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‣ cDNA microarray analysis of differentially expressed genes in penile tissue after treatment with tadalafil

ANDRADE, Enrico; ANDRADE, Priscila Maria; BORRA, Ricardo Carneiro; CLARO, Joaquim; Srougi, Miguel
Fonte: BLACKWELL PUBLISHING Publicador: BLACKWELL PUBLISHING
Tipo: Artigo de Revista Científica
Português
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To evaluate differential gene expression in penile tissue after treatment with the phosphodiesterase 5 (PDE5) inhibitor tadalafil, as of the three clinically available PDE5 inhibitors (sildenafil, tadalafil, and vardenafil) used for the treatment of erectile dysfunction (ED), tadalafil has a long half-life and low incidence of side-effects. In all, 32 adult rats were divided into two groups. The control group received 0.5 mL of drinking water alone, while the tadalafil group was treated with tadalafil at a dose of 0.27 mg/kg. At 4 h after treatment with water or tadalafil the rats were killed and the penile tissue was removed. The total RNA was isolated from the penile tissue from both groups and differentially expressed genes were identified by cDNA microarray analysis. To validate the expression data from the microarray analysis, quantitative real-time polymerase chain reaction (PCR) and immunohistochemistry were used. In all, 153 genes were differentially expressed between the control group and the tadalafil group. We validated the microarray results by quantitative PCR for the insulin-like growth factor binding protein 6 (IGFBP-6) gene and the neuronal calcium sensor 1 (NCS-1) gene, both of which were up-regulated in the tadalafil group...

‣ Avaliação da mudança na expressão gênica em tumores de mama após tratamento com rapamicina; Rapamycin induced transcriptional profile of breast cancer mantained in organ culture

Grosso, Stana Helena Giorgi
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 19/09/2008 Português
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A via AKT/PI3K apresenta-se geralmente alterada nos diversos tipos de cânceres humanos e a alteração dos componentes desta via ocorre através da ativação de oncogenes ou inativação de genes supressores tumorais levando a transformações celulares que podem promover a tumorigênese. No câncer de mama a via AKT/PI3K pode ser ativada por Erb-B2, receptores dos fatores de crescimento de insulina (IGF), receptores de estrógeno e perda da expressão do gene PTEN. mTOR (proteína alvo da rapamicina em mamíferos) é uma serina treonina quinase, membro da via AKT/PI3K que se encontra envolvida em múltiplas funções biológicas como controle da tradução, transcrição, degradação protéica e biogênese ribossomal. A ativação desta proteína resulta na fosforilação e ativação de seus principais substratos 4EBP1 e S6K1, requeridos para a biossíntese ribossomal e tradução de RNAms importantes para controle e progressão no ciclo celular. A rapamicina é uma droga com propriedades fungicidas, imunossupressoras e anticancerígenas que atua na inibição de mTOR afetando a expressão de genes envolvidos no metabolismo e síntese protéica. No nosso estudo avaliamos os elementos da via do AKT através de análise imunoistoquímica em fatias de tumores mantidos em cultura de órgão antes e depois do tratamento com rapamicina. A cultura de órgão mantém uma interação entre o epitélio mamário e estroma podendo-se preservar o microambiente que reconstitui o comportamento da célula tumoral. Nesta análise imunoistoquímica observamos uma diminuição significativa de 4EBP1 nas fatias dos tumores tratados com rapamicina em relação aos casos controles. Além disso...

‣ Hybridizing sparse component analysis with genetic algorithms for microarray analysis

Stadlthanner, K.; Theis, F. J.; Lang, E. W.; Tomé, A. M.; Puntonet, C. G.; Górriz, J. M.
Fonte: Elsevier Publicador: Elsevier
Tipo: Artigo de Revista Científica
Português
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Nonnegative Matrix Factorization (NMF) has proven to be a useful tool for the analysis of nonnegative multivariate data. However, it is known not to lead to unique results when applied to Blind Source Separation (BSS) problems. In this paper we present an extension of NMF capable of solving the BSS problem when the underlying sources are sufficiently sparse. In contrast to most well-established BSS methods, the devised algorithm is capable of solving the BSS problem in cases where the underlying sources are not independent or uncorrelated. As the proposed fitness function is discontinuous and possesses many local minima, we use a genetic algorithm for its minimization. Finally, we apply the devised algorithm to real world microarray data.; Siemens AG, Corporate Technology, Munich - Biomarker; DFG - GRK 638: Nonlinearity and Nonequilibrium in Condensed Matter; DAAD-GRICES Acções Integradas Luso-Alemãs - GEVD-MP; DAAD Acciones Integradas Hispano-Alemanas - Microarrays

