RESUMEN
Present study reports the identification of genomic and proteomic signatures of endosulfan exposure in hepatocellular carcinoma cells (HepG2). HepG2 cells were exposed to sublethal concentration (15µM) of endosulfan for 24h. DNA microarray and MALDI-TOF-MS analyses revealed that endosulfan induced significant alterations in the expression level of genes and proteins involved in multiple cellular pathways (apoptosis, transcription, immune/inflammatory response, carbohydrate metabolism, etc.). Furthermore, downregulation of PHLDA gene, upregulation of ACIN1 protein and caspase-3 activation in exposed cells indicated that endosulfan can trigger apoptotic cascade in hepatocellular carcinoma cells. In total 135 transcripts and 19 proteins were differentially expressed. This study presents an integrated approach to identify the alteration of biological/cellular pathways in HepG2 cells upon endosulfan exposure.
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Carcinoma Hepatocelular/genética , Endosulfano/toxicidad , Genómica/métodos , Insecticidas/toxicidad , Neoplasias Hepáticas/genética , Proteínas/química , Proteómica/métodos , Carcinoma Hepatocelular/química , Carcinoma Hepatocelular/metabolismo , Perfilación de la Expresión Génica , Células Hep G2 , Humanos , Neoplasias Hepáticas/química , Neoplasias Hepáticas/metabolismo , Proteínas/genética , Proteínas/metabolismoRESUMEN
Toll-like receptors (TLRs) are proteins that play key role in the innate immune system. In the present study, -1000 base pairs upstream are taken from the transcription start site of the various TLR genes (10 known) in human. About 40 microRNAs have been identified that share 12-19 nucleotide sequence similarity with the promoter regions of 10 TLRs. It is proposed that the microRNA performs potential role in identification of promoter sequence and initiation of transcription.
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Estudios de Asociación Genética/métodos , Genoma Humano/genética , MicroARNs/genética , Regiones Promotoras Genéticas/genética , Receptores Toll-Like/genética , Activación Transcripcional/genética , HumanosRESUMEN
Exposure to environmental mutagens results in alteration of microRNA expression mainly oriented towards down-regulation, as typically observed in cigarette smoke. However, the molecular mechanism triggering this event is still unknown. To shed light on this issue, we developed an 'in silico' analysis testing 25 established environmental mutagens (polycyclic aromatic hydrocarbons, heterocyclic compounds, nitrosoamines, morpholine, ethylnitrosurea, benzene derivatives, hydroxyl amines, alkenes) for their potential to interfere with the function of DICER, the enzyme involved in the cytoplasmic phase of microRNA maturation. In order to analyse the binding affinity between DICER and each mutagen, the three-dimensional bioinformatic structures of DICER-RNase III domains and of mutagens have been constructed. The binding affinity of mutagens for each DICER's RNase III domain was estimated by calculating the global contact-energy and the number of intermolecular contacts. These two parameters reflect the stability of the DICER-mutagen complexes. All the 25 mutagens tested form stable complexes with DICER, 20 of which form a complex with DICER A domain, that is more stable than those formed by DICER with its natural substrate, i.e. double strand short RNAs. These mutagens are benzo(a)pyrene diol epoxide, nitroimidazoles, fluorenes, naphthalene, morpholine, stilbenes, hydroxylamines, fecapentenes. In the case of exposure to mutagen mixtures (benzo(a)pyrene-diolepoxide and 4-acetylaminostilbene), synergistic or less than addictive effects occur depending on the docking order of the compounds. A group of 8 mutagens with the highest ability to interfere with this DICER function, was identified by hierarchical cluster analysis. This group included 1-ethyl-1-nitrosourea and 4-nitrosomorpholine. Herein, presented data support the view that mutagens interfere with microRNA maturation by binding DICER. This finding sheds light on a new epigenetic mechanism exerted by environmental mutagens in inducing cell damage.
