Conserved syntenic clusters of protein coding genes are missing in
... Results: Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian saurop ...
... Results: Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian saurop ...
Conserved syntenic clusters of protein coding genes are missing in birds
... many conserved genes that could not be found in the previous assembly (for example, [20]), and yielded significant BLAT-alignments for approximately 96% of genes from a positive control search set consisting of randomly selected lizard gene models with known orthologs in birds). Lastly, this subset ...
... many conserved genes that could not be found in the previous assembly (for example, [20]), and yielded significant BLAT-alignments for approximately 96% of genes from a positive control search set consisting of randomly selected lizard gene models with known orthologs in birds). Lastly, this subset ...
Phylogenetic Relationships between the Western Aster Yellows
... the basis of the presence and number of base pair matches, mismatches, and gaps in the compared sequences. Distance matrix (9, 36, 54) and maximum parsimony (25, 36, 54) analyses have been used to generate phylogenetic trees from aligned 16s rRNA sequences. The plant-pathogenic mycoplasmalike organi ...
... the basis of the presence and number of base pair matches, mismatches, and gaps in the compared sequences. Distance matrix (9, 36, 54) and maximum parsimony (25, 36, 54) analyses have been used to generate phylogenetic trees from aligned 16s rRNA sequences. The plant-pathogenic mycoplasmalike organi ...
RNA interference pathways display high rates of adaptive protein
... between C. nigoni and C. afra, and excluded regions that were greater than 6 standard deviations from the mean divergence. Published reference assemblies were not available for Apis cerana and Heliconius hecale. To generate outgroup sequences for these species we iteratively remapped reads (H. hecal ...
... between C. nigoni and C. afra, and excluded regions that were greater than 6 standard deviations from the mean divergence. Published reference assemblies were not available for Apis cerana and Heliconius hecale. To generate outgroup sequences for these species we iteratively remapped reads (H. hecal ...
A Pneumocystis carinii multi-gene family with
... EcoRI restriction endonuclease site incorporated at the 5' end to facilitate cloning of the amplification products into EcoRIdigested plasmid vectors pBluescript SK( - ) (Stratagene) or pUC18 (Pharmacia). The final concentration of the amplification reaction mix was 50 mM KCl, 10 mM Tris (pH 8-0), 0 ...
... EcoRI restriction endonuclease site incorporated at the 5' end to facilitate cloning of the amplification products into EcoRIdigested plasmid vectors pBluescript SK( - ) (Stratagene) or pUC18 (Pharmacia). The final concentration of the amplification reaction mix was 50 mM KCl, 10 mM Tris (pH 8-0), 0 ...
Expression of floricaula in single cell layers of
... may be involved in the genetic control of meristem behaviour. To investigate this possibility on a molecular level, it is important to know the expression pattern of the gene under study, both in wild type and in the chimeras. For example, is the gene normally expressed in one layer or in several, a ...
... may be involved in the genetic control of meristem behaviour. To investigate this possibility on a molecular level, it is important to know the expression pattern of the gene under study, both in wild type and in the chimeras. For example, is the gene normally expressed in one layer or in several, a ...
Predicting_tRNA_and_tmRNA_genes_12-2-16
... distant genomically from all the others within its genome found by the programs, or encoded on the opposite strand as all the others, or encoded within a ORF called by GeneMark or Glimmer that has high coding potential. In general, violation of either of the two latter of the three preceding conditi ...
... distant genomically from all the others within its genome found by the programs, or encoded on the opposite strand as all the others, or encoded within a ORF called by GeneMark or Glimmer that has high coding potential. In general, violation of either of the two latter of the three preceding conditi ...
The universal reagent for genome tailoring
... control that the remaining loxP site does not create a disturbance in the gene function after the selectable marker is removed. Interestingly, this allele without the marker removal (Fig. 3B) can provide a useful tool for learning more about the function of the gene of interest. If the marker was de ...
... control that the remaining loxP site does not create a disturbance in the gene function after the selectable marker is removed. Interestingly, this allele without the marker removal (Fig. 3B) can provide a useful tool for learning more about the function of the gene of interest. If the marker was de ...
Predicting tRNA and tmRNA genes Aragorn - SEA
... distant genomically from all the others within its genome found by the programs, or encoded on the opposite strand as all the others, or encoded within a ORF called by GeneMark or Glimmer that has high coding potential. In general, violation of either of the two latter of the three preceding conditi ...
