RBM38 Mediates the Proliferation of Acute Myeloid Leukemia Cells HL-60 by Regulating FZD1 mRNA Stability / 中国实验血液学杂志

OBJECTIVE@#To explore the regulatory function of RNA binding motif protein 38 (RBM38) in human acute myeloid leukemia cells HL-60 and its mechanism.@*METHODS@#The lentivirus carriers of overexpressed and knockdown RBM38 were constructed. After HL-60 cells were transfected, Western blot was used to analyze the expression level of RBM38 in HL-60 cells. The cell proliferation and cycle of HL-60 were detected by CCK-8 assay and flow cytometry assay, respectively. RNA immunoprecipitation coupled real-time PCR (RIP-qPCR) was used to detect the combination of RBM38 with mRNAs. Actinomycin D treatment followed by real-time PCR (AcD-qPCR) was used to detect the effect of RBM38 on the stability of target mRNAs.@*RESULTS@#RBM38 in HL-60 cells was overexpressed or inhibited by lentivirus transduction. Overexpressed RBM38 promoted the cell cycle and proliferation of HL-60, while RBM38 knockdown repressed the two processes. RBM38 showed an interaction with FZD1 mRNA and enhancement of its stability.@*CONCLUSION@#RBM38 can regulate cell proliferation of HL-60 by improving the stability of FZD1 mRNA.

Effect of encephalomyocarditis virus 3'Untranslated region on GFP transient expression: implications in recombinant protein production / Efecto de la Región 3'-no traducida del virus de la encefalomiocarditis sobre la expresión transitoria de GFP: implicaciones en la producción de proteínas recombinantes

The enrichment of therapeutic protein production yield in mammalian cell cultures by modulating mRNA stability is a fairly new strategy in biotechnological applications. Here, we describe the application of 3'-untranslated region (3'UTR) from RNA viral genome to modulate mRNA stability.The data obtained showed that the use of the 3 'UTR sequence of the encephalomyocarditis virus (EMCV 3'UTR) downstream of the target gene was not able to significantly modulate the free energy density indicators of the RNA. However, the sequence influenced the stability of the mRNA (and, therefore, the amount of protein production) in a cell type and time-dependent manner, indicating a central role of mRNA-stabilizing binding sites/cellular factors in this process. Our data might be of interest for the biotechnology community to improve recombinant protein production in mammalian cell cultures and RNA-based therapy/vaccination approaches.

El enriquecimiento de la producción terapéutica de proteínas en cultivos de células de mamíferos mediante la modulación de la estabilidad del ARNm es una estrategia nueva en aplicaciones biotecnológicas. Se describe la aplicación de la región 3'-no traducida (3'UTR) del genoma viral ARN para modular la estabilidad del ARNm. Los datos obtenidos mostraron que el uso de la secuencia 3'UTR del virus de la encefalomiocarditis (EMCV 3'UTR) aguas abajo del gen objetivo no pudo modular significativamente los indicadores de densidad de energía libre del ARN. Sin embargo, la secuencia influyó en la estabilidad del ARNm (y, por lo tanto, en la cantidad de producción de proteínas) dependiente de la célula y del tiempo, lo que indica un papel central de los sitios de unión estabilizadores de ARNm/factores celulares en este proceso. Nuestros datos podrían ser de interés para la comunidad biotecnológica para mejorar la producción de proteínas recombinantes en cultivos de células de mamíferos y en enfoques de terapia/vacunación basados en ARN.

Isolation and genetic stability of an infectious bronchitis virus strain (IBV) / Isolamento e estabilidade genética de uma cepa do vírus da bronquite infecciosa (IBV)

O vírus da bronquite infecciosa (IBV) é um importante patógeno respiratório presente na avicultura comercial e tem provocado grandes perdas econômicas em todo o mundo. A vacinação é realizada pela indústria produtora de aves, mas continuam surgindo novos sorotipos e variações antigênicas, dificultando o controle de IBV. Nós realizamos uma caracterização molecular de uma cepa de IBV obtida diretamente de tecidos e comparamos com a mesma cepa que havia sido passada três vezes em ovo embrionado. Nós mostramos uma variação significante na sequência viral depois de ter sido isolada em ovo embrionado.(AU)

