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1.
Arq. bras. med. vet. zootec. (Online) ; 73(3): 742-746, May-June 2021. tab
Article in English | ID: biblio-1278357

ABSTRACT

Objetivou-se neste estudo relatar a frequência e a identidade de patógenos transmitidos por carrapatos em cães residentes de uma área caracterizada por brejo de alta altitude. Amostras sanguíneas (n=203) foram coletadas e molecularmente analisadas via PCR (Babesia spp., Hepatozoon spp., Anaplasma spp. e Ehrlichia spp.) e sequenciamento de DNA. De todas as amostras analisadas, 8,87% (18/203) foram positivas a algum patógeno transmitido por carrapato. Especificamente, 5,42% (11/203) e 3,45% (7/203) foram positivos a Anaplasma platys e Ehrlichia canis, respectivamente. Este estudo fornece, pela primeira vez, evidência científica de infecção de cães por esses patógenos nessa área de alta altitude e reforça o provável papel de R. sanguineus s.l. como vetor de A. platys, principalmente considerando.se que muitos animais positivos eram infestados por essa espécie de carrapato.(AU)


Subject(s)
Animals , Dogs , Ehrlichiosis/epidemiology , Ehrlichia canis/isolation & purification , Anaplasma/isolation & purification , Anaplasmosis/epidemiology , Brazil , Polymerase Chain Reaction/veterinary , Sequence Analysis, DNA/veterinary , Wetlands , Altitude
2.
Article in Chinese | WPRIM | ID: wpr-879610

ABSTRACT

OBJECTIVE@#To explore the correlation between DSG2, TTN and GATA4 genes and Brugada syndrome in Henan Province of China.@*METHODS@#From February 2017 to February 2019, 100 patients with Brugada syndrome and 100 healthy individuals were selected as the study and the control groups, respectively. Electrocardiogram and echocardiography were carried out, and peripheral blood samples was collected. Coding regions of DSG2, TTN and GATA4 genes were amplified by PCR and sequenced. The results were compared with standard sequences from GenBank.@*RESULTS@#Electrocardiogram showed that all patients from the study group had ventricular arrhythmia, 87 cases (87%) presented ventricular tachycardia (VT), 84 cases (84%) presented T wave inversion, and 51 cases (51%) presented Epsilon wave. Echocardiography showed that the right ventricle in the study group was enlarged with the inner diameter of the right ventricle being (40.0±13.3) mm, and the right ventricle showed various degree of abnormal systolic function. The enlargement of right atrium accounted for 64%, and the involvement of the left ventricle accounted for 27%. The right ventricular diameter and left ventricular diastolic diameter of the study group were significantly greater than those of the control group (P< 0.05). DNA sequencing showed that 60 patients carried DSG2 gene variants, among which 18 had missense variant of exon 8. Fifty patients carried TTN gene variants, including 8 in the A-band domain and 3 in the I-band domain. Twenty patients carried 3 variants of the GATA4 gene.@*CONCLUSION@#Variants of the DSG2, TTN and GATA4 genes in Henan region are correlated with the onset of Brugada syndrome.


Subject(s)
Arrhythmogenic Right Ventricular Dysplasia , Brugada Syndrome/genetics , China , Connectin , Desmoglein 2/genetics , GATA4 Transcription Factor , Humans , Pedigree , Sequence Analysis, DNA
3.
Article in Chinese | WPRIM | ID: wpr-879602

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a patient with primary ciliary dyskinesia (PCD).@*METHODS@#High-throughput sequencing and bioinformatic analysis were carried out to identify pathogenic variant in the patient. Suspected variant was verified by Sanger sequencing among the family members, and intracytoplasmic sperm injection (ICSI) was used to achieve the pregnancy.@*RESULTS@#The patient had obstructive azoospermia, measurement of nasal NO exhalation at 84 ppb, and typical symptoms of PCD in nasal sinuses and lungs. DNA sequencing showed that he had carried biallelic variants of the DNAH5 gene, namely c.1489C>T (p.Q497X) in exon 11 and c.6304C>T (p.R2102C) in exon 38. His wife achieved clinical pregnancy with the assistance of ICSI.@*CONCLUSION@#Above finding has enriched the spectrum of DNAH5 gene variants, though the latters did not affect the outcome of pregnancy by ICSI.