‣ Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress

Coito, João L.; Rocheta, Margarida; Carvalho, Luísa; Amâncio, Sara
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em //2012 Português
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Research Article; Background: Quantitative real time polymerase chain reaction is becoming the primary tool for detecting mRNA and transcription data analysis as it shows to have advantages over other more commonly used techniques. Nevertheless, it also presents a few shortcomings, with the most import being the need for data normalisation, usually with a reference gene. Therefore the choice of the reference gene(s) is of great importance for correct data analysis. Microarray data, when available, can be of great assistance when choosing reference genes. Grapevine was submitted to water stress and heat stress as well as a combination of both to test the stability of the possible reference genes. Results: Using the analysis of microarray data available for grapevine, six possible reference genes were selected for RT-qPCR validation: PADCP, ubiq, TIF, TIF-GTP, VH1-IK, aladin-related. Two additional genes that are commonly used as reference genes were included: act and L2. The stability of those genes was tested in leaves of grapevine in both field plants and in greenhouse plants under water or heat stress or a combination of both. Gene stability was analyzed with the softwares GeNorm, NormFinder and the ΔCq method resulting in several combinations of reference genes suitable for data normalisation. In order to assess the best combination...

‣ D-MaPs - DNA-microarray projects: web-based software for multi-platform microarray analysis

Carazzolle,Marcelo F.; Herig,Taís S.; Deckmann,Ana C.; Pereira,Gonçalo A.G.
Fonte: Sociedade Brasileira de Genética Publicador: Sociedade Brasileira de Genética
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/01/2009 Português
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The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix). Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus) submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner). In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core.

‣ Microarray analysis of evolution of RNA viruses: Evidence of circulation of virulent highly divergent vaccine-derived polioviruses

Cherkasova, Elena; Laassri, Majid; Chizhikov, Vladimir; Korotkova, Ekaterina; Dragunsky, Eugenia; Agol, Vadim I.; Chumakov, Konstantin
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
Português
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Two approaches based on hybridization of viral probes with oligonucleotide microarrays were developed for rapid analysis of genetic variations during microevolution of RNA viruses. Microarray analysis of viral recombination and microarray for resequencing and heterogeneity analysis were able to generate instant genetic maps of vaccine-derived polioviruses (VDPVs) and reveal the degree of their evolutionary divergence. Unlike conventional methods based on cDNA sequencing and restriction fragment length polymorphism, the microarray approaches are better suited for analysis of heterogeneous populations and mixtures of different strains. The microarray hybridization profile is very sensitive to the cumulative presence of small quantities of different mutations, including those that cannot be revealed by sequencing, making this approach useful for characterization of profiles of nucleotide sequence diversity in viral populations. By using these methods, we identified a type-3 VDPV isolated from a healthy person and missed by conventional methods of screening. The mutational profile of the polio strain was consistent with >1 yr of circulation in human population and was highly virulent in transgenic mice, confirming the ability of VDPV to persist in communities despite high levels of immunity. The proposed methods for fine genotyping of heterogeneous viral populations can also have utility for a variety of other applications in studies of genetic changes in viruses...

‣ Mouse genomic representational oligonucleotide microarray analysis: Detection of copy number variations in normal and tumor specimens