ADAR1-mediated RNA-editing of 3'UTRs in breast cancer

BACKGROUND: Whole transcriptome RNA variant analyses have shown that adenosine deaminases acting on RNA ( ADAR ) enzymes modify a large proportion of cellular RNAs, contributing to transcriptome diversity and cancer evolution. Despite the advances in the understanding of ADAR function in breast cancer, ADAR RNA editing functional consequences are not fully addressed. RESULTS: We characterized A to G(I) mRNA editing in 81 breast cell lines, showing increased editing at 3'UTR and exonic regions in breast cancer cells compared to immortalized non-malignant cell lines. In addition, tumors from the BRCA TCGA cohort show a 24% increase in editing over normal breast samples when looking at 571 well-characterized UTRs targeted by ADAR1. Basal-like subtype breast cancer patients with high level of ADAR1 mRNA expression shows a worse clinical outcome and increased editing in their 3'UTRs. Interestingly, editing was particularly increased in the 3'UTRs of ATM, GINS4 and POLH transcripts in tumors, which correlated with their mRNA expression. We confirmed the role of ADAR1 in this regulation using a shRNA in a breast cancer cell line (ZR-75-1). CONCLUSIONS: Altogether, these results revealed a significant association between the mRNA editing in genes related to cancer-relevant pathways and clinical outcomes, suggesting an important role of ADAR1 expression and function in breast cancer.

The Role of MicroRNAs in Oncogenesis and Progression of Prostate Cancer

MicroRNAs (miRNAs) are small noncoding RNAs that target mRNA to reduce gene and protein expression by repressing their targets' translation or inducing mRNA degradation. They play fundamental roles in various cancers, including prostate cancer. Each single miRNA may regulate hundreds of genes, and a certain gene may serve as a target by multiple miRNAs. Hence, miRNAs modulate, cell cycle, apoptosis, epithelial-mesenchymal transition (EMT), and metastasis, etc. In this review, we will summarize the several miRNAs that may function as oncogenes and tumor suppressors. And we will describe the each miRNAs associated with cell cycle, apoptosis, EMT, and metastasis in prostate cancer.

Effect of BIS depletion on HSF1-dependent transcriptional activation in A549 non-small cell lung cancer cells

The expression of BCL-2 interacting cell death suppressor (BIS), an anti-stress or anti-apoptotic protein, has been shown to be regulated at the transcriptional level by heat shock factor 1 (HSF1) upon various stresses. Recently, HSF1 was also shown to bind to BIS, but the significance of these protein-protein interactions on HSF1 activity has not been fully defined. In the present study, we observed that complete depletion of BIS using a CRISPR/Cas9 system in A549 non-small cell lung cancer did not affect the induction of heat shock protein (HSP) 70 and HSP27 mRNAs under various stress conditions such as heat shock, proteotoxic stress, and oxidative stress. The lack of a functional association of BIS with HSF1 activity was also demonstrated by transient downregulation of BIS by siRNA in A549 and U87 glioblastoma cells. Endogenous BIS mRNA levels were significantly suppressed in BIS knockout (KO) A549 cells compared to BIS wild type (WT) A549 cells at the constitutive and inducible levels. The promoter activities of BIS and HSP70 as well as the degradation rate of BIS mRNA were not influenced by depletion of BIS. In addition, the expression levels of the mutant BIS construct, in which 14 bp were deleted as in BIS-KO A549 cells, were not different from those of the WT BIS construct, indicating that mRNA stability was not the mechanism for autoregulation of BIS. Our results suggested that BIS was not required for HSF1 activity, but was required for its own expression, which involved an HSF1-independent pathway.

