WheatNet: A genome-scale functional network for hexaploid bread
... genome-scale network, which facilitates the prediction of novel candidate genes for a trait, can be constructed. Network-based predictions have been useful in the model plant Arabidopsis thaliana (Lee et al., 2010). However, such a predictive gene network is not yet available for bread wheat, Tritic ...
... genome-scale network, which facilitates the prediction of novel candidate genes for a trait, can be constructed. Network-based predictions have been useful in the model plant Arabidopsis thaliana (Lee et al., 2010). However, such a predictive gene network is not yet available for bread wheat, Tritic ...
The molecular evolution of development
... the HOM/Hox genes in the arthropod Drosophila melanogaster, the vertebrates Homo sapiens and Mus musculus, the cephalochordate Amphioxus and the nematode Caenorhabditis elegans (Fig. 1), Zhang and Nei(24) suggest that extant members of the HOM/Hox gene family were derived not from three precursors, ...
... the HOM/Hox genes in the arthropod Drosophila melanogaster, the vertebrates Homo sapiens and Mus musculus, the cephalochordate Amphioxus and the nematode Caenorhabditis elegans (Fig. 1), Zhang and Nei(24) suggest that extant members of the HOM/Hox gene family were derived not from three precursors, ...
10709_2015_9875_MOESM4_ESM
... Thus, we repeated our key chemogenetic and GI network analyses with datasets from this study. Unfortunately, the results based on the Deutschbauer et al. datasets are not in agreement with the results observed for the Pir et al. dataset. We analyzed the Deutschbauer et al. datasets thoroughly and sp ...
... Thus, we repeated our key chemogenetic and GI network analyses with datasets from this study. Unfortunately, the results based on the Deutschbauer et al. datasets are not in agreement with the results observed for the Pir et al. dataset. We analyzed the Deutschbauer et al. datasets thoroughly and sp ...
Correlation between sequence divergence and polymorphism
... level of repeats [29]. The plastid genomes of the Campanulaceae family have also been found to contain many inversions [13,14,29]. Likely this propensity for structural instability explains why mapping C. americanum reads to T. caeruleum’s plastid genome was not helpful in further assembly of C. ame ...
... level of repeats [29]. The plastid genomes of the Campanulaceae family have also been found to contain many inversions [13,14,29]. Likely this propensity for structural instability explains why mapping C. americanum reads to T. caeruleum’s plastid genome was not helpful in further assembly of C. ame ...
TTEST – Between subjects
... SAM -2 • SAM gives estimates of the False Discovery Rate (FDR), which is the proportion of genes likely to have been wrongly identified by chance as being significant. • It is a very interactive algorithm – allows users to dynamically change thresholds for significance (through the tuning parameter ...
... SAM -2 • SAM gives estimates of the False Discovery Rate (FDR), which is the proportion of genes likely to have been wrongly identified by chance as being significant. • It is a very interactive algorithm – allows users to dynamically change thresholds for significance (through the tuning parameter ...
Rice Bioinformatics. Analysis of Rice Sequence Data and
... that represent diverse physiological and developmental programs, complete genomic sequencing is unlikely to be completed in the foreseeable future. Thus, sequencing of ESTs remains the primary tool for genomic exploration and for functional genomics analyses. The value of EST resources can be greatl ...
... that represent diverse physiological and developmental programs, complete genomic sequencing is unlikely to be completed in the foreseeable future. Thus, sequencing of ESTs remains the primary tool for genomic exploration and for functional genomics analyses. The value of EST resources can be greatl ...
Theoretical and Applied Genetics
... effective method to control this disease in canola production. In particular, blackleg resistance is considered as one of the most important traits in the canola breeding programs of all seed companies in Canada, Europe and Australia. Mapping blackleg resistance genes and eventually cloning these ge ...
... effective method to control this disease in canola production. In particular, blackleg resistance is considered as one of the most important traits in the canola breeding programs of all seed companies in Canada, Europe and Australia. Mapping blackleg resistance genes and eventually cloning these ge ...
Gene Expression Programming: A New Adaptive
... The flowchart of a gene expression algorithm (GEA) is shown in Figure 1. The process begins with the random generation of the chromosomes of the initial population. Then the chromosomes are expressed and the fitness of each individual is evaluated. The individuals are then selected according to fitn ...
... The flowchart of a gene expression algorithm (GEA) is shown in Figure 1. The process begins with the random generation of the chromosomes of the initial population. Then the chromosomes are expressed and the fitness of each individual is evaluated. The individuals are then selected according to fitn ...
Aucun titre de diapositive - Universidad Nacional De Colombia
... trEST is an attempt to produce contigs from clusters of ESTs and to translate them into proteins. trEST uses UniGene clusters and clusters produced from inhouse software. To assemble clusters trEST uses Phrap and CAP3 algorithms. Contigs produced by the assembling step are translated into protein se ...