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ARN Helicasas DEAD-box/antagonistas & inhibidores , ARN Helicasas DEAD-box/metabolismo , MicroARNs/metabolismo , Mutágenos/metabolismo , Ribonucleasa III/antagonistas & inhibidores , Ribonucleasa III/metabolismo , Animales , Análisis por Conglomerados , Biología Computacional/métodos , ARN Helicasas DEAD-box/química , ARN Helicasas DEAD-box/genética , Contaminantes Ambientales/metabolismo , Humanos , MicroARNs/genética , Modelos Moleculares , Conformación Proteica , Ribonucleasa III/química , Ribonucleasa III/genéticaRESUMEN
Although microRNAs have been investigated extensively in cancer research, little is known regarding their response to noxious agents in apparently healthy tissues. We analyzed the expression of 484 miRNAs in the lungs of rats exposed to environmental cigarette smoke (ECS) for 28 days. ECS down-regulated 126 miRNAs (26.0%) at least 2-fold and 24 miRNAs more than 3-fold. We previously demonstrated that 107 of 4858 genes (2.9%) and 50 of 518 proteins (9.7%) were up-regulated by ECS in the same tissue, which is consistent with the role of microRNAs as negative regulators of gene expression. The most remarkably down-regulated microRNAs belonged to the families of let-7, miR-10, miR-26, miR-30, miR-34, miR-99, miR-122, miR-123, miR-124, miR-125, miR-140, miR-145, miR-146, miR-191, miR-192, miR-219, miR-222, and miR-223, which regulate stress response, apoptosis, proliferation, angiogenesis, and expression of genes. In contrast, miR-294, an inhibitor of transcriptional repressor genes, was up-regulated by ECS. There was a strong parallelism in dysregulation of rodent microRNAs and their human homologues, which are often transcribed from genes localized in fragile sites deleted in lung cancer. Five ECS-down-regulated microRNAs are known to be affected by single nucleotide polymorphisms. Thus, changes in microRNA expression are an early event following exposure to cigarette smoke.
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Regulación hacia Abajo/efectos de los fármacos , Lesión Pulmonar/metabolismo , MicroARNs/metabolismo , Contaminación por Humo de Tabaco , Animales , Perfilación de la Expresión Génica , Humanos , Pulmón/metabolismo , Lesión Pulmonar/etiología , Análisis por Micromatrices , Ratas , Ratas Sprague-Dawley , Contaminación por Humo de Tabaco/efectos adversosRESUMEN
Lipoprotein lipase (LPL) is a key enzyme in lipid metabolism. Decrease of the LPL enzymatic activity leads to elevated triglycerides (TG) and reduced high-density lipoprotein (HDL-C levels), both risk factors for cardiovascular disease (CVD). Therefore, mutations, which decrease the LPL activity, may confer susceptibility to CVD. Here, the informational spectrum method (ISM), a virtual spectroscopy method for structure/function analysis of nucleotide and protein sequences, is applied for identification of evolutionary highly conserved information encoded by the primary structure of LPL. It was demonstrated that mutations, which alter the LPL enzymatic activity also alter this information. On the basis of this finding, an efficient and simple bioinformatics criterion for assessment of the pathogenic effect of LPL nonsynonymous single nucleotide substitution as a risk factor of CVD has been proposed.
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Enfermedades Cardiovasculares/genética , Biología Computacional/métodos , Lipoproteína Lipasa/genética , Mutación , Secuencia de Aminoácidos , Animales , Apolipoproteínas/química , Apolipoproteínas/metabolismo , Dimerización , Humanos , Lipoproteína Lipasa/química , Modelos Moleculares , Factores de Riesgo , Relación Estructura-ActividadRESUMEN
The present study demonstrates apoptosis-inducing potential and mechanism of action of Tribulus terristris alkaloid extract in Jurkat E6-1 cancer cell line. Liquid Chromatography-Mass Spectrometry and High Resolution-Mass Spectrometry analysis identified the presence of four N-feruloyltyramine derivatives, namely trans-N-feruloyl-3-hydroxytyramine (1), trans-N-coumaroyltyramine (2), trans-N-feruloyltyramine (3) and trans-N-feruloyl-3-ethoxytyramine (4) in the alkaloid extract. Compounds 2 and 3 have not been yet reported in the alkaloid extract of T. terristris. In silico analysis revealed therapeutic potential of N-feruloyltyramine derivatives and strong binding efficiency to both chains of Tumor Necrosis Factor Receptor 1. Treatment of alkaloids extract to Jurkat E6-1 clone induced dose-dependent cytotoxicity (LC50 140.4 µg mL-1). Jurkat cells treated with alkaloids extract at sub-lethal concentration showed DNA fragmentation, enhancement in caspase-3 activity and phosphatidylserine translocation (apoptosis indicator) compared to control cells. Gene expression analysis using Human Apoptosis RT2 Profiler PCR Array analysis upon alkaloid treatment was found to significantly alter expression of critical genes such as TNFR1, FADD, AIFM, CASP8, TP53, DFFA and NFKB1. These genes are predicted to mediate apoptotic cell death via both intrinsic and extrinsic apoptosis pathway. In summary, we report the identification of new N-feruloyltyramine derivatives from alkaloid extract of T. terristris fruit with probable anti-leukemic and pharmacological potential.