Improving the expression of recombinant pullulanase by increasing mRNA stability in Escherichia coli

Background: Pullulanase production in both wild-type strains and recombinantly engineered strains remains low. The Shine-Dalgarno (SD) sequence and stem-loop structure in the 5' or 3' untranslated region (UTR) are well-known determinants of mRNA stability. This study investigated the effect of mRNA stability on pullulanase heterologous expression. Results: We constructed four DNA fragments, pulA, SD-pulA, pulA-3t, and SD-pulA-3t, which were cloned into the expression vector pHT43 to generate four pullulanase expression plasmids. The DNA fragment pulA was the coding sequence (CDS) of pulA in Klebsiella variicola Z-13. SD-pulA was constructed by the addition of the 5' SD sequence at the 5' UTR of pulA. pulA-3t was constructed by the addition of a 3' stem-loop structure at the 3' UTR of pulA. SD-pulA-3t was constructed by the addition of the 5' SD sequence at the 5' UTR and a 3' stem-loop structure at the 3' UTR of pulA. The four vectors were transformed into Escherichia coli BL21(DE3). The pulA mRNA transcription of the transformant harboring pHT43-SD-pulA-3t was 338.6%, 34.9%, and 79.9% higher than that of the other three transformants, whereas the fermentation enzyme activities in culture broth and intracellularly were 107.0 and 584.1 times, 1.2 and 2.0 times, and 62.0 and 531.5 times the amount of the other three transformants (pulA, SD-pulA, and pulA-3 t), respectively. Conclusion: The addition of the 5' SD sequence at the 5' UTR and a 3' stem-loop structure at the 3' UTR of the pulA gene is an effective approach to increase pulA gene expression and fermentation enzyme activity.

Circular RNA in human disease and their potential clinic significance / 中华医学遗传学杂志

Circular RNAs (circ RNAs) are a novel type of RNA that, unlike linear RNAs, form a covalently closed continuous loop and are highly represented in the eukaryotic transcriptome. They share a stable structure, high expression and often exhibit tissue/developmental-stage-specific expression. Emerging evidence indicates that circRNAs might play important roles in human disease, such as cancer, neurological disorders and atherosclerotic vascular disease risk. The huge potentials of circRNAs are recently being discovered from the laboratory to the clinic. CircRNAs might be developed as a potential novel and stable biomarker and potential drugs used in disease diagnosis and treatment. Here, we review the current understanding of the roles of circRNAs in human disease and their potential clinic significance in disease.

Mammalian mitochondrial RNAs are degraded in the mitochondrial intermembrane space by RNASET2

Mammalian mitochondrial genome encodes a small set of tRNAs, rRNAs, and mRNAs. The RNA synthesis process has been well characterized. How the RNAs are degraded, however, is poorly understood. It was long assumed that the degradation happens in the matrix where transcription and translation machineries reside. Here we show that contrary to the assumption, mammalian mitochondrial RNA degradation occurs in the mitochondrial intermembrane space (IMS) and the IMS-localized RNASET2 is the enzyme that degrades the RNAs. This provides a new paradigm for understanding mitochondrial RNA metabolism and transport.

Correlation between RNA Expression Level and Early PMI in Human Brain Tissue / 法医学杂志

OBJECTIVES@#To explore the correlation between the expression levels of several RNA markers in human brain tissue and early postmortem interval （PMI）.@*METHODS@#Twelve individuals with known PMI （range from 4.3 to 22.5 h） were selected and total RNA was extracted from brain tissue. Eight commonly used RNA markers were chosen including β-actin, GAPDH, RPS29, 18S rRNA, 5S rRNA, U6 snRNA, miRNA-9 and miRNA-125b, and the expression levels were detected in brain tissue by real-time fluorescent quantitative PCR. The internal reference markers with stable expression in early PMI were screened using geNorm software and the relationship between its expression level and some relevant factors such as age, gender and cause of death were analyzed. RNA markers normalized by internal reference were inserted into the mathematic model established by previous research for PMI estimation using R software. Model quality was judged by the error rate calculated with estimated PMI.@*RESULTS@#5S rRNA, miRNA-9 and miRNA-125b showed quite stable expression and their expression levels had no relation with age, gender and cause of death. The error rate of estimated PMI using β-actin was 24.6%, while GAPDH was 41.0%.@*CONCLUSIONS@#5S rRNA, miRNA-9 and miRNA-125b are suitable as internal reference markers of human brain tissue owing to their stable expression in early PMI. The expression level of β-actin correlates well with PMI, which can be used as an additional index for early PMI estimation.

