ELMER: An R/Bioconductor Tool Inferring Regulatory Element
... DNA methyaltion data feeding to ELMER should be a matrix of DNA methylation beta (β) value for samples (column) and probes (row) processed from row HM450K array data. If TCGA data were used, level 3 processed data from TCGA website will be downloaded and automatically transformed to the matrix by EL ...
... DNA methyaltion data feeding to ELMER should be a matrix of DNA methylation beta (β) value for samples (column) and probes (row) processed from row HM450K array data. If TCGA data were used, level 3 processed data from TCGA website will be downloaded and automatically transformed to the matrix by EL ...
Recent highlights of the China Rice Functional Genomics Program
... and its promoter, to produce stable transgenic lines with a range of reduced amylose contents. This trait has been incorporated into elite fertility restorer lines as well as cultivars commonly grown in China [23]. In addition, reliable transformation procedures have been developed for most recalcit ...
... and its promoter, to produce stable transgenic lines with a range of reduced amylose contents. This trait has been incorporated into elite fertility restorer lines as well as cultivars commonly grown in China [23]. In addition, reliable transformation procedures have been developed for most recalcit ...
Application of a Real Time Polymerase Chain Reaction Method to
... Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710 ...
... Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710 ...
Quantification and Classification1 - IC
... it has become clear that archaeal proteins split into those genes that were most similar to their bacterial homologs and that looked “eukaryotic” (24, 56, 70). Some exceptions notwithstanding, the bacterial and eukaryotic proteins in archaea were neatly divided along functional lines, with those inv ...
... it has become clear that archaeal proteins split into those genes that were most similar to their bacterial homologs and that looked “eukaryotic” (24, 56, 70). Some exceptions notwithstanding, the bacterial and eukaryotic proteins in archaea were neatly divided along functional lines, with those inv ...
Preliminary Examination of the Bacterial Diversity
... and plated on nutrient agar plates and incubated overnight at 37o C. After incubation, colonies were scored for morphological characteristics and subjected to a variety of biochemical tests. The results of these analyses revealed 65 unique isolates, four of which could not be sequenced. The 16s rRNA ...
... and plated on nutrient agar plates and incubated overnight at 37o C. After incubation, colonies were scored for morphological characteristics and subjected to a variety of biochemical tests. The results of these analyses revealed 65 unique isolates, four of which could not be sequenced. The 16s rRNA ...
Mycobacterium tuberculosis: Potassium uptake systems of
... of MTB and other mycobacterial species, some of which are clinically relevant in humans or animals, while others are non-pathogenic, are illustrated in Figure 1. Most of the mycobacterial species encode at least two trk (ceoBC) genes, which vary in size and orientation between species. Only ceoB and ...
... of MTB and other mycobacterial species, some of which are clinically relevant in humans or animals, while others are non-pathogenic, are illustrated in Figure 1. Most of the mycobacterial species encode at least two trk (ceoBC) genes, which vary in size and orientation between species. Only ceoB and ...
Extrachromosomal DNA Transformationof Caenorhabditis elegans
... amount of pBR322 hybridization expected for each worm DNA preparation if the plasmid sequences were present in one copy per genome (see Table 2). The percentage of transformed worms in each population was used to derive the copy number per genome per transformant. It should be noted that the copy nu ...
... amount of pBR322 hybridization expected for each worm DNA preparation if the plasmid sequences were present in one copy per genome (see Table 2). The percentage of transformed worms in each population was used to derive the copy number per genome per transformant. It should be noted that the copy nu ...
Positional dependence of transcriptional inhibition by DNA torsional
... telomere increased gradually towards the chromosomal end. At this time point, about half of the over-represented transcripts (445% of total, P ¼ 1.4 1095, w2 test) were from genes located at o50 kb from the telomere, a compartment that confines about 15% of yeast genes. Conversely, decreased tran ...
... telomere increased gradually towards the chromosomal end. At this time point, about half of the over-represented transcripts (445% of total, P ¼ 1.4 1095, w2 test) were from genes located at o50 kb from the telomere, a compartment that confines about 15% of yeast genes. Conversely, decreased tran ...
A B - Drug Metabolism and Disposition
... Inactivation of species-specific genes such as CYP2C76 could lead to a better animal model in monkeys. However, the techniques of gene knockout or knockdown in vivo, have not been available in this species (Norgren, 2004). Our results present an alternative way to produce animals lacking the functio ...
... Inactivation of species-specific genes such as CYP2C76 could lead to a better animal model in monkeys. However, the techniques of gene knockout or knockdown in vivo, have not been available in this species (Norgren, 2004). Our results present an alternative way to produce animals lacking the functio ...
