Gene expression analysis identifies hypothetical genes that may be critical during the infection process of Xanthomonas citri subsp. citri

Background: Gene expression analysis via microarray is widely used in phytobacteria to validate differential gene expression associated with virulence or to compare biological profiles of wild type and mutant strains. Here, we employed DNA microarrays to study the early stages of the infection process (24, 72 and 120 h post-inoculation) of Xanthomonas citri subsp. citri (Xac) infecting Citrus sinensis to interrogate the expression profiles of hypothetical genes. Results: Under infective conditions, 446 genes were up- and 306 downregulated. Outstanding among genes upregulated during infection were those involved in synthesizing the Type 3 Secretion System and effectors, xanthan gum and quorum-sensing induction, and flagellum synthesis and regulation. Additionally, 161 hypothetical genes were up- and 100 were downregulated, 49 of which are known to have a significant biological role. To understand hypothetical gene co-regulation or -expression, nine expression profiles including 158 genes were identified during the three infection phases. Of these, 47 hypothetical genes were identified as having expression profiles associated with at least one connected to a gene associated with adaptation and virulence. Conclusions: Expression patterns of six differentially expressed genes were validated by quantitative reverse transcription polymerase chain reaction, thus demonstrating the effectiveness of this tool in global gene expression analysis in Xac.

Complejidad de la expresión de genes asociados a obesidad en el tejido adiposo humano / Complexity of the expression of genes associated with obesity in human adipose tissue / Complexidade da expressão de genes associados à obesidade no tecido adiposo humano

Resumen Objetivo: Analizar la complejidad de la expresión génica en tejido adiposo de genes asociados con obesidad, mediante simulación computacional con diferentes herramientas bioinformáticas. Métodos: Después de una búsqueda bibliográfica en PubMed, se seleccionaron 37 genes asociados con obesidad con fold change mayor a 1,5. A partir del cálculo de valores de los z-score obtenidos de experimentos de micromatrices de ADN de muestras de tejido adiposo de personas obesas y de control, se construyó una red de interacción con el programa Cytoscape 3.2. La información detallada sobre las características genómicas de estos genes se extrajo de las bases de datos Genome Browser de la UCSC y del NCBI. Utilizando herramientas de análisis de multivariado, se hizo un análisis de componentes principales y uno de agrupación. Resultados: La red construida mostró que los genes con mayor número de interacciones fueron: 1) el factor nuclear respiratorio (NRF1), 2) el canal activado de potasio activado por calcio alfa 1 (KCNMA1) y 3) la sintasa de ácidos grasos (FASN). Los que tuvieron mayores valores de expresión fueron: 1) el factor de crecimiento endotelial vascular A (VEGFA), 2) la dioxigenasa dependiente de alfa-cetoglutarato (FTO) y 3) el regulador de crecimiento neuronal 1 (NEGR1). Las proteínas IL6, BDNF y HLC tuvieron los mayores valores de interacción con IL6R, NRF1 y ACACB, respetivamente. Las categorías ontológicas más importantes se relacionaron con procesos metabólicos de lipoproteínas, el ciclo de los ácidos tricarboxílicos, la activación de las MAP-quinasas y la cascada JNK. Conclusiones: En su conjunto los resultados obtenidos de sobreexpresión diferencial de genes asociados con el metabolismo de lípidos en el tejido adiposo de personas obesas podría ser un criterio para discriminar a nivel de diagnóstico esta patología.

Summary Objective: To analyze the complexity of gene expression in the adipose tissue of genes associated with obesity, by computer simulation with different bioinformatics tools. Methods: After conducting a PubMed literature search, 37 genes associated with obesity with a fold change greater than 1.5 were selected. An interaction network was cons tructed using the Cytoscape 3.2 program from the calculation of z-score values obtained from DNA microarray experiments of adipose tissue samples collected from obese and control people. Detailed information on the genomic characteristics of these genes was extracted from the UCSC and NCBI Genome Browser databases. Using multivariate analysis tools, a principal component analysis and a cluster analysis were carried out. Results: The constructed network showed that the genes with the greatest number of interactions were: 1) the nuclear respiratory factor (NRF1), 2) the activated channel of potassium activate by calcium alpha 1 (KCNMA1), and 3) the fatty acid synthase (FASN). Those with the higher expression values were: 1) vascular endothelial growth factor A (VEGFA), 2) alpha-ketoglutarate-dependent dioxygenase (FTO), and 3) neuronal growth regulator 1 (NEGR1). The IL6, BDNF and HLC proteins had the highest interaction values with IL6R, NRF1 and ACACB, respectively. The most important ontological categories were related to lipoprotein metabolic processes, the tricarboxylic acid cycle, the activation of the MAP kinases, and the JNK cascade. Conclusions: As a whole, the results obtained from differential overexpression of genes associated with lipid metabolism in the adipose tissue of obese people could be a criterion to discriminate this pathology at a diagnostic level.

