Practical: Ranges
... strand returns the strand information in a compact representation called a run-length encoding. The ‘names’ could have been specified when the instance was constructed; once named, the GRanges instance can be subset by name like a regular vector. As the GRanges function suggests, the GRanges class e ...
... strand returns the strand information in a compact representation called a run-length encoding. The ‘names’ could have been specified when the instance was constructed; once named, the GRanges instance can be subset by name like a regular vector. As the GRanges function suggests, the GRanges class e ...
A wide-range phylogenetic analysis of Zic proteins: Implications for
... and Urochordata. Interestingly, the ZOC domain was confined to the conserved class, not the diverged class (Figs. 2B and 3). Exon–intron organization of Zic genes reveals the existence of a single ancestral bilateralian Zic gene In our examination of genomic organization we focused on the exon–intro ...
... and Urochordata. Interestingly, the ZOC domain was confined to the conserved class, not the diverged class (Figs. 2B and 3). Exon–intron organization of Zic genes reveals the existence of a single ancestral bilateralian Zic gene In our examination of genomic organization we focused on the exon–intro ...
The Organellar Genome and Metabolic Potential
... organelles that are intimately associated with endosymbiotic methane–producing archaea that use the hydrogen produced by the organelles. Despite the hydrogenosomal metabolism of this organelle, we have found that it actually has a genome (Akhmanova, Voncken, van Alen, et al. 1998), that similar to m ...
... organelles that are intimately associated with endosymbiotic methane–producing archaea that use the hydrogen produced by the organelles. Despite the hydrogenosomal metabolism of this organelle, we have found that it actually has a genome (Akhmanova, Voncken, van Alen, et al. 1998), that similar to m ...
Quantitative genetics of gene expression during fruit fly - EMBL-EBI
... Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes, by exploiting naturally occurring genetic variation in large cohorts of individuals. More recently, the GWAS approach has also ...
... Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes, by exploiting naturally occurring genetic variation in large cohorts of individuals. More recently, the GWAS approach has also ...
Identifying key developments, issues and
... genome editing comprises a Cas9 endonuclease guided to its target sequence by a specifically designed guide RNA (gRNA) of around 20 base pairs. It is a naturally occurring system in prokaryotic (simple) cells 17 but works in both simple and more complex cells. 18 17. The CRISPR-Cas9 approach involve ...
... genome editing comprises a Cas9 endonuclease guided to its target sequence by a specifically designed guide RNA (gRNA) of around 20 base pairs. It is a naturally occurring system in prokaryotic (simple) cells 17 but works in both simple and more complex cells. 18 17. The CRISPR-Cas9 approach involve ...
Application of the new manP counter-selection system for B. subtilis
... the two repeats come together, the plasmid cannot be replicated (Altenbuchner et al., ...
... the two repeats come together, the plasmid cannot be replicated (Altenbuchner et al., ...
Nixon Evidence
... organisms selected in vitro have decreased levels of PFOR and a 6-kDa ferredoxin (51, 87), while antisense inhibition of PFOR mRNAs causes transfected giardia organisms to become metronidazole resistant (15). Metronidazole-resistant amebae show increased expression of iron-containing superoxide dism ...
... organisms selected in vitro have decreased levels of PFOR and a 6-kDa ferredoxin (51, 87), while antisense inhibition of PFOR mRNAs causes transfected giardia organisms to become metronidazole resistant (15). Metronidazole-resistant amebae show increased expression of iron-containing superoxide dism ...
Introduction: - Statistical Science
... 0.25. For example, the table shows the differences between phenotype label and gene tag permutations for the Gender dataset example. The large number of gene sets passing the test using gene tag permutations (38) is likely to include many false positives. This is an extreme case. In general the gene ...
... 0.25. For example, the table shows the differences between phenotype label and gene tag permutations for the Gender dataset example. The large number of gene sets passing the test using gene tag permutations (38) is likely to include many false positives. This is an extreme case. In general the gene ...
Genomic Analysis of Hox Clusters in the Sea Lamprey
... genes to Hox cognate groups, the complete homeodomain amino acid sequences from P. marinus were aligned with those from mouse and amphioxus. This alignment was then used in a neighbor-joining analysis resulting in the bootstrapped tree of Figure 3. The known mouse Hox gene cognates cluster together ...