Base-pair neutral homozygotes can be discriminated by calibrated
... by 2–88C and is easily detected by standard methods. This large Tm separation occurs with probes of 15–35 bases that are perfectly matched to one allele. High-resolution melting analysis of amplicons is an attractive genotyping method because it eliminates the need for oligonucleotide probes (4,5). ...
... by 2–88C and is easily detected by standard methods. This large Tm separation occurs with probes of 15–35 bases that are perfectly matched to one allele. High-resolution melting analysis of amplicons is an attractive genotyping method because it eliminates the need for oligonucleotide probes (4,5). ...
Lecture #7
... Small branches within a clade indicate sexual reproduction is ongoing within that group of individuals ...
... Small branches within a clade indicate sexual reproduction is ongoing within that group of individuals ...
The costs of environmental degradation in the Marine Strategy
... In this context, it is inappropriate to provide a TEV resulting from individual aggregated preferences,6 since that would be based on a different normative principle from the GES, namely the maximum of welfare. But it might seem meaningful to know the current maintenance costs devoted to marine envi ...
... In this context, it is inappropriate to provide a TEV resulting from individual aggregated preferences,6 since that would be based on a different normative principle from the GES, namely the maximum of welfare. But it might seem meaningful to know the current maintenance costs devoted to marine envi ...
Matrix-assisted laser desorption/ionisation time-of
... biovars by MALDI-TOF MS seems currently not to be reliable, since the available database of reference spectra and the routine analysis tools contain so far only one single strain for each biovar. Therefore, the generation of a database comprising several reference spectra for each of the four biova ...
... biovars by MALDI-TOF MS seems currently not to be reliable, since the available database of reference spectra and the routine analysis tools contain so far only one single strain for each biovar. Therefore, the generation of a database comprising several reference spectra for each of the four biova ...
introduction
... cytochrome oxidases typical of the mitochondrial genome (Feagin, 1992). Additionally, the 6kb linear genome encoded bacterial-type rRNAs which were different from those encoded by the 35kb circle (Feagin et aI., 1997). Sequence analysis revealed that the 35kb element was similar to chloroplast genom ...
... cytochrome oxidases typical of the mitochondrial genome (Feagin, 1992). Additionally, the 6kb linear genome encoded bacterial-type rRNAs which were different from those encoded by the 35kb circle (Feagin et aI., 1997). Sequence analysis revealed that the 35kb element was similar to chloroplast genom ...
Integrating genome and transcriptome resources into the TreeGenes
... Integrating Genome and Transcriptome Resources into TreeGenes Jill Wegrzyn David Neale Doreen Main Keithanne Mockaitis University of California at Davis Washington State University Indiana University/Center for Genomics and Bioinformatics ...
... Integrating Genome and Transcriptome Resources into TreeGenes Jill Wegrzyn David Neale Doreen Main Keithanne Mockaitis University of California at Davis Washington State University Indiana University/Center for Genomics and Bioinformatics ...
PDF ( 27 ) - DergiPark
... (Tcr) genes for 46 tetracycline- and 18 erythromycin-resistant isolates. Tcr gene sequence identity between different species of isolates was identified to investigate the dissemination of resistance genes. All of the 151 bacteria belonged to 4 different phyla: Proteobacteria, Bacteroidetes, Actinob ...
... (Tcr) genes for 46 tetracycline- and 18 erythromycin-resistant isolates. Tcr gene sequence identity between different species of isolates was identified to investigate the dissemination of resistance genes. All of the 151 bacteria belonged to 4 different phyla: Proteobacteria, Bacteroidetes, Actinob ...
Localization and structural analysis of the ribosomal RNA operons of
... E. coli rRNA operons. The fact that insertion of a cartridge resulted in the loss of the wild type signal, leads to the conclusion that there are only three rRNA operons in R. sphaeroides. Thus rmA can be assigned to the 10 kb BamYU signal, rrnB to the 14 kb BamYU signal, and rmC to the 13 kb BamYU ...
... E. coli rRNA operons. The fact that insertion of a cartridge resulted in the loss of the wild type signal, leads to the conclusion that there are only three rRNA operons in R. sphaeroides. Thus rmA can be assigned to the 10 kb BamYU signal, rrnB to the 14 kb BamYU signal, and rmC to the 13 kb BamYU ...
Real-time Quantification of HER2/neu Gene Amplification by
... The techniques used to evaluate the HER2/neu gene status have included gene-based assays such as Southern and slot blotting, in-situ hybridization (fluorescent and nonfluorescent) and PCR methods [7]. Each of the techniques mentioned has its advantages and disadvantages. In order to perform a fast p ...