Subject(s)
Axonemal Dyneins/genetics , Exons , High-Throughput Nucleotide Sequencing , Humans , Kartagener Syndrome/genetics , Male , Sequence Analysis, DNA , Sperm Injections, Intracytoplasmic
4.
Article in Chinese | WPRIM | ID: wpr-879581

ABSTRACT

OBJECTIVE@#To apply nanopore third-generation sequencing for the detection of chromosomal aneuploidy samples, and explore its performance and application prospects.@*METHODS@#DNA extracted from two human cell lines with X chromosome monosomy and 22.5 Mb deletion in 7q11.23-q21.3 region was sequenced with a MinION sequencer, and the results were analyzed.@*RESULTS@#Respectively, 555 872 and 2 679 882 reads were obtained from the two samples within 24 hours, with genome coverage being 53.75% and 88.63%. With a sequencing depth of 0.81× and 2.40× , respectively, the abnormal chromosomal regions could be detected by comparative analysis using Minimap2.@*CONCLUSION@#With low-depth whole genome sequencing, the use of nanopore third-generation sequencing is expected to complete the detection and analysis of chromosomal aneuploidy samples within 24 hours, but its further application and promotion needs to overcome the cost constraints.


Subject(s)
Aneuploidy , Chromosomes , High-Throughput Nucleotide Sequencing , Humans , Sequence Analysis, DNA , Technology
5.
Article in Chinese | WPRIM | ID: wpr-879572

ABSTRACT

OBJECTIVE@#To delineate the characteristics of a novel HLA-DQB1 allele identified during routine HLA matching in a leukemia family.@*METHODS@#The mother and brother of the patient were subjected to PCR sequence-specific oligonucleotide probe (SSOP), PCR sequence-based typ1ing (SBT), as well as next-generation sequencing (NGS).@*RESULTS@#PCR-SBT revealed that the patient's mother and brother's HLA-DQB1 sequences did not fully match with any known allele combination. NGS revealed that the novel allele has differed from the closest matched DQB1*03:02 with a T>G substitution at position 233 in exon 2, which resulted in substitution of Valine at codon 46 by Glycine. Pedigree analysis confirmed that the novel HLA-DQB1 allele was inherited from his mother.@*CONCLUSION@#A novel HLA-DQB1 allele has been identified through next generation sequencing and was officially named as HLA-DQB1*03:362 by the World Health Organization HLA Factor Nomenclature Committee.


Subject(s)
Alleles , Base Sequence , HLA-DQ beta-Chains/genetics , Humans , Male , Nucleotides , Polymorphism, Single Nucleotide , Sequence Analysis, DNA
6.
Article in Chinese | WPRIM | ID: wpr-880843

ABSTRACT

OBJECTIVE@#To explore the feasibility of detecting maternal hereditary mitochondrial tRNA@*METHODS@#We performed sequence analysis of mitochondrial DNA in blood samples from 2070 cases of maternal hereditary mitochondrial disease in the First Affiliated Hospital of Wenzhou Medical University, and identified 3 patients with m.15927G>A mutation.Buccal swabs and blood samples were obtained from the 3 patients (mutation group) and 3 normal volunteers (control group).After extracting whole genomic DNA from all the samples, the DNA concentration and purity were analyzed.The PCR products were subjected to dot blot hybridization, Southern blot hybridization, and DNA sequencing analysis to verify the feasibility of detecting m.15927G>A mutation using buccal swabs.@*RESULTS@#There was no significant difference in DNA concentration extracted from buccal swabs and blood samples in either the mutation group or the control group (@*CONCLUSIONS@#Buccal swabs collection accurate is an accurate and sensitive method for the detection of m.15927G>A mutation.