... genes to Hox cognate groups, the complete homeodomain amino acid sequences from P. marinus were aligned with those from mouse and amphioxus. This alignment was then used in a neighbor-joining analysis resulting in the bootstrapped tree of Figure 3. The known mouse Hox gene cognates cluster together ...
Multiple Domains Exist within the Upstream Activator
... and sugar derivatives called opines. The inciting strain of Agrobacterium can utilize these opines as a carbon and sometimes a nitrogen source. Agrobacterium strains can be classified based upon their ability to catabolize particular opines. (For recent reviews of the crown gall tumorigenesis proces ...
... and sugar derivatives called opines. The inciting strain of Agrobacterium can utilize these opines as a carbon and sometimes a nitrogen source. Agrobacterium strains can be classified based upon their ability to catabolize particular opines. (For recent reviews of the crown gall tumorigenesis proces ...
Coordination of replication and transcription along a Drosophila
... arrays of cDNAs have demonstrated a correlation between time of replication and the probability that a specific gene is expressed, it remained to be determined what step(s) in the replication initiation process are influenced by transcription. Similarly, because the prior studies lacked contiguous i ...
... arrays of cDNAs have demonstrated a correlation between time of replication and the probability that a specific gene is expressed, it remained to be determined what step(s) in the replication initiation process are influenced by transcription. Similarly, because the prior studies lacked contiguous i ...
BROWSING GENES AND GENOMES WITH ENSEMBL
... and which strand of the genome is this gene located? How many transcripts (splice variants) have been annotated for it? (b) What is the longest transcript? How long is the protein it encodes? Has this transcript been annotated automatically (by Ensembl) or manually (by Havana)? How many exons does i ...
... and which strand of the genome is this gene located? How many transcripts (splice variants) have been annotated for it? (b) What is the longest transcript? How long is the protein it encodes? Has this transcript been annotated automatically (by Ensembl) or manually (by Havana)? How many exons does i ...
Transposon stability and a role for conjugational transfer in adaptive mutability
... cells as well as self-transfer between lacI33 bacteria. We found that TetR was frequently lost in episomal Lac⫹ revertant colonies that accumulate during selection with and without an imposed requirement for conjugal transfer. This loss was found many orders of magnitude more frequently than had bee ...
... cells as well as self-transfer between lacI33 bacteria. We found that TetR was frequently lost in episomal Lac⫹ revertant colonies that accumulate during selection with and without an imposed requirement for conjugal transfer. This loss was found many orders of magnitude more frequently than had bee ...
A method for fast database search for all k-nucleotide repeats
... number of repeats to balloon from 50 to hundreds or thousands [29]. Individuals with this defect su er from fragile-X mental retardation. Several other diseases are also now known to have their basis in huge expansions of di erent trinucleotide repeats [8, 17, 23]. Besides their importance in DNA fu ...
... number of repeats to balloon from 50 to hundreds or thousands [29]. Individuals with this defect su er from fragile-X mental retardation. Several other diseases are also now known to have their basis in huge expansions of di erent trinucleotide repeats [8, 17, 23]. Besides their importance in DNA fu ...
FEMS Microbiology Letters
... In the pyruvate clastic reaction [1], PFO catalyses the oxidative cleavage of pyruvate and coenzyme A to acetylcoenzyme A and CO2 with concomittant reduction of ferredoxin. The enzyme has been described for strictly anaerobic bacteria like Clostridium spp. [1], diverse archaea [2] and some eukaryote ...
... In the pyruvate clastic reaction [1], PFO catalyses the oxidative cleavage of pyruvate and coenzyme A to acetylcoenzyme A and CO2 with concomittant reduction of ferredoxin. The enzyme has been described for strictly anaerobic bacteria like Clostridium spp. [1], diverse archaea [2] and some eukaryote ...
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... characterized with terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes and the nucleotide sequence responsible for each terminal restriction fragment (T-RF) was determined by 16S rRNA gene cloning and sequencing [18]. Two major populations, one assigned to the genus ...
... characterized with terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes and the nucleotide sequence responsible for each terminal restriction fragment (T-RF) was determined by 16S rRNA gene cloning and sequencing [18]. Two major populations, one assigned to the genus ...
Recombination and clonal groupings within Helicobacter pylori from
... bacteria from different continents or that particular alleles are selected for in certain populations. However, a different segment of the vacA gene was found to have recombined freely in bacteria isolated from Canada and South Africa (Suerbaum et al ., 1998). The virulence-associated cagA gene enco ...
