Statistical analysis of simple repeats in the human genome
... base pairs (bp) long, among which belong the Alu families. A link between homo- and dipolymeric tracts and mobile elements has been recently highlighted. In particular, the mobility of Alu repeats, which form 10% of the human genome, has been correlated with the length of poly(A) tracts located at o ...
... base pairs (bp) long, among which belong the Alu families. A link between homo- and dipolymeric tracts and mobile elements has been recently highlighted. In particular, the mobility of Alu repeats, which form 10% of the human genome, has been correlated with the length of poly(A) tracts located at o ...
Supplementary Figures (doc 9746K)
... FGFR2 are shown. From right to left, they are exon 7, exon 8, exon 9, and exon 10. Exon 8 is the IIIb-specific exon, whereas exon 9 is IIIc-specific. The blue exon peaks are the alignment results of normal RNA-Seq reads, while the yellow ones are from tumor reads. The arcs with numbers in them show ...
... FGFR2 are shown. From right to left, they are exon 7, exon 8, exon 9, and exon 10. Exon 8 is the IIIb-specific exon, whereas exon 9 is IIIc-specific. The blue exon peaks are the alignment results of normal RNA-Seq reads, while the yellow ones are from tumor reads. The arcs with numbers in them show ...
Alu - Environmental
... National Geographic articles on using the Y-chromosome to trace migration out of Africa ...
... National Geographic articles on using the Y-chromosome to trace migration out of Africa ...
Male-Biased Mutation Rate and Divergence in Autosomal, Z
... by use of ClustalW on default settings (Thompson, Higgins, and Gibson 1994), although some manual adjustment was required to improve the alignment of repetitive sequences. Pairwise distances were estimated by use of the baseml program in PAML version 3.11 (Yang 1997), with the Tamura-Nei (Tamura and ...
... by use of ClustalW on default settings (Thompson, Higgins, and Gibson 1994), although some manual adjustment was required to improve the alignment of repetitive sequences. Pairwise distances were estimated by use of the baseml program in PAML version 3.11 (Yang 1997), with the Tamura-Nei (Tamura and ...
Antisense Transcript and RNA Processing
... was required for viability but could not produce stable atpB transcripts. Based on strand-specific RT-PCR, S1 nuclease protection, and RNA gel blots, evidence was obtained that the PSþ genome stabilizes atpB mRNA by generating an atpB antisense transcript, which attenuates the degradation of the pol ...
... was required for viability but could not produce stable atpB transcripts. Based on strand-specific RT-PCR, S1 nuclease protection, and RNA gel blots, evidence was obtained that the PSþ genome stabilizes atpB mRNA by generating an atpB antisense transcript, which attenuates the degradation of the pol ...
Reference genome sequence of the model plant Setaria
... element classes, insertion dates were approximated for each element family (Supplementary Fig. 3). The data indicate a very recent burst of LTR retrotransposon amplification, peaking within the last few hundred thousand years, whereas the LINE and CACTA elements exhibit a broader range of activity o ...
... element classes, insertion dates were approximated for each element family (Supplementary Fig. 3). The data indicate a very recent burst of LTR retrotransposon amplification, peaking within the last few hundred thousand years, whereas the LINE and CACTA elements exhibit a broader range of activity o ...
here
... The Problem with Keeping the Current Classification Current classification is fundamentally anchored in a division that is not biologically based. This division artificially partitions the scientific community This situation leads to erroneous conclusions based on ...
... The Problem with Keeping the Current Classification Current classification is fundamentally anchored in a division that is not biologically based. This division artificially partitions the scientific community This situation leads to erroneous conclusions based on ...
Touring Ensembl: A practical guide to genome browsing Open Access
... [12-14]. Within only 200 bp upstream of the translational start site, binding sites for proteins such as NF-κB, AP-1, and NFAT (nuclear factor of activated T-cells), DNase I hypersensitive sites and a TATA box can all be found. These regions have been shown to be involved in the control of T-cell me ...
... [12-14]. Within only 200 bp upstream of the translational start site, binding sites for proteins such as NF-κB, AP-1, and NFAT (nuclear factor of activated T-cells), DNase I hypersensitive sites and a TATA box can all be found. These regions have been shown to be involved in the control of T-cell me ...
Chapter 18: Gene Mutation and DNA Repair
... Having discussed spontaneous mutations we now move on to induced mutations, which are those caused by environmental agents. These agents are called mutagens, and can be physical or chemical. As you proceed through this section, you should become familiar with the major classes of mutagens, which are ...
