Fine mapping of Restorer-of-fertility in pepper (Capsicum
... The majority of cloned Rf genes are members of the pentatricopeptide repeat (PPR) gene family. Through genetic mapping, co-segregation of PPR genes with Rf has also been identified in several crops including sorghum, Mimulus, and maize (CMS-S) (Barr and Fishman 2010; Klein et al. 2005; Xu et al. 200 ...
... The majority of cloned Rf genes are members of the pentatricopeptide repeat (PPR) gene family. Through genetic mapping, co-segregation of PPR genes with Rf has also been identified in several crops including sorghum, Mimulus, and maize (CMS-S) (Barr and Fishman 2010; Klein et al. 2005; Xu et al. 200 ...
ATP16 Genes and Neighboring ORFs Are Duplicated on
... enzymes, EcoRI, BamHI, HindIII, SalI, PvuII, PstI, XbaI, NcoI, and SphI. In the gene disruption experiments, the undisrupted ATP16 (YDL004w, 1.0 kb) was detected in all laboratory strains used in this study, but some His+-transformants yielded undisrupted ATP16 (YDL004w, 1.0 kb) in addition to the d ...
... enzymes, EcoRI, BamHI, HindIII, SalI, PvuII, PstI, XbaI, NcoI, and SphI. In the gene disruption experiments, the undisrupted ATP16 (YDL004w, 1.0 kb) was detected in all laboratory strains used in this study, but some His+-transformants yielded undisrupted ATP16 (YDL004w, 1.0 kb) in addition to the d ...
Identification of a Novel Streptococcal Gene
... of mutagenic DNA repair. For example, in Streptococcus pyogenes, essential DnaE has been characterized as a highly errorprone DNA polymerase capable of TLS in vitro (11). Recently, Streptococcus pneumoniae cells were shown to respond, upon exposure to the DNA-damaging agent mitomycin C, by RecAdepen ...
... of mutagenic DNA repair. For example, in Streptococcus pyogenes, essential DnaE has been characterized as a highly errorprone DNA polymerase capable of TLS in vitro (11). Recently, Streptococcus pneumoniae cells were shown to respond, upon exposure to the DNA-damaging agent mitomycin C, by RecAdepen ...
Prioritizing curation of mouse genes by paucity of annotations and
... Our goal is to achieve comprehensive annotation of ciliary genes in the laboratory mouse based on experimental data by mid 2015. Based on our early results, we were able to annotate some genes that were not associated in the Mouse Genome Database (MGD) with literature tagged to be curated for Gene O ...
... Our goal is to achieve comprehensive annotation of ciliary genes in the laboratory mouse based on experimental data by mid 2015. Based on our early results, we were able to annotate some genes that were not associated in the Mouse Genome Database (MGD) with literature tagged to be curated for Gene O ...
Features and phylogeny of the six compared Plasmodium genomes
... [PlasmoDB, news item from Feb 1, 2008]. Indeed, the first in-depth sequencing-based analysis of the P. falciparum transcriptome using high-throughput sequencing (RNA-Seq) led to the revision of only one out of ten gene models and could not find evidence for new protein-coding genes [5]. Thus, P. fal ...
... [PlasmoDB, news item from Feb 1, 2008]. Indeed, the first in-depth sequencing-based analysis of the P. falciparum transcriptome using high-throughput sequencing (RNA-Seq) led to the revision of only one out of ten gene models and could not find evidence for new protein-coding genes [5]. Thus, P. fal ...
Sequence analysis of three mitochondrial DNA molecules reveals
... exonic ORFs (the eight structural genes only) is 79.6 and 77.5%, respectively. VAR1 differs from the average by having an A+T content at 94.2%, and ATP9 differs by having only 65.8% A+T. The intronic ORF encoded by S.castellii COX1.2 has an A+T content (76.9%) close to the average. For S.servazzii, ...
... exonic ORFs (the eight structural genes only) is 79.6 and 77.5%, respectively. VAR1 differs from the average by having an A+T content at 94.2%, and ATP9 differs by having only 65.8% A+T. The intronic ORF encoded by S.castellii COX1.2 has an A+T content (76.9%) close to the average. For S.servazzii, ...
New Perspectives on Rickettsial Evolution from New
... A wide variety of repetitive sequence elements are found in bacteria. These range from duplicated genes which exhibit varying degrees of homology like the ATP/ADP translocase genes, proline-betaine transporters, and sca gene families in Rickettsia, to the small palindromic repeat elements which are ...
... A wide variety of repetitive sequence elements are found in bacteria. These range from duplicated genes which exhibit varying degrees of homology like the ATP/ADP translocase genes, proline-betaine transporters, and sca gene families in Rickettsia, to the small palindromic repeat elements which are ...
12859_2006_1447_MOESM4_ESM
... 65,960 introns. A keyword search as well as a BLAST search is available. Submission of the gene DDR1 did not yield any results. Submission of the Affymetrix probe also did not yield results. The database can be downloaded in whole for high-throughput analysis. The Xpro (http://origin.bic.nus.edu.sg ...