Correlation between RNA Degradation Patterns of Rat's Brain and Early PMI at Different Temperatures / 法医学杂志

OBJECTIVES@#To explore the correlation between early postmortem interval （PMI） and eight RNA markers of rat's brain at different temperatures.@*METHODS@#Total 222 SD rats were randomly divided into control group （PMI=0 h） and four experimental groups. And the rats in the experimental groups were sacrificed by cervical dislocation and respectively kept at 5 ℃, 15 ℃, 25 ℃ and 35 ℃ in a controlled environment chamber. The RNA was extracted from brain tissues, which was taken at 9 time points from 1 h to 24 h postmortem. The expression levels of eight markers, β-actin, GAPDH, RPS29, 18S rRNA, 5S rRNA, U6 snRNA, miRNA-9 and miRNA-125b, were detected using real-time fluorescent quantitative PCR, respectively. Proper internal reference was selected by geNorm software. Regression analysis of normalized RNA markers was performed by SPSS software. Mathematical model for PMI estimation was established using R software. Another 6 SD rats with known PMI were used to verify the mathematical model.@*RESULTS@#5S rRNA, miR-9 and miR-125b were suitable as internal reference markers for their stable expression. Both β-actin and GAPDH had well time-dependent degradation patterns and degraded continually with prolongation of PMI in 24 h postmortem. The mathematical model of the variation of ΔCt values with PMI and temperature was set up by R software and the model could be used for PMI estimation. The average error rates of model validation using β-actin and GAPDH were 14.1% and 22.2%, respectively.@*CONCLUSIONS@#The expression levels of β-actin and GAPDH are well correlated with PMI and environmental temperature. The mathematical model established in present study can provide references for estimating early PMI under various temperature conditions.

Otimização da RT-PCR Multiplex para detecção de vírus dengue em amostras de Aedes aegypti infectados artificialmente / Optimization of Multiplex RT-PCR for Dengue virus detection in artificially infected Aedes aegypti samples

A dengue é a mais importante doença viral transmitida por mosquitos, no que diz respeito à morbidade e mortalidade, que afeta os seres humanos. Este vírus é transmitido pelos vetores Aedes albopictus e Aedes aegypti, este último é o principal vetor nas Américas. O controle da doença se baseia na vigilância laboratorial e vigilância entomológica. A vigilância laboratorial visa aprimorar a capacidade do diagnóstico, detectando precocemente a circulação viral e monitorando os sorotipos circulantes. Dentro deste tipo de vigilância, a RT-PCR é um método bastante usado no diagnóstico da doença em humanos e mosquitos, porém, a má conservação do material pode comprometer a integridade do RNA e trazer resultados falso-negativos. O desenvolvimento de melhores métodos de vigilância do vírus dengue (DENV) em mosquitos é de grande valor para os programas de controle. Desta maneira, o presente projeto visou otimizar a técnica de RT-PCR Multiplex para detecção de DENV em amostras de Ae. aegypti infectadas artificialmente pelo vírus. Primers que amplificam uma região de 80 pb do gene rpL8 de mosquito foram desenhados no site Primer3 e avaliados na ferramenta online Multiple Primer Analyzer, junto com primers que amplificam os sorotipos DENV. Não houve competição de primers e foi observado bandas distintas no gel de agarose. Foi avaliado o efeito de diferentes formas de preservação do material genético das amostras (RNA later®, freezer -80°C e nitrogênio líquido) por 7 dias, onde não houve diferenças significativas em relação à integridade do RNA. O efeito de diferentes formas de extração de RNA (Kit da QIAGEN®, TRIzol® e Chomczymski-Sacchi) também foi avaliado e o método Chomczymski-Sacchi obteve o melhor desempenho. A otimização desta técnica permitirá uma maior confiabilidade nos resultados, já que além da detecção dos sorotipos, haverá uma confirmação da qualidade do RNA, aprimorando a capacidade do diagnóstico e auxiliando a prevenção e controle da transmissão da dengue.

