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A phage display combined with DNA affinity magnetic system can be applied to a screening of DNA binding proteins, such as transcription factors Electron. J. Biotechnol.
Yulita,Kusumadewi Sri; Kouno,Takafumi; Ezaki,Bunichi.
Here we introduce a new approach for the screening of DNA binding proteins, using a phage library based on a phage display technique. In principal, a complementary DNA (cDNA) library based on the recombinant bacteriophage T7 expressing target proteins on its capsid (phage display) is constructed. These phage particles are hybridized with a biotinylated target DNA fragment which is immobilized on the surface of streptavidin paramagnetic particle (SA-PMP). The phage particles are released from the target DNA fragment by a nuclease treatment and the recovered phages are used to the next round of hybridization. These processes are repeated three times to amplify the target phages in the population. This simple method is faster, and more systemic than other...
Tipo: Journal article Palavras-chave: AtGST11 gene; Biopanning; DNA binding proteins; T7 phage differential display; Transcription factors.
Ano: 2010 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582010000100014
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A practical approach to the understanding and teaching of RNA silencing in plants Electron. J. Biotechnol.
Bazzini,Ariel A; Mongelli,Vanesa C; Hopp,H. Esteban; del Vas,Mariana; Asurmendi,Sebastián.
Gene silencing, also called RNA interference (RNAi) is a specific mechanism of RNA degradation involved in gene regulation, development and defense in eukaryotic organisms. It became an important subject in the teaching programs of molecular biology, genetics and biotechnology courses in the last years. The aim of this work is to provide simple and inexpensive assays to understand and teach gene silencing using plants as model systems. The use of transient and permanent transgenic plants for expressing reporter genes, like those derived from jellyfish green fluorescent protein (gfp) encoding gene, provides a nice, colorful and conclusive image of gene silencing. Three experimental approaches to evidence RNA silencing are depicted. In the first approach...
Tipo: Journal article Palavras-chave: Gene silencing; GFP; HC-Pro; PDS; Protocols; PTGS; Teaching; Transgenic; Transient expression; TRV; VIGS.
Ano: 2007 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582007000200002
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A predicted structure of the cytochrome c oxidase from Burkholderia pseudomallei Electron. J. Biotechnol.
Mohd. Raih,Mohd. Firdaus; Sailan,Ahmad Tarmidi; Zamrod,Zulkeflie; Embi,Mohd. Noor; Mohamed,Rahmah.
Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen. The enzyme belongs to the haem-copper-containing oxidases superfamily. A recombinant plasmid carrying a 2.0 kb insert from a Burkholderia pseudomallei genomic library was subjected to automated DNA sequencing utilizing a primer walking strategy. Analysis of the 2002 bp insert revealed a 1536 bp open reading frame predicted to encode a putative cytochrome c oxidase. Further analysis using sequence alignments and tertiary structure analysis tools demonstrated that the hypothetical B. pseudomallei cytochrome c oxidase is similar to cytochrome c oxidases from other organisms such as Thermus...
Tipo: Journal article
Ano: 2003 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582003000100005
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A preferable approach to clone hLIF cDNA from the genomic DNA Electron. J. Biotechnol.
Cui,Yihong; Zhu,Guangqin; Chen,Qiuju; Wang,Yunfei; Yang,Mingming; Song,Yuxuan; Wang,Jiangang; Cao,Binyun.
Complementary DNA (cDNA) is valuable for investigating protein structure and function in the research of life science, but it is difficult to obtain by traditional reverse transcription. In this study, we employed a novel strategy to clone the human leukemia inhibitory factor (hLIF) gene cDNA from genomic DNA directly isolated from the mucous membrane of mouth. The hLIF sequence can be acquired within a few hours by means of amplification of each exon and splicing using overlap-PCR. Thus, the new approach developed in this study is simple, time- and cost-effective, and it is not limited to particular gene expression levels of each tissue.
Tipo: Journal article Palavras-chave: CDNA cloning; HLIF; Oral mucous membrane; Overlap PCR.
Ano: 2011 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000300012
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A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber Electron. J. Biotechnol.
Rubio-Piña,Jorge; Quiroz-Moreno,Adriana; Sánchez-Teyer,L. Felipe.
