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Biomédica (Bogotá) ; 37(supl.2): 143-154, jul.-set. 2017. tab, graf
Article in English | LILACS | ID: biblio-888533


Abstract Introduction: Mitochondrial DNA has proven its utility for the study of insect evolution. Genes such as cytochrome b (Cytb) and the transfer gene for serine (SertRNA) can be used to compare closely related organisms. Objective: The phylogenetic utility of Cytb-SertRNA-IG1-ND1 was tested for polymorphisms, and secondary structure modeling in SertRNA was done to detect possible cryptic species in Anopheles neivai. Materials and methods: Specimens from Colombia, Guatemala, and the type locality in Panamá were collected and sequenced for specimen comparison based on DNA polymorphisms, and secondary structure modeling for the SertRNA gene. Results: Thirty-six sequences for A. neivai and A. pholidotus were obtained. Conclusions: Polymorphic variants were detected in A. neivai for Cytb-SertRNA-IG1- ND1. Despite this variation in A. neivai, cryptic species could not be detected.

Resumen Introducción. El ADN mitocondrial ha demostrado su utilidad para el estudio de la evolución en los insectos. Existen algunos genes mitocondriales como el citocromo b (Cytb) y el gen de transferencia para el aminoácido serina (SertRNA) que pueden usarse en el diagnóstico de especies estrechamente relacionadas. Objetivo. Explorar la utilidad filogenética de la región Cytb-SertRNA-IG1-ND1 para detectar posibles especies crípticas en Anopheles neivai. Materiales y métodos. Se recolectaron especímenes en Colombia, Guatemala y en la localidad tipo en Panamá, los cuales se secuenciaron y se compararon mediante el polimorfismo de ADN en toda la región y mediante la simulación de estructuras secundarias del gen SertRNA. Resultados. Se obtuvieron las secuencias de especímenes de A. neivai (34) y A. pholidotus (2). Conclusiones. Se detectaron algunos polimorfismos para la regiónCytb-SertRNA-IG1-ND1 en A. neivai, pero no así especies crípticas.

Animals , DNA, Mitochondrial/genetics , Anopheles/genetics , Panama , Phylogeny , Polymorphism, Genetic , Species Specificity , DNA/analysis , DNA/genetics , RNA, Transfer, Ser/genetics , Genes, Insect , Colombia , Insect Proteins/genetics , Cytochromes b/genetics , Guatemala , Anopheles/classification , Nucleic Acid Conformation
Article in Chinese | WPRIM | ID: wpr-335167


Mitochondrial tRNAgene mutation is closely related to acoustic nerve deafness. Some mutations can affect the structure and transcriptional processing of tRNA, for instance m.7444G>A mutation in tRNAprecursor 3' side, m.7472 insC as well as m.7511T>C mutations in the stem and ring of tRNA, may influence tRNAstability, thus affect the synthesis of mitochondrial peptides, reduce the production of ATP and cause deafness. This article focuses on mitochondrial tRNAgene mutations as well as the mechanism underlying hearing loss.

Amino Acid Sequence , Base Sequence , Genetic Predisposition to Disease , Genetics , Hearing Loss , Genetics , Humans , Mitochondrial Proteins , Genetics , Mutation , Nucleic Acid Conformation , RNA , Chemistry , Genetics , RNA, Transfer, Ser , Chemistry , Genetics
Article in Chinese | WPRIM | ID: wpr-335138


A high proportion of modified nucleotides has been found in mitochondrial tRNA. Such modification can promote accurate folding of tRNA and its stability, while unmodified mitochondrial tRNA may fold into various 2D-structures with impaired functions. Therefore, modification of mitochondrial tRNA is closely related to mitochondrial diseases. Particularly, positions 9, 34, 37, 54 and 55 of the mitochondrial tRNA are critical for such modification. Mutations at these positions are important cause for mitochondrial dysfunction and have been associated with various mitochondrial diseases.

