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1.
Braz. j. med. biol. res ; 54(5): e10743, 2021. tab, graf
Article in English | LILACS | ID: biblio-1180738

ABSTRACT

Amphiphilic copolymers have a wide variety of medical and biotechnological applications, including DNA transfection in eukaryotic cells. Still, no polymer-primed transfection of prokaryotic cells has been described. The reversible addition-fragmentation chain transfer (RAFT) polymer synthesis technique and the reversible deactivation radical polymerization variants allow the design of polymers with well-controlled molar mass, morphology, and hydrophilicity/hydrophobicity ratios. RAFT was used to synthesize two amphiphilic copolymers containing different ratios of the amphiphilic poly[2-(dimethyl-amino) ethyl methacrylate] and the hydrophobic poly [methyl methacrylate]. These copolymers bound to pUC-19 DNA and successfully transfected non-competent Escherichia coli DH5α, with transformation efficiency in the range of 103 colony-forming units per µg of plasmid DNA. These results demonstrate prokaryote transformation using polymers with controlled amphiphilic/hydrophobic ratios.


Subject(s)
Polymers , DNA/genetics , Bacteria , Transfection , Cations
2.
Chinese Journal of Biotechnology ; (12): 1120-1130, 2021.
Article in Chinese | WPRIM | ID: wpr-878618

ABSTRACT

As the demand for high-performance computing continues to grow, traditional computing models are facing unprecedented challenges. Among the many emerging computing technologies, DNA computing has attracted much attention due to its low energy consumption and parallelism. The DNA circuit, which is the basis for DNA computing, is an important technology for the regulation and processing of the molecular information. This review highlights the basic principles of DNA computing, summarizes the latest research progress, and concludes with a discussion of the challenges of DNA computing. Such integrated molecular computing systems are expected to be widely used in the fields of aerospace, information security and defense system.


Subject(s)
DNA/genetics
4.
Rev. Soc. Bras. Med. Trop ; 53: e20200189, 2020. tab, graf
Article in English | LILACS, ColecionaSUS, SES-SP | ID: biblio-1143863

ABSTRACT

Abstract INTRODUCTION: Knowledge of triatomine bloodmeal sources is essential for understanding vector-host interactions in Trypanosoma cruzi transmission cycles. Expensive commercial deoxyribonucleic acid (DNA) extraction kits are widely used for bloodmeal identification. This study assessed the performance of an inexpensive phenol-chloroform DNA extraction protocol for identification of triatomine bloodmeal sources, comparing it with a commercially available kit. METHODS: Both methods were used to obtain DNA from the intestinal contents of Triatoma brasiliensis blood-fed on either Columba sp., Mus musculus, or Gallus gallus. Subsequently, the mitochondrial 12S ribosomal ribonucleic acid (rRNA) gene was amplified by polymerase chain reaction, sequenced, and compared with GenBank data. RESULTS: Twelve (80%) samples extracted with the commercial kit and four (26.7%) with phenol-chloroform were pure (according to the A260/A280 ratio). Samples extracted with phenol-chloroform, except for Columba sp. samples, had higher DNA concentration than those extracted with the commercial kit. Samples extracted using phenol-chloroform and blood-fed on G. gallus had significantly higher DNA concentration than those blood-fed on Columba sp. (p-value <0.001) and M. musculus (p-value <0.001). The 215-base-pair 12S rRNA fragment was amplified from all samples and produced reliable sequences, enabling the identification of the bloodmeal source, most of which showed identity and coverage above 95%. The phenol-chloroform method was much less expensive than the commercial kit but took considerably more time to perform. CONCLUSIONS: Our data showed that both DNA extraction methods produced reliable sequences enabling identification of triatomine bloodmeal sources but differed greatly in cost and time required.


Subject(s)
Animals , Triatoma/genetics , Trypanosoma cruzi/genetics , DNA/genetics , Chloroform , Phenol , Mice
5.
Article in Chinese | WPRIM | ID: wpr-878790