Background: Agave tequilana has a great economic importance in Mexico in order to produce alcoholic beverages and bioenergy. However, in this species the structure and organization of the rDNAs in the genome are limited, and it represents an obstacle both in their genetic research and improvement as well. rDNA copy number variations per eukaryotic genome have been considered as a source of genetic rearrangements. In this study, the copy number of 18S and 5S rDNAs in the A. tequilana genome was estimated, and an absolute quantitative qPCR assay and genome size was used. In addition, an association between the rDNAs copy number and physical mapping was performed to confirm our results. Results: The analysis were successfully applied to determine copy number...
Tipo: Journal article Palavras-chave: Agave tequilana; Copy number; Fluorescent in situ hybridization; Ribosomal DNA; Quantitative PCR.
Ano: 2016 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000400002
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A rapid and cheap protocol for preparation of PCR templates in peanut Electron. J. Biotechnol.
Wang,Chuan Tang; Wang,Xiu Zhen; Tang,Yue Yi; Zhang,Jian Cheng; Yu,Shan Lin; Xu,Jian Zhi; Bao,Zhen Min.
This paper describes a simple, low cost and reliable DNA template preparation protocol for polymerase chain reaction (PCR) using immature leaves from peanut seeds or leaves from field-grown plants. The technique may find wide utility in studies involving PCR-based molecular markers, rapid screening for transformants and gene cloning.
Tipo: Journal article Palavras-chave: DNA extraction; Groundnut; PCR; Peanut.
Ano: 2009 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582009000200009
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A rapid method for an offline glycerol determination during microbial fermentation Electron. J. Biotechnol.
Kuhn,Jennifer; Müller,Hagen; Salzig,Denise; Czermak,Peter.
Background The purpose of this work was to find a rapid method for glycerol detection during microbial fermentations. The method requirements were, first, to avoid sample pretreatment, and second, to measure glycerol precisely especially out of fermentation broth. Results This was achieved by combining two reaction principles - the Malaprade reaction and the Hantzsch reaction. In the Malaprade reaction, glycerol is converted into formaldehyde. This forms a dye in the Hantzsch reaction after which adsorption is than detected. The subsequent assay was investigated with two different fermentation media, a chemically undefined and a chemically defined media, used for Pichia pastoris fermentation. In both media, as well as in real fermentation samples, glycerol...
Tipo: Journal article Palavras-chave: Glycerol determination; Fermentation broth; Hantzsch reaction; Malaprade reaction.
Ano: 2015 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000300017
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A real-time PCR genotyping assay to detect FAD2A SNPs in peanuts (Arachis hypogaea L.) Electron. J. Biotechnol.
Barkley,Noelle A; Wang,Ming Li; Pittman,Roy N.
The high oleic (C18:1) phenotype in peanuts has been previously demonstrated to result from a homozygous recessive genotype (ol1ol1ol2ol2) in two homeologous fatty acid desaturase genes (FAD2A and FAD2B) with two key SNPs. These mutant SNPs, specifically G448A in FAD2A and 442insA in FAD2B, significantly limit the normal function of the desaturase enzyme activity which converts oleic acid into linoleic acid by the addition of a second double bond in the hydrocarbon chain. Previously, a genotyping assay was developed to detect wild type and mutant alleles in FAD2B. A real-time PCR assay has now been developed to detect wild type and mutant alleles (G448A) in FAD2A using either seed or leaf tissue. This assay was demonstrated to be applicable for the...
Tipo: Journal article Palavras-chave: Fatty acid composition; Gas chromatography; Peanut (Arachis hypogaea L.); Real-time PCR; SNP genotyping.
Ano: 2011 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000100009
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A simple and efficient method for extraction of Taq DNA polymerase Electron. J. Biotechnol.
Chen,Sique; Zheng,Xiujuan; Cao,Hongrui; Jiang,Linghui; Liu,Fangqian; Sun,Xinli.