... trEST is an attempt to produce contigs from clusters of ESTs and to translate them into proteins. trEST uses UniGene clusters and clusters produced from inhouse software. To assemble clusters trEST uses Phrap and CAP3 algorithms. Contigs produced by the assembling step are translated into protein se ...
Multiple Mechanisms Contribute to Lateral Transfer of an
... et al. 2011), and a 7 kb region around the opd gene apparently constituted the only identity between these two dissimilar plasmids (Mulbry et al. 1986; Pandeeti et al. 2011; Siddavattam et al. 2003). However the sequence of the opd gene cluster in the self-transmissible pCMS1 showed no features of a ...
... et al. 2011), and a 7 kb region around the opd gene apparently constituted the only identity between these two dissimilar plasmids (Mulbry et al. 1986; Pandeeti et al. 2011; Siddavattam et al. 2003). However the sequence of the opd gene cluster in the self-transmissible pCMS1 showed no features of a ...
1 Transcription in eukaryotes Eukaryotic RNA polymerases
... But: It was not yet possible to reconstitute RNA polymerase from separate subunits •Another option: find genes for all putative subunits, mutate them and look for the function. All the genes were discovered, cloned and sequenced. They clone for 12 putative subunits of yeast polymerase II. Each of po ...
... But: It was not yet possible to reconstitute RNA polymerase from separate subunits •Another option: find genes for all putative subunits, mutate them and look for the function. All the genes were discovered, cloned and sequenced. They clone for 12 putative subunits of yeast polymerase II. Each of po ...
Nucleotide Sequence and Organization of the Rat Heme Oxygenase
... which contains two copies of core sequences of metal regulatory elements found in metallothionein genes (34). However, the heme oxygenase gene contains no heme-responsive element of the yeast iso-1-cytochrome c gene (17). We are particularly interested in the presence of a heat shock element because ...
... which contains two copies of core sequences of metal regulatory elements found in metallothionein genes (34). However, the heme oxygenase gene contains no heme-responsive element of the yeast iso-1-cytochrome c gene (17). We are particularly interested in the presence of a heat shock element because ...
SGD: Saccharomyces Genome Database.
... Sequence Similarity View and Stripe View. Pattern Matching, Sequence Similarity View and Stripe View are all programs created by SGD staff. Pattern Matching allows users to perform a variety of motif searches, using degenerate search sequences. Sequence Similarity View and Stripe View provide a visu ...
... Sequence Similarity View and Stripe View. Pattern Matching, Sequence Similarity View and Stripe View are all programs created by SGD staff. Pattern Matching allows users to perform a variety of motif searches, using degenerate search sequences. Sequence Similarity View and Stripe View provide a visu ...
An Investigation of Codon Usage Bias Including
... in translating the mRNA transcripts into the protein macromolecules. When the codon associated with the highest tRNA abundance is utilized, efficiencies in translation can be realized due to the higher relative availability. Biases associated with translational efficiency are not the only biases fou ...
... in translating the mRNA transcripts into the protein macromolecules. When the codon associated with the highest tRNA abundance is utilized, efficiencies in translation can be realized due to the higher relative availability. Biases associated with translational efficiency are not the only biases fou ...
Evolution of antifreeze glycoprotein gene from a trypsinogen gene in
... of notothenioid trypsinogen cDNA (accession no. U58945) and gene (accession no. U58835) are shown in Figs. 1 C and D, respectively. The intronyexon boundaries were established by comparing the two sequences. The trypsinogen gene contains six exons (E1-E6) and five introns (I1-I5). Exon 1 encodes a 2 ...
... of notothenioid trypsinogen cDNA (accession no. U58945) and gene (accession no. U58835) are shown in Figs. 1 C and D, respectively. The intronyexon boundaries were established by comparing the two sequences. The trypsinogen gene contains six exons (E1-E6) and five introns (I1-I5). Exon 1 encodes a 2 ...
splicing
... genetic change to the sequence of the DNA • Although it is every bit as important as a genetic change because it can cause the silencing of a gene or even heterochromatization of a whole region of a chromosome ...
... genetic change to the sequence of the DNA • Although it is every bit as important as a genetic change because it can cause the silencing of a gene or even heterochromatization of a whole region of a chromosome ...
Structural Domains and Matrix Attachment Regions
... genes are located ⵑ140 kb apart (Civardi et al., 1994), separated by blocks of repeats of retroelements (P. SanMiguel, unpublished observations), whereas no large repeats were found in the orthologous regions of sorghum and rice (Chen and Bennetzen, 1996; Chen et al., 1997). Given the established im ...