Resumo Objetivo: Analisar a complexidade da expressão gênica no tecido adiposo de genes associados com obesidade, por meio de simulação por computador com diferentes ferramentas bioinformáticas. Métodos: Após uma busca bibliográfica em PubMed, foram selecionados 37 genes associados com obesidade com fold change superior a 1,5. A partir do cálculo de valores dos z-score obtidos de experimentos de micro matrizes de ADN de amostras de tecido adiposo de pessoas obesas e de controle, construiu-se uma rede de interação com o programa Cytoscape 3.2. A informação detalhada sobre as características genômicas destes genes foi obtida das bases de dados Genome Browser da UCSC e do NCBI. Utilizando ferramentas de análise de multivariado, fez-se uma análise de componentes principais e um de agrupação. Resultados: A rede construída mostrou que os genes com maior número de interações foram: 1) o fator nuclear respiratório (NRF1), 2) o canal ativado de potássio ativado por cálcio alfa 1 (KCNMA1) e 3) ácido graxo sintase (FASN). Os que tiveram maiores valores de expressão foram: 1) o fator de crescimento endo-telial vascular A (VEGFA), 2) a dioxigenase dependente de alfa-cetoglutarato (FTO) e 3) o regulador de crescimento neuronal 1 (NEGR1). As proteínas IL6, BDNF e HLC tiveram os maiores valores de interação com IL6R, NRF1 e ACACB, respectivamente. As categorias ontológicas mais importantes se relacionaram com processos metabólicos de lipoproteínas, o ciclo dos ácidos tri carboxílicos, a ativação das MAP-quinases e a cascata JNK. Conclusões: Em seu conjunto, os resultados obtidos de superexpressão diferencial de genes associados com o metabolismo de lipídios no tecido adiposo de pessoas obesas poderia ser um critério para discriminar a nível de diagnóstico esta patologia.

Diagnóstico clínico en saliva. Revisión

El odontólogo está llamado a convertirse en un elemento importante en el desarrollo de estudios de fenotipado de poblaciones para impulsar la aplicación de la medicina personalizada y la razón se debe a la saliva, que además de resultar un fluido imprescindible para la conservación de las funciones orales, se perfila con cualidades importantes para el diagnóstico clínico con base genética. Con el desarrollo de potentes técnicas de laboratorio, como el inmunoensayo, electroforesis, fluorescencia, cromatografía (HPLC y CG), espectrometría de masa (EM), la reacción en cadena de la polimerasa (PCR) y pruebas genéticas de fenotipado, se ha podido correlacionar la presencia de ciertos biomarcadores de daño tisular en la saliva con los niveles de esas especies en sangre. Estos biomarcadores constituyen señales del daño tisular o de respuestas del organismo a esas injurias, cuando aun no se pueden observar las evidencias clínicas del mismo. Esta aplicación de la saliva le confiere una importancia especial en lo referente al diagnóstico clínico. Al estudio de los biomarcadores orales se ha unido, de forma más reciente, el desarrollo de protocolos para la obtención de ADN genómico de la saliva que permite, por la viabilidad en la colección de muestras, su conservación y facilidades en su traslado, realizar estudios poblacionales para conocer la funcionalidad de ciertos genes que se relacionan con la biotransformación de los medicamentos, una causa importante de las variaciones interindividuales a los tratamientos farmacológicos. El conocimiento de polimorfismos en genes que expresan las enzimas que metabolizan fármacos específicos, permite realizar cambios en los principios activos o ajustes en las dosis de tratamientos individuales, que es el objetivo de la medicina personalizada o farmacogenética. Estos estudios también permiten conocer la predisposición genética de poblaciones al desarrollo de ciertas enfermedades, tanto orales como sistémicas, lo que propicia el establecimiento de nuevas políticas en la profilaxis y medicina preventiva. El uso de la saliva con estos fines abre nuevas perspectivas en la atención odontológica, y requiere de esfuerzos interdisciplinarios y cooperación en el equipo de salud.