... Having discussed spontaneous mutations we now move on to induced mutations, which are those caused by environmental agents. These agents are called mutagens, and can be physical or chemical. As you proceed through this section, you should become familiar with the major classes of mutagens, which are ...
RecA maintains the integrity of chloroplast DNA molecules in
... nuclear genomes of many organisms, including plants (Lin et al., 2006). Repair and recombination of chloroplast DNA (cpDNA) in Chlamydomonas reinhardtii is suppressed when a dominant-negative version of E. coli RecA is targeted to chloroplasts (Cerutti et al., 1995). The prevalence of chloroplast-ta ...
... nuclear genomes of many organisms, including plants (Lin et al., 2006). Repair and recombination of chloroplast DNA (cpDNA) in Chlamydomonas reinhardtii is suppressed when a dominant-negative version of E. coli RecA is targeted to chloroplasts (Cerutti et al., 1995). The prevalence of chloroplast-ta ...
How were introns inserted into nuclear genes?
... removed in the course of evolution, there must be a long-term balance between removal and insertion. A consequence (regrettable from a Popperian point of view) is that in this situation one can give a probable explanation of any intron distribution but a definite explanation of none. But the operati ...
... removed in the course of evolution, there must be a long-term balance between removal and insertion. A consequence (regrettable from a Popperian point of view) is that in this situation one can give a probable explanation of any intron distribution but a definite explanation of none. But the operati ...
The Use of Cytochrome B Sequence Variation in Estimation of
... Wilson (1990), Johnsonand Cicero (199 l), Richman and Price (1992) and Lanyon (1992) mitochondrial variation was characterized through restriction fragment analysis. In the latter papers, cytochrome b sequence variation was used to estimate genetic variation. Cytochrome b is essential for the proper ...
... Wilson (1990), Johnsonand Cicero (199 l), Richman and Price (1992) and Lanyon (1992) mitochondrial variation was characterized through restriction fragment analysis. In the latter papers, cytochrome b sequence variation was used to estimate genetic variation. Cytochrome b is essential for the proper ...
Evolution of mating types driven by purifying selection
... develop the ability to recognize a universal mitochondrial marker protein, at the same time protecting its own organelles from degradation, e.g. by ceasing the expression of the marker in its own mitochondria (allele Um, Fig. 1b). I term this mechanism the “maternal” mode of UPI, and the gamete dest ...
... develop the ability to recognize a universal mitochondrial marker protein, at the same time protecting its own organelles from degradation, e.g. by ceasing the expression of the marker in its own mitochondria (allele Um, Fig. 1b). I term this mechanism the “maternal” mode of UPI, and the gamete dest ...
Caenorhabditis elegans chromosome arms are anchored to the
... found to be associated with large domains up to several megabases in length, which cover about 40% of the genome in mouse and human cells [6,7]. In flies, however, the size and the coverage of lamin-associated regions were not determined precisely because the cDNA microarrays used for detection cont ...
... found to be associated with large domains up to several megabases in length, which cover about 40% of the genome in mouse and human cells [6,7]. In flies, however, the size and the coverage of lamin-associated regions were not determined precisely because the cDNA microarrays used for detection cont ...
Gene transfer in bacteria - McGraw Hill Higher Education
... The E. coli genome was sequenced in 1997 Genome of K12 strain was sequenced ...
... The E. coli genome was sequenced in 1997 Genome of K12 strain was sequenced ...
—1— User Guide © Copyright 2009 Robert C. Edgar, all rights
... (inter) once for the entire genome, then the intra-chromosome simulator (intra) once for each chromosome. This process is called a cycle. The output from one cycle can be used as input to another cycle. It is generally better to run many short cycles rather than one or a few long cycles as longer cy ...
... (inter) once for the entire genome, then the intra-chromosome simulator (intra) once for each chromosome. This process is called a cycle. The output from one cycle can be used as input to another cycle. It is generally better to run many short cycles rather than one or a few long cycles as longer cy ...
Approaches to Repeat Finding
... Processed Pseudogenes, Retrotranscripts, SINES - Non-functional copies of RNA genes which have been reintegrated into the genome with the assitance of a reverse transcriptase. DNA Transposons Retrovirus Retrotransposons Non-Retrovirus Retrotransposons ( LINES ) ...
... Processed Pseudogenes, Retrotranscripts, SINES - Non-functional copies of RNA genes which have been reintegrated into the genome with the assitance of a reverse transcriptase. DNA Transposons Retrovirus Retrotransposons Non-Retrovirus Retrotransposons ( LINES ) ...