... bacteria from different continents or that particular alleles are selected for in certain populations. However, a different segment of the vacA gene was found to have recombined freely in bacteria isolated from Canada and South Africa (Suerbaum et al ., 1998). The virulence-associated cagA gene enco ...
A global picture of tRNA genes in plant genomes
... annotated a few genes or pseudogenes that were misannotated, correctly annotated numerous non-expressed mitochondrial or plastidial tDNA sequences inserted into the nuclear genome and recognized by tRNAscan-SE, re-annotated some tRNAs in terms of amino acid and codon recognition due to the presence ...
... annotated a few genes or pseudogenes that were misannotated, correctly annotated numerous non-expressed mitochondrial or plastidial tDNA sequences inserted into the nuclear genome and recognized by tRNAscan-SE, re-annotated some tRNAs in terms of amino acid and codon recognition due to the presence ...
Origin and Distribution of Calvin Cycle Fructose and
... streptophytes), rhodophytes and representatives of all lineages of complex algae including a cryptophyte (Guillardia), a haptophyte (Emiliania), two heterokonts (Thalassiosira, Phaeodactylum), two dinoflagellates (Lingulodinium, Amphidinium), a chlorarachniophyte (Bigelowiella), and a euglenophyte ( ...
... streptophytes), rhodophytes and representatives of all lineages of complex algae including a cryptophyte (Guillardia), a haptophyte (Emiliania), two heterokonts (Thalassiosira, Phaeodactylum), two dinoflagellates (Lingulodinium, Amphidinium), a chlorarachniophyte (Bigelowiella), and a euglenophyte ( ...
First genomic insights into members of a candidate bacterial
... issues have emerged such as the sudden washout of granular sludge biomass due to overgrowth of filamentous bacteria (bulking), which can lead to complete loss of performance. Bulking of anaerobic digestion systems can be caused by a variety of filamentous microorganisms (Hulshoff Pol et al., 2004; ...
... issues have emerged such as the sudden washout of granular sludge biomass due to overgrowth of filamentous bacteria (bulking), which can lead to complete loss of performance. Bulking of anaerobic digestion systems can be caused by a variety of filamentous microorganisms (Hulshoff Pol et al., 2004; ...
Large-scale Analysis of Pseudogenes in the Human Genome
... pseudogenes (also called processed pseudogenes). Duplicated pseudogenes arose from tandem duplication or unequal crossing-over, thus they often have retained the original exon-intron structures of the parental genes, though sometimes incompletely. In contrast, retrotransposed pseudogenes were create ...
... pseudogenes (also called processed pseudogenes). Duplicated pseudogenes arose from tandem duplication or unequal crossing-over, thus they often have retained the original exon-intron structures of the parental genes, though sometimes incompletely. In contrast, retrotransposed pseudogenes were create ...
Extrapolation to the whole human genome
... Main non-processed pseudogene populations We examined the non-processed pseudogene populations for chromosomes 21 and 22 for their prevalent functional classes and compared them to the classes for genes predicted using GenomeScan (Yeh et al., 2001). The total number of InterPro motif assignments and ...
... Main non-processed pseudogene populations We examined the non-processed pseudogene populations for chromosomes 21 and 22 for their prevalent functional classes and compared them to the classes for genes predicted using GenomeScan (Yeh et al., 2001). The total number of InterPro motif assignments and ...
... gene dose determination by quantitative real-time PCR. The high similarity in the genome structures of the S. cerevisiae ⴛ S. kudriavzevii hybrids under study indicates that they originated from a single hybridization event. After hybridization, the hybrid genome underwent extensive chromosomal rear ...
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... The presence of a copper-containing dissimilatory nitrite reductase gene (nirK) was discovered in several isolates of -subdivision ammonia-oxidizing bacteria using PCR and DNA sequencing. PCR primers Cunir3 and Cunir4 were designed based on published nirK sequences from denitrifying bacteria and us ...
... The presence of a copper-containing dissimilatory nitrite reductase gene (nirK) was discovered in several isolates of -subdivision ammonia-oxidizing bacteria using PCR and DNA sequencing. PCR primers Cunir3 and Cunir4 were designed based on published nirK sequences from denitrifying bacteria and us ...
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.