ABSTRACT

A highly specific electrochemical biosensor based on T-Hg~(2+)-T structure for fast screening trace Hg~(2+) in complex animal drug matrix was constructed by cyclic voltammetry(CV) and differential pulse voltammetry(DPV). In the presence of Hg~(2+), it can be specifically binded to the T base of DNA sequence on the surface of modified gold electrode, which changes the conformation of DNA molecule and the electrochemical signal. The concentration ratio of EDC/NHS, the concentration ratio of FC-DNA and the reaction time of the biosensor were optimized by the index of sensitivity and reproducibility in CV. The results showed that the stability of the biosensor was good within 3 days(RSD≤1.3%), the difference between batches was low(RSD=4.7%), and the specificity of the biosensor was high in the presence of interfering ions(As~(3+), Cd~(2+), Cu~(2+), Pb~(2+), Zn~(2+) and Fe~(3+)). DPV results showed that the peak current signal value has a linear relationship with the lgC_((Hg)) over a concentration range from 0.1 nmol·L~(-1) to 1.0 μmol·L~(-1) with a detection limit of 0.066 nmol·L~(-1). Finally, the recovery rate tested in the matrix of animal medicine was satisfactory as 99.17%-101.3%, which can meet the needs of the determination of trace Hg~(2+) in the matrix of Bombyx Batryticatus, and provide a new idea for the rapid screening of trace heavy metals in the matrix of other types of complex traditional Chinese medicine.


Subject(s)
Animals , Biosensing Techniques , DNA/genetics , Electrochemical Techniques , Gold , Mercury , Reproducibility of Results
6.
Chinese Journal of Biotechnology ; (12): 2877-2891, 2020.
Article in Chinese | WPRIM | ID: wpr-878537

ABSTRACT

Studies on the interaction between small organic molecules and DNA are important means to explore drug mechanism and new drugs. Quercetin is a polyhydroxy flavone compound with activities such as anti-cancer, anti-inflammatory, antibacterial, antiviral, hypoglycemic and anti-hypertensive, immunomodulation and cardiovascular protection. Experimental studies aim at confirming if an interaction exists between quercetin and DNA, and determining the type of interaction. The interaction between quercetin and herring DNA can be detected by fluorescence spectrometry and resonance scattering fluorescence spectrometry analysis. The mode of the interaction between quercetin and herring DNA can be detected by UV-Vis spectrophotometry and fluorescence polarization analysis. This review helps understand the in vitro interaction between quercetin and DNA, and assist the development of drugs for corresponding diseases.


Subject(s)
DNA/genetics , Quercetin , Spectrometry, Fluorescence
8.
Braz. dent. j ; 29(2): 179-183, Mar.-Apr. 2018. tab
Article in English | LILACS | ID: biblio-951532

ABSTRACT

Abstract Persistent apical periodontitis (AP) is a situation involving an inflammatory and immune response caused mainly by anaerobic polymicrobial infection of the root canal system and the outcome and follow-up of the root canal treatment has been reported as intimately related to host response. The apical periodontitis repair might be associated with genetic polymorphisms. This study aimed to evaluate the association between HIF1A genetic polymorphisms (rs2301113 and rs2057482) with PAP in Brazilian patients. Subjects with at least 1 year of follow-up after root canal therapy (RCT) were recalled. Sixty-four subjects with signs/symptoms of PAP and 84 subjects with root canal-treated teeth exhibiting healthy perirradicular tissues (healed) were included. Genomic DNA was extracted from saliva and used for HIF1A genotyping by real-time PCR. Genotype and allele frequencies were compared by c2 or Fisher's exact tests and odds ratio was implemented, using Epi Info 3.5.2. All tests were performed with an established alpha of 0.05. There was no association between allele and genotype distribution for HIF1As polymorphisms and PAP (p>0.05). The genetic polymorphisms in HIF1A were not associated with persistent apical periodontitis.


Resumo A periodontite apical persistente (PAP) é uma condição que envolve uma resposta inflamatória e imunológica causada principalmente por infecções polimicrobianas de origem anaeróbia no sistema de canais radiculares, tornando o resultado e o acompanhamento do tratamento do canal radicular intimamente relacionados à resposta do hospedeiro. O reparo da periodontite apical pode estar associado a polimorfismos genéticos. Este estudo teve como objetivo avaliar a associação entre os polimorfismos genéticos do HIF1A (rs2301113 e rs2057482) com a PAP em pacientes brasileiros. Indivíduos com pelo menos 1 ano de acompanhamento após o tratamento do canal radicular (TCR) foram agendados para consulta de acompanhamento. Sessenta e quatro indivíduos com sinais/sintomas de PAP e 84 indivíduos com dentes tratados endodonticamente e tecidos perirradiculares saudáveis (cicatrizados) foram incluídos no presente estudo. O DNA genômico foi extraído da saliva e utilizado para a genotipagem do HIF1A por PCR em tempo real. O genótipo e as frequências alélicas foram comparados por teste c2 ou exato de Fisher e odds-ratio foi implementado por meio do software Epi Info 3.5.2. Todos os testes realizados foram estabelecidos com a=0,05. Não houve associação entre alelo e distribuição genotípica para polimorfismos do HIF1A e PAP (p> 0,05). Os polimorfismos genéticos em HIF1A não foram associados à periodontite apical persistente.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Periapical Periodontitis/genetics , Polymorphism, Genetic , Bone Remodeling/genetics , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Neovascularization, Pathologic/genetics , Periapical Periodontitis/pathology , Root Canal Therapy , Brazil , DNA/genetics , Real-Time Polymerase Chain Reaction , Gene Frequency , Genotype
9.
Salud pública Méx ; 59(5): 532-539, Sep.-Oct. 2017. tab, graf
Article in English | LILACS | ID: biblio-903800