... The techniques used to evaluate the HER2/neu gene status have included gene-based assays such as Southern and slot blotting, in-situ hybridization (fluorescent and nonfluorescent) and PCR methods [7]. Each of the techniques mentioned has its advantages and disadvantages. In order to perform a fast p ...
Analyses of human–chimpanzee orthologous gene
... model systems from the GenAge dataset (de Magalhaes et al., 2005). These genes are candidates for determinants of human longevity and aging, though none of them have been proven to play a causal role in human aging and the degree of evolutionary conservation in function of genes and pathways that co ...
... model systems from the GenAge dataset (de Magalhaes et al., 2005). These genes are candidates for determinants of human longevity and aging, though none of them have been proven to play a causal role in human aging and the degree of evolutionary conservation in function of genes and pathways that co ...
Guidelines for Human Gene Nomenclature (1997)
... gene) to which a name is being attached and then tracking the change of that concept over time. In one of the most thought-provoking talks for many participants, Carl Price (Rutgers) described the system of the Commission Plant Gene Nomenclature (CPGN) system. Angiosperms, with the ability and prope ...
... gene) to which a name is being attached and then tracking the change of that concept over time. In one of the most thought-provoking talks for many participants, Carl Price (Rutgers) described the system of the Commission Plant Gene Nomenclature (CPGN) system. Angiosperms, with the ability and prope ...
Semiconservative Replication in the Quasispecies Model
... As strand separation occurs, daughter strand synthesis is catalyzed via enzymes known as DNA replicases. However, due to errors in the base pairing process, σ is not necessarily paired with σ̄. Rather, once cell division is finished, the original σ is paired with some σ ′ , and similarly for σ̄. Eac ...
... As strand separation occurs, daughter strand synthesis is catalyzed via enzymes known as DNA replicases. However, due to errors in the base pairing process, σ is not necessarily paired with σ̄. Rather, once cell division is finished, the original σ is paired with some σ ′ , and similarly for σ̄. Eac ...
Complex Signatures of Natural Selection at the Duffy Blood Group
... candidates for use in the exploration of the effects of positive natural selection on patterns of linked neutral variation. Detection of the signature of natural selection requires one to distinguish between the effects of natural selection and those of population history. This is a particularly dif ...
... candidates for use in the exploration of the effects of positive natural selection on patterns of linked neutral variation. Detection of the signature of natural selection requires one to distinguish between the effects of natural selection and those of population history. This is a particularly dif ...
Type-2 fuzzy Approach for Disease-Associated Gene Identification on Microarrays Yan-Fei Wang
... word “different” itself is a fuzzy concept and fuzzy theory has many advantages in dealing with data containing uncertainty; therefore fuzzy approaches have been taken into consideration to analyze DNA microarrays. Liang et al. [1] proposed a fuzzy set theory based approach, namely a fuzzy membershi ...
... word “different” itself is a fuzzy concept and fuzzy theory has many advantages in dealing with data containing uncertainty; therefore fuzzy approaches have been taken into consideration to analyze DNA microarrays. Liang et al. [1] proposed a fuzzy set theory based approach, namely a fuzzy membershi ...
A Step-by-Step Tutorial: Divergence Time Estimation with
... calculated, there is no way MCMCTREE can tell what type of data was used to generate the in.BV file. We will now analyse the amino acid data set for the 23 fish species together with the tRNA and RNA genes (the last two partitions in the nucleotide data set). Copy the in.BV file from 12tr into AAtr. ...
... calculated, there is no way MCMCTREE can tell what type of data was used to generate the in.BV file. We will now analyse the amino acid data set for the 23 fish species together with the tRNA and RNA genes (the last two partitions in the nucleotide data set). Copy the in.BV file from 12tr into AAtr. ...
An S Receptor Kinase Gene in Self-Compatible
... 1988). To determine in which tissues the SRK-A10 gene was expressed, W1 and Westar RNA samples were analyzed by RNA PCR. As shown in Figure 4, the SRK-A10 gene is predominantly expressed in the pistils throughout bud development in both W1 and Westar RNA samples. This is the primary site of expressi ...
... 1988). To determine in which tissues the SRK-A10 gene was expressed, W1 and Westar RNA samples were analyzed by RNA PCR. As shown in Figure 4, the SRK-A10 gene is predominantly expressed in the pistils throughout bud development in both W1 and Westar RNA samples. This is the primary site of expressi ...
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use either ""shotgun"" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.