The dentist is called to become an important element in the development of studies phenotyping of populations to advance the implementation of personalized medicine and the reason is because saliva, which besides being a prerequisite for the preservation of oral functions fluid , is emerging with important qualities for clinical diagnosis with genetic basis. With the development of powerful laboratory techniques, such as immunoassay, electrophoresis, fluorescence, chromatography (HPLC and GC), mass spectrometry (MS), polymerase chain reaction (PCR) and genetic testing phenotyping, it has been correlate the presence of certain biomarkers of tissue damage in saliva levels of these species in blood. These biomarkers are signs of tissue damage or agency responses to these injuries, when not even be seen clinical evidence of it. This application saliva attaches special importance with regard to clinical diagnosis. The study of oral biomarkers has joined, more recently, the development of protocols for obtaining genomic DNA from saliva that allows for viability in sample collection, preservation of the same and facilities during transport, conduct population studies to determine the function of certain genes that are related to biotransformation of drugs, a major cause of differences among individuals to drug treatments. Knowledge of polymorphisms in genes that express enzymes that metabolize specific drugs can make changes or adjustments active principles in doses of individual treatments, which is the goal of personalized medicine or pharmacogenetics. These studies also provide insight into the genetic predisposition of populations to the development of certain diseases, both oral and systemic, which favors the establishment of new policies in the prophylaxis and preventive medicine. The use of saliva for this purpose opens new perspectives in care dental and requires interdisciplinary efforts and cooperation in the health team.

From Faulty Biochemical Assumptions to Poor Diagnostic Performance: Reflections on the Failure of DNA Microarrays to Become a Reliable Clinical Diagnostic Tool.

Since their inception about two decades ago, DNA microarrays have been considered as a great hope in translational research and personalized medicine. Although DNA microarrays for gene expression profiling proved to be an indispensable tool in the laboratory settings, their applications as an instrument for clinical diagnostics have not yet produced tangible results. In this paper, we convey the idea that, apart from notoriously poor reproducibility and complexities of experimental validations, there exist other reasons hindering clinical application of DNA microarrays. These reasons are rooted in the very core of the DNA microarrays methodology, that is, in faulty biochemical assumptions underlying microarray measurements. A key premise the microarray measurements are based on is that mRNA abundances harvested from the eukaryotic cytoplasm are indicative of the activity levels of corresponding genes. There are at least two reasons why this premise is questionable. First, each transcription is supported by a number of transcription factors expressed by many genes. Due to this reason, relations between the transcription rates of genes and the mRNA abundances are the 'many-to-one', not the 'one-to-one'; therefore, abnormality in a certain mRNA abundance does not unequivocally indicate abnormality of the gene bearing its complimentary code. Second, mRNA copy numbers in cytoplasm are regulated by a number of epigenetic factors among which the post-transcriptional mRNA stability is of primary importance. Abnormal concentration of certain mRNA may result from deviant Opinion Article British Journal of Medicine & Medical Research, 4(27): 4511-4522, 2014 4512 mRNA stability, thus mimicking, but having nothing to do with, presumed abnormality in transcription rates of corresponding genes. An instrument built upon so poorly understood biochemical basis can hardly serve as a reliable tool in the delicate task of diagnosis of human disease in clinical settings.

Investigating the Effects of Imputation Methods for Modelling Gene Networks Using a Dynamic Bayesian Network from Gene Expression Data

Background: Gene expression data often contain missing expression values. Therefore, several imputation methods have been applied to solve the missing values, which include k-nearest neighbour (kNN), local least squares (LLS), and Bayesian principal component analysis (BPCA). However, the effects of these imputation methods on the modelling of gene regulatory networks from gene expression data have rarely been investigated and analysed using a dynamic Bayesian network (DBN). Methods: In the present study, we separately imputed datasets of the Escherichia coli S.O.S. DNA repair pathway and the Saccharomyces cerevisiae cell cycle pathway with kNN, LLS, and BPCA, and subsequently used these to generate gene regulatory networks (GRNs) using a discrete DBN. We made comparisons on the basis of previous studies in order to select the gene network with the least error. Results: We found that BPCA and LLS performed better on larger networks (based on the S. cerevisiae dataset), whereas kNN performed better on smaller networks (based on the E. coli dataset). Conclusion: The results suggest that the performance of each imputation method is dependent on the size of the dataset, and this subsequently affects the modelling of the resultant GRNs using a DBN. In addition, on the basis of these results, a DBN has the capacity to discover potential edges, as well as display interactions, between genes.

