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Questions and Answers (10) View all
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Answer added in MEME7 Consensus motif using MEME program. Is it real or is it only a statistically significant repetition?By Laura España Serrano · University of FloridaLaura España Serrano · University of FloridaThank you all for your time! I think I'm going to continue with an EMSA to assay the binding activity of my protein and this DNA sequence. As Marcelo ... [more]Thank you all for your time! I think I'm going to continue with an EMSA to assay the binding activity of my protein and this DNA sequence. As Marcelo advised me, I'll use a mutant in the sequence as control. Do you think is a good idea?Following
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Answer added in Plant Tissue Culture2 Is it possible to use frozen tissue for Chip-seq?By Pasquale Termolino · National Research CouncilLaura España Serrano · University of FloridaCan you do the first step (crosslinking and sonication) immediately? If you can do this step then you can freeze your samples at -80°C during months.... [more]Can you do the first step (crosslinking and sonication) immediately? If you can do this step then you can freeze your samples at -80°C during months. I'm not sure if you can use later your frozen tomatos... I hope it helps.Following
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Answer added in Gene Expression39 English language usage: gene expression or gene transcription in describing RT-PCR results?By Felix Toka · Szkoła Główna Gospodarstwa WiejskiegoLaura España Serrano · University of FloridaIn my opinion for an RTPCR assay is more commonly used , analysis of gene expression at RNA level. In the case of translation, for example in a Wester... [more]In my opinion for an RTPCR assay is more commonly used , analysis of gene expression at RNA level. In the case of translation, for example in a Western blot assay, gene expression at protein level.Following
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Question asked in MEME7 Consensus motif using MEME program. Is it real or is it only a statistically significant repetition?I did a Chip Seq analysis and I used a MEME program to analyze the consensus motif for the transcription factor binding site. I obtained a long sequen... [more]I did a Chip Seq analysis and I used a MEME program to analyze the consensus motif for the transcription factor binding site. I obtained a long sequence (24 nucleotides). I did a search of this sequence and I found that it is one of the most frequent n-mers in the human genome. What does this mean exactly? Is there any way to know if my consensus motif is real or only a statistically significant repetition?By Laura España Serrano · University of FloridaFollowing
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Question asked in MEMEOpen How can I be sure if a TF predicted Consensus motif is real or only a frequent repeated sequence?I used MEME program to analyze the consensus motif of the transcription factor binding site for a Chip Seq analysis. I did a search of this sequence (... [more]I used MEME program to analyze the consensus motif of the transcription factor binding site for a Chip Seq analysis. I did a search of this sequence (15 nucleotides) and I found that it is one of the most frequent n-mers in the human genome. What does it means exactly? How can I be sure if my consensus motif is real or only a repetition?By Laura España Serrano · University of FloridaFollowing
Publications (3) View all
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Article: The D2 dopamine receptor gene variant C957T affects human fear conditioning and aversive priming.
E Huertas, G Ponce, M A Koeneke, C Poch, L España-Serrano, T Palomo, M A Jiménez-Arriero, J Hoenicka[show abstract] [hide abstract]
ABSTRACT: Polymorphisms of DRD2 and ANKK1 have been associated with psychiatric syndromes where there is believed to be an underlying learning process deficit such as addiction, post-traumatic stress disorder and psychopathy. We investigated the effects of the DRD2 C957T and ANKK1 TaqIA single nucleotide polymorphism (SNP), which have been associated with psychopathic traits in alcoholic patients, on fear conditioning and aversive priming in healthy volunteers. We found that the DRD2 C957T SNP, but not the ANKK1 TaqIA SNP, was associated with both differential conditioning of the skin conductance response and the aversive priming effect. There were no differences between the genotype groups with respect to the extinction of the skin-conductance conditioned response. These results suggest that the C957T SNP could be related to learning differences associated with the risk of developing psychiatric disorders in individuals that are carriers of the C homozygous genotype. Our genetic data raise the possibility that the dopaminergic system functional variations determined by this SNP could affect fear learning.Genes Brain and Behavior 10/2010; 9(1):103-9. · 3.48 Impact Factor -
Article: The ANKK1 gene associated with addictions is expressed in astroglial cells and upregulated by apomorphine.