Lakshmi, B.; Hall, Ira M.; Egan, Christopher; Alexander, Joan; Leotta, Anthony; Healy, John; Zender, Lars; Spector, Mona S.; Xue, Wen; Lowe, Scott W.; Wigler, Michael; Lucito, Robert
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
Português
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Genomic amplifications and deletions, the consequence of somatic variation, are a hallmark of human cancer. Such variation has also been observed between “normal” individuals, as well as in individuals with congenital disorders. Thus, copy number measurement is likely to be an important tool for the analysis of genetic variation, genetic disease, and cancer. We developed representational oligonucleotide microarray analysis, a high-resolution comparative genomic hybridization methodology, with this aim in mind, and reported its use in the study of humans. Here we report the development of a representational oligonucleotide microarray analysis microarray for the genomic analysis of the mouse, an important model system for many genetic diseases and cancer. This microarray was designed based on the sequence assembly MM3, and contains ≈84,000 probes randomly distributed throughout the mouse genome. We demonstrate the use of this array to identify copy number changes in mouse cancers, as well to determine copy number variation between inbred strains of mice. Because restriction endonuclease digestion of genomic DNA is an integral component of our method, differences due to polymorphisms at the restriction enzyme cleavage sites are also observed between strains...

‣ Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data

Hsiao, Albert; Subramaniam, Shankar
Fonte: Springer Netherlands Publicador: Springer Netherlands
Tipo: Artigo de Revista Científica
Português
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Conventional statistical methods for interpreting microarray data require large numbers of replicates in order to provide sufficient levels of sensitivity. We recently described a method for identifying differentially-expressed genes in one-channel microarray data 1. Based on the idea that the variance structure of microarray data can itself be a reliable measure of noise, this method allows statistically sound interpretation of as few as two replicates per treatment condition. Unlike the one-channel array, the two-channel platform simultaneously compares gene expression in two RNA samples. This leads to covariation of the measured signals. Hence, by accounting for covariation in the variance model, we can significantly increase the power of the statistical test. We believe that this approach has the potential to overcome limitations of existing methods. We present here a novel approach for the analysis of microarray data that involves modeling the variance structure of paired expression data in the context of a Bayesian framework. We also describe a novel statistical test that can be used to identify differentially-expressed genes. This method, bivariate microarray analysis (BMA), demonstrates dramatically improved sensitivity over existing approaches. We show that with only two array replicates...

‣ Unraveling the ischemic brain transcriptome in a permanent middle cerebral artery occlusion mouse model by DNA microarray analysis

Hori, Motohide; Nakamachi, Tomoya; Rakwal, Randeep; Shibato, Junko; Nakamura, Keisuke; Wada, Yoshihiro; Tsuchikawa, Daisuke; Yoshikawa, Akira; Tamaki, Keiji; Shioda, Seiji
Fonte: The Company of Biologists Limited Publicador: The Company of Biologists Limited
Tipo: Artigo de Revista Científica
Português
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Brain ischemia, also termed cerebral ischemia, is a condition in which there is insufficient blood flow to the brain to meet metabolic demand, leading to tissue death (cerebral infarction) due to poor oxygen supply (cerebral hypoxia). Our group is interested in the protective effects of neuropeptides for alleviating brain ischemia, as well as the underlying mechanisms of their action. The present study was initiated to investigate molecular responses at the level of gene expression in ischemic brain tissue. To achieve this, we used a mouse permanent middle cerebral artery occlusion (PMCAO) model in combination with high-throughput DNA microarray analysis on an Agilent microarray platform. Briefly, the right (ipsilateral) and left (contralateral) hemispheres of PMCAO model mice were dissected at two time points, 6 and 24 hours post-ischemia. Total RNA from the ischemic (ipsilateral) hemisphere was subjected to DNA microarray analysis on a mouse whole genome 4x44K DNA chip using a dye-swap approach. Functional categorization using the gene ontology (GO, MGD/AMIGO) of numerous changed genes revealed expression pattern changes in the major categories of cellular process, biological regulation, regulation of biological process, metabolic process and response to stimulus. Reverse-transcriptase PCR (RT-PCR) analysis on randomly selected highly up- or downregulated genes validated...