Biogenesis and regulation of the let-7 miRNAs and their functional implications

The let-7 miRNA was one of the first miRNAs discovered in the nematode, Caenorhabditis elegans, and its biological functions show a high level of evolutionary conservation from the nematode to the human. Unlike in C. elegans, higher animals have multiple isoforms of let-7 miRNAs; these isoforms share a consensus sequence called the 'seed sequence' and these isoforms are categorized into let-7 miRNA family. The expression of let-7 family is required for developmental timing and tumor suppressor function, but must be suppressed for the self-renewal of stem cells. Therefore, let-7 miRNA biogenesis must be carefully controlled. To generate a let-7 miRNA, a primary transcript is produced by RNA polymerase II and then subsequently processed by Drosha/DGCR8, TUTase, and Dicer. Because dysregulation of let-7 processing is deleterious, biogenesis of let-7 is tightly regulated by cellular factors, such as the RNA binding proteins, LIN28A/B and DIS3L2. In this review, we discuss the biological functions and biogenesis of let-7 miRNAs, focusing on the molecular mechanisms of regulation of let-7 biogenesis in vertebrates, such as the mouse and the human.

Depression help-seeking attitudes and behaviors among an Internet-based sample of Spanish-speaking perinatal women / Actitudes y comportamientos de búsqueda de ayuda para la depresión en una muestra basada en internet de mujeres de habla hispana en período perinatal

OBJECTIVE: To examine attitudes and beliefs related to help-seeking for depression among an international sample of pregnant women, a majority of whom were Spanish-speakers residing in Latin America. METHODS: More than 6 000 (n = 6 672) pregnant women met eligibility criteria and consented to participate between 15 January 2009-12 August 2011. Of these, 1 760 with a Latino/Hispanic background completed a baseline survey as part of a larger study. Group comparisons analyzed attitudes and behaviors related to seeking help for depression, while a logistic regression was conducted to identify demographic characteristics related to help-seeking support. RESULTS: Of the participants, three-fourths reported experiencing depression during or after their current or past pregnancies. The majority of participants did not seek help, and generally reported ambivalence about their depressive symptoms and uncertainty as to the helpfulness of others. However, 44.8% did seek help, mostly by speaking to family or partners and reported feeling fear, shame, and embarrassment about their symptoms. A current major depressive episode and an income less than or equal to US$ 10 000 were significant predictors of help-seeking behaviors. CONCLUSIONS: Data from this study suggest that when feeling sad or depressed, perinatal Latinas tend to seek emotional support first from family and friends and may underutilize mental health services when needed. The Internet is an effective means for reaching perinatal women, especially those in areas of the world where there may be barriers to accessing psychological resources.

OBJETIVO: Analizar las actitudes y las creencias relacionadas con la búsqueda de ayuda para la depresión en una muestra internacional de mujeres embarazadas, la mayor parte de ellas hispanohablantes y residentes en América Latina. MÉTODOS: Más de 6 000 mujeres embarazadas (n = 6 672) cumplieron los criterios de selección y aceptaron participar entre el 15 de enero del 2009 y el 12 de agosto del 2011. De estas, 1 760 de origen latino o hispano completaron una encuesta básica que formaba parte de un estudio más amplio. Mediante comparaciones de grupo, se analizaron las actitudes y los comportamientos relacionados con la búsqueda de ayuda para la depresión, mientras que, mediante regresión logística, se determinaron las características demográficas relacionadas con la búsqueda de ayuda o apoyo. RESULTADOS: De todas las participantes, tres cuartas partes notificaron sentimientos de depresión durante o después de los embarazos actuales o pasados. La mayor parte de ellas no buscaron ayuda, y en general manifestaron ambivalencia acerca de sus síntomas depresivos e incertidumbre en cuanto a la capacidad de ayuda de otras personas. Sin embargo, 44,8% buscaron ayuda, principalmente hablando con familiares o compañeros, y notificaron sentimientos de temor, culpabilidad y vergüenza acerca de sus síntomas. Un episodio depresivo mayor actual y unos ingresos iguales o inferiores a US$ 10 000 fueron factores predictivos significativos de comportamientos de búsqueda de ayuda. CONCLUSIONES: Los datos de este estudio indican que, cuando se sienten tristes o deprimidas, las mujeres latinas en período perinatal tienden a buscar en primer lugar el apoyo emocional de la familia y los amigos, y podrían subutilizar los servicios de salud mental cuando son necesarios. La internet es un medio eficaz para llegar a las mujeres en período perinatal, especialmente a las que viven en zonas del mundo donde pueden existir barreras para el acceso a los recursos psicológicos.