Subject(s)
DNA, Mitochondrial/genetics , Humans , Mitochondria , Mutation , RNA, Transfer , Sequence Analysis, DNA
7.
Neotrop. ichthyol ; 19(2): e200109, 2021. tab, graf
Article in English | ID: biblio-1279484

ABSTRACT

The fishes of the Haemulidae family are currently allocated to 19 genera with a worldwide distribution in the tropical and subtropical waters of the world's oceans. Brachygenys and Haemulon are important genera of reef fish in Brazil, as they occur in large shoals, which are both ecologically and commercially valuable. This study identified the Brazilian species of the genera Brachygenys and Haemulon using DNA barcodes. While we found only a single lineage in Brachygenys chrysargyrea, Haemulon melanurum, H. parra, and H. squamipinna, more than one molecular operational taxonomic unit (MOTU) was identified in H. atlanticus, H. aurolineatum, and H. plumieri, indicating the possible existence of discrete populations or cryptic species.(AU)


Os peixes da família Haemulidae estão atualmente distribuídos em 19 gêneros, com distribuição mundial em águas oceânicas tropicais e subtropicais. Brachygenys e Haemulon são importantes gêneros de peixes recifais do Brasil, visto que ocorrem em grandes cardumes, de valores ecológicos e comerciais. Este estudo identificou as espécies brasileiras dos gêneros Brachygenys e Haemulon usando o código de barras de DNA. Embora apenas uma única linhagem de Brachygenys chrysargyrea, Haemulon melanurum, H. parra e H. squamipinna tenha sido encontrada em nosso conjunto de dados, mais de uma unidade taxonômica operacional molecular (MOTU) foi identificada em H. atlanticus, H. aurolineatum e H. plumieri, indicando a possível existência de populações discretas ou espécies crípticas.(AU)


Subject(s)
Animals , Perciformes , Products Distribution , Molecular Biology , Sequence Analysis, DNA , Fishes
8.
Article in Chinese | WPRIM | ID: wpr-879175

ABSTRACT

Resina Draconis, a rare and precious traditional medicine in China, is known as the "holy medicine for promoting blood circulation". According to the national drug standard, it's derived from the resin extracted from the wood of Dracaena cochinchinensis, a Liliaceae plant. In addition, a variety of Dracaena species all over the world can form red resins, and there is currently no molecular identification method that can efficiently identify the origin of Dracaena medicinal materials. In this study, seven species of Dracaena distributed in China were selected as the research objects. Four commonly used DNA barcodes(ITS2, matK, rbcL and psbA-trnH), and four highly variable regions(trnP-psaJ, psbK-psbI, trnT-trnL, clpP) in chloroplast genome were used to evaluate the identification efficiency of Dracaena species. The results showed that clpP sequence fragment could accurately identify seven species of Dracaena plants. However, due to the long sequence of clpP fragment, there were potential problems in the practical application process. We found that the combined fragment "psbK-psbI+ trnP-psaJ" can also be used for accurate molecular identification of the Resina Draconis origin plants and relative species of Dracaena, which were both relatively short sequences in the combined fragment, showing high success rates of amplification and sequencing. Therefore, the "psbK-psbI+ trnP-psaJ" combined fragment can be used as the DNA barcode fragments for molecular identification of Resina Dracon's origin plants and relative species of Dracaena. Research on the identification of Dracaena species, the results of this study can be used to accurately identify the original material of Resina Draconis, and providing effective means for identification, rational development and application of Resina Draconis base source.


Subject(s)
China , DNA Barcoding, Taxonomic , DNA, Plant/genetics , Dracaena/genetics , Plants , Resins, Plant , Sequence Analysis, DNA
9.
Bol. latinoam. Caribe plantas med. aromát ; 19(3): 300-313, mayo 2020. ilus, tab
Article in English | LILACS | ID: biblio-1116300

ABSTRACT

Every 3 to 7 year angiosperms species of the flowering desert appear in the Atacama Region of Chile, as a result of the climatic phenomenon "El Niño". Our objective was to evaluate the universality of matK and rbcL barcode markers of these species, and validate their taxon through phylogenetic relationships. Argemone hunnemannii, Oenothera coquimbensis, Malesherbia humilis, Leucocoryne appendiculata, Loasa elongata, Nicotiana solanifolia, Stachys grandidentata, Aristolochia chilensis, Alstroemeria kingii and Adesmia eremophila, almost all classified as endemic to Chile, were collected in Pan de Azúcar and Llanos de Challe National Park (Atacama Region, Chile) at the end of October 2017. The phylogeny of these ten angiosperm species from the flowering desert was analyzed using rbcL and matK markers with the maximum likelihood and Bayesian inference methods. The results showed that 70% of the species can be distinguished with the matK or rbcL locus, however, 100% were distinguished using both loci. The phylogenetic results showed that the species formed clades with high reliability and high support with both the matK and rbcL genes, when comparing our results with sequences obtained from GenBank. The matK and rbcL genes are efficient markers for analyzing phylogenetic relationships and validating the taxonomy of flowering species.