RESUMEN
BACKGROUND: Burkholderia cenocepacia is recognized as opportunistic pathogen that can cause lung infections in cystic fibrosis patients. A hallmark of B. cenocepacia infections is the inability to eradicate the organism because of multiple intrinsic antibiotic resistance. As Resistance-Nodulation-Division (RND) efflux systems are responsible for much of the intrinsic multidrug resistance in Gram-negative bacteria, this study aims to identify RND genes in the B. cenocepacia genome and start to investigate their involvement into antimicrobial resistance. RESULTS: Genome analysis and homology searches revealed 14 open reading frames encoding putative drug efflux pumps belonging to RND family in B. cenocepacia J2315 strain. By reverse transcription (RT)-PCR analysis, it was found that orf3, orf9, orf11, and orf13 were expressed at detectable levels, while orf10 appeared to be weakly expressed in B. cenocepacia. Futhermore, orf3 was strongly induced by chloramphenicol. The orf2 conferred resistance to fluoroquinolones, tetraphenylphosphonium, streptomycin, and ethidium bromide when cloned and expressed in Escherichia coli KAM3, a strain lacking the multidrug efflux pump AcrAB. The orf2-overexpressing E. coli also accumulate low concentrations of ethidium bromide, which was restored to wild type level in the presence of CCCP, an energy uncoupler altering the energy of the drug efflux pump. CONCLUSION: The 14 RND pumps gene we have identified in the genome of B. cenocepacia suggest that active efflux could be a major mechanism underlying antimicrobial resistance in this microorganism. We have characterized the ORF2 pump, one of these 14 potential RND efflux systems. Its overexpression in E. coli conferred resistance to several antibiotics and to ethidium bromide but it remains to be determined if this pump play a significant role in the antimicrobial intrinsic resistance of B. cenocepacia. The characterization of antibiotic efflux pumps in B. cenocepacia is an obligatory step prior to the design of specific, potent bacterial inhibitors for the improved control of infectious diseases. Consequently, the topic deserves to be further investigated and future studies will involve systematic investigation on the function and expression of each of the RND efflux pump homologs.
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Proteínas de la Membrana Bacteriana Externa/genética , Complejo Burkholderia cepacia/efectos de los fármacos , Farmacorresistencia Bacteriana Múltiple/genética , Genoma Bacteriano , Fijación del Nitrógeno/genética , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Antibacterianos/farmacología , Proteínas de la Membrana Bacteriana Externa/química , Proteínas de la Membrana Bacteriana Externa/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Complejo Burkholderia cepacia/genética , Complejo Burkholderia cepacia/crecimiento & desarrollo , Medios de Cultivo , Escherichia coli/genética , Escherichia coli/metabolismo , Etidio/metabolismo , Humanos , Pruebas de Sensibilidad Microbiana , Datos de Secuencia Molecular , Sistemas de Lectura Abierta/genética , Reacción en Cadena de la Polimerasa de Transcriptasa InversaRESUMEN
For sustainable development, biodiversity conservation and life-quality improvement must be simultaneously considered. Molecular techniques have greatly impacted biotechnology. These methods have, in particular, improved the capability to investigate the fine differences among organisms and, as a consequence, to better investigate the effects on environmental factors on them. We propose an approach to support the optimal selection of molecular probes for barcoding application in many biotechnological fields. The aim of our work is specificity maximization. To this purpose, we have integrated a filter system based on wavelet transforms with biological knowledge about the sequence proneness to mutation and post-translational modification. Specifically, we have tested the proposed method on ITS1 sequences that are a region of the rRNA locus. Our analysis has shown the presence of other local relative stable conformations in addition to known cleavage site. Their characteristics differ within the group of mammals selected for our analysis. These variations could be used to design new species-specific barcoding probes or other quick molecular screening tools.