Janet Hoenicka, Adolfo Quiñones-Lombraña, Laura España-Serrano, Ximena Alvira-Botero, Leonor Kremer, Rocío Pérez-González, Roberto Rodríguez-Jiménez, Miguel Angel Jiménez-Arriero, Guillermo Ponce, Tomás Palomo[show abstract] [hide abstract]
ABSTRACT: TaqIA, the most widely analyzed genetic polymorphism in addictions, has traditionally been considered a gene marker for association with D2 dopamine receptor gene (DRD2). TaqIA is located in the coding region of the ANKK1 gene that overlaps DRD2 and encodes a predicted kinase ANKK1. The ANKK1 protein nonetheless had yet to be identified. This study examined the ANKK1 expression pattern as a first step to uncover the biological bases of TaqIA-associated phenotypes. Northern blot and quantitative reverse-transcriptase polymerase chain reaction analyses were performed to analyze the ANKK1 mRNA. To study ANKK1 protein expression, we developed two polyclonal antibodies to a synthetic peptides contained in the putative Ser/Thr kinase domain. We demonstrate that ANKK1 mRNA and protein were expressed in the adult central nervous system (CNS) in human and rodents, exclusively in astrocytes. Ankk1 mRNA level in mouse astrocyte cultures was upregulated by apomorphine, suggesting a potential relationship with the dopaminergic system. Developmental studies in mice showed that ANKK1 protein was ubiquitously located in radial glia in the CNS, with an mRNA expression pick around embryonic Day 15. This time expression pattern coincided with that of the Drd2 mRNA. On induction of differentiation by retinoic acid, a sequential expression was found in human neuroblastoma, where ANKK1 was expressed first, followed by that of DRD2. An opposite time expression pattern was found in rat glioma. Spatial and temporal regulation of the expression of ANKK1 suggest an involvement of astroglial cells in TaqIA-related neuropsychiatric phenotypes both during development and adult life.Biological psychiatry 10/2009; 67(1):3-11. · 8.93 Impact Factor -
Article: Gender-specific COMT Val158Met polymorphism association in Spanish schizophrenic patients.
Janet Hoenicka, Elena Garrido, Isabel Martínez, Guillermo Ponce, María Aragüés, Roberto Rodríguez-Jiménez, Laura España-Serrano, Ximena Alvira-Botero, José Luis Santos, Gabriel Rubio, Miguel Angel Jiménez-Arriero, Tomás Palomo[show abstract] [hide abstract]
ABSTRACT: The functional Val158Met polymorphism (rs4680) located at the gene that codes for the catechol-O-methyltransferase (COMT) has been extensively investigated in schizophrenia although current data are still controversial. Since COMT activity is sexually dimorphic, we carried out two independent studies in homogeneous samples of male and female Spanish schizophrenic patients. In males, we found an association between the homozygous Val genotype and the disorder, which resembled a recessive model (P = 0.022; odds ratio [OR] = 1.67). This Val homozygotes overrepresentation is produced at the expense of the heterozygous individuals decrease, whilst the Met homozygotes showed no differences when compared controls and patients. As a consequence, the heterozygous genotype in this sample had a protective effect (P = 0.03; OR = 0.65) and a strong deviation from Hardy-Weinberg equilibrium in male cases was observed (P = 0.006). In addition, a 2-SNP haplotype analysis (rs4818-Val158Met) confirmed there is an overrepresentation of the different homozygous Val genotypes in the male schizophrenic sample. Regarding females, we did not find any statistically significant association between COMT SNP and schizophrenia. In the light of this we suggest that the Val158Met SNP is involved in risk and protective genotypes for the vulnerability to schizophrenia in Spanish male population.American Journal of Medical Genetics Part B Neuropsychiatric Genetics 05/2009; 153B(1):79-85. · 3.70 Impact Factor