TGF-beta Suppresses COX-2 Expression by Tristetraprolin-Mediated RNA Destabilization in A549 Human Lung Cancer Cells / Journal of the Korean Cancer Association, 대한암학회지

PURPOSE: Overexpression of cyclooxygenase 2 (COX-2) is thought to promote survival of transformed cells. Transforming growth factor beta (TGF-beta) exerts anti-proliferative effects on a broad range of epithelial cells. In the current study, we investigated whether TGF-beta can regulate COX-2 expression in A549 human lung adenocarcinoma cells, which are TGF-beta-responsive and overexpress COX-2. MATERIALS AND METHODS: Western blotting, Northern blotting, and mRNA stability assays were performed to demonstrate that COX-2 protein and mRNA expression were suppressed by TGF-beta. We also evaluated the effects of tristetraprolin (TTP) on COX-2 mRNA using RNA interference. RESULTS: We demonstrated that COX-2 mRNA and protein expression were both significantly suppressed by TGF-beta. An actinomycin D chase experiment demonstrated that COX-2 mRNA was more rapidly degraded in the presence of TGF-beta, suggesting that TGF-beta-induced inhibition of COX-2 expression is achieved via decreased mRNA stability. We also found that TGF-beta rapidly and transiently induced the expression of TTP, a well-known mRNA destabilizing factor, before suppression of COX-2 mRNA expression was observed. Using RNA interference, we confirmed that increased TTP levels play a pivotal role in the destabilization of COX-2 mRNA by TGF-beta. Furthermore, we showed that Smad3 is essential to TTP-dependent down-regulation of COX-2 expression in response to TGF-beta. CONCLUSION: The results of this study show that TGF-beta down-regulated COX-2 expression via mRNA destabilization mediated by Smad3/TTP in A549 cells.

ATF3 Mediates Anti-Cancer Activity of Trans-10, cis-12-Conjugated Linoleic Acid in Human Colon Cancer Cells

Conjugated linoleic acids (CLA) are a family of isomers of linoleic acid. CLA increases growth arrest and apoptosis of human colorectal cancer cells through an isomer-specific manner. ATF3 belongs to the ATF/CREB family of transcription factors and is associated with apoptosis in colorectal cancer. The present study was performed to investigate the molecular mechanism by which t10, c12-CLA stimulates ATF3 expression and apoptosis in human colorectal cancer cells. t10, c12-CLA increased an apoptosis in human colorectal cancer cells in dose dependent manner. t10, c12-CLA induced ATF3 mRNA and luciferase activity of ATF3 promoter in a dose-dependent manner. The responsible region for ATF3 transcriptional activation by t10, c12-CLA is located between -147 and -1850 of ATF3 promoter. mRNA stability of ATF3 was not affected by t10, c12-CLA treatment. t10, c12-CLA increases GSK3beta expression and suppresses IGF-1-stimulated phosphorylation of Akt. The knockdown of ATF3 suppressed expression of GSK3beta and NAG-1 and PARP cleavage. The results suggest that t10, c12-CLA induces apoptosis through ATF3-mediated pathway in human colorectal cancer cells.

