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DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols ArchiMer
Alain, Karine; Callac, Nolwenn; Ciobanu, Maria Cristina; Reynaud, Yann; Duthoit, Frederique; Jebbar, Mohamed.
Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low bio-masses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor (R)) were compared. Effective DNA extraction was evaluated in terms of...
Tipo: Text Palavras-chave: Sediment; DNA extraction; Deep subsurface biosphere.
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00056/16691/14364.pdf
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An efficient and rapid DNA minipreparation procedure suitable for PCR/SSR and RAPD analyses in tropical forest tree species BABT
Alzate-Marin,Ana Lilia; Guidugli,Marcela Corbo; Soriani,Hilda Hildebrand; Martinez,Carlos Alberto; Mestriner,Moacyr Antônio.
An efficient and rapid DNA minipreparation modified method for frozen samples was developed for five tropical tree species: Copaifera langsdorffii, Hymenaea courbaril, Eugenia uniflora, Tabebuia roseo alba and Cariniana estrellensis. This procedure that dispenses the use of liquid nitrogen, phenol and the addition of proteinase K, is an adaptation of the CTAB-based DNA extraction method. The modifications included the use of PVP to eliminate the polyphenols, only one chloroform-isoamyl alcohol step and the addition of RNase immediately after extraction with chloroform. The yields of the DNA samples ranged from 25.7 to 42.1 µg from 100 mg leaf tissue. The DNA samples extracted by this method were successfully used for PCR (SSR and RAPD) analyses in these...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Copaifera langsdorffii; Hymenaea courbaril; Eugenia uniflora; Tabebuia roseo alba; Cariniana estrellensis; DNA extraction.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132009000500020
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Direct RAPD evaluation of bacteria without conventional DNA extraction BABT
Araújo,Welington Luiz; Angellis,Derlene Attili de; Azevedo,João Lúcio.
The present work reports successful DNA amplification of Pantoea agglomerans and Bacillus pumilus through Random Amplified Polymorphic DNA (RAPD). For this, template DNA was obtained without conventional DNA extraction. The procedure was as follows: cultures grown for 20 hours in 5 mL LB medium were centrifuged and the resulting preparation was suspended in TE buffer. After boiling, the cell suspension was diluted and 2.0 µl were used in reactions of 15 µl. The results showed no significant differences among the RAPD profile of the PCR reactions derived from the boiling and phenol extraction methods, suggesting the utilization of this method for genetic population analysis.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bacteria; Boiling method; DNA extraction; RAPD.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132004000300006
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Simple and robust DNA extraction method for the large-scale analysis of genotypes containing high polyphenolic content, such as landracesof Solanum tuberosum and Zea mays Ciencia e Investigación Agraria
Barra,Macarena; Salazar,Erika; Beltrán,María; Sagredo,Boris.
The extraction of high-quality DNA is essential for studies conducted at the molecular level in species with an abundance of contaminants in their tissues, such as some landraces of potato and maize, in which it is difficult to extract good-quality genomic DNA. Compounds such as polyphenols interfere with the amplification of DNA during polymerase chain reaction (PCR), which makes it difficult to conduct PCR-based studies ofmolecular markers. This article describes a simple and robust protocol for DNA isolation that was applied to potato and maize landraces and resulted in a high DNA concentration with excellent purity and quality. This method is based on the method of Krizman et al. (2006) with some modifications and was tested on potato leaves and young...
Tipo: Journal article Palavras-chave: Activated charcoal; DNA extraction; Genomic DNA; Polyphenols.
Ano: 2012 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-16202012000300019
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Detection of ostreid herpesvirus-1 (OsHV-1) by PCR using a rapid and simple method of DNA extraction from oyster larvae ArchiMer
Batista, Frederico; Taris, Nicolas; Boudry, Pierre; Renault, Tristan.
A DNA extraction procedure was developed for the detection of ostreid herpesvirus-1 (OsHV-1) using the polymerase chain reaction (PCR) in oyster larvae. The DNA extraction procedure developed was tested on 8 larval samples. Abnormal nuclei with characteristic features associated with OsHV-1 infections were only observed in samples in which the viral DNA was detected by PCR. A previously described competitive PCR method was applied to detect inhibition during PCR reactions. The results show that the method can be used on small amounts of oyster larvae (3 mg) for the detection of OsHV-1 DNA by PCR.
Tipo: Text Palavras-chave: DNA extraction; Detection; Larvae; Oyster; OsHV 1; Herpesvirus.
Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/publication-2916.pdf
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Urine as a promising sample for Leishmania DNA extraction in the diagnosis of visceral leishmaniasis - a review BJID
Bezerra,Gilberto Silva Nunes; Barbosa Júnior,Walter Lins; Silva,Elis Dionísio da; Leal,Nilma Cintra; Medeiros,Zulma Maria de.
ABSTRACT Visceral leishmaniasis is a serious and debilitating infection with high fatality rate in tropical and subtropical countries. As clinical symptoms of visceral leishmaniasis are not so specific, confirmatory diagnostic methods with high sensitivity and specificity are needed. Noninvasive methods have been developed using urine as a clinical sample for visceral leishmaniasis diagnosis. In fact, there is a clear correlation between kidney impairment and Leishmania DNA in urine. However, it has been proved that Leishmania nucleic acid may also be isolated from patients without any sign of renal involvement. Even though urine has become a promissing biological sample, it is still not widely used due to several issues, such as (i) incomprehension of the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Visceral leishmaniasis; Renal involvement; Diagnosis; Urine sample; DNA extraction.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702019000200111
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Protocol for extraction of genomic DNA from swine solid tissues Genet. Mol. Biol.
Biase,Fernando Henrique; Franco,Maurício Machaim; Goulart,Luiz Ricardo; Antunes,Robson Carlos.
Molecular diagnostics are performed by using DNA from different body tissues. However, it is necessary to obtain genomic DNA of good quality. Due to the impossibility of collecting blood from slaughtered animals, DNA extraction from solid tissues is necessary. The objective of this study was to describe a protocol of DNA extraction from swine skin, adipose, brain, liver, kidney and muscle tissues. We obtained high molecular weight DNA of good quality, shown by agarose gel and amplification of two DNA fragments, 605bp and 891pb, by PCR. Spectrophotometric analysis of DNA concentration showed variation among the DNA from different tissues, with the liver and adipose tissues presenting the greatest and the smallest concentration, respectively. The described...
Tipo: Info:eu-repo/semantics/other Palavras-chave: DNA extraction; Swine tissues.
Ano: 2002 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572002000300011
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Comparison of different methodologies for DNA extraction from Aegla longirostri BABT
Bitencourt,João Vitor Trindade; Roratto,Paula Angélica; Bartholomei-Santos,Marlise Ladvocat; Santos,Sandro.
The aim of this study was to compare some DNA extraction methodologies for Aegla longirostri. The protocols were based on the traditional phenol-chloroform DNA extraction methodology and using a commercial kit for DNA extraction. They differed in tissues used, the addition - or not - of beta-mercaptoethanol to the lysis buffer, times and methods for the animal's conservation (frozen, in ethanol or fresh). Individuals stored at -20°C for a long time supplied lower molecular weight DNA than those stored for a short time. The best yield for the specimens preserved in ethanol was obtained for 15 days storage in 95% ethanol. The kit resulted in a low quantity of high molecular weight DNA. The best protocol for DNA extraction from Aeglidae, and probably for...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Anomura; Aeglidae; Freshwater crab; DNA extraction.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132007000700010
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Use of real-time PCR to evaluate two DNA extraction methods from food Ciênc. Tecnol. Aliment.
Branquinho,Maria Regina; Ferreira,Renata Trotta Barroso; Cardarelli-Leite,Paola.
The DNA extraction is a critical step in Genetically Modified Organisms analysis based on real-time PCR. In this study, the CTAB and DNeasy methods provided good quality and quantity of DNA from the texturized soy protein, infant formula, and soy milk samples. Concerning the Certified Reference Material consisting of 5% Roundup Ready® soybean, neither method yielded DNA of good quality. However, the dilution test applied in the CTAB extracts showed no interference of inhibitory substances. The PCR efficiencies of lectin target amplification were not statistically different, and the coefficients of correlation (R²) demonstrated high degree of correlation between the copy numbers and the threshold cycle (Ct) values. ANOVA showed suitable adjustment of the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: DNA extraction; Genetically modified organisms; GMO; Food analysis; Real-time PCR; Linearity.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0101-20612012000100017
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Extração de DNA a partir de coágulos sanguíneos bovinos. Infoteca-e
BRITO, L. G.; OLIVEIRA, M. C. de S.; MOURA, M. M. da F.; SILVA NETTO, F. G. da S.; CAVALCANTE, F. A.; MARIM, A. D.; SOUZA, G. C. R. de; SILVA, J. L. da.