Diseño de microsondas mediante hibridación virtual para el estudio de variantes en los sitios REP-CMT1A / Microarray design using virtual hybridization to study variations in REP-CMT1A sites

Antecedentes: El gen PMP22 se encuentra duplicado en pacientes con Charcot-Marie-Tooth 1A (CMT1A); se ha descrito que el origen de la duplicación es el intercambio desigual de las cromátidas durante la meiosis entre dos regiones de 24 kb denominadas sitios REPCMT1A, encontrándose un REP proximal y un REP distal, los cuales tienen una homología de 98%. Dentro de cada uno de estos sitios existen zonas denominadas puntos calientes de mutación (hot spot), donde se presenta el mayor número de variantes y mutaciones que pudieran dar origen al intercambio desigual. El objetivo de este trabajo fue diseñar un conjunto de microsondas para elaborar un microarreglo con el cual pueda detectarse la presencia de variantes y puntos de mutación en los sitios REP-proximal y REP-distal CMT1A. Material y métodos A partir de las secuencias informadas de los REP distal y proximal, se delimitaron los sitios hot spot dentro de las regiones proximal y distal. Estas secuencias se alinearon, se empalmaron y se detectaron 12 zonas de diferencia secuencial. Resultados y conclusiones. Se diseñaron y analizaron 24 microsondas mediante el programa Genosensor Probe Designer. Las sondas podrán ser sintetizadas y utilizadas en un microarreglo que permita encontrar variaciones, puntos de mutación, y facilitar el diagnóstico de pacientes con CMT1A.

BACKGROUND: Gene PMP22 is duplicated in patients with CMT1A. Duplication is due to an unequal chromatid interchange during meiosis that takes place between two 24 Kb regions named REP-CMT1A proximal and distal sites. Homology is approximately 98%. Within each one of the sites we find zones termed hot spots where a greater number of variants and mutations could give origin to an unequal interchange. The aim of this study was to design a set of probes to create a microarray that could detect the presence of variants and mutation points in distal and proximal REP sites among patients with CMT1A. MATERIAL AND METHODS: With reported sequences of distal and proximal REPs, we determined hot spot sites within proximal and distal regions. These sequences were aligned and matched, hence 12 zones were detected. RESULTS AND CONCLUSIONS: Twenty four probes were designed and analyzed using the Genosensor Probe Designer program. Probes could be synthesized and used in a microarray that is able to find variations and mutation points and facilitates diagnosis of patients with CMT1A.

Variaciones genéticas del gen supresor de tumores TP53: relevancia y estrategias de análisis / Genetic variations of the tumor suppressor TP53: Outstanding and strategies of analysis

In the modern society, cancer remains an important cause of death. Cancer development is a very complex process that involves alterations in genes regulating cellular growth. Among these alterations or variations, are included point mutations, genetic susceptibility by single nucleotide polymorphisms or "SNP" and alteration or loss in tumor suppressor genes functions. The tumor suppressor TP53 is one of the most important and studied genes on cancer genetics. Therefore, it has been demonstrated that TP53 present mutations in more than 50% of all types of human cancer and encodes a multifunctional protein whose absence contributes to genomic instability, the accumulation of mutations and increased tumor development. The identification of such alterations in cancerous cells at level of single nucleotide is very important, because its implication in the loss or alteration in the function of this gene, its clinical relevance and finally, its association with response to therapy and prognosis. Due to the large interesting issue, in this work we are focused only in two of the most common genetic variations present in this gene: the point mutations and SNP remarking some outstanding molecular characteristics needed for design its analysis.