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Código de Barras del ADN Taxonómico , ADN Espaciador Ribosómico , Análisis de Ondículas , Animales , Sitios de Unión , Biología Computacional/métodos , Código de Barras del ADN Taxonómico/métodos , Enzimas de Restricción del ADN/metabolismo , Humanos , Unión ProteicaRESUMEN
In the last decade the role of noncoding RNAs (ncRNAs) emerges not only as key elements of posttranscriptional gene silencing, but also as important players of epigenetic regulation. New kind and new functions of ncRNAs are continuously discovered and one of their most important roles is the mediation of environmental signals, both physical and chemical. The activity of cytoplasmic short ncRNA is extensively studied, in spite of the fact that their function and role in the nuclear compartment are not yet completely unraveled. Cellular nucleus contains a multiplicity of long and short ncRNAs controlling at different levels transcriptional and epigenetic processes. In addition, some ncRNAs are involved in RNA editing and quality control. In this paper we review the existing knowledge dealing with how chemical stressors can influence the functionality of short nuclear ncRNAs. Furthermore, we perform bioinformatics analyses indicating that chemical environmental stressors not only induce DNA damage but also influence the mechanism of ncRNAs production and control.
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Núcleo Celular/genética , Epigénesis Genética/genética , ARN Largo no Codificante/genética , ARN Pequeño no Traducido/genética , Núcleo Celular/metabolismo , Daño del ADN/genética , Edición de ARN/genética , Interferencia de ARNRESUMEN
Fluorosis is caused by excess of fluoride intake over a long period of time. Aberrant change in the Runt-related transcription factor 2 (RUNX2) mediated signaling cascade is one of the decisive steps during the pathogenesis of fluorosis. Up to date, role of fluoride on the epigenetic alterations is not studied. In the present study, global expression profiling of short noncoding RNAs, in particular miRNAs and snoRNAs, was carried out in sodium fluoride (NaF) treated human osteosarcoma (HOS) cells to understand their possible role in the development of fluorosis. qPCR and in silico hybridization revealed that miR-124 and miR-155 can be directly involved in the transcriptional regulation of Runt-related transcription factor 2 (RUNX2) and receptor activator of nuclear factor κ-B ligand (RANKL) genes. Compared to control, C/D box analysis revealed marked elevation in the number of UG dinucleotides and D-box sequences in NaF exposed HOS cells. Herein, we report miR-124 and miR-155 as the new possible players involved in the development of fluorosis. We show that the alterations in UG dinucleotides and D-box sequences of snoRNAs could be due to NaF exposure.