... genes are located ⵑ140 kb apart (Civardi et al., 1994), separated by blocks of repeats of retroelements (P. SanMiguel, unpublished observations), whereas no large repeats were found in the orthologous regions of sorghum and rice (Chen and Bennetzen, 1996; Chen et al., 1997). Given the established im ...
Non-Mendelian inheritance
... mtDNAs occur in all aerobic eukaryotic cells and generate energy for cell function by oxidative phosphorylation (OXPHOS) producing ATP. ...
... mtDNAs occur in all aerobic eukaryotic cells and generate energy for cell function by oxidative phosphorylation (OXPHOS) producing ATP. ...
Control of Chromosome Pairing and Genome Evolution in Disomic
... the parents? Why do the F5s sometimes differ from the F2s? All of their data are summarized in Table 1. They suggested the following mechanisms for the observed results: They suggested the following mechanisms for the observed results: “The changes we observed could have resulted from several differ ...
... the parents? Why do the F5s sometimes differ from the F2s? All of their data are summarized in Table 1. They suggested the following mechanisms for the observed results: They suggested the following mechanisms for the observed results: “The changes we observed could have resulted from several differ ...
Identifying a Novel Isoform of the AZIN1 Gene by Combining High
... reading frame that would change the terminus of the subsequent protein from Ser-Asp-Glu-Asp-stop to PheArg-stop. Follow-up studies could validate this finding on the protein level and then measure gene expression of this new isoform in various tissues, subjects, and time-points. Moreover, the method ...
... reading frame that would change the terminus of the subsequent protein from Ser-Asp-Glu-Asp-stop to PheArg-stop. Follow-up studies could validate this finding on the protein level and then measure gene expression of this new isoform in various tissues, subjects, and time-points. Moreover, the method ...
not a plastid specific promoter but is also capable of
... indicated that either the psbA promoter is not plastid specific but is recognized by the RNA polymerase II transcription complex as well, or that the regions upstream from the psbA promoter located either on the T-DNA or on the plant nuclear genome, contain an RNA polymerase II transcription start s ...
... indicated that either the psbA promoter is not plastid specific but is recognized by the RNA polymerase II transcription complex as well, or that the regions upstream from the psbA promoter located either on the T-DNA or on the plant nuclear genome, contain an RNA polymerase II transcription start s ...
Genome-Wide Analysis of Core Cell Cycle Genes in
... other hand, no B1- or B2-like destruction box was detected. The phylogenetic position of this gene within the B cluster depended on the number of positions used for the analysis. Because cyclin sequences are known to be saturated with substitutions (Renaudin et al., 1996), a technique was applied to ...
... other hand, no B1- or B2-like destruction box was detected. The phylogenetic position of this gene within the B cluster depended on the number of positions used for the analysis. Because cyclin sequences are known to be saturated with substitutions (Renaudin et al., 1996), a technique was applied to ...
Conspiracy of silence among repeated transgenes
... comparable impact in agriculture and medicine. Researchers usually assume that an integrated transgene’s behavior reflects normal influences at the site of insertion. However, genomes have mechanisms for recognizing potentially threatening sequence elements, like transposons, and silencing them. Cyt ...
... comparable impact in agriculture and medicine. Researchers usually assume that an integrated transgene’s behavior reflects normal influences at the site of insertion. However, genomes have mechanisms for recognizing potentially threatening sequence elements, like transposons, and silencing them. Cyt ...
Ovation™ RNA Amplification System
... Approximately 20 ng of reverse transcribed RNA equivalents was loaded into each PCR well. For amplified product, 20 ng of total RNA was used to ...
... Approximately 20 ng of reverse transcribed RNA equivalents was loaded into each PCR well. For amplified product, 20 ng of total RNA was used to ...
Applied and Environmental Microbiology
... orf2110). Isolates of lineage I exhibit higher hemolytic and phospholipase activities on selective agars than those of lineage II (Fig. 3). ActA sequences of lineage II exhibit a high variability on the protein level (from 79.0% to 99.5% identity), resulting in six different actA subtypes (Fig. 1). ...
... orf2110). Isolates of lineage I exhibit higher hemolytic and phospholipase activities on selective agars than those of lineage II (Fig. 3). ActA sequences of lineage II exhibit a high variability on the protein level (from 79.0% to 99.5% identity), resulting in six different actA subtypes (Fig. 1). ...
Transposable element
A transposable element (TE or transposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.TEs make up a large fraction of the C-value of eukaryotic cells. There are at least two classes of TEs: class I TEs generally function via reverse transcription, while class II TEs encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. It has been shown that TEs are important in genome function and evolution. In Oxytricha, which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.