Consulta: subjectFacets:"Sequence"
Registros recuperados: 9
Data/hora: 10/06/2024 13:57:47

Sucrose synthase molecular marker associated with sugar content in elite sugarcane progeny
Provedor de dados: Genetics and Molecular Biology
Autores: Silva,Jorge A. da; Bressiani,Jose A.
We describe the development and application of an expressed sequence tag (EST)-derived restriction fragment length polymorphism (RFLP) marker for sugarcane elite genotypes which can be used for quantitative trait loci (QTL) tagging for sugar content. EST-derived RFLP markers for proteins involved in sucrose metabolism have been used in Southern analysis for mapping and gene tagging in elite sugarcane clones. A single dose marker, obtained from a sucrose synthase EST associated with sugar content at the alpha = 0.01 probability level, is presented for sugarcane breeding. Utilization of EST homologues to known genes for generation of molecular markers accelerated the identification of a QTL controlling an important trait-sugar content. Sugarcane bacterial...
Tipo: Info:eu-repo/semantics/other
Palavras-chave: Sucrose; Synthase; Expressed; Sequence; Tag.
Ano: 2005
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000200020

Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: implication in virus taxonomy
Provedor de dados: Genetics and Molecular Biology
Autores: Boulila,Moncef.
A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31β algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher's Exact Test of Neutrality, positive...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bioinformatics; Phylogeny; Recombination; Positive selection; Tombusviridae; Sequence; Taxonomy.
Ano: 2011
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000400018

Mark-recapture cloning: a straightforward and cost-effective cloning method for population genetics of single-copy nuclear DNA sequences in diploids
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Bierne, Nicolas; Tanguy, A; Faure, Michel; Faure, B; David, E; Boutet, I; Boon, E; Quere, N; Plouviez, S; Kemppainen, P; Jollivet, D; Moraga, D; Boudry, Pierre; David, P.
We describe a simple protocol to reduce the number of cloning reactions of nuclear DNA sequences in population genetic studies of diploid organisms. Cloning is a necessary step to obtain correct haplotypes in such organisms, and, while traditional methods are efficient at cloning together many genes of a single individual, population geneticists rather need to clone the same locus in many individuals. Our method consists of marking individual sequences during the polymerase chain reaction (PCR) using 5'-tailed primers with small polynucleotide tags. PCR products are mixed together before the cloning reaction and clones are sequenced with universal plasmid primers. The individual from which a sequence comes from is identified by the tag sequences upstream...
Tipo: Text
Palavras-chave: Sequence; Population genetics; High throughput allele recognition; DNA polymorphism.
Ano: 2007
URL: http://archimer.ifremer.fr/doc/2007/publication-4222.pdf

A Computer-Assisted Method for Depositional Model Determination
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Ndiaye, Mapathe; Davaud, Eric; Jorry, Stephan.
A software has been developed to overcome the difficulties related to depositional model determination in Geosciences. The implemented methods, Walker, Harper and Turk methods, based on Markov process and Markov chain analysis, have been used in a case study. The results of the analysis are consistent with previous works. The analysis shows also that the results are accurate and do not rely on the used method. Therefore, the obtained depositional sequence is suitable to build a depositional model on which reliable sequence stratigraphic studies can be based.
Tipo: Text
Palavras-chave: Depositional Model; Sequence; Log; Markov Chain; Transition Matrix; Walker; Harper; Turk; El Garia Formation.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00248/35880/35376.pdf

Phylogeny of Cyperaceae based on DNA sequence data - a new rbcL analysis
Provedor de dados: Naturalis Digital Academic Repository
Autores: Simpson, D.A.; Muthama Muasya, A.; Alves, M.V.; Bruhl, J.J.; Dhooge, S.; Chase, M.W.; Furness, C.A.; Ghamkhar, K.; Goetghebeur, P.; Hodkinson, T.D.; Marchant, A.D.; Reznicek, A.A.; Nieuwborg, R.; Roalson, E.H.; Smets, E.; Starr, J.R.; Thomas, W.W.; Wilson, K.L.; Zhang, X.
Since the Monocots II meeting in 1998, significant new data have been published that enhance our systematic knowledge of Cyperaceae. Phylogenetic studies in the family have also progressed steadily. For this study, a parsimony analysis was carried out using all rbcL sequences currently available for Cyperaceae, including data for two new genera. One of the four subfamilies (Caricoideae) and seven of the 14 tribes (Bisboeckelereae, Cariceae, Cryptangieae, Dulichieae, Eleocharideae, Sclerieae, Trilepideae) are monophyletic. Subfamily Mapanioideae and tribe Chrysitricheae are monophyletic if, as the evidence suggests, Hellmuthia is considered a member of Cypereae. Some other features of our analysis include: well-supported Trilepideae and...
Tipo: Article / Letter to the editor
Palavras-chave: Cyperaceae; Monocotyledons; Phylogeny; RbcL; Sequence; 42.48.
Ano: 2007
URL: http://www.repository.naturalis.nl/record/414071