... 65,960 introns. A keyword search as well as a BLAST search is available. Submission of the gene DDR1 did not yield any results. Submission of the Affymetrix probe also did not yield results. The database can be downloaded in whole for high-throughput analysis. The Xpro (http://origin.bic.nus.edu.sg ...
High-resolution mapping of the leaf rust disease resistance gene Lr1
... large and small grass genomes (Feuillet and Keller 1999). Therefore, gene-rich regions in the wheat genome may be amenable to molecular manipulations as are the small genomes of plants such as rice (Faris et al. 2000). The leaf rust disease resistance gene 1 (Lr1) described by Ausemus et al. (1946) ...
... large and small grass genomes (Feuillet and Keller 1999). Therefore, gene-rich regions in the wheat genome may be amenable to molecular manipulations as are the small genomes of plants such as rice (Faris et al. 2000). The leaf rust disease resistance gene 1 (Lr1) described by Ausemus et al. (1946) ...
PDF
... At first, such a model seems to be in contradiction to some observations that suggest that, in some systeffiS, posterior body parts can regenerate anterior portions (e.g.Slack, 1980). However, it is not clear whether, in these particular cases, anterior regeneration does require posterior cells (as ...
... At first, such a model seems to be in contradiction to some observations that suggest that, in some systeffiS, posterior body parts can regenerate anterior portions (e.g.Slack, 1980). However, it is not clear whether, in these particular cases, anterior regeneration does require posterior cells (as ...
Polygenic inheritance and micro/minisatellites
... Figure 1 Illustrative examples of the association between alleles of repeat polymorphisms at a variety of genes and quantitative behavioral traits. (a) Monoamine oxidase A gene (MAOA) and VNTR polymorphism alleles divided into four groups. There was a significant association with a number of quantit ...
... Figure 1 Illustrative examples of the association between alleles of repeat polymorphisms at a variety of genes and quantitative behavioral traits. (a) Monoamine oxidase A gene (MAOA) and VNTR polymorphism alleles divided into four groups. There was a significant association with a number of quantit ...
Genetics 184 - Ronin Genetics
... from the discovery of mobile DNA elements. (By coincidence, the research to be described was carried out independently by the late Burke Judd and by the author with only trivial differences. We used different w alleles and different mobile elements. Because I am more familiar with my own research, I ...
... from the discovery of mobile DNA elements. (By coincidence, the research to be described was carried out independently by the late Burke Judd and by the author with only trivial differences. We used different w alleles and different mobile elements. Because I am more familiar with my own research, I ...
Paper
... Li et al. (Research Articles, 1 July 2011, p. 53; published online 19 May 2011) reported more than 10,000 mismatches between messenger RNA and DNA sequences from the same individuals, which they attributed to previously unrecognized mechanisms of gene regulation. We found that at least 88% of these ...
... Li et al. (Research Articles, 1 July 2011, p. 53; published online 19 May 2011) reported more than 10,000 mismatches between messenger RNA and DNA sequences from the same individuals, which they attributed to previously unrecognized mechanisms of gene regulation. We found that at least 88% of these ...
Is it Good to Share? The Parallel between Information
... Vertical and Horizontal Transmission Vertical Transmission – from a parent Natural Selection works by Vertical Transmission of Genes: A gene increases fitness of an organism. The organism multiplies more rapidly. The gene is passed to the offspring. The gene increases in frequency. Conversely, bad ...
... Vertical and Horizontal Transmission Vertical Transmission – from a parent Natural Selection works by Vertical Transmission of Genes: A gene increases fitness of an organism. The organism multiplies more rapidly. The gene is passed to the offspring. The gene increases in frequency. Conversely, bad ...
towards synthetic plant genomes, transcriptomes and epigenomes
... However, figuratively, it seems that developing new synthetic biological tools can help pull synthetic biology itself out of the swamp by its own hair. During the last decade, the most widely used class of artificial tools was synthetic DNA-binding domains that consist of either proteins or protein ...
... However, figuratively, it seems that developing new synthetic biological tools can help pull synthetic biology itself out of the swamp by its own hair. During the last decade, the most widely used class of artificial tools was synthetic DNA-binding domains that consist of either proteins or protein ...
Supplementary Information 410 475
... Genetics Computer Group. (B) Percentages of similarity and percentages of identity (parentheses) between the various TSG sequences were obtained by alignment using the GAP program (Genetics Computer Group). The Drosophila melanogaster genome contains a gene product (CG12410) highly similar in sequen ...
... Genetics Computer Group. (B) Percentages of similarity and percentages of identity (parentheses) between the various TSG sequences were obtained by alignment using the GAP program (Genetics Computer Group). The Drosophila melanogaster genome contains a gene product (CG12410) highly similar in sequen ...
AGRA: analysis of gene ranking algorithms
... rows represent ranked genes with the most important gene on the top and the least important gene on the bottom of the list. Due to the calculation complexity and limitation of the FACTA+ system, the input file should contain maximum 7 different gene lists with maximum 100 genes in each list. When th ...