Las especies de angiospermas del Desierto Florido de la Región de Atacama de Chile aparecen cada 3 a 7 años, influenciado por el fenómeno climático "El Niño". Nuestro objetivo fue evaluar la universalidad de los marcadores de código de barra matK y rbcL de estas especies, y validar su taxón por medio de relaciones filogenéticas. Las especies Argemone hunnemannii, Oenothera coquimbensis, Malesherbia humilis, Leucocoryne appendiculata, Loasa elongata, Nicotiana solanifolia, Stachys grandidentata, Aristolochia chilensis, Alstroemeria kingii y Adesmia eremophila son clasificadas la mayoría endémicas de Chile. Estas especies fueron colectadas en el Parque Nacional Pan de Azúcar y Llanos de Challe, Región de Atacama, Chile. La colecta se realizó a fines de octubre de 2017. Con los marcadores rbcL y matK se analizó la filogenia con los métodos máxima verosimilitud e inferencia bayesiana en diez especies de angiosperma del Desierto Florido. Los resultados mostraron que el 70% de las especies pueden ser distinguidas con un locus matK o rbcL, sin embargo, el 100% se distinguió usando ambos locus. Los resultados filogenéticos mostraron que las especies formaron clados con alta fiabilidad y alto soporte tanto con los genes matK y rbcL, al comparar con accesos de secuencias obtenidas de GenBank. Lo genes matK y rbcL son marcadores eficientes para analizar relaciones filogenéticas y validar el taxón de las especies de flor.


Subject(s)
Phylogeny , Plants/genetics , Desert , DNA Barcoding, Taxonomic/methods , Ribulose-Bisphosphate Carboxylase , Chile , Sequence Analysis, DNA
10.
Arq. bras. med. vet. zootec. (Online) ; 72(2): 312-316, Mar./Apr. 2020. ilus
Article in English | ID: biblio-1128168

ABSTRACT

Cercopithifilaria bainae is a nematode belonging to the family Onchocercidae that parasitizes the subcutaneous tissue of dogs. Its transmission occurs through the tick Rhipicephalus sanguineus and its geographical distribution overlaps that of this vector. The present study reports the detection of microfilaremia by C. bainae in an eight-year-old male dog that presented anorexia, hyperthermia, motor incoordination, mydriasis, a nodule in the left testicle and concomitant infection by Ehrlichia sp. Blood samples were analyzed using microscopy, PCR and DNA sequencing. Microfilariae measuring 150±5.5µm in length and 7±1.8µm in width were retrieved. The DNA sequence exhibited 98% identity with C. bainae sequences available in Genbank. This is the first report of microfilaremia by C. bainae in a dog in the central western region of Brazil.(AU)


Cercopithifilaria bainae é um nematoide pertencente à família Onchocercidae, que parasita o tecido subcutâneo de cães. Sua transmissão ocorre pelo carrapato Rhipicephalus sanguineus, e sua distribuição geográfica se sobrepõe ao espalhamento desse vetor. O presente estudo relata a detecção de microfilaremia por C. bainae em um cão macho de oito anos que apresentava anorexia, hipertermia, incoordenação motora, midríase e nódulo no testículo esquerdo e infecção concomitante por Ehrlichia sp. A coleta de sangue foi realizada, e o material analisado por meio dos exames de microscopia, PCR e sequenciamento de DNA. Microfilárias medindo 150±5,5µm de comprimento e 7±1,8µm de largura foram recuperadas. A sequência de DNA obtida mostrou 98% de identidade com sequências de C. bainae disponíveis no Genbank. Este é o primeiro relato de microfilaremia de C. bainae em um cão na região Centro-Oeste do Brasil.(AU)