Correlation between five RNA markers of rat's skin and PMI at different temperatures / 法医学杂志

OBJECTIVE@#To explore the correlation between postmortem interval (PMI) and five RNA markers of rat's skin--β-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA(18S rRNA), 5S ribosomal RNA (5S rRNA), and microRNA-203 (miR-203), at different temperatures.@*METHODS@#Eighteen SD rats were randomly divided into three environmental temperature groups: 4 °C, 15 °C and 35 °C, respectively. Skin samples were taken at 11 time points from 0 h to 120 h post-mortem. The total RNA was extracted from the skin samples and the five RNA levels were detected by real-time fluorescent quantitative PCR. Proper internal reference was selected by geNorm software. Regression analysis of the RNA markers was conducted by GraphPad software.@*RESULTS@#5S rRNA and miR-203 were most suitable internal references. A good linear relationship between PMI and RNA levels (β-actin and GAPDH) was observed in two groups (4 °C and 15 °C), whereas the S type curve relationship between the expression levels of the two markers (β-actin and GAPDH) and PMI was observed in the 35 °C group. The partial linear relationship between 18S rRNA and PMI was observed in the groups (15 °C and 35 °C).@*CONCLUSION@#Skin could be a suitable material for extracting RNA. The RNA expression levels of β-actin and GAPDH correlate well with PMI, and these RNA markers of skin tissue could be additional indice for the estimation of PMI.

Relation between RNA sequences, structures, and shapes via variation networks

RNA plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. RNA secondary structure represents various significant portions of RNA tertiary structure. Since the biological function of RNA is concluded indirectly from its primary structure, it would be important to analyze the relations between the RNA sequences and their structures. One important tool to perform this kind of analysis is the neutral network which is a collection of RNA sequences, all coding the same secondary structure, where each RNA sequence is distinguished from the others by no more than a single base mutation. Another high level and useful representation of an RNA secondary structure is the RNA shape, where it is holding the vicinity and nesting of structural components and reducing their lengths to one unit. This allows us to analyze the huge structural space corresponding to the larger RNA sequences. In this study, a new concept, entitled Variation Network, over the set of all RNA shapes is introduced. Based on this concept, the potential relations between random and natural RNA sequences, as well as their corresponding structures are analyzed. To explore the relations between random and natural RNA sequences and their corresponding structures, different properties including frequency, normalized frequency, shape energy average, variation rate, normalized variation rate, neighborhood energy average, and stability were obtained and analyzed. The correlations among these properties of random and natural Variation Networks are presented. Base on the obtained correlations, all the employed datasets are highly correlated to each other from the frequency point of view, whereas they are not well correlated from the thermodynamic energy point of view. Since the thermodynamic energy value of an RNA sequence over its secondary structure plays a key role in its function, this research conclude that the natural RNA sequences are not generated randomly

Suppression of miR-155 Expression in IFN-gamma-Treated Astrocytes and Microglia by DJ-1: A Possible Mechanism for Maintaining SOCS1 Expression

Previously, we reported that DJ-1, encoded by a Parkinson's disease (PD)-associated gene, inhibits expression of proinflammatory mediators in interferon-gamma (IFN-gamma)-treated astrocytes and microglia through inhibition of STAT1 activation. Here, using microglia and astrocytes cultured from wild-type (WT) and DJ-1-knockout (KO) mouse brains, we examined how DJ-1 regulates suppressor of cytokine signaling 1 (SOCS1), a negative feedback regulator of STAT1 (signal transducer and activator of transcription) that is also induced by STAT1. We found that IFN-gamma significantly increased SOCS1 mRNA expression in WT microglia and astrocytes, but not in KO cells, although STAT1 was highly activated in these latter cells. We further found that SOCS mRNA stability was decreased in DJ-1-KO cells, an effect that appeared to be mediated by the microRNA, miR-155. IFN-gamma increased the levels of miR-155 in DJ-1-KO cells but not in WT cells. In addition, an miR-155 inhibitor rescued SOCS1 expression and decreased STAT1 activation in DJ-1-KO cells. Taken together, these results suggest that DJ-1 efficiently regulates inflammation by maintaining SOCS1 expression through regulation of miR-155 levels, even under conditions in which STAT1 activation is decreased.