ABSTRACT

Abstract: Objective: To determine the number of micronuclei and nuclear anomalies in Mexico's indigenous population. Materials and methods: One hundred twenty indigenous individuals were evaluated, including thirty from the ethnicities Cora, Huichol, Tarahumara and Tepehuano. The number of micronuclei (MN) and any nuclear abnormality (NA) in oral mucosa cells, including cells with nuclear buds, binucleated cells, cells with karyolysis, karyorrhetic, condensed chromatin and pyknotic cells were determined for each participant. Results: Tepehuano and Tarahumaras showed the greatest damage to DNA. The Tepehuano group presented the highest number of MN and NA, this being a significant difference (p < 0.05) compared with the rest of the studied groups. This group also presented the highest herbicide exposure (46.7%). In relation to the smoking and drinking habits, these were more frequent in the Tarahumara group (33.3 and 50% respectively). Conclusion: The ethnic diversity, habits and customs may influence the DNA nuclear integrity in the Amerindian groups.


Resumen: Objetivo: Determinar el número de micronúcleos y anomalías nucleares en la población indígena de México. Material y métodos: Se evaluó a ciento veinte indígenas, incluyendo treinta individuos de las etnias cora, huichol, tarahumara y tepehuana. A cada participante se le determinó el número de micronúcleos (MN) y de alguna anomalía nuclear (AN) en células de mucosa bucal, incluyendo células con brotes nucleares, binucleadas, cariolisis, cariorrexis, cromatina condensada y picnóticas. Resultados: Los tepehuanos y tarahumaras mostraron el mayor daño al ADN. El grupo tepehuano presentó el mayor número de MN y AN, con una diferencia significativa (p < 0.05) en comparación con el resto de los grupos estudiados; este grupo presentó también la mayor exposición a herbicidas (46.7%). En relación con los hábitos de fumar y beber, se presentaron con mayor frecuencia en el grupo tarahumara (33.3 y 50%, respectivamente). Conclusión. La diversidad étnica, hábitos y costumbres pueden influir la integridad del ADN en los grupos amerindios.


Subject(s)
Humans , Male , Female , Adolescent , Adult , Middle Aged , Young Adult , Indians, North American/genetics , Cell Nucleus/ultrastructure , Micronuclei, Chromosome-Defective , Alcohol Drinking/epidemiology , DNA/genetics , Ethnic Groups/genetics , Smoking/epidemiology , Diet , Feeding Behavior , Herbicides , Mexico , Mouth Mucosa/ultrastructure
10.
Braz. dent. j ; 28(2): 148-151, mar.-Apr. 2017. tab, graf
Article in English | LILACS | ID: biblio-839142

ABSTRACT

Chromosomal instability, leading to aneuploidy, is one of the hallmarks of human cancers. USP44 (ubiquitin specific peptidase 44) is an important molecule that plays a regulatory role in the mitotic checkpoint and USP44 loss causes chromosome mis-segregation, aneuploidy and tumorigenesis in vivo. In this study, it was investigated the immunoexpression of USP44 in 28 malignant salivary gland neoplasms and associated the results with DNA ploidy status assessed by image cytometry. USP44 protein was widely expressed in most of the tumor samples and no clear association could be established between its expression and DNA ploidy status or tumor size. On this basis, it may be concluded that the aneuploidy of the salivary gland cancers included in this study was not driven by loss of USP44 protein expression.