DNA, Mitochondrial , Chemistry , Genetics , Humans , Mitochondrial Diseases , Genetics , Mutation , Nucleic Acid Conformation , RNA, Transfer , Chemistry , Genetics
Rev. bras. oftalmol ; 75(2): 144-146, Mar.-Apr. 2016. graf
Article in English | LILACS | ID: lil-779959


ABSTRACT This article presents a case of tick infestation of the lower eyelid by a previously unreported species. A 71-year-old male presented with a tick attached to the lower eyelid. The tick was identified morphologically, and then molecularly via polymerase chain reaction (PCR) and sequencing of its DNA. In addition, a review of the literature relevant to the genera of ticks associated with infestation of the human eye is provided. The tick, which was in the nymphal developmental stage, was first identified according to taxonomic keys as Dermacentor sp. For complete species identification, 16s rDNA gene PCR and sequencing were performed, which showed that the tick was D. marginatus. Systematizing tick species could assist physicians in determining the potential for transmission of tick-borne human diseases.

RESUMO Este artigo apresenta um caso de infestação por carrapatos da pálpebra inferior por uma espécie previamente não declarada. Um homem de 71 anos de idade apresentou-se com um carrapato grudado na pálpebra inferior. O carrapato foi identificado morfologicamente, e, em seguida, uma estrutura molecular através de reacção em cadeia da polimerase (PCR) e a sequenciação do seu DNA. Além disso, uma análise da literatura pertinente aos gêneros de carrapatos associados à infestação do olho humano é fornecido. O carrapato, que estava em fase de desenvolvimento das ninfas, foi identificado pela primeira vez de acordo com chaves taxonômicas com o Dermacentor sp. Para identificação de espécies completa, gene 16S rDNA PCR e sequenciamento foram realizadas, que mostrou que o carrapato foi D. marginatus. Sistematizando espécie de carrapato poderia ajudar os médicos a determinar o potencial de transmissão de doenças humanas transmitidas por carrapatos.

Humans , Male , Aged , Tick Infestations/parasitology , Ticks/classification , Ticks/genetics , Ticks/parasitology , Eye Infections, Parasitic , Eyelids/parasitology , Phylogeny , DNA/isolation & purification , DNA/chemistry , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 16S/chemistry , Polymerase Chain Reaction , Eyelid Diseases/parasitology , Nucleic Acid Conformation
Article in English | WPRIM | ID: wpr-296542


In the present study, the complete genomes of four common (4/EV71/Wenzhou/CHN/2014, 15/ EV71/Wenzhou/CHN/2014, 116/EV71/Wenzhou/ CHN/2014, and 120/EV71/Wenzhou/CHN/2014) and two virulent (11/EV71/Wenzhou/CHN/2014 and 109/EV71/Wenzhou/CHN/2014) enterovirus 71 (EV71) isolates were sequenced and described. They are 7405 bp in length and belong to EV71 sub-genotype C4 (C4a cluster). Nucleotide sequence alignment revealed six nucleotide variations (GP151→TP151, GP199→AP199, GP261→TP261, AP328→CP328, GP422→AP422, and GP437→TP437) in the two virulent isolates within the 5'UTR of the IRES element. RNA secondary structure predictions of IRES and FCE indicated that the common isolates shared similar structures, which were different from those of the virulent isolates. Moreover, the GP114→CP114 and GP151→TP151 mutations in the virulent isolates contributed to the formation of the unique RNA secondary structures in SL II. Furthermore, nucleotide/amino acid sequence alignments of 82 EV71 isolates indicated that six sites (TP488 and CP577 in the 5'UTR; AsnP57 in 2A; IleP56 in 3C; CP10 and AP47 in the 3'UTR) are potentially associated with the neurovirulence of EV71. Finally, the 3D structures of 2A were analogous, whereas the structures of VP1 and 3C were variable.