... distant genomically from all the others within its genome found by the programs, or encoded on the opposite strand as all the others, or encoded within a ORF called by GeneMark or Glimmer that has high coding potential. In general, violation of either of the two latter of the three preceding conditi ...
RT-PCR Analysis - Shiu Lab - Michigan State University
... the largest hydrolase families (9, 10). PG activities have been shown to be associated with a wide range of plant developmental programs such as seed germination, organ abscission, pod and anther dehiscence, pollen grain maturation, xylem cell formation, and pollen tube growth (5, 11-13). Over-expre ...
... the largest hydrolase families (9, 10). PG activities have been shown to be associated with a wide range of plant developmental programs such as seed germination, organ abscission, pod and anther dehiscence, pollen grain maturation, xylem cell formation, and pollen tube growth (5, 11-13). Over-expre ...
A pair of Sox: distinct and overlapping functions of
... A pair of Sox: distinct and overlapping functions of zebrafish sox9 co-orthologs in craniofacial and pectoral fin development Yi-Lin Yan1,*, John Willoughby1,2,*, Dong Liu1, Justin Gage Crump1, Catherine Wilson1, Craig T. Miller1,3, Amy Singer1, Charles Kimmel1, Monte Westerfield1 and John H. Postle ...
... A pair of Sox: distinct and overlapping functions of zebrafish sox9 co-orthologs in craniofacial and pectoral fin development Yi-Lin Yan1,*, John Willoughby1,2,*, Dong Liu1, Justin Gage Crump1, Catherine Wilson1, Craig T. Miller1,3, Amy Singer1, Charles Kimmel1, Monte Westerfield1 and John H. Postle ...
factor occupancy and gene expression Effects of sequence variation
... A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this proble ...
... A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this proble ...
factor occupancy and gene expression Effects of
... A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this proble ...
... A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this proble ...
Analysis of Cross Sequence Similarities for Multiple - PolyU
... In Figure 2(a), a set of 12 nucleotides ‘ACGCTTACGCAT’ is a sample sequence. The subsequence ‘ACGCTT’ shown between 1 and 6 indicates the first six bases of the sample sequence while the subsequence ‘ACGCAT’ listed between 7 and 12 is the 7th to 12th bases of the sample sequence. The vertical line l ...
... In Figure 2(a), a set of 12 nucleotides ‘ACGCTTACGCAT’ is a sample sequence. The subsequence ‘ACGCTT’ shown between 1 and 6 indicates the first six bases of the sample sequence while the subsequence ‘ACGCAT’ listed between 7 and 12 is the 7th to 12th bases of the sample sequence. The vertical line l ...
factor occupancy and gene expression Effects of sequence variation
... A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this proble ...
... A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this proble ...
Conservation of Brachyury (T) genes in amphioxus and vertebrates
... transcripts are not detectable in cells fated to give rise to any non-notochordal cells. Hence, expression of Brachyury in notochord development preceded vertebrate origins; in contrast, expression in early mesoderm (other than notochord) probably evolved later. The data do not resolve whether this ...
... transcripts are not detectable in cells fated to give rise to any non-notochordal cells. Hence, expression of Brachyury in notochord development preceded vertebrate origins; in contrast, expression in early mesoderm (other than notochord) probably evolved later. The data do not resolve whether this ...
Epigenetic Interactions among Three dTph1 Transposons in Two
... By analyzing (phenotypic) reversions of unstable transposon insertion alleles, one can monitor the excisions of these transposons. Strikingly, P, Ac, and Tam insertion alleles appear to revert by different mechanisms in their cognate hosts (reviewed in Rommens et al., 1993). This may be due to diffe ...
... By analyzing (phenotypic) reversions of unstable transposon insertion alleles, one can monitor the excisions of these transposons. Strikingly, P, Ac, and Tam insertion alleles appear to revert by different mechanisms in their cognate hosts (reviewed in Rommens et al., 1993). This may be due to diffe ...
Two distinct teleost hepatocyte nuclear factor 1 genes, hnf1a/tcf1
... by using TRIZOL reagent (Invitrogen). Using 1 Ag of total RNA, the first-strand cDNAs (20 Al) were synthesized with oligo(dT) by SUPERSCRIPT III reverse transcriptase (Invitrogen) according to manufacturer’s protocol. After reverse transcription, 2-Al first-strand cDNAs were subjected to PCR by usin ...