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Subunidad alfa 1 del Factor de Unión al Sitio Principal/biosíntesis , Fluorosis Dental/genética , MicroARNs/biosíntesis , Osteosarcoma/genética , Ligando RANK/biosíntesis , Diferenciación Celular/efectos de los fármacos , Línea Celular Tumoral , Supervivencia Celular/efectos de los fármacos , Subunidad alfa 1 del Factor de Unión al Sitio Principal/genética , Fluorosis Dental/patología , Regulación de la Expresión Génica/efectos de los fármacos , Humanos , MicroARNs/genética , Osteosarcoma/complicaciones , Osteosarcoma/tratamiento farmacológico , Osteosarcoma/patología , Ligando RANK/genética , ARN Nucleolar Pequeño/genética , Transducción de Señal/efectos de los fármacos , Fluoruro de Sodio/toxicidadRESUMEN
The SH3 binding glutamic acid-rich (SH3BGR) gene was cloned in an effort to identify genes located to human chromosome 21, within the congenital heart disease region, and expressed in the developing heart. After the identification of SH3BGR, two human homologous genes, SH3BGRL and SH3BGRL3, were identified and mapped to chromosome Xq13.3 and 1p34.3-35, respectively. SH3BGRL and SH3BGRL3 code for small proteins similar to the N-terminal region of the SH3BGR protein. SH3BGRL3 protein shows a significant similarity to Glutaredoxin 1 of Escherichia coli, and all the three proteins are predicted to belong to Thioredoxin-like protein Superfamily. Here we describe the identification and characterization of an additional human homologue of SH3BGR, named SH3BGRL2. The SH3BGRL2 gene maps to chromosome 6q13-15 and its messenger RNA has a large 3' untranslated region containing several AUUUA repeats. SH3BGRL2 codes for a protein of 107 amino acids, which, like SH3BGRL and SH3BGRL3 proteins, is highly homologous to the N-terminal region of the SH3BGR protein and appears to be related to Glutaredoxins and to PKC-interacting cousin of thioredoxin homology domain. We propose that the identification of SH3BGRL2 establishes a novel family of human genes, coding for highly conserved small proteins belonging to Thioredoxin-like protein Superfamily.
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Proteínas Portadoras/genética , Proteínas Musculares/genética , Tiorredoxinas/genética , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Northern Blotting , Células COS , Núcleo Celular/metabolismo , Clonación Molecular , Secuencia Conservada/genética , ADN Complementario/química , ADN Complementario/genética , Femenino , Expresión Génica , Proteínas Fluorescentes Verdes , Células HeLa , Humanos , Proteínas Luminiscentes/genética , Proteínas Luminiscentes/metabolismo , Datos de Secuencia Molecular , ARN Mensajero/genética , ARN Mensajero/metabolismo , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Alineación de Secuencia , Análisis de Secuencia de ADN , Homología de Secuencia de AminoácidoRESUMEN
One of the major fallouts of the human genome project relates to the investigation of the molecular mechanisms of diseases. Identification of genes which are involved in a specific pathological process and characterization of their interactions is of fundamental importance for supporting the drug design processes. Discovery of targets and the related experimental validation is a critical step in the development of new drugs. The new experimental methods for gene expression analysis, such as microarray technology, allows for the concurrent evaluation of the expression of multiple genes. The outcome of these new experimental methods requires a subsequent validation of the gene function by using in vitro or in vivo models. In the last decade, one of the most promising methodologies for the investigation of gene function relies upon antisense oligonucleotides (ASO). The crucial step in antisense experiment design is the characterization of the nucleotide domains that can efficiently be targeted by this kind of synthetic molecule. At present, no standardized procedures for target selection are available. In this paper, we propose an integrative approach to ASO target selection: the proposed tool Automatic Gene Walk (AgeWa) combines a neural filter with database mining for the prediction of the optimal target for antisense action.
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Algoritmos , Inteligencia Artificial , Mapeo Cromosómico/métodos , Marcación de Gen/métodos , Oligodesoxirribonucleótidos Antisentido/química , Oligodesoxirribonucleótidos Antisentido/genética , Análisis de Secuencia de ADN/métodos , Sistemas de Administración de Bases de Datos , Bases de Datos Genéticas , Hibridación in Situ/métodos , Integración de SistemasRESUMEN
Noncoding RNAs (ncRNAs) are ribonucleic acids capable of controlling different genetic and metabolic functions. These molecules have been recently organized into different classes, and among them microRNAs (miRNAs) are extensively studied. MicroRNAs are short oligomers mainly involved in posttranscriptional gene silencing. The specific research field, focused on structural and functional characterization of microRNAs, is commonly called mirnomics. The exploitation of the interest in microRNAs has stimulated the organization of several databases that are often integrated with analytical tools in order to predict microRNA targets, or to find those miRNAs capable to inhibit the expression of a specific protein. This work attempts to provide an overview of accessible information about microRNAs and other noncoding RNAs that has been gathered in curated databases.