Resumo Instabilidade cromossômica acarretando aneuploidia é um dos fatores marcantes de neoplasias malignas humanas. USP44 (peptidase específica de ubiquitina 44) é uma importante molécula que exerce um papel regulador no ciclo celular e sua perda pode acarretar em segregação cromossômica deficiente, aneuploidia e desenvolvimento de tumores in vivo. Neste estudo, investigou-se a expressão imuno-histoquímica da proteína USP44 em 28 neoplasias malignas de glândulas salivares, associando-se os resultados com o estado de ploidia do DNA avaliado por citometria de fluxo. A proteína USP44 apresentou ampla expressão na maioria das amostras avaliadas e não foi observada associação entre a expressão protéica e o estado de ploidia do DNA ou extensão do tumor. Baseando-se nos resultados, concluiu-se que a aneuploidia das neoplasias malignas de glândulas de salivares incluídas neste estudo não foi influenciada pela perda de expressão da proteína USP44.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Aged , Aged, 80 and over , Young Adult , Aneuploidy , DNA/genetics , Salivary Gland Neoplasms/genetics , Ubiquitin-Specific Proteases/metabolism
11.
Rev. cuba. invest. bioméd ; 35(2): 184-194, abr.-jun. 2016.
Article in Spanish | LILACS, CUMED | ID: lil-783764

ABSTRACT

Desde hace varias décadas el ensayo Cometa, o electroforesis alcalina de células individuales, se ha convertido en un método establecido para el estudio del daño de ácido desoxirribonucleico, con múltiples aplicaciones en ensayos de genotoxicidad, estudios de biomonitoreo en humanos, epidemiologia molecular y ecotoxicología; así como una herramienta fundamental para investigaciones sobre daño y reparación del ácido desoxirribonucleico. Este ensayo se distinguió por su simplicidad, sensibilidad, versatilidad, rapidez y economía. Es una poderosa técnica que se basa en la visualización microscópica de las imágenes del ácido desoxirribonucleico después que las células son embebidas en agarosa, lisadas y sometidas a una electroforesis alcalina. Esta metodología básica ha sido ampliada, y permite ahora, detectar con alta sensibilidad una gran variedad de daños del ácido desoxirribonucleico en cualquier tipo de células. La inclusión en este ensayo, de enzimas capaces de producir lesiones específicas en la hebra de ácido desoxirribonucleico, ha incrementado su rango de detección y sensibilidad. Pero es importante tener claro que su especificidad no es absoluta. El propósito es destacar algunos aspectos útiles de este método y sus ventajas; describir la experiencia en algunos aspectos técnicos del proceder, normalizado según las condiciones del laboratorio en el instituto para ampliar su utilización en el país.


For several decades now the comet assay (single cell gel electrophoresis assay) has been the method used for the study of deoxyribonucleic acid damage, with multiple applications in genotoxicity assays, biomonitoring studies in humans, molecular epidemiology and ecotoxicology, and a fundamental tool for research into deoxyribonucleic acid damage and repair. The comet assay has stood out for its simplicity, sensitivity, versatility, rapidity and economy. It is a powerful technique based on microscopic visualization of deoxyribonucleic acid images after the cells have been embedded in agarose, lysed and subjected to alkaline electrophoresis. This basic methodology has been broadened, and may now detect with great sensitivity a large variety of deoxyribonucleic acid damage in any type of cell. Inclusion in the assay of enzymes capable of producing specific lesions on the deoxyribonucleic strand has broadened its detection range and sensitivity. However, it is important to bear in mind that its specificity is not absolute. The purpose of the present study is to point out some useful aspects and advantages of the method, and describe the experience with some technical aspects of the procedure, standardized in keeping with the conditions in the laboratory at the institute to extend its use in the country.


Subject(s)
Humans , DNA/genetics , Comet Assay/methods
12.
Article in English | WPRIM | ID: wpr-89401

ABSTRACT

PURPOSE: To describe clinical findings in a Korean family with Axenfeld-Rieger syndrome. METHODS: A retrospective review of clinical data about patients with diagnosed Axenfeld-Rieger syndrome. Five affected members of the family underwent a complete ophthalmologic examination. We screened the forkhead box C1 gene and the pituitary homeobox 2 gene in patients. Peripheral blood leukocytes and buccal mucosal epithelial cells were obtained from seven members of a family with Axenfeld-Rieger syndrome. DNA was extracted and amplified by polymerase chain reaction, followed by direct sequencing. RESULTS: The affected members showed iris hypoplasia, iridocorneal adhesions, posterior embryotoxon, and advanced glaucoma in three generation. None had systemic anomalies. Two mutations including c.1362_1364insCGG and c.1142_1144insGGC were identified in forkhead box C1 in four affected family members. CONCLUSIONS: This study may help to understand clinical findings and prognosis for patients with Axenfeld-Rieger syndrome.