Foi otimizada uma metodologia de extração de DNA genômico a partir de coágulo sanguíneo. Amostras de sangue com e sem anticoagulante EDTA para a obtenção dos coágulos sanguíneos foram coletadas em bovinos nos estados de Rondônia e Acre para pesquisa de Anaplasma marginale. Para a extração de DNA a partir do coágulo sanguíneo testaram-se dois tipos de tecido de nylon: no tratamento 1, o tecido utilizado apresentava diâmetro dos poros de 200 µm e no tratamento 2, tecido com poros de diâmetro de 1.200 µm. As amostras de sangue com anticoagulante representaram o tratamento 3, sendo este considerado como tratamento controle. Após a quebra mecânica, os coágulos sofreram centrifugação a 7.000 RPM por 15 minutos passando através das malhas dos tecidos utilizados...
Tipo: Boletim de Pesquisa e Desenvolvimento (INFOTECA-E) Palavras-chave: Extração de DNA; Coágulo sanguíneo; Epidemiologia molecular; Doenças de bovinos; DNA extraction; Blood clot; Molecular epidemiology; Bovine diseases.
Ano: 2006 URL: http://www.infoteca.cnptia.embrapa.br/handle/doc/710703
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Comparison of preservation methods of Atta spp. (Hymenoptera: Formicidae) for RAPD analysis Anais da SEB
Carvalho,Alfredo O. R.; Vieira,Luiz G. E..
High quality DNA for molecular studies can be easily extracted from fresh specimens. However, live samples are difficult to keep for long periods thus making their preservation a serious problem, specially when they are collected and transported from remote locations. In order to establish an efficient method to preserve Atta spp. (leaf-cutting ants) for RAPD analysis, six different storage methods were examined: 1) -70°C; 2) 95% ethanol at -20°C; 3) 95% ethanol at 4°C; 4) 95% ethanol at room temperature; 5) silica gel at room temperature; and 6) buffer (0.25 M EDTA, 2.5% SDS, 0.5 M Tris-HCl, pH 9.2) at room temperature. DNA was extracted (Cheung et al., 1993 - modified) and examined after 90, 210 and 360 days of storage. Freshly killed specimens were used...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Insecta; Leaf-cutting ants; DNA extraction; Storage conditions.
Ano: 2000 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0301-80592000000300011
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The use of museum specimens as source of DNA Naturalis
Cibois, A..
Tipo: Article / Letter to the editor Palavras-chave: Aves; Museum specimens; DNA extraction; 42.83.
Ano: 2005 URL: http://www.repository.naturalis.nl/record/210819
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Enhancement of soil DNA extraction by the use of a hand held mixer BJM
Costa,Jefferson Luis da Silva; Oliveira,Virgínia Carla de.
The efficiency of soil DNA extraction using a bead beater homogenizer (Biospec Products - Germany) was compared to that obtained with a hand held mixer (Moulinex - Brazil). The hand held mixer costs 100 times less and extracted seven times more crude DNA than the bead beater.
Tipo: Info:eu-repo/semantics/other Palavras-chave: Molecular tools; DNA extraction.
Ano: 2003 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822003000400004
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A simple method for isolation of genomic DNA from fresh and dry leaves of Terminalia arjuna (Roxb.) Wight and Arnot Electron. J. Biotechnol.
Deshmukh,Vishal P; Thakare,Prashant V; Chaudhari,Uddhav S; Gawande,Prashant A.
Current protocols for isolation of genomic DNA from Terminalia arjuna have their own limitations due to the presence of high content of gummy polysaccharides and polyphenols. DNA isolated by these protocols is contaminated with a yellowish, sticky and viscous matrix. In our modified DNA isolation method polysaccharides and polyphenols are removed prior to the precipitation of the DNA. Then the genomic DNA was precipitated using isopropanol. This protocol yielded a high molecular weight DNA isolated from fresh as well as dry leaves of T. arjuna, which was free from contamination and colour. Isolated DNA can be used for restriction digestion and PCR amplification. The main objective of the present protocol is to provide a simple method of isolation of DNA,...
Tipo: Journal article Palavras-chave: Ayurveda; DNA extraction; Medicinal plant; Terminalia species.
Ano: 2007 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582007000300014
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Evaluation of six methods for total dna extraction from gut earthworms for microbial community diversity and metagenomics. Repositório Alice
ESTEVES, E. D.; BROWN, G. G.; PEDROSA, F. de O.; SOUZA, E. M. de; CHUBATSU, L. S..
2015
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Minhoca; Extração de DNA; Método; Earthworm; DNA extraction.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1029457
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Use of a cysteine proteinase from Carica candamarcensis as a protective agent during DNA extraction BJMBR
Genelhu,M.S.; Zanini,M.S.; Veloso,I.F.; Carneiro,A.M.D.; Lopes,M.T.P.; Salas,C.E..