Subject(s)
Animals , Male , Dogs , Onchocerca , Subcutaneous Tissue/parasitology , Microfilariae , Nematoda , Brazil , Base Sequence , Anorexia , Polymerase Chain Reaction , Sequence Analysis, DNA , Disease Transmission, Infectious
11.
Arq. bras. med. vet. zootec. (Online) ; 72(1): 33-39, Jan.-Feb. 2020. graf
Article in Portuguese | ID: biblio-1088915

ABSTRACT

A biópsia embrionária associada à genotipagem permite a obtenção de informações genômicas antes mesmo da transferência dos embriões. Neste estudo, foram avaliadas amostras biopsiadas de blastocistos bovinos transferidos para receptoras (n=47), sob a hipótese de que a raça (Gir ou Girolando), o estádio embrionário (blastocisto ou blastocisto expandido) e a competência para estabelecimento de prenhez (positiva ou negativa) afetariam a quantidade e a qualidade do DNA da amostra obtida. O DNA foi extraído, amplificado, quantificado por eletroferograma e genotipado. O parâmetro call rate (CR) foi adotado para mensurar a qualidade da genotipagem. Obteve-se concentração de DNA de 86,07±171,66ng/µL e CR 0,73±0,17. O CR não variou em função da quantidade de DNA nas amostras. As variáveis raça e estádio embrionário não influenciaram a concentração de DNA, nem o CR. Houve efeito da prenhez sobre o CR (P=0,0187), mas, como houve maior CR nas amostras provenientes do grupo prenhez negativa, não foi possível associar esse parâmetro à qualidade embrionária. Concluiu-se que a raça e a qualidade embrionária não afetam os parâmetros aqui estudados em amostras embrionárias, ou seja, embriões com maiores chances de implantação não refletem alta qualidade nas amostras de biópsia genotipadas.(AU)


Embryo biopsy associated with genotyping allows genomic information before embryo transfer. In this study, blastocyst biopsy samples from embryos transferred to recipients (n= 47) were evaluated, under the hypothesis that breed (Gyr or Girolando), embryonic stage (blastocyst or expanded blastocyst) and competence to establish pregnancy (positive or negative) would affect the quantity and DNA quality of samples. DNA was extracted, amplified, quantified by electropherogram and genotyped. The parameter call rate (CR) was used to measure the quality of genotyping. DNA concentration of 86.07±171.66ng/µl, and CR 0.73±0.17 was obtained. CR did not vary according to the amount of DNA in the samples. The variables breed and embryonic stage had no influence on DNA concentration or CR. There was pregnancy effect on the CR (P= 0.0187), but since there was a higher CR in the samples from the negative pregnancy group, it was not possible to associate this parameter with the embryonic quality. We conclude that the breed and embryo quality do not affect the evaluated parameters in embryonic samples. Embryos with higher chances of implantation do not reflect high quality in embryo biopsy genotyped samples.(AU)


Subject(s)
Animals , Cattle , Selection, Genetic , Biopsy/veterinary , Sequence Analysis, DNA/veterinary , Embryo, Mammalian , Genotyping Techniques/veterinary , In Vitro Techniques/veterinary
12.
Braz. j. med. biol. res ; 53(11): e9056, 2020. tab, graf
Article in English | LILACS, ColecionaSUS | ID: biblio-1132484

ABSTRACT

Cryptococcal meningitis affects normal hosts and immunocompromised patients exhibiting high mortality rates. The objective of this study was to design two molecular assays, visible microarray platforms and loop-mediated isothermal amplification (LAMP), to identify Cryptococcus spp. and the species neoformans and gattii from the cerebral spinal fluid (CSF). To identify Cryptococcus and the two species, we designed two microarrays DNA platforms based on the internal transcribed spacer (ITS) region and CAP59 gene and LAMP assays specific for Cryptococcus species. The assays were tested using CSF from patients with cryptococcal meningitis. CSF from patients with cryptococcal meningitis was cultured in Sabouraud culture medium, and the Cryptococcus spp. grown in the culture medium were also tested for LAMP and microarray platforms. The results were compared to DNA sequencing of the same genetic regions. A total of 133 CSF samples were studied. Eleven CSFs were positive for Cryptococcus (9 C. neoformans and 2 C. gattii), 15 were positive for bacteria, and 107 were negative. The CAP59 platform correctly identified 73% of the CSF samples, while the ITS platform identified 45.5%. CAP59 platform correctly identified 100% of the Cryptococcus isolates, and ITS platform identified 70%. The two sets of LAMP primers correctly identified 100% of the Cryptococcus isolates. However, for CSF samples, the amplification occurred only in 55.5% of C. neoformans. The methodologies were reliable in the identification of Cryptococcus species, mainly for isolates from culture medium, and they might be applied as adjunctive tests to identify Cryptococcus species.