Background Thermostable DNA polymerase (Taq Pol ?) from Thermus aquaticus has been widely used in PCR, which was usually extracted with Pluthero's method. The method used ammonium sulfate to precipitate the enzyme, and it saved effort and money but not time. Moreover, we found that 30-40% activity of Taq Pol I was lost at the ammonium sulfate precipitation step, and the product contained a small amount of DNA. Results We provided a novel, simplified and low-cost method to purify the Taq Pol ? after overproduction of the enzyme in Escherichia coli, which used ethanol instead of ammonium sulfate to precipitate the enzyme. The precipitate can be directly dissolved in the storage buffer without dialysis. In addition, DNA and RNA contamination was removed with...
Tipo: Journal article Palavras-chave: Ethanol precipitation; PCR; Purification; Taq DNA polymerase.
Ano: 2015 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000500005
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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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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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A simple negative selection method to identify adenovirus recombinants using colony PCR Electron. J. Biotechnol.
Zhao,Yongliang; Dong,Zongming; Li,Tengfei; Huang,Gang.
Background: The AdEasy system is a fast-track system for generating recombinant adenoviruses using the efficient homologous recombination machinery between shuttle and adenovirus backbone plasmids in Escherichia coli BJ5183 cells. The key step is homologous recombination in BJ5183 cells, which is driven by RecA activity. However, culture time is stringently limited to reduce the damage to recombinant plasmids by RecA activity. Therefore, rapid identification of recombinant adenoviruses within the limited time-period is critical. Results: We developed a simple negative selection method to identify recombinant adenoviruses using colony PCR, which improves the efficiency of adenovirus recombination screening and packaging. Conclusions: The negative selection...
Tipo: Journal article Palavras-chave: Adenovirus; AdEasy; Colony PCR; Homologous recombination; RecA.
Ano: 2014 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000100008
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A standardized protocol for genomic DNA isolation from Terminalia arjuna for genetic diversity analysis Electron. J. Biotechnol.
Sarwat,Maryam; Singh Negi,Madan; Lakshmikumaran,Malathi; Kumar Tyagi,Akhilesh; Das,Sandip; Shankar Srivastava,Prem.
For studying genetic diversity in natural populations of Terminalia, a medicinal plant, our attempts to isolate high quality DNA using several previously reported protocols and even modifications were unsuccessful. We therefore combined CTAB based isolation, and column based purification step, to isolate DNA from Terminalia arjuna. The DNA isolated using this standardized protocol was high in quality and suitable for restriction digestion and generation of random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP).
Tipo: Journal article Palavras-chave: DNA extraction; Medicinal plants; Molecular markers; Terminalia species.
Ano: 2006 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582006000100011
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A strategy to identify genomic expression at single-cell level or a small number of cells Electron. J. Biotechnol.
Li,Biaoru.
Recent advances in functional genomics allow us to estimate the expression of several thousands of genes in the mammalian genome. Techniques such as microarrays, expressed tag sequencing (EST), serial analysis of gene expression (SAGE), subtractive cloning and differential display (DD), and two-dimensional electrophoresis gel have been extensively used to screen and analyze parallel gene expression. Some pathological processes, for example, tumorigenesis and solid tumour growth, in which the former is derived from a single-cell and the latter has a mixed-cell problem, present new challenges to the limit of these functional genomic techniques. To fully understand the functions of cells in tumorigenesis or in heterogeneous solid tumour masses, it is...
Tipo: Journal article Palavras-chave: Genome; Genomic expression; Genomic expression analysis at single cell; Single cell.
Ano: 2005 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582005000100011
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Academic Manpower Training Policy in Israel in the Area of Biotechnology Electron. J. Biotechnol.
Herskovic,Shlomo.
Tipo: Journal article
Ano: 2002 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582002000200003
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Accommodating the difference in students' prior knowledge of cell growth kinetics Electron. J. Biotechnol.
Seters,Janneke van; Ossevoort,Miriam; Goedhart,Martin; Tramper,Johannes.
This paper describes the development and benefits of an adaptive digital module on cell growth to tackle the problem of educating a heterogeneous group of students at the beginning of an undergraduate course on process engineering. Aim of the digital module is to provide students with the minimal level of knowledge on cell growth kinetics they need to comprehend the content knowledge of the subsequent lectures and pass the exam. The module was organised to offer the subject matter in a differentiated manner, so that students could follow different learning paths. Two student groups were investigated, one consisting of students who had received their prior education abroad and one of students that had not. Exam scores, questionnaires, and logged user data...