We describe the use of a plant cysteine proteinase isolated from latex of Carica candamarcensis as a protective agent during isolation of bacterial DNA following growth in culture of these cells. Between 100 to 720 units of proteinase (1 µg = 6 units) afforded good DNA protection when incubated with various kinds of microorganisms. Agarose gel electrophoresis showed that the resulting DNA was similar in size to DNA preparations obtained by treatment with proteinase K. The viability of the resulting material was checked by PCR amplification using species-specific primers. After standing at room temperature (25oC) for 35 days, the enzyme lost 10% of its initial activity. The enzyme stability and good yield of DNA suggest the use of this proteinase as an...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Cysteine proteinase; Proteinase K; C. candamarcensis; DNA extraction.
Ano: 1998 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X1998000900005
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Comparison of three methods of DNA extraction from cold-smoked salmon and impact of physical treatments ArchiMer
Giacomazzi, Sophie; Leroi, Francoise; Joffraud, Jean-jacques.
Aims: To compare three bacterial DNA extraction procedures on cold-smoked salmon (CSS) and assess the impact on their efficiency of two physical treatments of the food matrix, ionizing irradiation and freezing. Methods and Results: As molecular methods for bacterial detection have become an important analytical tool, we compared bacterial DNA extraction procedures on CSS. Working with frozen and irradiated CSS, we obtained negative responses from samples known to be highly contaminated. Thus, we decided to study the impact of these two physical treatments on bacterial DNA extraction procedures. The efficiency of bacterial DNA extraction directly from the fish matrix suspension was measured by an rpoB PCR-based reaction. The results demonstrated that the...
Tipo: Text Palavras-chave: RpoB gene; PCR; Ionizing irradiation; Freezing; DNA extraction; Cold smoked salmon.
Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/publication-1106.pdf
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A simple ethanol wash of the tissue homogenates recovers high-quality genomic DNA from Corchorus species characterized by highly acidic and proteinaceous mucilages Electron. J. Biotechnol.
Kundu,Avijit; Sarkar,Debabrata; Bhattacharjee,Amit; Topdar,Niladri; Sinha,Mohit Kumar; Mahapatra,Bikash Sinha.
A simple miniprep based on early elimination of highly acidic and proteinaceous mucilages through ethanol washing of the tissue homogenates has been developed for the extraction of genomic DNA from mature leaves and seeds of Corchorus spp. As compared to high cetyltrimethylammonium bromide (CTAB)-NaCl DNA extraction followed by ethanol-based removal of remnant mucilages from the DNA pellet, this simple miniprep consistently and reproducibly recovers high amounts of DNA with good spectral qualities at A260/A280 and A260/A230. The purified DNA is efficiently digested by restriction endonucleases, and is suitable for PCR amplification of nuclear microsatellites with expected allele sizes.
Tipo: Journal article Palavras-chave: Corchorus; DNA extraction; Microsatellite; Mucilage; PCR; Restriction digestion.
Ano: 2011 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000100010
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Comparison of DNA extraction protocols for microbial communities from soil treated with biochar BJM
Leite,D.C.A.; Balieiro,F.C.; Pires,C.A.; Madari,B.E.; Rosado,A.S.; Coutinho,H.L.C.; Peixoto,R.S..
Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Biochar; DNA extraction; PCR-DGGE; Microbial communities; DNA purity indices.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822014000100023
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Extraction of high-quality host DNA from feces and regurgitated seeds: a useful tool for vertebrate ecological studies Biol. Res.
MARRERO,PATRICIA; FREGEL,ROSA; CABRERA,VICENTE M; NOGALES,MANUEL.
DNA extraction methods for genotyping non-invasive samples have led to great advances in molecular research for ecological studies, and have been particularly useful for analyzing threatened species. However, scarce amounts of fragmented DNA and the presence of Taq polymerase inhibitors in non-invasive samples are potential problems for subsequent PCR amplifications. In this study we describe a novel technique for extracting DNA from alimentary tract cells found on external surfaces of feces and regurgitated seeds. The presence of contaminants and inhibitors is minimized and samples are preserved intact for use in other ecological research (e.g. trophic studies). The amplification efficiency and purity of the extracted DNA from feces were significantly...
Tipo: Journal article Palavras-chave: DNA extraction; Ecological studies; Guanidine thiocyanate; Non-invasive method; Pigeons; Seed dispersal.
Ano: 2009 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602009000200002
Registros recuperados: 38
Primeira ... 12 ... Última
 

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