Subject(s)
Humans , Meningitis, Cryptococcal/diagnosis , Cryptococcus neoformans/genetics , Sequence Analysis, DNA , Oligonucleotide Array Sequence Analysis , Nucleic Acid Amplification Techniques
13.
Article in Chinese | WPRIM | ID: wpr-879481

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a pedigree affected with hereditary spastic paraplegia type 4 (HSP4).@*METHODS@#Peripheral venous blood samples were taken from members of the four-generation pedigree and 50 healthy controls for the extraction of genomic DNA. Genes associated with peripheral neuropathy and hereditary spastic paraplegia were captured and subjected to targeted capture and next-generation sequencing. The results were confirmed by Sanger sequencing.@*RESULTS@#DNA sequencing suggested that the proband has carried a heterozygous c.1196C>G variant in exon 9 of the SPAST gene, which can cause substitution of serine by threonine at position 399 (p.Ser399Trp) and lead to change in the protein function. The same variant was also detected in other patients from the pedigree but not among unaffected individuals or the 50 healthy controls. Based on the ACMG 2015 guidelines, the variant was predicted to be possibly pathogenic.@*CONCLUSION@#The c.1196C>G variant of the SPAST gene probably underlay the HSP4 in this pedigree.


Subject(s)
Base Sequence , Humans , Mutation , Paraplegia/genetics , Pedigree , Sequence Analysis, DNA , Spastic Paraplegia, Hereditary/genetics , Spastin/genetics
14.
Chinese Journal of Biotechnology ; (12): 772-781, 2020.
Article in Chinese | WPRIM | ID: wpr-826899

ABSTRACT

Rhus chinensis is an important economic species, which could provide raw materials for pharmaceutical and industrial dyes. Rhus chinensis is famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. We report here Rhus chinensis chloroplast genomes by de novo sequencing. The results show that the length of Rhus chinensis was 159 082 bp, exhibiting a typical four-part structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The length of LSC and SSC was 85 394 bp and 18 663 bp, respectively. The genomes contained 126 genes, including 88 protein encoding genes, 8 rRNA and 30 tRNA genes. In the chloroplast genome, 61.97% of the sequence were gene coding region. In the sequence of gene encoding region, the vast majority of sequences were protein encoding region, accounting for 86.65%, followed by rRNA (10 620 bp, 10.77%) and tRNA (2 540 bp, 2.58%). In Rhus chinensis chloroplast genome, only 8 genes contain introns, all containing 1 intron except ycf3 gene (2 introns). The Rhus chinensis chloroplast genome contains 755 SSR locies. SSR mainly consists of dinucleotide and mononucleotide, accounting for 60% (453) and 28.74% (217) respectively. The clustering results show that Anacardiaceae were closest to Rhus chinensis, followed by Aceraceae and Sapindaceae. This study provides a molecular basis for the classification of Rhus chinensis.


Subject(s)
Genome, Chloroplast , Genetics , Open Reading Frames , Phylogeny , Rhus , Classification , Genetics , Sequence Analysis, DNA
15.
Chinese Journal of Biotechnology ; (12): 811-819, 2020.
Article in Chinese | WPRIM | ID: wpr-826895

ABSTRACT

Sequencing technology has been greatly improved in terms of throughput and cost. The single-molecule nanopore DNA sequencing, one of the major branches of the third-generation sequencing technology, has made great contributions in the fields of medicine and life sciences due to its advantages of ultra-long reading length, real-time detection and direct detection of base methylation modification, etc. This article briefly describes the principle of nanopore sequencing technology, and discusses its application in clinical, animal, plant, bacterial and virus fields and its future development direction.