Base Sequence , Central Nervous System , Virology , Enterovirus A, Human , Classification , Genetics , Virulence , Enterovirus Infections , Virology , Genome, Viral , Genomics , Genotype , Humans , Molecular Sequence Data , Nucleic Acid Conformation , Phylogeny , RNA, Viral , Chemistry , Genetics , Virulence
Clinics ; 70(5): 363-368, 05/2015. tab, graf
Article in English | LILACS | ID: lil-748276


OBJECTIVES: To evaluate the clinical outcomes and identify the predictors of mortality in elderly patients undergoing peritoneal dialysis. METHODS: We conducted a retrospective study including all incident peritoneal dialysis cases in patients ≥65 years of age treated from 2001 to 2014. Demographic and clinical data on the initiation of peritoneal dialysis and the clinical events during the study period were collected. Infectious complications were recorded. Overall and technique survival rates were analyzed. RESULTS: Fifty-eight patients who began peritoneal dialysis during the study period were considered for analysis, and 50 of these patients were included in the final analysis. Peritoneal dialysis exchanges were performed by another person for 65% of the patients, whereas 79.9% of patients preferred to perform the peritoneal dialysis themselves. Peritonitis and catheter exit site/tunnel infection incidences were 20.4±16.3 and 24.6±17.4 patient-months, respectively. During the follow-up period, 40 patients were withdrawn from peritoneal dialysis. Causes of death included peritonitis and/or sepsis (50%) and cardiovascular events (30%). The mean patient survival time was 38.9±4.3 months, and the survival rates were 78.8%, 66.8%, 50.9% and 19.5% at 1, 2, 3 and 4 years after peritoneal dialysis initiation, respectively. Advanced age, the presence of additional diseases, increased episodes of peritonitis, the use of continuous ambulatory peritoneal dialysis, and low albumin levels and daily urine volumes (<100 ml) at the initiation of peritoneal dialysis were predictors of mortality. The mean technique survival duration was 61.7±5.2 months. The technique survival rates were 97.9%, 90.6%, 81.5% and 71% at 1, 2, 3 and 4 years, respectively. None of the factors analyzed were predictors of technique survival. CONCLUSIONS: Mortality was higher in elderly patients. Factors affecting mortality in elderly patients included advanced age, ...

Gene Expression Regulation , Bacterial Proteins/chemistry , Computational Biology , Kinetics , Ligands , Nucleic Acid Conformation , Nucleotides/chemistry , Protein Binding , Protein Conformation , Protein Structure, Secondary , Protein Structure, Tertiary , RNA , Thermodynamics
Cad. saúde pública ; 31(3): 451-462, 03/2015. tab, graf
Article in English | LILACS | ID: lil-744830


The aim of this systematic review was to identify and characterize articles in indexed scientific journals with quantitative data surveys on administrative or legal proceedings for access to medicines. The SciELO, LILACS, MEDLINE via PubMed, Embase, and Scopus databases were used. We identified 45 articles, of which 17 were selected. The larger studies, each covering between 2,000 and 2,927 lawsuits, were done in the states of São Paulo, Rio de Janeiro, and Santa Catarina, Brazil. Eleven studies specified the type of legal representation, of which six examined cases with public attorneys and five with private attorneys. Only two studies reported whether the lawsuit was individual or class action, and in both the claims were individual. Since the majority of the medicines requested in the lawsuits were medium to high-cost, the review indicates that lawsuits contributed to the incorporation of these drugs into current pharmaceutical care in Brazil.

El objetivo de esta revisión sistemática fue identificar y caracterizar los artículos disponibles en revistas científicas indexadas en bases de datos electrónicas, que llevaron a cabo un estudio cuantitativo de datos, procedimientos administrativos o judiciales sobre la cuestión del acceso a los medicamentos a través de demandas judiciales. Los estudios fueron localizados en las bases de datos SciELO, LILACS, MEDLINE vía PubMed, Embase, Scopus. Se identificaron 45 artículos, de los cuales se seleccionaron 17. Los estudios que se llevaron a cabo engloban de 2.000 a 2.927 procesos judiciales en São Paulo, Río de Janeiro y Santa Catarina, Brasil. En once estudios se realizaron encuestas a los representantes legales de la acción judicial. En seis estudios predominó la representación pública legal y en cinco abogados privados. Sólo dos estudios examinaron si la acción era individual o colectiva y en los dos hubo prevalencia de acciones individuales. Como la mayoría de los medicamentos estaba involucrada en acciones legales de medio y alto coste, se cree que las demandas han contribuido a la incorporación de fármacos en la política pública actual.