Avaliação do impacto da implantação do controle de qualidade em um banco de amostras teciduais criopreservadas / Evaluating the impact of implementation of quality control in a bank of cryopreserved tissue samples

Bancos de tumores foram criados para organizar a coleta, arm azenamento e distribuição de amostras biológicas de pacientes oncológicos, favorecendo seu uso nas pesquis as sobre o cân cer. Amostras ade quadas devem ter RNA, DNA e proteínas de boa qualidade. RNA de boa qualidade deve estar íntegro e puro e DNA deve ter boa c oncentração e pur eza. Basea do em norm as in ternacionais, f oi elaborado e implantado um abrangente sistema de controle de qualidade no banco de tumores do Hospital de Câncer de Barretos, que para fins de estudo foi dividido em banco pré-controle de qu alidade (den ominado b anco pré) e em ban co pós- controle de qualidade (denominado banco pós). Objetivando comparar a qualidade das amostras n os dois bancos, atra vés d a extração d e R NA total e d e DNA (utilizando-se homogeneizador de tecidos e Kits), selecionou-se de forma aleatória 200 a mostras tumorais, distribuídas ig ualitariamente entre mama, co lorreto, estômago, pulmão e tireóide, sendo 100 do banco pré e 100 do banco pós. Para se avaliar a influência do tempo de isquemia fria (tempo entre a excisão do e spécime cirúrgico e o congelamento rápido da amostra armazenada) na qualidade do RNA total de amostras tumorais do banco pós, foram coletadas 200 amostras tumorais, distribuídas igualitariamente entre mama, co lorreto, estômago, pulmão e ti reóide, de 100 doadores diferentes, metade com o tempo de isquemia fria (TIF) de até 30 minutos e a o utra metade do mesmo espécime com TIF de 45 minutos. Extraiu-se RNA total dessas amostras (com maceração manual e Trizol) e comparou-se a sua qualidade, através do núm ero de i ntegridade do RNA (RIN), dentr o dos d ois intervalos de tempo e nas diferentes top ografias. Ao c omparar-se amostras com RIN acima de 7 (consideradas ideais para experimentos de microarray), do banco pré e do b anco pó s, for am enc ontrados 73 (73%) no p rimeiro e 87 (87%) no segundo (p=0,013). Ao comparar-se o intervalo de TIF de até 30 minutos com o de 45...

Tumor banks were created to or ganize the collection, storage and d istribution of biological samples of cancer pa tients, favoring it's use in cancer rese arches. Appropriate samples should have good quality of RNA, DNA and p roteins. RNA of good quality should be intact and pure and DNA should have good concentration and pu rity. Ba sed on international sta ndards, we elabo rated and imp lanted an comprehensive s ystem of qu ality control in the tu mor bank of Ba rretos Cancer Hospital, w hich was divided for st udy purposes i n pre bank quality control (denominated pre bank) and post bank qu ality control (denominated post bank). Aiming to compare the quality of the samples in two banks, through the extraction of total RNA and DNA (b y tissue homogenizer and Kits), we se lected 200 tumor samples in a random way, distributed equally among breast, colorectal, stomach, lung and thyroid, being 100 of the pre-bank and 100 of the post bank. To evaluate the influence o f cold ischem ia time (time b etween t he ex cision o f the su rgical specimen and the fast freezing of the stored sample) in the quality of total of RNA tumor sa mples of th e po st bank , we collected 2 00 t umor s amples, distrib uted equally among breast, colorectal, stom ach, lung and th yroid, fro m 100 different donors, half with the cold ischemia time (CIT) up to 30 minutes and the other ha lf of the sam e specimen with CIT exact ly 45 minutes. We ex tracted total RNA of these samples (with manual maceration and T rizol) and c ompared their qu ality, through the RNA integri ty number (RIN), ins ide tw o intervals of time a nd in different topographies. Comparing samples with RIN above 7 (considered ideals for microarray experiments), of the pre bank and of the post bank, we found 73 (73%) in the first and 87 (87%) in the second (p=0,013). Comparing the interval of CIT up to 30 m inutes with the ex actly 45 minutes, we found respectively 63 (64,3%)...