‣ Comparative RNA-Seq and Microarray Analysis of Gene Expression Changes in B-Cell Lymphomas of Canis familiaris

Mooney, Marie; Bond, Jeffrey; Monks, Noel; Eugster, Emily; Cherba, David; Berlinski, Pamela; Kamerling, Steve; Marotti, Keith; Simpson, Heather; Rusk, Tony; Tembe, Waibhav; Legendre, Christophe; Benson, Hollie; Liang, Winnie; Webb, Craig Paul
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 04/04/2013 Português
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Comparative oncology is a developing research discipline that is being used to assist our understanding of human neoplastic diseases. Companion canines are a preferred animal oncology model due to spontaneous tumor development and similarity to human disease at the pathophysiological level. We use a paired RNA sequencing (RNA-Seq)/microarray analysis of a set of four normal canine lymph nodes and ten canine lymphoma fine needle aspirates to identify technical biases and variation between the technologies and convergence on biological disease pathways. Surrogate Variable Analysis (SVA) provides a formal multivariate analysis of the combined RNA-Seq/microarray data set. Applying SVA to the data allows us to decompose variation into contributions associated with transcript abundance, differences between the technology, and latent variation within each technology. A substantial and highly statistically significant component of the variation reflects transcript abundance, and RNA-Seq appeared more sensitive for detection of transcripts expressed at low levels. Latent random variation among RNA-Seq samples is also distinct in character from that impacting microarray samples. In particular, we observed variation between RNA-Seq samples that reflects transcript GC content. Platform-independent variable decomposition without a priori knowledge of the sources of variation using SVA represents a generalizable method for accomplishing cross-platform data analysis. We identified genes differentially expressed between normal lymph nodes of disease free dogs and a subset of the diseased dogs diagnosed with B-cell lymphoma using each technology. There is statistically significant overlap between the RNA-Seq and microarray sets of differentially expressed genes. Analysis of overlapping genes in the context of biological systems suggests elevated expression and activity of PI3K signaling in B-cell lymphoma biopsies compared with normal biopsies...

‣ Automatic Spot Identification for High Throughput Microarray Analysis

Wu, Eunice; Su, Yan A.; Billings, Eric; Brooks, Bernard R.; Wu, Xiongwu
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Português
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High throughput microarray analysis has great potential in scientific research, disease diagnosis, and drug discovery. A major hurdle toward high throughput microarray analysis is the time and effort needed to accurately locate gene spots in microarray images. An automatic microarray image processor will allow accurate and efficient determination of spot locations and sizes so that gene expression information can be reliably extracted in a high throughput manner. Current microarray image processing tools require intensive manual operations in addition to the input of grid parameters to correctly and accurately identify gene spots. This work developed a method, herein called auto-spot, to automate the spot identification process. Through a series of correlation and convolution operations, as well as pixel manipulations, this method makes spot identification an automatic and accurate process. Testing with real microarray images has demonstrated that this method is capable of automatically extracting subgrids from microarray images and determining spot locations and sizes within each subgrid, regardless of variations in array patterns and background noises. With this method, we are one step closer to the goal of high throughput microarray analysis.

‣ Identification of differentially expressed genes between osteoarthritic and normal trabecular bone from the intertrochanteric region of the proximal femur using cDNA microarray analysis

Hopwood, B.; Gronthos, S.; Kuliwaba, J.; Robey, P.; Findlay, D.; Fazzalari, N.
Fonte: Elsevier Science Inc Publicador: Elsevier Science Inc
Tipo: Artigo de Revista Científica
Publicado em //2005 Português
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Osteoarthritis (OA) is a common age-related joint disease resulting in progressive degenerative damage to articular cartilage. The etiology of primary OA has not yet been determined. However, there is evidence supporting the hypothesis that primary OA is a disease affecting bone remodeling in addition to articular cartilage. In this study, we have used cDNA microarray analysis to compare gene expression in bone between normal (CTL) and OA individuals. Trabecular bone was sampled from the intertrochanteric region of the proximal femur, a site distal to the diseased hip joint. Total RNA was extracted from three pairs of age- and sex-matched CTL and OA bone samples, reverse-transcribed and radioactively labeled to generate cDNA probes, before hybridization with the Research Genetics GF211 human gene microarray filter. The CTL and OA samples were found to have similar levels of gene expression for more than 4000 known human genes. However, forty-one genes were identified that were differentially expressed, twofold or more, between all three CTL–OA sample pairs. Using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis, three genes, fms-like tyrosine kinase 1 (FLT1), plexin B1 (PLXNB1), and small inducible cytokine A2 (SCYA2)...