O objetivo desta revisão sistemática foi identificar e caracterizar artigos disponíveis em periódicos científicos indexados em bases eletrônicas, que realizaram levantamento de dados quantitativo, em processos administrativos ou judiciais, sobre a questão do acesso a medicamentos por meio de ações judiciais. Foram usadas as bases de dados SciELO, LILACS, MEDLINE via PubMed, Embase e Scopus. Identificamos 45 artigos, dos quais foram selecionados 17 artigos. Os estudos com faixa de 2.000 a 2.927 processos foram conduzidos em São Paulo, Rio de Janeiro e Santa Catarina, Brasil. Em 11 estudos foram pesquisadas qual a representação jurídica da ação. Em seis estudos predominaram a representação de advogados públicos e em cinco particulares. Somente dois estudos observaram se a ação era coletiva ou individual, sendo que nas duas pesquisas a prevalência era de ações individuais. Como a maioria dos medicamentos envolvidos nas ações é de médio e alto custo, acredita-se que as demandas judiciais tenham contribuído para incorporação de medicamentos nas ações de assistência farmacêutica atuais.

Bacteriophage lambda/genetics , DNA, Viral/physiology , Genes, Switch , Genomic Instability , Binding Sites , DNA, Viral/chemistry , Gene Expression Regulation, Viral , Lysogeny/genetics , Models, Genetic , Mutation , Nucleic Acid Conformation , Operator Regions, Genetic , Stochastic Processes
Cad. saúde pública ; 31(3): 620-632, 03/2015. tab
Article in Portuguese | LILACS | ID: lil-744835


O estudo descreve os pontos de venda de alimentos e sua associação com sobrepeso/obesidade em escolares de Florianópolis, Santa Catarina, Brasil. Desenho transversal com amostra probabilística de 2.506 escolares de escolas públicas (n = 19) e privadas (n = 11). O sobrepeso/obesidade foi classificado pela referência da Organização Mundial da Saúde de 2007. Foram realizadas análises brutas e ajustadas por meio de regressão de Poisson. A prevalência de sobrepeso/obesidade foi de 34,2%. Na rede pública, foram verificados 19,6% de sobrepeso e 13,5% de obesidade. Na rede privada, observaram-se 22,4% de sobrepeso e 11,1% de obesidade. Na rede pública, foi encontrada associação entre sobrepeso/obesidade e utilização da padaria (p = 0,004). Na rede privada, observou-se que os escolares de famílias que utilizaram o supermercado apresentaram 26% menos de sobrepeso/obesidade do que os escolares que não utilizam esses pontos de venda de alimentos (p = 0,003). Os dados encontrados evidenciam a existência de associação entre a utilização de alguns tipos de pontos de venda de alimentos (supermercado e padaria) e a prevalência de sobrepeso/obesidade na população escolar.

The study analyzes retail food outlets and their association with overweight/obesity in schoolchildren from Florianópolis, Santa Catarina State, Brazil. The study used a cross-sectional design with a random sample of 2,506 schoolchildren from public (n = 19) and private schools (n = 11). Overweight and obesity were classified according to World Health Organization guidelines for 2007, and crude and adjusted analyses were performed using Poisson regression. Prevalence of overweight/obesity was 34.2%. In public schools, 19.6% of the children were overweight and 13.5% were obese, as compared to 22.4% and 11.1% in private schools. An association was found in the public school system between overweight/obesity and the use of bakeries for food purchases (p = 0.004). In the private school system, children of families that bought groceries at the supermarket showed 26% less overweight/obesity compared to those who did not (p = 0.003). The data show an association between some types of food outlets (supermarkets and bakeries) and prevalence of overweight/obesity in the school-age population.