Subject(s)
Aged, 80 and over , Anterior Eye Segment/abnormalities , DNA/genetics , DNA Mutational Analysis , Eye Abnormalities/diagnosis , Female , Forkhead Transcription Factors/genetics , Genetic Testing , Homeodomain Proteins/genetics , Humans , Male , Middle Aged , Mutation , Pedigree , Retrospective Studies , Transcription Factors/genetics , Young Adult
13.
São Paulo; s.n; s.n; 2015. 133 p. tab, graf, ilus.
Thesis in Portuguese | LILACS | ID: biblio-847321

ABSTRACT

O tratamento padrão para pacientes com câncer de reto localmente avançado consiste no uso de quimioradioterapia neoadjuvante (QRTn), seguida por cirurgia. Uma fração significativa dos pacientes responde completamente ao tratamento e no momento da reavaliação não apresenta evidência clínica nem radiológica de doença. Uma abordagem alternativa, Watch and Wait, propõe não operar imediatamente esses pacientes e submetê-los a um protocolo de observação frequente, a fim de evitar as morbidades associadas à cirurgia. No entanto, a avaliação da resposta ao tratamento ainda é um desafio, devido à subjetividade da avaliação clínica e a ausência de exames radiológicos suficientemente sensíveis e específicos para garantir a ausência de células tumorais residuais ou capazes de detectar a recorrência precoce da doença. DNA circulante contendo alterações genéticas específicas do tumor (ctDNA) pode ser encontrado na fração livre de células do sangue e tem sido utilizado para monitorar a dinâmica tumoral em tumores sólidos. Avanços recentes das tecnologias de sequenciamento permitem a identificação eficiente e rápida e a um custo relativamente baixo de alterações genéticas em tumores individuais, superando o problema imposto pela ausência de alterações genéticas recorrentes nesses tumores. Essas alterações podem ser utilizadas como biomarcadores personalizados para monitorar a resposta ao tratamento, detectar doença residual e a recidiva precoce do tumor. O objetivo deste trabalho foi identificar e estudar biomarcadores personalizados em pacientes com câncer de reto localmente avançado tratados com QRTn e avaliar a capacidade desses biomarcadores para monitorar a dinâmica tumoral, e auxiliar na definição da conduta cirúrgica e na detecção da recidiva precoce da doença. Biópsias de seis pacientes com adenocarcinoma de reto distal (cT2- 3N0-1M0), foram coletadas prospectivamente pré-tratamento. O DNA genômico extraído a partir das biópsias foi usado para construir bibliotecas tipo mate-pair para o sequenciamento do genoma completo, utilizando a plataforma SOLiD. Rearranjos inter e intracromossômicos foram identificados utilizando programas computacionais desenvolvidos pelo nosso grupo de pesquisa e em seguida foram validados utilizando PCR e sequenciamento Sanger. Foram validadas, pelo menos, três variações estruturais para cada paciente. Amostras de plasma foram coletadas no momento do diagnóstico, depois da QRTn e durante o seguimento. DNA circulante total foi extraído a partir das amostras de plasma e ensaios personalizados foram desenvolvidos para monitorar a presença de variações estruturais através de PCR Digital. ctDNA foi detectado em todas amostras de plasma pré-tratamento de pacientes com tumores T3. A detecção desses biomarcadores apresentou boa correlação com a resposta ao tratamento, no entanto, esta abordagem não foi sensível o suficiente para detectar doença residual. Para dois pacientes que desenvolveram doença metastática foi verificado um aumento nos níveis de ctDNA com pelo menos 36 semanas antes do diagnóstico clínico de doença metastática, sendo possível correlacionar os níveis de ctDNA detectados em coletas subsequentes com a resposta ao tratamento sistêmico de segunda linha. Este estudo, embora de caráter exploratório, gerou dados relevantes e suficientes para justificar a realização de estudos adicionais para avaliar a aplicação dos biomarcadores personalizados na definição da conduta cirúrgica e no acompanhamento de pacientes com câncer de reto tratados com QRTn