‣ Microarray gene expression profiling of osteoarthritic bone suggests altered bone remodelling, WNT and transforming growth factor-β/bone morphogenic protein signalling; Microarray gene expression profiling of osteoarthritic bone suggests altered bone remodelling, WNT and transforming growth factor-beta/bone morphogenic protein signalling

Hopwood, B.; Tsykin, A.; Findlay, D.; Fazzalari, N.
Fonte: BioMed Central Ltd. Publicador: BioMed Central Ltd.
Tipo: Artigo de Revista Científica
Publicado em //2007 Português
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Osteoarthritis (OA) is characterized by alterations to subchondral bone as well as articular cartilage. Changes to bone in OA have also been identified at sites distal to the affected joint, which include increased bone volume fraction and reduced bone mineralization. Altered bone remodelling has been proposed to underlie these bone changes in OA. To investigate the molecular basis for these changes, we performed microarray gene expression profiling of bone obtained at autopsy from individuals with no evidence of joint disease (control) and from individuals undergoing joint replacement surgery for either degenerative hip OA, or fractured neck of femur (osteoporosis [OP]). The OP sample set was included because an inverse association, with respect to bone density, has been observed between OA and the low bone density disease OP. Compugen human 19K-oligo microarray slides were used to compare the gene expression profiles of OA, control and OP bone samples. Four sets of samples were analyzed, comprising 10 OA-control female, 10 OA-control male, 10 OA-OP female and 9 OP-control female sample pairs. Print tip Lowess normalization and Bayesian statistical analyses were carried out using linear models for microarray analysis, which identified 150 differentially expressed genes in OA bone with t scores above 4. Twenty-five of these genes were then confirmed to be differentially expressed (P < 0.01) by real-time PCR analysis. A substantial number of the top-ranking differentially expressed genes identified in OA bone are known to play roles in osteoblasts...

‣ Microarray analysis identifies candidate genes for key roles in coral development

Grasso, L.; Maindonald, J.; Rudd, S.; Hayward, D.; Saint, R.; Miller, D.; Ball, E.
Fonte: BioMed Central Ltd. Publicador: BioMed Central Ltd.
Tipo: Artigo de Revista Científica
Publicado em //2008 Português
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Background: Anthozoan cnidarians are amongst the simplest animals at the tissue level of organization, but are surprisingly complex and vertebrate-like in terms of gene repertoire. As major components of tropical reef ecosystems, the stony corals are anthozoans of particular ecological significance. To better understand the molecular bases of both cnidarian development in general and coral-specific processes such as skeletogenesis and symbiont acquisition, microarray analysis was carried out through the period of early development – when skeletogenesis is initiated, and symbionts are first acquired. Results: Of 5081 unique peptide coding genes, 1084 were differentially expressed (P ≤ 0.05) in comparisons between four different stages of coral development, spanning key developmental transitions. Genes of likely relevance to the processes of settlement, metamorphosis, calcification and interaction with symbionts were characterised further and their spatial expression patterns investigated using whole-mount in situ hybridization. Conclusion: This study is the first large-scale investigation of developmental gene expression for any cnidarian, and has provided candidate genes for key roles in many aspects of coral biology, including calcification...

‣ Etablierung von Home-Made cDNA Microarrays und Untersuchung der Genexpression nach Hochleistungssport; Establishment of home-made cDNA Microarrays and cDNA-microarray analysis as a research tool for expression profiling in human peripheral blood following exhaustive exercise

Zieker, Derek
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
Português
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Stress kann in verschiedenen Varianten auftreten, und sich sehr unterschiedlich auf den Organismus auswirken. Im Rahmen dieses Forschungsprojektes wurde ein freiwillig auferlegter physischer Stress in Form von Hochleistungssport untersucht. Bei hohen Trainings- oder Wettkampfbelastungen werden Stressantworten im Immunsystem des Sportlers mobilisiert, die dann sekundäre Auswirkungen auf somatische Parameter zeigen. Diese Auswirkungen können zu Veränderungen in der zellulären Zusammensetzung im peripheren Blut führen. Des Weiteren, kann man eine Veränderung auf Genexpressionsebene beobachten. Im Rahmen der Dissertationsarbeit wurden home-made cDNA Microarrays hergestellt und etabliert. Die Herstellung und Etablierung sind im Abschnitt Methode dieser Arbeit ausführlich beschrieben. In dieser Studie wurde mit home-made cDNA Microarrays die Genexpression bei acht Halbmarathonläufern untersucht. Der eingesetzte cDNA Microarray enthielt ausgewählte Gene des Stress- und Entzündungsgeschehen. Das Besondere dieses Ansatzes ist, dass nicht nur ein einzelnes oder wenige Kandidatengene sondern eine größere Gruppe potentiell relevanter Gene auf mRNA- Ebene analysiert wurde. Die Abnahmezeitpunkte der Blutproben der Läufer waren, vor (t0)...