Do-it-yourself shuffling and the number of runs under randomness
Provedor de dados: Research in Agricultural & Applied Economics (AgEcon Searh)
Autores: Smeeton,   Nigel; Cox,   Nicholas J.
A common class of problem in statistical science is estimating, as a benchmark, the probability of some event under randomness. For example, in a sequence of events in which several outcomes are possible and the length of the sequence and number of outcomes of each type known, the number of runs gives an indication of whether the outcomes are random, clustered, or alternating. This note explains and illustrates a simple method of random shuffling that is often useful. We show how the conditional probability distribution of the number of runs may be derived easily in Stata, thus yielding p-values for testing the null hypothesis that the type of outcome is random. We also compare our direct approach with that using the simulate command.
Tipo: Journal Article
Palavras-chave: Alternation; Categorical data; Clustering; Conditional distribution; Forvalues; P-value; Permutation; Run; Sequence; Simulate; Simulation; Research Methods/ Statistical Methods.
Ano: 2003
URL: http://purl.umn.edu/116095

Molecular and functional characterization of ferredoxin NADP(H) oxidoreductase from Gracilaria chilensis and its complex with ferredoxin
Provedor de dados: Biological Research
Autores: Vorphal,María Alejandra; Bruna,Carola; Wandersleben,Traudy; Dagnino-Leone,Jorge; Lobos-González,Francisco; Uribe,Elena; Martínez-Oyanedel,José; Bunster,Marta.
Abstract  Backgroud Ferredoxin NADP(H) oxidoreductases (EC 1.18.1.2) (FNR) are flavoenzymes present in photosynthetic organisms; they are relevant for the production of reduced donors to redox reactions, i.e. in photosynthesis, the reduction of NADP+ to NADPH using the electrons provided by Ferredoxin (Fd), a small FeS soluble protein acceptor of electrons from PSI in chloroplasts. In rhodophyta no information about this system has been reported, this work is a contribution to the molecular and functional characterization of FNR from Gracilaria chilensis, also providing a structural analysis of the complex FNR/Fd.  Methods The biochemical and kinetic characterization of FNR was performed from the enzyme purified from phycobilisomes enriched fractions. The...
Tipo: Journal article
Palavras-chave: Ferredoxin NADP+ reductase; Ferredoxin; Sequence; Kinetic parameters; Structural features.
Ano: 2017
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602017000100228

UL146 variability among clinical isolates of Human Cytomegalovirus from Japan
Provedor de dados: Biological Research
Autores: Aguayo,Francisco; Murayama,Tsugiya; Eizuru,Yoshito.
Human Cytomegalovirus (HCMV) is a herpesvirus associated with serious diseases in immunocompromised subjects. The region between ORF UL133 and UL151 from HCMV, named ULb' is frequently deleted in attenuated AD169 and in highly passaged laboratory strains. However, this region is conserved in low-passaged and more virulent HCMV, like the Toledo strain. The UL146 gene, which is located in the ULb' region, encodes a CXC-chemokine analogue. The diversity of UL146 gene was evaluated among fifty-six clinical isolates of HCMV from Japan. Results show that UL146 gene was successfully amplified by the polymerase chain reaction (PCR) in only 17/56 strains (30%), while the success rate for UL145/UL147 gene was 18/56 strains (32%). After DNA sequencing, the 35...
Tipo: Journal article
Palavras-chave: Cytomegalovirus; UL146; Sequence; V.
Ano: 2010
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602010000400013

De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies
Provedor de dados: Biological Research
Autores: Thunders,Michelle; Cavanagh,Jo; Li,Yinsheng.
Abstract  Background  Earthworms are sensitive to toxic chemicals present in the soil and so are useful indicator organisms for soil health. Eisenia fetida are commonly used in ecotoxicological studies; therefore the assembly of a baseline transcriptome is important for subsequent analyses exploring the impact of toxin exposure on genome wide gene expression.  Results  This paper reports on the de novo transcriptome assembly of E. fetida using Trinity, a freely available software tool. Trinotate was used to carry out functional annotation of the Trinity generated transcriptome file and the transdecoder generated peptide sequence file along with BLASTX, BLASTP and HMMER searches and were loaded into a Sqlite3 database. To identify differentially expressed...
Tipo: Journal article
Palavras-chave: Earthworm; Trinity; Transcriptome; E. fetida; Ecotoxicology; RNA; Sequence; Gene expression.
Ano: 2017
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602017000100401