Subject(s)
Animals , Base Sequence , DNA , Chemistry , Genetics , Humans , Nanopore Sequencing , Nanopores , Research , Sequence Analysis, DNA
16.
Article in Chinese | WPRIM | ID: wpr-880812

ABSTRACT

OBJECTIVE@#To study the difference in age estimation based on quantitative analysis of DNA methylation by MassARRAY and pyrosequencing techniques.@*METHODS@#The methylation levels of 9 CpG sites from two independent whole blood sample sets (containing 65 and 62 samples) were detected using MassARRAY and pyrosequencing techniques. Z-score transformation was used to remove the batch effects of different techniques, and a linear regression model was used for age prediction.@*RESULTS@#For age prediction using the MassARRAY system, the 65 samples showed a mean absolute difference (MAD) of 2.49 years before Z-score transformation of the data and 2.44 years after the transformation, similar to the results in the 62 samples (MAD of 3.36 years before and 3.42 years after Z-score transformation). For data typed from pyrosequencing, the 65 samples showed a MAD of 4.20 years before and 2.76 years after data Z-score transformation, also similar to the results in the 62 samples (MAD of 3.92 years before and 3.63 years after data transformation).@*CONCLUSIONS@#Z-score transformation can effectively reduce the system batch effect between MassARRAY and pyrosequencing. Data from the MassARRAY system allows direct age estimation without further data processing, while the pyrosequencing data may increase the error in age estimation, which can be corrected by Z-score transformation of the data.


Subject(s)
CpG Islands/genetics , DNA Methylation , High-Throughput Nucleotide Sequencing , Linear Models , Sequence Analysis, DNA
17.
Journal of Experimental Hematology ; (6): 1791-1795, 2020.
Article in Chinese | WPRIM | ID: wpr-879973

ABSTRACT

OBJECTIVE@#To analyze the characteristics of gene mutation in adult ALL and its clinical significance.@*METHODS@#Clinical data of 134 primary adult ALL patients and DNA sequencing results of 16 kinds of gene mutation were collected. The characteristic of gene mutation and clinical significances were statistically analyzed.@*RESULTS@#In 31 cases of 134 ALL cases (23.13%) the gene mutations were detected as follows: 19 cases of 114 B-ALL cases (16.67%), 11 cases of 19 T-ALL cases (57.89%) and 1 case of T/B-ALL. The incidence of T-ALL gene mutation was significantly higher than that of B-ALL (χ@*CONCLUSION@#There may be multiple gene mutations in adult ALL patients. IL7R and NOTCH1 are the most common gene mutations and NOTCH1 mutation may indicate poor prognosis. Detection of gene mutations is helpful to understand the pathogenesis of ALL and evaluate the prognosis of adult ALL patients.


Subject(s)
Adult , Humans , Mutation , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma , Prognosis , Receptor, Notch1/genetics , Sequence Analysis, DNA
18.
Mem. Inst. Oswaldo Cruz ; 115: e200208, 2020. tab, graf
Article in English | LILACS, SES-SP | ID: biblio-1135227

ABSTRACT

Paracoccidioides spp. isolation from environmental samples is rare and hardly reproducible. Molecular techniques have facilitated the fungal detection. However, it can be still difficult. Some strategies to enhance the capacity of DNA detection have been adopted, including the analysis of soil samples belonging to the habitat of animals from which Paracoccidioides spp. have already been isolated, notably armadillo burrows. To date, the detection of Paracoccidioides spp. has not yet been reported from outbreak hotspots. Clusters and outbreaks of acute paracoccidioidomycosis (PCM), usually a more severe clinical form, have currently occurred in urban areas being associated to climate changes, deforestation, and great constructions. These occurrences potentially signalise the fungus' environmental niche, a riddle not yet solved. The authors performed an environmental investigation in a deeply disturbed area, after a highway construction in Rio de Janeiro, Brazil, where a recent outbreak of acute PCM occurred. Specific DNA sequences of Paracoccidioides brasiliensis were detected in shallow soil samples around the highway, reinforcing the association between the road construction and this PCM outbreak.