‣ cDNA Microarray Analyse und Genexpressionprofil von sporadischen Vestibularisschwannomen verglichen mit gesundem Autopsiegewebe: Eine Betrachtungsweise auf molekularer Ebene unter Verwendung der Ingenuity Pathway Analysis Software; cDNA microarray analysis and gene expression profiling of sporadic vestibular schwannomas compared to healthy post-mortem tissue: a look at the molecular level using Ingenuity Pathway Analysis Software

Gugel, Isabel
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
Português
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Ziel: Die vorliegende Studie wurde durchgeführt um differentiell exprimierte Gene und Signalwege zwischen Tumor- und Kontrollgewebe zu identifizieren, die eine möglicherweise wichtige Rolle in der Krankheitsentstehung spielen. Zur Bestimmung des Expressionsprofils diente uns eine cDNA Microarray und die Auswertung der resultierenden Daten erfolgte mit der Ingenuity Pathway Analysis Software (IPA, www.ingenuity.com). Hintergrund: Vestibularisschwannome sind benigne Tumore, die von den Schwannzellen des VIII. Hirnnerven ausgehen. Mit einem Anteil von 80-86% aller raumfordernden Läsionen des Kleinhirnbrückenwinkels stellen sie somit die am häufigsten dort anzutreffende Tumorentität dar. Unter den Vestibularisschwannomen werden eine unilateral sporadische Form, eine zystische Variante und eine bilateral oder auch Neurofibromatose Typ 2 (NF2)-assoziierte Form unterschieden. Letztere ist eine charakteristische Manifestation innerhalb des autosomal-dominant vererbten Tumorsyndroms, der Neurofibromatose Typ 2 (NF2). Zudem weisen die Patienten mit einer NF2 weitere benigne Tumore des Nervensystems (z.B. Meningeome), okuläre Veränderungen (z.B. Katarakte) aber auch Hautläsionen, wie beispielsweise die typischen Café-au-lait Flecken...

‣ Fetal ocular movements and retinal cell differentiation: analysis employing DNA microarrays

Baguma-Nibasheka, M.; Reddy, T.; Abbas-Butt, A.; Kablar, B.
Fonte: Murcia : F. Hernández Publicador: Murcia : F. Hernández
Tipo: Artigo de Revista Científica Formato: application/pdf
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As developmental biologists we study the role of fetal movements in providing continuity between prenatal and postnatal life. There are two major categories of fetal motility. The first category consists of movements that have an obvious effect on the survival or development of the fetus (e.g., changes of position, sucking and swallowing). The second category consists of fetal movements that anticipate postnatal functions. For example, fetal ocular movements (FOMs) predict postnatal eye function (e.g., motion vision) of the newborn and therefore represent an important indicator of fetal health. However, while the clinical significance of fetal motility is obvious, its biological significance is elusive. We propose to use retina of genetically modified mouse embryos to study the biological role of FOMs in the genesis of cell diversity and organ functional maturation. Our results have already demonstrated the importance of fetal eye motility in the differentiation of cholinergic amacrine cells (CACs) in the retina (Kablar, 2003). Apparently, these cells are sensitive to motion and also responsible for motion vision. In the current report, we suggest employing the unique opportunity provided by the mouse Myf5-/-:MyoD-/- knock-outs that lack skeletal musculature and FOMs...