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MicroARNs/genética , ARN no Traducido/genética , Bases de Datos Genéticas , Resonancia Magnética Nuclear BiomolecularRESUMEN
Noncoding RNAs (ncRNAs) constitute an evolutionary conserved system involved in the regulation of biological functions at posttranscriptional level. The capability to rapidly adapt their metabolism is essential for the survival of organisms. NcRNAs are a valuable means used by cells to rapidly transfer and internalize an external signal. NcRNAs are capable not only to influence the translational phase but also to affect epigenetic processes. They have been identified in almost all kingdoms of life (from archaea to human and plants). In this chapter we outline the currently available resources that could be used for the screening of viral and bacterial ncRNAs.
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Genes Bacterianos , Genes Virales , MicroARNs/genéticaRESUMEN
The CELLmicrocosmos PathwayIntegration (CmPI) was developed to support and visualize the subcellular localization prediction of protein-related data such as protein-interaction networks. From the start it was possible to manually analyze the localizations by using an interactive table. It was, however, quite complicated to compare and analyze the different localization results derived from data integration as well as text-mining-based databases. The current software release provides a new interactive visual workflow, the Subcellular Localization Charts. As an application case, a MUPP1-related protein-protein interaction network is localized and semi-automatically analyzed. It will be shown that the workflow was dramatically improved and simplified. In addition, it is now possible to use custom protein-related data by using the SBML format and get a view of predicted protein localizations mapped onto a virtual cell model.
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Gráficos por Computador , Bases de Datos de Proteínas , Imagenología Tridimensional/métodos , Modelos Biológicos , Mapeo de Interacción de Proteínas/métodos , Proteoma/metabolismo , Fracciones Subcelulares/metabolismo , Simulación por Computador , Distribución TisularRESUMEN
The focal adhesion pathway has a great impact on cellular growth and survival. Its disregulation is correlated with the loss of cellular mechanical properties. Such modifications are, in many cases, associated with pathologies such as cancer and cardiovascular diseases. Actin remodeling is a critical reaction cascade embedded in focal adhesion pathway, and Rac1 is one of the proteins involved in actin remodeling. In order to design highly selective pharmacophores against this target, it is necessary to maximize the binding affinity of chemical entities against Rac1. To this purpose we propose an integrative chemo-bioinformatics tool to screen ligand specificity for a target protein. Our integrative workflow includes chemo-informatics data mining (Chemical System), structural bioinformatics and combined exploratory data analysis. We have applied this integrative chemo-bioinformatics workflow to a comparative analysis of three different classes of ligands (morpholines, flavonoids and imidazoles) against the Rac1 protein. Our analysis emphasizes the presence of several ligands that preferentially dock Rac1 in the domain that seems to be responsible for Rac1-phospholipase C gamma 1 interaction. Recent studies have highlighted the Rac1 and PLC interactions in platelet adhesion. Our study has highlighted the role of Rac1-PLC gamma1 interaction in cytoskeleton remodeling associated with cardiovascular diseases. Rac1 PLC interaction is Calcium dependent. This suggest that some of the analysed ligands, could be used to control the Calcium dependent cytoskeleton remodeling since they dock Rac1 in the switch 2 domain. Our results, in a nanotechnology perspective, also endorse the use Rac1's switch 2 domain suitable for new highly specific biosensors.
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Flavonoides/metabolismo , Imidazoles/metabolismo , Morfolinas/metabolismo , Proteína de Unión al GTP rac1/metabolismo , Análisis por Conglomerados , Descubrimiento de Drogas , Flavonoides/química , Interacciones Hidrofóbicas e Hidrofílicas , Imidazoles/química , Ligandos , Modelos Moleculares , Morfolinas/química , Unión Proteica , Termodinámica , Proteína de Unión al GTP rac1/químicaRESUMEN
MicroRNAs (miRNAs) are small non-coding RNAs that regulate fundamental cellular processes in diverse organisms and that have an important function in gene expression regulation. miRNAs seem capable to concurrently modulate hundreds of target genes. Their abnormal expression is emerging as important element in many pathological conditions. The identification of microRNA binding sites on those proteins that can be disease biomarker is fundamental to design synthetic artificial oligomers. In this paper we suggest a method, based on signal processing, to filter out potential miRNA recognition sites in the 3' UTR region of mRNAs.