Tipo: Journal article Palavras-chave: Adaptive digital learning material; Bioreactor design; Biotechnology; Education; Intelligent tutoring system; Intelligent Web-based educational system.
Ano: 2011 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000200001
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Active anti-acetylcholinesterase component of secondary metabolites produced by the endophytic fungi of Huperzia serrata Electron. J. Biotechnol.
Wang,Zhejian; Ma,Zhao; Wang,Lili; Tang,Chengchen; Hu,Zhibi; Chou,GuiXin; Li,Wankui.
Background An endophytic fungus lives within a healthy plant during certain stages of, or throughout, its life cycle. Endophytic fungi do not always cause plant disease, and they include fungi that yield different effects, including mutual benefit, and neutral and pathogenic effects. Endophytic fungi promote plant growth, improve the host plant's resistance to biotic and abiotic stresses, and can produce the same or similar biologically active substances as the host. Thus, endophytic fungal products have important implications in drug development. Result Among the numerous endophytic fungi, we identified two strains, L10Q37 and LQ2F02, that have anti-acetylcholinesterase activity, but the active compound was not huperzine A. The aim of this study was to...
Tipo: Journal article Palavras-chave: Anti-acetylcholinesterase activity; Acetylcholinesterase inhibitor; Biological characteristics; Endophytic fungi.
Ano: 2015 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000600003
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Advances in improving mammalian cells metabolism for recombinant protein production Electron. J. Biotechnol.
Altamirano,Claudia; Berrios,Julio; Vergara,Mauricio; Becerra,Silvana.
Background: The production of recombinant proteins for therapeutic use represents a great impact on the biotechnology industry. In this context, established mammalian cell lines, especially CHO cells, have become a standard system for the production of such proteins. Their ability to properly configure and excrete proteins in functional form is an enormous advantage which should be contrasted with their inherent technological limitations. These cell systems exhibit a metabolic behaviour associated with elevated cell proliferation which involves a high consumption of glucose and glutamine, resulting in the rapid depletion of these nutrients in the medium and the accumulation of ammonium and lactate. Both phenomena contribute to the limitation of cell...
Tipo: Journal article Palavras-chave: Aerobic glycolysis; Cell engineering; CHO cells; Glutaminolysis; Metabolism.
Ano: 2013 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582013000300010
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Advances in the development of a noninvasive embryo model for the evaluation of the quality of cloned embryos subjected to different treatments Electron. J. Biotechnol.
Felmer,Ricardo; Arias,María Elena.
Total number of cells in cloned embryos is generally lower than that of in vivo derived embryos and in bovines cell allocation at the blastocyst stage, has been observed to be affected in a large proportion of cloned embryos. The current embryo staining procedures are toxic for mammalian cells and thus can not be used to determine the developmental potential of a stained embryo. Therefore, in the present study we sought to assess the feasibility to develop a noninvasive embryo model that would be suitable for the evaluation of cloned embryos subjected to different nuclear transfer and embryo culture procedures. For doing this, we stably transfected a bovine embryonic fibroblast cell line and generated a number of clones that constitutively expressed a red...
Tipo: Journal article
Ano: 2008 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582008000500002
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Aerobic biodegradation of nonylphenol ethoxylates in shaking-flask test Electron. J. Biotechnol.
Wang,Ping; Nong,Xu-Hua; Ge,Jie-Hong.
Nonylphenol ethoxylates (NPEOs), which are widely used for industrial and domestic purposes, exert adverse effects on wildlife after being used and discharged into the environment. However, their ultimate biodegradability and biodegradation pathway remains unclear. In this study, the aerobic degradability of nonylphenol ethoxylates (NPEOs) by the acclimated microorganisms in active sludge was examined using shaking-flask tests. The degradation of benzene rings in NPEOs was determined using UV spectroscopy and high performance liquid chromatography (HPLC). Results showed that more than 80% of benzene rings were removed after 8-10 days of degradation, and the majority of NPEOs were also removed after 9 days of degradation, indicating NPEOs and the benzene...
Tipo: Journal article Palavras-chave: Aerobic biodegradation; Degradation pathway; ESI-MS; HPLC; Nonylphenol ethoxylates.
Ano: 2011 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000400001
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