... rows represent ranked genes with the most important gene on the top and the least important gene on the bottom of the list. Due to the calculation complexity and limitation of the FACTA+ system, the input file should contain maximum 7 different gene lists with maximum 100 genes in each list. When th ...
Human housekeeping genes are compact
... Length analysis of HK genes Table 1 compares the lengths of various parts of the HK genes and the background genes. The alignment data was taken from the UCSC genome browser (http://genome. ucsc.edu) [16]. We excluded 322 genes that do not have a unique alignment, as well as 1242 genes that were not ...
... Length analysis of HK genes Table 1 compares the lengths of various parts of the HK genes and the background genes. The alignment data was taken from the UCSC genome browser (http://genome. ucsc.edu) [16]. We excluded 322 genes that do not have a unique alignment, as well as 1242 genes that were not ...
Characteristic Features of the Nucleotide Sequences of Yeast
... data of the three yeast chromosomal sequence data that have recently become available. In addition, the data for indicated. All four genes were predicted to be likely genes chromosomes III and V were extracted from the Gen- when the sc_cul.5 (order 5) matrix was used (Fig. la). In Bank database and ...
... data of the three yeast chromosomal sequence data that have recently become available. In addition, the data for indicated. All four genes were predicted to be likely genes chromosomes III and V were extracted from the Gen- when the sc_cul.5 (order 5) matrix was used (Fig. la). In Bank database and ...
Functional constraints and frequency of deleterious mutations in
... depends critically on the genomic deleterious mutation rate, U. For example, under a multiplicative model the load is 1 ⫺ e⫺U (where U is the mutation rate per diploid; ref. 4). The mutation load also depends on the manner in which mutations interact with one another between and within loci (4), and ...
... depends critically on the genomic deleterious mutation rate, U. For example, under a multiplicative model the load is 1 ⫺ e⫺U (where U is the mutation rate per diploid; ref. 4). The mutation load also depends on the manner in which mutations interact with one another between and within loci (4), and ...
Analysis of GDSL lipase (GLIP) family genes in rice (Oryza sativa)
... (Fig. 4), 8 were found to be up-regulated by more than 2-fold and 15 down-regulated at desiccation stress (Fig. 6 A, B). In 7-day-old rice shooting, genes were more sensitive to desiccation stress, 14 down- and 7 up-regulated significantly. Meantime, 7 genes were down-regulated and 2 induced in salt ...
... (Fig. 4), 8 were found to be up-regulated by more than 2-fold and 15 down-regulated at desiccation stress (Fig. 6 A, B). In 7-day-old rice shooting, genes were more sensitive to desiccation stress, 14 down- and 7 up-regulated significantly. Meantime, 7 genes were down-regulated and 2 induced in salt ...
deschamp_2009_sequencing
... Mapping SNP-containing HQ unitags to reference sequence (genome), using a k-mer table (k=length of trimmed tags), and find copy numbers and locations. Capturing single-copy HQ unitags with up to a single-base mismatch to the reference sequence at the exact location of the putative SNP site for one o ...
... Mapping SNP-containing HQ unitags to reference sequence (genome), using a k-mer table (k=length of trimmed tags), and find copy numbers and locations. Capturing single-copy HQ unitags with up to a single-base mismatch to the reference sequence at the exact location of the putative SNP site for one o ...
Life: The Science of Biology, 10e
... Promoters bind and orient RNA polymerase so that the correct DNA strand is transcribed. All promoters have consensus sequences that allow them to be recognized by RNA polymerase. Different classes of consensus sequences are recognized by regulatory proteins called sigma factors. ...
... Promoters bind and orient RNA polymerase so that the correct DNA strand is transcribed. All promoters have consensus sequences that allow them to be recognized by RNA polymerase. Different classes of consensus sequences are recognized by regulatory proteins called sigma factors. ...
Comparative day/night metatranscriptomic analysis of microbial
... based on abundance (35% of cell counts and 21% 16S rRNA of libraries), and may represent the most actively transcribing cells in this surface ocean community in both the day and night. Major heterotrophic taxa contributing to the community transcriptome included a-Proteobacteria (19% of annotated se ...
... based on abundance (35% of cell counts and 21% 16S rRNA of libraries), and may represent the most actively transcribing cells in this surface ocean community in both the day and night. Major heterotrophic taxa contributing to the community transcriptome included a-Proteobacteria (19% of annotated se ...
Genome Evolution in an Insect Cell: Distinct
... genetic distance under the maximum likelihood model used. This phylogeny strongly supports the following hypotheses: (i) a single origin of endosymbionts in the ancestor of the ant genera Camponotus, Colobopsis, and Polyrhachis, (ii) independent origins of symbiosis in the ants Formica and Plageolep ...
... genetic distance under the maximum likelihood model used. This phylogeny strongly supports the following hypotheses: (i) a single origin of endosymbionts in the ancestor of the ant genera Camponotus, Colobopsis, and Polyrhachis, (ii) independent origins of symbiosis in the ants Formica and Plageolep ...
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.