El cáncer continúa siendo una importante causa de muerte en la sociedad moderna. Los procesos en el desarrollo del cáncer son muy complejos e involucran alteraciones en genes implicados en la proliferación celular. Entre estas alteraciones o variaciones genéticas se incluyen las mutaciones puntuales, la susceptibilidad genética por polimorfismos de un solo nucleótido o "SNP", así como la pérdida o alteración en la función de genes supresores de tumores. El gen supresor de tumores TP53 es uno de los genes más importantes y estudiados en la genética del cáncer, ya que se encuentra mutado en más del 50% de todos los tipos de cáncer humano y codifica para una proteína multifuncional cuya deficiencia contribuye a la inestabilidad genómica que conduce a la acumulación de mutaciones y a la aceleración en el desarrollo del tumor. Es importante el estudio de dichas alteraciones genéticas presentes en las células cancerosas que puedan ser detectadas a nivel de un solo nucleótido, por su implicación en la pérdida o alteración en la función del gen TP53, así como por la relevancia clínica que ellas puedan tener al ser asociadas a la respuesta de una terapia particular o al pronóstico. Debido a la extensión de este trabajo solamente revisaremos dos de las variaciones genéticas importantes en este gen: las mutaciones puntuales y los SNP, haciendo ánfasis en algunas características moleculares que son relevantes en el diseño de estrategias de análisis para su detección.

Clinical detection and identification of seven species human herpesviruses by DNA microarray technique / 临床检验杂志

Objective To establish a method for rapid diagnosis and identification of seven species human herpesviruses infection.Methods Primers and oligonucleotide probes were designed and synthesized based on the highly conserved regions of the DNA polymerase genes in human herpesviruses, namely herpes simplex virus type 1 (HSV-1),HSV-2,varicella-zoster virus (VZV),Epstein-Barr virus (EBV),cytomegalovirus (CMV),and human herpes virus 6 (HHV-6A/6B).DNA microarrays were made by printing the oligonucleotide probes on the special glass slides.A total of 282 blood specimens from children with suspected infection were analyzed by this DNA microarray technique,and the results were compared with those of TaqMan PCR.Results The products of the seven human herpesviruses after PCR amplification could be used to identify the virus species with DNA microarrays.The detection limits were 10 copies/?l for HSV-1,HSV-2,VZV,EBV,CMV,HHV-6A,and HHV-6B,respectively.The assay did not show cross-reaction to the DNA extract of hepatitis B virus,staphylococcus aureus,E.coli,Candia albicans and human genome.Among the 282 samples,59 were positive for human herpesviruses DNA.Compared with those of TaqMan PCR,the sensitivity and specificity of the microarray assay were 96.7% and 99.5%,respectively,and the index of accurate diagnosis was 0.962.Conclusions This DNA microarray for identifying human herpesviruses species is specific and sensitive,and may serve as an efficient technique for simultaneous detection and species identification of human herpesviruses in clinical specimen.

Gene Expression Profile of Volume-Overloaded Human Ventricular Myocardium Prior to Developing Heart Failure

BACKGROUND AND OBJECTIVES: Left ventricle burdened by longstanding volume-overload, undergoes various structural and functional alterations. Accordingly, the expressions of multiple classes of genes are likely to be altered. However, the profile of gene expressions, specifically in a volume-overloaded left ventricle in humans, has not been explored. SUBJECTS AND METHODS: The pattern of gene expression was studied, using a cDNA microarray, in myocardium from 4 normal subjects and 5 patients with chronic regurgitant valvular heart disease whose end-diastolic left ventricular dimension measures 65 mm or more, but whose systolic function remained preserved. RESULTS: We identified 58 differentially expressed genes that were functionally classifiable in the volume-overloaded myocardium. Those genes involved in cell cycle/growth (up/down-regulation: 9/1), signal transduction (4/1) were mostly overexpressed in the volume-overloaded myocardium. The distributions of the gene expressions were variable for those involved in transcription/translation (up/down-regulation: 6/7) and apoptosis (2/2). The genes related to the myocyte structure (troponin T3, tropomyosin, etc)(up/down-regulation: 1/10), as well as those related to metabolism (2/5), were underexpressed. The gene expression patterns from RT-PCR and Western blot, with randomly selected genes, were similar to those from the cDNA microarray. CONCLUSION: Altered expression was identified in multiple genes in the volume-overloaded human left ventricle prior to the development of heart failure. The genes related to cell growth and signal transduction were mostly overexpressed, while those related to cellular structure and metabolism appeared to be underexpressed. These results might help in the elucidation of cellular mechanisms for the remodeling process associated with chronic volume-overloading.

Development of DNA microarrays in Sepsis / 肠外与肠内营养

Microarrays have been emerged as new research tools for high throughput parallel gene expression profiling, large scale gene discovery, mutation and polymorphism analysis in an automatic way. We present a review of development of DNA microarrays in sepsis