‣ Identification of differentially expressed genes in fetal rat forebrain exposed to a teratogen by cDNA microarray analysis

Dheen, S.T.; Hao, A.J.; Fu, J.; Gopalakrishnakone, P.; Ling, E. A.
Fonte: Murcia : F. Hernández Publicador: Murcia : F. Hernández
Tipo: Artigo de Revista Científica Formato: application/pdf
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In an attempt to understand the molecular basis underlying the neural tube defects induced by the teratogen, cyclophosphamide (CP), cDNA microarray analysis was carried out in neural tubes of embryos derived from normal and CP-treated rats. Genes found to have altered expression levels in CP-treated group were clustered into groups on the basis of their biological functions. The expression profile of different genes involved in transcription of molecules related to cell adhesion, inflammation, metabolism and neurotrophic factors pathways as well as in still undefined processes was differentially affected by the teratogen treatment. The most remarkable change was the up-regulation of genes related to an inflammatory process dominated by the fetal brain macrophages viz. amoeboid microglia. Amoeboid microglia/brain macrophage expansion, based on gene expression and histological analysis, was found to be vigorous at the subventricular region. The present results suggest that a vigorous inflammatory response involving amoeboid microglia/brain macrophages primarily is an important component in CP-induced prenatal development disorder.

‣ Prenatal Investigation of a Familial Partial Monosomy 10q

Silva, Marisa; Marques, Bárbara; Brito, Filomena; Ferreira, Cristina; Furtado, José; Ventura, Catarina; Nunes, Luis; Kay, Teresa; Caetano, Paula; Correia, Hildeberto
Fonte: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP Publicador: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP
Tipo: Conferência ou Objeto de Conferência
Publicado em 28/09/2012 Português
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Objective: To present the clinical, cytogenetic and molecular findings of a prenatal study of a familial partial monosomy 10q. Distal 10q deletions are rare and the majority are terminal deletions involving bands 10q25 and 10q26. Patients typically present with facial dysmorphism, postnatal growth retardation, developmental and mental retardation, genitourinary anomalies and digital anomalies. Methods: Conventional cytogenetic analysis in metaphases obtained by chorionic villi long term cultures, multiplex ligation dependent probe amplification (MLPA), fluorescent in situ hybridization (FISH), microarray analysis. Results: A 24-year-old gravida was referred for chorionic villus sampling at 12+6 weeks of gestation due to a previous child with facial dysmorphism, bilateral inguinal hernia, short stature and mild to moderate psychomotor delay of whom a microarray analysis was underway. His karyotype was normal but array-CGH analysis disclosed a 10q24.33-q25.1 interstitial deletion. The deletion encompasses 987Kb to 1,14Mb and includes 20 genes, in particular the COL17A gene. Fetal and parental karyotypes were normal. FISH analysis with a BAC clone located within the 10q region deleted in the phenotypically abnormal sibling showed normal results for both the mother and the fetus and a deletion in the apparently normal father. Conclusion: In this case chorionic villi analysis as well as the application of FISH with a specific and targeted BAC clone allowed a shorter turnaround time for the prenatal investigation of the chromosomal abnormality. The authors discuss the challenges of microarray analysis application in the prenatal setting namely in cases like the one presented here where there seems to be phenotypic variability.

‣ Analysis-driven lossy compression of DNA microarray images

Hernández Cabronero, Miguel; Blanes Garcia, Ian; Pinho, Armando J.; Marcellin, Michael W.; Serra Sagristà, Joan
Fonte: Universidade Autônoma de Barcelona Publicador: Universidade Autônoma de Barcelona
Tipo: info:eu-repo/semantics/article; info:eu-repo/semantics/acceptedVersion Formato: application/pdf
Publicado em //2015 Português
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DNA microarrays are one of the fastest-growing new technologies in the field of genetic research, and DNA microarray images continue to grow in number and size. Since analysis techniques are under active and ongoing development, storage, transmission and sharing of DNA microarray images need be addressed, with compression playing a significant role. However, existing lossless coding algorithms yield only limited compression performance (compression ratios below 2:1), whereas lossy coding methods may introduce unacceptable distortions in the analysis process. This work introduces a novel Relative Quantizer (RQ), which employs non-uniform quantization intervals designed for improved compression while bounding the impact on the DNA microarray analysis. This quantizer constrains the maximum relative error introduced into quantized imagery, devoting higher precision to pixels critical to the analysis process. For suitable parameter choices, the resulting variations in the DNA microarray analysis are less than half of those inherent to the experimental variability. Experimental results reveal that appropriate analysis can still be performed for average compression ratios exceeding 4.5:1.