El estudio describe los puntos de venta de alimentos y su asociación con el sobrepeso/obesidad en escolares de Florianópolis, Santa Catarina, Brasil. Se trata de un estudio transversal con una muestra aleatoria de 2.506 escolares de las escuelas públicas (n = 19) y privadas (n = 11). El sobrepeso/obesidad se clasifica, en función de la OMS en 2007, con análisis ajustados y crudos que se realizaron mediante la regresión de Poisson. La prevalencia de sobrepeso/obesidad fue de un 34,2%. En el sistema público el resultado fue de un 19,6% sobrepeso y un 13,5% obesidad. En el privado se observó un 22,4% de sobrepeso y 11,1% obesidad. En el primero se encontró una correlación entre el sobrepeso/obesidad y el consumo de bollería (p = 0,004). En las escuelas privadas se observó que los escolares de familias que habían utilizado el supermercado tenían un 26% menos de sobrepeso/ obesidad que los niños en edad escolar que no utilizaron este punto de venta de alimentos (p = 0,003). En el momento del estudio existe una asociación entre el uso de algunos tipos de punto de venta de alimentos (supermercado y panadería) y la prevalencia de sobrepeso/obesidad en escolares.

DNA, Fungal/chemistry , HSP90 Heat-Shock Proteins/metabolism , Nucleic Acid Conformation , Saccharomyces cerevisiae , Saccharomyces cerevisiae Proteins/metabolism , Telomere/chemistry , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , DNA, Fungal/metabolism , Enzyme Activation , HSP90 Heat-Shock Proteins/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Telomerase/metabolism , Telomere-Binding Proteins/genetics , Telomere-Binding Proteins/metabolism , Telomere/metabolism
Article in English | WPRIM | ID: wpr-225151


The present study was performed to compare the mitochondrial genomes between 2 Spirometra tapeworms, Spirometra erinaceieuropaei and Spirometra decipiens (Cestoidea: Diphyllobothriidae), which larval stages are important etiological agents of sparganosis in humans. For each species, the full mitochondrial genome was amplified in 8 overlapping fragments using total genomic DNA purified from a single worm as the template. The mitochondrial genomes were 13,643 bp (S. erinaceieuropaei) and 13,641 bp (S. decipiens) in length and contained 36 genes; 12 protein-coding genes, 2 ribosomal RNA (rRNA, small and large subunits), and 22 transfer RNAs (tRNAs). The 12 protein-coding genes constituted 10,083 bp (S. erinaceieuropaei) and 10,086 bp (S. decipiens) of their respective mitochondrial genomes. The tRNA genes, ranging in length from 56 to 70 bp, were identified based on putative secondary structures such as the typical cloverleaf shape. A total of 23 intergenic sequences, varying from 1 to 204 bp in size, were interspersed in S. erinaceieuropaei (total, 504 bp) and S. decipiens (total, 496 bp) mtDNA. The 12 protein-coding genes of S. erinaceieuropaei and S. decipiens differed by 12.4%, whereas the overall difference in mtDNA sequence between S. erinaceieuropaei and S. decipiens was 12.9%. Thus, from the standpoint of the mitochondrial genome, S. decipiens represents a valid species that can be distinguished from S. erinaceieuropaei.

Animals , Base Sequence , Cestode Infections/parasitology , DNA, Mitochondrial/chemistry , Genome, Helminth , Genome, Mitochondrial , Humans , Molecular Sequence Data , Nucleic Acid Conformation , Open Reading Frames , Phylogeny , Spirometra/chemistry
Article in Chinese | WPRIM | ID: wpr-266719


Due to the minimum free energy model, it is very important to predict the RNA secondary structure accurately and efficiently from the suboptimal foldings. Using clustering techniques in analyzing the suboptimal structures could effectively improve the prediction accuracy. An improved k-medoids cluster method is proposed to make this a better accuracy with the RBP score and the incremental candidate set of medoids matrix in this paper. The algorithm optimizes initial medoids through an expanding medoids candidate sets gradually. The predicted results indicated this algorithm could get a higher value of CH and significantly shorten the time for calculating clustering RNA folding structures.