The standard treatment for patients with locally advanced rectal cancer comprises in neoadjuvant chemo radiotherapy (nCRT), followed by surgery. A significant fraction of these patients show complete response to the treatment and at the time of reassessment, there are no clinical and nor radiological evidence of residual tumor. An alternative approach, Watch and Wait, proposes not to immediately operate these patients, but to submit them to a protocol of frequent observation in order to avoid the morbidities associated with radical surgery. However, assessment of treatment response remains a significant challenge due to the subjectivity of the clinical examination and to the lack of sufficiently sensitive tools to ensure the absence of tumor cells or to detect early disease recurrence. Circulating DNA carrying tumor-specific genetic alterations (circulating tumor DNA - ctDNA) can be found in the cell-free fraction of the blood and has been successfully used to monitor the tumor dynamics in solid tumors. Recent advances in sequencing technologies have enabled the rapid and cost effective identification of genetic alterations in individual tumors, overcoming the problem imposed by the absence of recurrent genetic alterations in these tumors. These alterations can be used as personalized biomarkers to monitor treatment response, detect residual disease and early tumor recurrence. The purpose of this work was to identify and validate the use of personalized biomarkers for patients with locally advanced rectal cancer treated with nCRT and to evaluate the ability of these biomarkers to monitor the tumor dynamics, to define surgical approach and to detect early recurrence of the disease. Pre-treatment biopsies from 6 patients with cT2-3N0-1M0 distal rectal adenocarcinoma were prospectively collected. Genomic DNA extracted from the biopsies was used to construct mate-pair libraries for whole genome sequencing using SOLiD platform. Inter and intrachromosomal rearrangements were identified using an in-house bioinformatics pipeline and validated using PCR amplification and Sanger sequencing. At least three structural variations were validated for each patient. Plasma samples were collect at diagnosis, after nCRT and follow-up. Circulating DNA was obtained from the plasma samples and personalized assays were designed to monitor the presence of structural variations using Droplet Digital PCR. ctDNA was detected in all pre-treatment plasma samples for patients with T3 tumors. The detection of these biomarkers showed a good correlation with the treatment response, nonetheless, the approach was not sensitive enough to detect residual disease. In two patients who developed metastatic disease, an increase in ctDNA levels was observed at least 36 weeks before clinical detection of metastatic disease, and it was possible to correlate the level of ctDNA in subsequent plasma samples with response to the second-line treatment. This study, although exploratory, generated relevant and sufficient data to support additional studies to evaluate the use of personalized biomarkers in the surgical management and follow-up of rectal cancer patients treated with nCRT


Subject(s)
Male , Female , Biomarkers, Tumor/analysis , DNA/genetics , Neoadjuvant Therapy/classification , Rectal Neoplasms/pathology , Gene Library , Neoplastic Cells, Circulating/metabolism , Polymerase Chain Reaction/methods
14.
Indian J Exp Biol ; 2014 Oct; 52(10): 1011-1016
Article in English | IMSEAR | ID: sea-153801

ABSTRACT

DNA from molted feathers is being increasingly used for genetic studies on birds. However, the DNA obtained from such non-invasive sources is often not of enough quantity and quality for isolation of new microsatellite markers. The present study examined the potential of shed feathers of near threatened Painted Stork as a source of its DNA for cross-species amplification of microsatellites. Thirty-one shed feathers of varying conditions (‘good’ and ‘deteriorated’) and sizes (‘large’, ‘intermediate’ and ‘small’) collected in a north Indian population were used to isolate DNA by a standard isopropanol method and 11 microsatellite markers already developed in the Wood Stork were screened for amplification. Nine plucked feathers from two dead Painted Storks were also used to compare the DNA yield and amplification success. The DNA yield of feathers varied significantly in relation to the calamus size and condition. Among molted feathers, ‘good’ and ‘large’ samples provided more DNA than ‘deteriorated’ and ‘small’ ones, respectively. ‘Large’ plucked feathers yielded more DNA than ‘large’ molted feathers. DNA was almost degraded in all the samples and ratio of absorbance at 260/280 nm varied from 1.0 to 1.8, indicating impurity in many samples. Independent of DNA yields, all microsatellites were cross-amplified in all kinds of feathers, with >80% success in different feather categories. It is concluded that the shed feathers can be successfully used to isolate DNA in the Painted Stork and for cross-species amplification of microsatellites.