... by using TRIZOL reagent (Invitrogen). Using 1 Ag of total RNA, the first-strand cDNAs (20 Al) were synthesized with oligo(dT) by SUPERSCRIPT III reverse transcriptase (Invitrogen) according to manufacturer’s protocol. After reverse transcription, 2-Al first-strand cDNAs were subjected to PCR by usin ...
Epigenetic Interactions among Three dTph1
... By analyzing (phenotypic) reversions of unstable transposon insertion alleles, one can monitor the excisions of these transposons. Strikingly, P, Ac, and Tam insertion alleles appear to revert by different mechanisms in their cognate hosts (reviewed in Rommens et al., 1993). This may be due to diffe ...
... By analyzing (phenotypic) reversions of unstable transposon insertion alleles, one can monitor the excisions of these transposons. Strikingly, P, Ac, and Tam insertion alleles appear to revert by different mechanisms in their cognate hosts (reviewed in Rommens et al., 1993). This may be due to diffe ...
Package ‘GenomicFeatures’ October 14, 2014
... For asBED, a GRanges, with the columns name, thickStart, thickEnd, blockStarts, blockSizes added. The thick regions correspond to the CDS regions, and the blocks represent the exons. The transcript IDs are stored in the name column. The ranges are the transcript bounds. For asGFF, a GRanges, with co ...
... For asBED, a GRanges, with the columns name, thickStart, thickEnd, blockStarts, blockSizes added. The thick regions correspond to the CDS regions, and the blocks represent the exons. The transcript IDs are stored in the name column. The ranges are the transcript bounds. For asGFF, a GRanges, with co ...
Isolation, Characterization, and Annotation: The Search for Novel
... to the host, penetrates the cell membrane and injects its DNA. The genetic information can then follow two potential paths. In the lysogenic cycle, the DNA is incorporated into the host genome as a prophage and remains a part of the host’s genome as long as conditions remain stable for the prophage. ...
... to the host, penetrates the cell membrane and injects its DNA. The genetic information can then follow two potential paths. In the lysogenic cycle, the DNA is incorporated into the host genome as a prophage and remains a part of the host’s genome as long as conditions remain stable for the prophage. ...
Amplification of 16S rRNA Genes from Frankia Strains in Root
... Root nodules. The sources of the root nodules used in this study are listed in Table 1. In all cases the nodules were frozen at 2258C after collection or receipt at the University of Waikato. DNA isolation. Extreme care was used to avoid exogenous DNA in all solutions and during isolation of Frankia ...
... Root nodules. The sources of the root nodules used in this study are listed in Table 1. In all cases the nodules were frozen at 2258C after collection or receipt at the University of Waikato. DNA isolation. Extreme care was used to avoid exogenous DNA in all solutions and during isolation of Frankia ...
Evolution of Closely Linked Gene Pairs in
... of base pairs between the beginning and/or ends of the transcripts as annotated in Ensembl. In the better annotated genomes, this includes the 5# and 3# untranslated regions (UTR); in poorly annotated genomes, information about the UTRs may be incomplete, and the number of closely linked gene pairs ...
... of base pairs between the beginning and/or ends of the transcripts as annotated in Ensembl. In the better annotated genomes, this includes the 5# and 3# untranslated regions (UTR); in poorly annotated genomes, information about the UTRs may be incomplete, and the number of closely linked gene pairs ...
Comparative sequence analysis of the long repeat regions and
... sequence of herpes simplex virus type 1 (HSV-I) strain 17 (McGeoch et al., 1985, 1986, 1988; Perry & McGeoch, 1988). The 152 kbp sequence was interpreted as containing 70 distinct genes of which two, located in the major repeat elements of the genome, were present in two copies each. Many of the pro ...
... sequence of herpes simplex virus type 1 (HSV-I) strain 17 (McGeoch et al., 1985, 1986, 1988; Perry & McGeoch, 1988). The 152 kbp sequence was interpreted as containing 70 distinct genes of which two, located in the major repeat elements of the genome, were present in two copies each. Many of the pro ...
NIH Public Access
... The major features of the M. thermoacetica genome are listed in Table 1 and shown in Supplementary Figure S1. The genome consists of a single circular 2,628,784 bp chromosome that has a GC content of 56 % (Supplementary Figure S1). Base pair one of the chromosome was assigned within the putative ori ...
... The major features of the M. thermoacetica genome are listed in Table 1 and shown in Supplementary Figure S1. The genome consists of a single circular 2,628,784 bp chromosome that has a GC content of 56 % (Supplementary Figure S1). Base pair one of the chromosome was assigned within the putative ori ...
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.