Algorithms , Cluster Analysis , Nucleic Acid Conformation , RNA , Chemistry
Article in Chinese | WPRIM | ID: wpr-246079


The study is aimed to ensure the quality and safety of medicinal plants by using ITS2 DNA barcode technology to identify Corydalis boweri, Meconopsis horridula and their close related species. The DNA of 13 herb samples including C. boweri and M. horridula from Lhasa of Tibet was extracted, ITS PCR were amplified and sequenced. Both assembled and web downloaded 71 ITS2 sequences were removed of 5. 8S and 28S. Multiple sequence alignment was completed and the intraspecific and interspecific genetic distances were calculated by MEGA 5.0, while the neighbor-joining phylogenetic trees were constructed. We also predicted the ITS2 secondary structure of C. boweri, M. horridula and their close related species. The results showed that ITS2 as DNA barcode was able to identify C. boweri, M. horridula as well as well as their close related species effectively. The established based on ITS2 barcode method provides the regular and safe detection technology for identification of C. boweri, M. horridula and their close related species, adulterants and counterfeits, in order to ensure their quality control, safe medication, reasonable development and utilization.

Base Sequence , China , Corydalis , Chemistry , Classification , Genetics , DNA Barcoding, Taxonomic , Methods , DNA, Plant , Chemistry , Genetics , DNA, Ribosomal Spacer , Chemistry , Genetics , Molecular Sequence Data , Nucleic Acid Conformation , Papaveraceae , Chemistry , Classification , Genetics , Phylogeny , Plants, Medicinal , Chemistry , Classification , Genetics
Journal of Biomedical Engineering ; (6): 1065-1069, 2014.
Article in Chinese | WPRIM | ID: wpr-234457


This paper proposes algorithm in predicting the RNA secondary structure that combines several sequence comparisons, searches the eigenvalue for subsequence division with dynamic programing, utilizing the minimum free energy method. Moreover, the paper assesses the results derived from this new algorithm based on base-pairs distance, climbing distance and morphology distance. The paper also compares the assessment result and the prediction results of different prediction tools, and analyzes the advantages of the new method and its improvement direction.

Algorithms , Nucleic Acid Conformation , RNA , Chemistry
Article in Chinese | WPRIM | ID: wpr-299841


<p><b>OBJECTIVE</b>To analyse a special kind of Schisandra chinensis with the white fruit using ITS2 barcode at molecular levels.</p><p><b>METHOD</b>ITS2 regions were sequenced bidirectionally. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner, MEGA 5.0 software was used to align the sequences. The ITS2 secondary structure was predicted using ITS2 web server, BLAST 1 method was used to identify the S. chinensis with the white fruit.</p><p><b>RESULT</b>The length of the ITS2 sequence was 231 bp. And the sample was identified as S. chinensis using the method of BLAST 1. Their mean interspecific genetic distance (K2P distance) among the populations of the S. chinensis with the white fruit and S. chinensis was far lower than the mean interspecific genetic distance between the S. chinensis and S. sphenanthera.</p><p><b>CONCLUSION</b>By using ITS2 the S. chinensis with the white fruit was identified as S. chinensis, and the ITS2 barcode could be used to identify S. chinensis and S. sphenanthera.</p>

DNA, Plant , Chemistry , Genetics , DNA, Ribosomal Spacer , Chemistry , Genetics , Fruit , Chemistry , Classification , Genetics , Molecular Sequence Data , Nucleic Acid Conformation , Schisandra , Chemistry , Classification , Genetics , Sequence Analysis, DNA , Software
Chinese Journal of Virology ; (6): 257-262, 2014.
Article in Chinese | WPRIM | ID: wpr-356606