Subject(s)
Animals , Birds/genetics , DNA/genetics , Feathers/chemistry , Genetics, Population/methods , Microsatellite Repeats , Species Specificity
15.
Indian J Biochem Biophys ; 2014 Apr; 51(2): 115-120
Article in English | IMSEAR | ID: sea-154247

ABSTRACT

White matter disease refers to a set of diseases that affect the white matter of the brain and all of which have different consequences on brain function. Most of the studies have shown that it results from the defects during protein synthesis, with the gene defects in EIF2B1–5, encoding the five subunits of eukaryotic translation initiation factor 2B (eIF2B) α, β, γ, δ and ε, respectively. eIF2B plays a crucial role in protein translation and its regulation under different conditions. The previous studies have shown that mutations in five subunits of eIF2B cause white matter disease of the brain and thus EIF2B is the main culprit in development of white matter disease. In this study, the mutational screening of EIF2B5 gene encoding eIF2Bε was performed for the first time in 12 Kashmiri patients, each having a unique white matter disease condition. We found two novel missense mutations in EIF2B5: c.580A>G, p.Thr194Ala and c.611C>T, p.Ala204Val among the patients with demyelinating disease (multiple sclerosis), but no mutation was found in other patients. In conclusion our study suggests involvement of the EIF2B5 gene in MS development, thus suggesting p.Thr194Ala to be a susceptibility factor for the development of multiple sclerosis.


Subject(s)
Case-Control Studies , DNA/blood , DNA/genetics , Eukaryotic Initiation Factor-2B/chemistry , Eukaryotic Initiation Factor-2B/genetics , Exons/genetics , Genetic Predisposition to Disease , Humans , India , Leukoencephalopathies/genetics , Multiple Sclerosis/blood , Multiple Sclerosis/genetics , Mutation, Missense/genetics , Protein Conformation
16.
Article in English | WPRIM | ID: wpr-143101

ABSTRACT

An 87-year-old woman visited our clinic for a scheduled cataract surgery. At the time of preoperative evaluation, slit lamp examination showed lattice-shaped and granular deposits with asymmetrical patterns in the stroma of both corneas. Genomic DNA samples of the patient, amplified by polymerase chain reaction, showed a single nucleotide substitution, c. 1580T>G (p.L527R), in the transforming growth factor-beta-induced TGFBI gene. We also found two additional SNP mutations, c.1620T>C (p.F540F) and c.1678+23G>A, along with the well-known L527R mutation. This is the first report of lattice corneal dystrophy type IV with an L527R mutation outside of Japan, and could challenge the idea that L527R is caused by a mutation from a single Japanese ancestor.


Subject(s)
Aged, 80 and over , Corneal Dystrophies, Hereditary/diagnosis , DNA/genetics , DNA Mutational Analysis , Extracellular Matrix Proteins/genetics , Female , Humans , Mutation , Pedigree , Polymerase Chain Reaction , Transforming Growth Factor beta/genetics
17.
Article in English | WPRIM | ID: wpr-143096

ABSTRACT

An 87-year-old woman visited our clinic for a scheduled cataract surgery. At the time of preoperative evaluation, slit lamp examination showed lattice-shaped and granular deposits with asymmetrical patterns in the stroma of both corneas. Genomic DNA samples of the patient, amplified by polymerase chain reaction, showed a single nucleotide substitution, c. 1580T>G (p.L527R), in the transforming growth factor-beta-induced TGFBI gene. We also found two additional SNP mutations, c.1620T>C (p.F540F) and c.1678+23G>A, along with the well-known L527R mutation. This is the first report of lattice corneal dystrophy type IV with an L527R mutation outside of Japan, and could challenge the idea that L527R is caused by a mutation from a single Japanese ancestor.


Subject(s)
Aged, 80 and over , Corneal Dystrophies, Hereditary/diagnosis , DNA/genetics , DNA Mutational Analysis , Extracellular Matrix Proteins/genetics , Female , Humans , Mutation , Pedigree , Polymerase Chain Reaction , Transforming Growth Factor beta/genetics
18.
Indian J Exp Biol ; 2013 Dec; 51(12): 1130-1136
Article in English | IMSEAR | ID: sea-150302

ABSTRACT

The genomic and cDNA sequences of BnSUT1C were isolated from B. napus. Combination of cDNA and genomic DNA sequences revealed that the BnSUT1C gene contained three exons and two introns. The cDNA encodes a protein of 513 amino acids with a calculated molecular mass of 54.7 kDa and an isoelectric point of 9.12. It exhibits typical features of sucrose transporter with 12 trans-membranes spanning domains. BnSUT1C showed highly homologous with AtSUC1 and AtSUC5. A histidine residue, which is conserved across all functional sucrose transporter proteins in higher plants, is located at position 66 of the BnSUT1C. Two putative pollen-specific cis-elements, AGAAA and GTGA motifs, are located in 5′-upstream of BnSUT1C. The spatial and temporal expression patterns carried out by semi-quantitative RT-PCR and Real-Time PCR, which indicated that BnSUT1C predominantly expressed in later developmental stages of anther, as tapetal cells began to shrink and collapse. BnSUT1C could mediate the uptake of sucrose in the pollen and retrieval of tapetal degenerated products during pollen maturation.