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Regiones no Traducidas 3' , MicroARNs/genética , Regulación de la Expresión GénicaRESUMEN
Aicardi-Goutières syndrome is a rare encephalopathy of mutational origin characterized by increased levels of interferon alpha in cerebrospinal fluid. The aim of this study was to explore the influence of different Aicardi-Goutières syndrome genotypes on the clinical course of patients, seeking to identify specific gene expression profiles able to explain Aicardi-Goutières syndrome phenotype differences. We detected the occurrence of Aicardi-Goutières syndrome mutations in 21 patients and compared microarray gene-expression data of cerebrospinal fluid lymphocytes with clinical variables. The levels of interferon alpha in cerebrospinal fluid were high in all patients; we found differences in the expression of genes encoding for Toll-like receptor, endogenous RNases, T lymphocyte activation, angiogenesis inhibition, and peripheral interferon alpha production. These results indicate that further to interferon alpha production in the central nervous system, a variety of other pathogenic mechanisms is activated in Aicardi-Goutières syndrome to various degrees in different patients, thus explaining the interindividual difference in Aicardi-Goutières syndrome course.
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Enfermedades Autoinmunes del Sistema Nervioso/genética , Enzimas Reparadoras del ADN/genética , Exodesoxirribonucleasas/genética , Mutación/genética , Malformaciones del Sistema Nervioso/genética , Ribonucleasa H/genética , Análisis de Varianza , Enfermedades Autoinmunes del Sistema Nervioso/líquido cefalorraquídeo , Enfermedades Autoinmunes del Sistema Nervioso/patología , Niño , Preescolar , Femenino , Expresión Génica , Genotipo , Humanos , Interferón-alfa/líquido cefalorraquídeo , Linfocitosis/líquido cefalorraquídeo , Masculino , Análisis por Micromatrices/métodos , Malformaciones del Sistema Nervioso/líquido cefalorraquídeo , Malformaciones del Sistema Nervioso/patología , Receptores Toll-Like/metabolismoRESUMEN
'OMICS' techniques have deeply changed the drug discovery process. The availability of many different potential druggable genes, generated by these new techniques, have exploited the complexity of new lead compounds screening. 'Virtual screening', based on the integration of different analytical tools on high performance hardware platforms, has speeded up the search for new chemical entities suitable for experimental validation. Docking is a key step in the screening process. The aim of this paper is the evaluation of binding differences due to solvation. We have compared two commonly used software, one of which takes into account solvation, on a set of small molecules (Morpholines, flavonoids and imidazoles) which are able to target the RAC1 protein--a cardiovascular target. We have evaluated the degree of agreement between the two different programs using a machine learning approach combined with statistical test. Our analysis, on a sample of small molecules, has pointed out that 35% of the molecules seem to be sensitive to solvation. This result, even though quite preliminary, stresses the need to combine different algorithms to obtain a more reliable filtered set of ligands.
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Enfermedades Cardiovasculares/tratamiento farmacológico , Diseño de Fármacos , Proteína de Unión al GTP rac1/metabolismo , Humanos , Ligandos , SolubilidadRESUMEN
This paper addresses mutational events that give rise to differing response to drugs focusing on Rac1, a protein that has been recognized as a target for drug design for cardiovascular disease due its regulatory role of angiogenesis. Rac1 has been considered with reference to Single Nucleotide Polymorphism (SNP), which has become of great value for personalized medicine. We have considered four variation of Rac1 registered in UNIPROTKB. Two of these variations are due to the environmental or population factors and two are mutation that we have selected because they are located near the binding sites of Rac1. Rac1 has been modelled by Rosetta software and by i-Tasser web server. We have chosen i-Tasser based modelling because the Rac1 structure obtained was more closely resembling crystallography data. In silico model have been used as receptors for docking with a set of 20 morpholines. The results that have been obtained on SNPs shows that a single ligand can react very differently with a mutated structure. Our analysis shows that all mutations that have been considered change Rac1 conformation and increase the accessible surface of Rac1. Our analysis highlights the effect of two sources of genetic variability: single base variation and alternative splicing.