To obtain the genome sequence of human bocavirus 2 (HBoV2), different regions of HBoV2 genome were amplified through PCR in fecal specimens which had been identified as single-positive for HBoV2 in 2010. A genome sequence of HBoV2 (HBoV2-NC, 5444 bp) was obtained after sequence assembly. The phylogenetic analysis showed that HBoV2-NC had the closest evolutionary relationship with HBoV2 Lanzhou strain. The predication of inverted terminal repeats of HBoV2-NC by DINAMelt showed that inverted terminal repeats were contained in HBoV2-NC 5' terminal, which had the typical stem-loop structure in other parvoviruses. Finally, some flanking sequences of HBoV2-NC were amplified by linker-PCR.

Base Sequence , Gene Amplification , Genome, Viral , Human bocavirus , Chemistry , Classification , Genetics , Humans , Molecular Sequence Data , Nucleic Acid Conformation , Parvoviridae Infections , Virology , Phylogeny , RNA, Viral , Chemistry , Genetics , Terminal Repeat Sequences
Chinese Journal of Virology ; (6): 463-469, 2014.
Article in Chinese | WPRIM | ID: wpr-280342


Both sides of the picornavirus genome have 5'-untranslated region (5'UTR) and 3'- untranslated region (3'UTR). This study demontrated that both the 5'-and 3'-UTR can form complex structures, such as stem-loop, clover and pseudoknot structure, These structures play an important role in the regulaton of the replication and translation of the viruses. This article reviewed the progress of research on the structure and function of picornavirus' 3'-UTR over recent years.

3' Untranslated Regions , Animals , Humans , Nucleic Acid Conformation , Picornaviridae , Chemistry , Genetics , Metabolism , Picornaviridae Infections , Virology , RNA, Viral , Chemistry , Genetics , Metabolism
Journal of Experimental Hematology ; (6): 1369-1372, 2013.
Article in Chinese | WPRIM | ID: wpr-265011


Emerging evidence has demonstrated that genomes are organized into higher-order structures in vivo and long range interactions between genomic regions largely contribute to the regulation of gene expression. Hematopoiesis, orchestrated by the precise spatial regulation and organization of hematopoietic transcription factors, serves as a good model for exploring these issues. The chromosome conformation capture (3C) methodology and its high throughput based technology provide an innovative solution for analyzing the regulation of functional elements through inter-chromosomal and intra-chromosomal interactions, and contacts of functional components in nuclei, thus leading to a more comprehensive understanding of human genome and gene expression. This review focuses on the recent progress of 3C and its derivatives, and their applications in unraveling the mechanisms of transcriptional regulation in hematopoiesis.

Chromosomes , Gene Expression Regulation , Genetic Techniques , Genomics , Hematopoiesis , Genetics , Humans , Nucleic Acid Conformation
Article in Chinese | WPRIM | ID: wpr-306477


<p><b>OBJECTIVE</b>To select and identify ssDNA aptamers specific to Streptococcus mutans strains with different cariogenicity isolated from clinical specimens.</p><p><b>METHODS</b>Subtractive SELEX technology targeting the whole intact cells was used to screen for ssDNA aptamers specific to the clinical isolates Streptococcus mutans strains with different cariogenicity. Radioactive isotope, flow cytometry, gene cloning and sequencing, MEME online software and RNA structure analysis software were employed to analyze the first and secondary structures of the aptamers and identify the screened aptamers.</p><p><b>RESULTS</b>Detection by radioactive isotope showed sufficient pool enrichment after 9 rounds of subtractive SELEX. Flow cytometry showed that the selected aptamers H1, H16, H4, L1, L10 and H19 were capable of binding specifically with highly cariogenic Streptococcus mutans strains but not with strains with a low cariogenicity. The aptamer H19 had the strongest binding capacity to highly cariogenic Streptococcus mutans strains, with a dissociation constant of 69.45∓38.53 nmol/L.</p><p><b>CONCLUSION</b>We have obtained the ssDNA aptamers specific to the clinical isolates of highly cariogenic Streptococcus mutans strains.</p>

