of endogenous bacterial enzymes for use in a therapeutic setting. Native bacterial enzymatic activity (including NTR enzymes) was shown to be capable of activating multiple prodrugs, in isolation and in combination, and eliciting therapeutic responses in murine models of cancer. Overall, the data presented in this thesis advance the fields of bacterial therapy and imaging and introduce novel strategies for disease diagnosis and treatment. These preclinical studies demonstrate potential for clinical translation in multiple fields of research and medicine.

Efficient simulations with electronic open boundaries

We present a reformulation of the hairy-probe method for introducing electronic open boundaries that is appropriate for steady-state calculations involving nonorthogonal atomic basis sets. As a check on the correctness of the method we investigate a perfect atomic wire of Cu atoms and a perfect nonorthogonal chain of H atoms. For both atom chains we find that the conductance has a value of exactly one quantum unit and that this is rather insensitive to the strength of coupling of the probes to the system, provided values of the coupling are of the same order as the mean interlevel spacing of the system without probes. For the Cu atom chain we find in addition that away from the regions with probes attached, the potential in the wire is uniform, while within them it follows a predicted exponential variation with position. We then apply the method to an initial investigation of the suitability of graphene as a contact material for molecular electronics. We perform calculations on a carbon nanoribbon to determine the correct coupling strength of the probes to the graphene and obtain a conductance of about two quantum units corresponding to two bands crossing the Fermi surface. We then compute the current through a benzene molecule attached to two graphene contacts and find only a very weak current because of the disruption of the π conjugation by the covalent bond between the benzene and the graphene. In all cases we find that very strong or weak probe couplings suppress the current.

Exopolysaccharides produced by Bifidobacterium longum IPLA E44 and Bifidobacterium animalis subsp lactis IPLA R1 modify the composition and metabolic activity of human faecal microbiota in pH-controlled batch cultures

Exopolysaccharides (EPS) isolated from two Bifidobacterium strains, one of human intestinal origin (Bifidobacterium longum subsp. longum IPLA E44) and the other from dairy origin (Bifidobacterium animalis subsp. lactis IPLA R1), were subjected to in vitro chemically simulated gastrointestinal digestion. which showed the absence of degradation of both polymers in these conditions. Polymers were then used as carbon sources in pH-controlled faecal batch cultures and compared with the non-prebiotic carbohydrate glucose and the prebiotic inulin to determine changes in the composition of faecal bacteria. A set of eight fluorescent in situ hybridisation oligonucleotide probes targeting 16S rRNA sequences was used to quantify specific groups of microorganisms. Growth of the opportunistic pathogen Clostridium histolyticum occurred with all carbohydrates tested similarly to that found in negative control cultures without added carbohydrate and was mainly attributed to the culture conditions used rather than enhancement of growth by these substrates. Polymers E44 and RI stimulated growth of Lactobacillus/Enterococcus, Bifidobacterium, and Bacteroides/Prevotella in a similar way to that seen with inulin. The EPS RI also promoted growth of the Atopobium cluster during the first 24 h of fermentation. An increase in acetic and lactic acids was found during early stages of fermentation (first 10-24 h) correlating with increases of Lactobacillus, Bifidobacterium, and Atopobium. Propionic acid concentrations increased in old cultures, which was coincident with the enrichment of Clostridium cluster IX in cultures with EPS RI and with the increases in Bacteroides in cultures with both microbial EPS (RI and E44) and inulin. The lowest acetic to propionic acid ratio was obtained for EPS E44. None of the carbohydrates tested supported the growth of microorganisms from Clostridium clusters XIVa+b and IV, results that correlate with the poor butyrate production in the presence of EPS. Thus, EPS synthesized by bifidobacteria from dairy and intestinal origins can modulate the intestinal microbiota in vitro, promoting changes in some numerically and metabolically relevant microbial populations and shifts in the production of short chain fatty acids. (C) 2009 Elsevier B.V. All rights reserved.