Subject(s)
Animals , Paracoccidioides/isolation & purification , Paracoccidioidomycosis/microbiology , Armadillos , DNA, Fungal/genetics , Paracoccidioides/growth & development , Paracoccidioides/genetics , Soil Microbiology , Brazil , Base Sequence , Sequence Analysis, DNA , Ecosystem
19.
Mem. Inst. Oswaldo Cruz ; 115: e200370, 2020. tab, graf
Article in English | LILACS, SES-SP | ID: biblio-1135225

ABSTRACT

BACKGROUND Bacillus anthracis is the aetiologic agent of anthrax, a re-emerging, septicaemic, haemorrhagic and lethal disease that affects humans, domestic ruminants and wildlife. Plasmids pXO1 and pXO2 are attributes that confer pathogenicity to B. anthracis strains. This bacterium was used as biological weapon in the World Wars and in the biological attack in the United States of America at 2001. B. anthracis is classified as a Tier 1 bioterrorism agent by the Centers for Diseases Control and Prevention. Anthrax is recognised as a re-emerging disease. Several studies concerning the dynamics of B. anthracis cycle in soil revealed that nonpathogenic B. anthracis strains due to lack of pXO2 plasmid are commonly found in some types of soil. OBJECTIVES This study aimed isolation and identification of B. anthracis spores in soil samples of the state of Rio de Janeiro, Brazil. METHODS Phenotypic and genotypic approaches were used to identify isolates including MALDI-TOF/MS, motility test, susceptibility to gamma phage and penicillin, survey for pag and cap genes as surrogates of pXO1 and pXO2 plasmids, respectively, and sequencing of 16SrRNA-encoding gene. Physicochemical analysis of the soil samples were carried out to describe soil characteristics. FINDINGS We observed the presence of one B. anthracis pXO1+ and pXO2- isolated from clay loam soil; one B. anthracis-like strain pXO1+ and pXO2-isolated from loamy sand; and 10 Bacillus spp. strains sensitive to phage-gamma that need better characterisation to define which their species were recovered from loamy sand. MAIN CONCLUSIONS This work showed promising results and it was the first study to report results from an active surveillance for B. anthracis in Brazil.


Subject(s)
Humans , Plasmids/analysis , Soil Microbiology , Spores, Bacterial , Bacillus anthracis/isolation & purification , DNA, Bacterial/genetics , Polymerase Chain Reaction/methods , Virulence Factors/genetics , Plasmids/genetics , Soil , Bacillus anthracis/genetics , Bacillus anthracis/pathogenicity , Bacterial Toxins , Virulence , Brazil , DNA, Bacterial/analysis , Sequence Analysis, DNA , Antigens, Bacterial
20.
Mem. Inst. Oswaldo Cruz ; 115: e200220, 2020. tab, graf
Article in English | LILACS, SES-SP | ID: biblio-1135253

ABSTRACT

BACKGROUND The Nyssomyia genus and Lutzomyia subgenus include medical important species that are Latin American leishmaniases vectors. Little is known about the phylogenetic relationships of closely-related species in each of these taxonomic groups that are morphologically indistinguishable or differentiated by very subtle details. OBJECTIVES We inferred the phylogenetic relationships of closely-related species within both the Nyssomyia genus and the Lutzomyia subgenus using a cytochrome c oxidase subunit I (COI) fragment. METHODS The sampling was carried out from 11 Argentinean localities. For genetic analyses, we used GenBank sequences in addition to our sequences from Argentina. Kimura 2-parameter (K2P) genetic distance and nucleotide divergence (Da) was calculated between closely-related species of Nyssomyia genus, Lutzomyia subgenus and between clades of Lutzomyia longipalpis complex. FINDINGS The K2P and Da values within species of Nyssomyia genus and Lutzomyia subgenus were lower than the divergence detected between clades of Lu. longipalpis complex. The haplotype network analyses within Lutzomyia subgenus showed shared haplotypes between species, contrary to Nyssomyia genus with none haplotype shared. Bayesian inference within Nyssomyia genus presented structuring by species. MAIN CONCLUSIONS This study evidences the phylogenetic proximity among closely-related species within Nyssomyia genus and Lutzomyia subgenus. The COI sequences of Nyssomyia neivai derived from the present study are the first available in GenBank.


Subject(s)
Animals , Psychodidae/classification , Psychodidae/genetics , Phylogeny , Argentina , Base Sequence , Leishmaniasis , Polymerase Chain Reaction/methods , Bayes Theorem , Sequence Analysis, DNA/methods
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