Subject(s)
Amino Acid Sequence , Arabidopsis/genetics , Base Sequence , Brassica napus/genetics , Cloning, Molecular , DNA/genetics , DNA, Complementary/genetics , Membrane Transport Proteins/genetics , Membrane Transport Proteins/isolation & purification , Plant Proteins/genetics , Plant Proteins/isolation & purification , RNA, Messenger/genetics , Sequence Homology, Amino Acid , Transcriptome
19.
Article in English | IMSEAR | ID: sea-159949

ABSTRACT

Background: Fine needle aspiration cytology (FNAC) is most commonly used in first line investigation for tuberculous lymphadenopathy (TBLAP). Real-time polymerase chain reaction (PCR) an extremely versatile technique is being used for diagnosis and follow up of patients with infectious diseases. It can also be used for detecting Mycobacterium tuberculosis (Mtb) DNA in FNAC samples of TBLAP for rapid diagnosis and treatment. Aim: Detection of Mtb DNA on FNAC samples of tuberculous lymphadenopathy using Real-time PCR. Material and Methods: Twelve clinico-cytologically diagnosed TBLAP cases and five controls were included in the study. FNA samples were used for studying morphology, AFB demonstration, culture and for detecting Mtb DNA using Real-time PCR. Results: Mtb DNA was detected in ten cases (83.33 %) by Real-time PCR. ZN stain was positive in eight cases and culture in six cases. Conclusion: Detection of Mtb DNA in FNAC samples using Real-time PCR is a time saving, logical, economical approach over the culture based method.


Subject(s)
Adolescent , Adult , Child , DNA/analysis , DNA/genetics , Humans , Middle Aged , Mycobacterium/genetics , Real-Time Polymerase Chain Reaction/statistics & numerical data , Tuberculosis, Lymph Node/cytology , Tuberculosis, Lymph Node/genetics
20.
Indian J Hum Genet ; 2013 Jan; 19(1): 78-83
Article in English | IMSEAR | ID: sea-147640

ABSTRACT

CONTEXT: Amplification of Guanine-Cytosine (GC) -rich sequences becomes important in screening and diagnosis of certain genetic diseases such as diseases arising due to expansion of GC-rich trinucleotide repeat regions. However, GC-rich sequences in the genome are refractory to standard polymerase chain reaction (PCR) amplification and require a special reaction conditions and/or modified PCR cycle parameters. AIM: Optimize a cost effective PCR assay to amplify the GC-rich DNA templates. SETTINGS AND DESIGN: Fragile X mental retardation gene (FMR 1) is an ideal candidate for PCR optimization as its GC content is more than 80%. Primers designed to amplify the GC rich 5’ untranslated region of the FMR 1 gene, was selected for the optimization of amplification using DNA extracted from buccal mucosal cells. MATERIALS AND METHODS: A simple and rapid protocol was used to extract DNA from buccal cells. PCR optimization was carried out using three methods, (a) substituting a substrate analog 7-deaza-dGTP to dGTP (b) in the presence of a single PCR additive and (c) using a combination of PCR additives. All PCR amplifications were carried out using a low-cost thermostable polymerase. RESULTS: Optimum PCR conditions were achieved when a combination of 1M betaine and 5% dimethyl sulfoxide (DMSO) was used. CONCLUSIONS: It was possible to amplify the GC rich region of FMR 1 gene with reproducibility in the presence of betaine and DMSO as additives without the use of commercially available kits for DNA extraction and the expensive thermostable polymerases.


Subject(s)
Cheek/cytology , Cytosine/analogs & derivatives , DNA/genetics , Enhancer Elements, Genetic/genetics , Fragile X Syndrome/genetics , Guanine/analogs & derivatives , Nucleic Acid Amplification Techniques , Polymerase Chain Reaction/methods
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