Aptamers, Nucleotide , Genetics , Cloning, Molecular , DNA Primers , Dental Caries , Microbiology , Gene Library , Humans , Nucleic Acid Conformation , SELEX Aptamer Technique , Species Specificity , Streptococcus mutans , Classification , Genetics
Mem. Inst. Oswaldo Cruz ; 107(4): 522-531, June 2012. ilus
Article in English | LILACS | ID: lil-626447


The addition of a capped mini-exon [spliced leader (SL)] through trans-splicing is essential for the maturation of RNA polymerase (pol) II-transcribed polycistronic pre-mRNAs in all members of the Trypanosomatidae family. This process is an inter-molecular splicing reaction that follows the same basic rules of cis-splicing reactions. In this study, we demonstrated that mini-exons were added to precursor ribosomal RNA (pre-rRNA) are transcribed by RNA pol I, including the 5' external transcribed spacer (ETS) region. Additionally, we detected the SL-5'ETS molecule using three distinct methods and located the acceptor site between two known 5'ETS rRNA processing sites (A' and A1) in four different trypanosomatids. Moreover, we detected a polyadenylated 5'ETS upstream of the trans-splicing acceptor site, which also occurs in pre-mRNA trans-splicing. After treatment with an indirect trans-splicing inhibitor (sinefungin), we observed SL-5'ETS decay. However, treatment with 5-fluorouracil (a precursor of RNA synthesis that inhibits the degradation of pre-rRNA) led to the accumulation of SL-5'ETS, suggesting that the molecule may play a role in rRNA degradation. The detection of trans-splicing in these molecules may indicate broad RNA-joining properties, regardless of the polymerase used for transcription.

Leishmania mexicana/genetics , RNA Precursors/genetics , RNA, Spliced Leader/genetics , Trans-Splicing/genetics , Exons/genetics , Nucleic Acid Conformation , Reverse Transcriptase Polymerase Chain Reaction
Article in Chinese | WPRIM | ID: wpr-262422


<p><b>OBJECTIVE</b>To investigate mutational spectrum and frequency of the mitochondrial 12S rRNA gene in Chinese subjects with aminoglycoside-induced and non-syndromic hearing loss.</p><p><b>METHODS</b>Total of 456 subjects with non-syndromic hearing loss were recruited from seven schools for deaf-mutes in Zhejiang province. Genomic DNA was extracted from the whole blood, and then the DNA fragment was amplified spanning the 12S rRNA gene, followed by sequencing and analyzed.</p><p><b>RESULTS</b>Thirty-one variants were identified by mutation analysis of 12S rRNA gene in these subjects. The frequency of the known 1555A > G mutation was 4.4% (20/456). Prevalence of other putative deafness-associated mutation at positions 961 and 1095 were 2.0% (9/456) and 0.7% (3/456) respectively. Furthermore, the 1027A > G, 1109T > C and 1431G > A variants conferred increased sensitivity to ototoxic drugs or non-syndromic deafness as they were absent in 449 Chinese controls and localized at highly conserved nucleotides of this 12S rRNA gene. Moreover, clinical data showed a wide range of age-of-onset, variety of severity and various audiometric configurations in subjects carrying the 1555A > G mutation.</p><p><b>CONCLUSIONS</b>Our data demonstrated that the mitochondrial 12S rRNA gene is the hot spot for mutations associated with aminoglycoside ototoxicity and non-syndromic hearing loss. Nuclear modifier genes, mitochondrial haplotypes and environmental factors might play a role in the phenotypic manifestation of these mutations.</p>

Adolescent , Aminoglycosides , Genetics , Asians , Genetics , Base Sequence , Child , DNA Mutational Analysis , DNA, Mitochondrial , Genetics , Deafness , Genetics , Female , Humans , Male , Mutation , Nucleic Acid Conformation , Pedigree , RNA, Ribosomal , Genetics , Young Adult