Participation of the proteasomal lid subunit Rpn11 in mitochondrial
... be hydrolytic enzymes for removal of ubiquitin or ubiquitin-like proteins from their targets. Thus Rpn11 partakes in removal of ubiquitin from substrates bound to the proteasome [11–13,28], and the CSN subunit Csn5/Jab1 is responsible for removal of the ubiquitin-like modifier Rub1/Nedd8 from the cu ...
... be hydrolytic enzymes for removal of ubiquitin or ubiquitin-like proteins from their targets. Thus Rpn11 partakes in removal of ubiquitin from substrates bound to the proteasome [11–13,28], and the CSN subunit Csn5/Jab1 is responsible for removal of the ubiquitin-like modifier Rub1/Nedd8 from the cu ...
transcription factor binding site
... approach that accounts for the ratio as well as the absoThis strand-specific pattern can be used for the optimal detection of enriched ...
... approach that accounts for the ratio as well as the absoThis strand-specific pattern can be used for the optimal detection of enriched ...
genetic introgression: an integral but neglected component of
... several hybrid zones are called “suture zones.” The Great Plains suture zone, where eastern and western Nearctic sister species come into contact, is one of the most important (e.g., Carling and Brumfield 2008, 2009; Mettler and Spellman 2009; Carling and Zuckerberg 2011; Carling et al. 2011). Many ...
... several hybrid zones are called “suture zones.” The Great Plains suture zone, where eastern and western Nearctic sister species come into contact, is one of the most important (e.g., Carling and Brumfield 2008, 2009; Mettler and Spellman 2009; Carling and Zuckerberg 2011; Carling et al. 2011). Many ...
Whole genome analyses using PopGenome and VCF files
... This module provides a wide range of FST as well as diversity measurenments. There exists two main classes. First, calculations which are either based on haplotypes mode=ḧaplotype¨ or second, the sequence based methods focussing on nucleotides mode="nucleotide". Note, be careful with haplotype base ...
... This module provides a wide range of FST as well as diversity measurenments. There exists two main classes. First, calculations which are either based on haplotypes mode=ḧaplotype¨ or second, the sequence based methods focussing on nucleotides mode="nucleotide". Note, be careful with haplotype base ...
Alu Human Polymorphism
... inherited from each parent – Most occurred millions of years ago and are often on both pairs of chromosomes – There are Alu elements that have occurred since humans branched from other primates – This gives rise to dimorphic Alus from the last hundreds of thousands of years – Estimated to jump 1:200 ...
... inherited from each parent – Most occurred millions of years ago and are often on both pairs of chromosomes – There are Alu elements that have occurred since humans branched from other primates – This gives rise to dimorphic Alus from the last hundreds of thousands of years – Estimated to jump 1:200 ...
An extreme cytoplasmic bottleneck in the modern European
... Burbank, possessed cpSSR haplotype A and comparisons with previous cpRFLP studies which included this cultivar (Hosaka & Hanneman 1988b; Waugh et al. 1990; Powell et al. 1993) con¢rm that the predominant A haplotype corresponds to the T-type cytoplasm. Between four and nine alleles were detected at ...
... Burbank, possessed cpSSR haplotype A and comparisons with previous cpRFLP studies which included this cultivar (Hosaka & Hanneman 1988b; Waugh et al. 1990; Powell et al. 1993) con¢rm that the predominant A haplotype corresponds to the T-type cytoplasm. Between four and nine alleles were detected at ...
Arabidopsis thaliana: A Model Plant for Genome Analysis
... Arabidopsis thaliana has recently become the organism of choice for a wide range of studies in plant sciences (1). The current visibility of Arabidopsis research reflects the growing realization among biologists that this simple angiosperm can serve as a convenient model not only for plant biology b ...
... Arabidopsis thaliana has recently become the organism of choice for a wide range of studies in plant sciences (1). The current visibility of Arabidopsis research reflects the growing realization among biologists that this simple angiosperm can serve as a convenient model not only for plant biology b ...
Pleistocene Speciation and the Mitochondrial DNA Clock
... of substitution estimated for the cytochrome b gene under the best-fit model (the gammaHKY85 model in each case) was 0.0278 and 0.0252 substitutions per site per lineage per My, respectively, or more than 2.5 times faster than the rate predicted by a 2% per My mtDNA clock (0.01 substitutions per sit ...
... of substitution estimated for the cytochrome b gene under the best-fit model (the gammaHKY85 model in each case) was 0.0278 and 0.0252 substitutions per site per lineage per My, respectively, or more than 2.5 times faster than the rate predicted by a 2% per My mtDNA clock (0.01 substitutions per sit ...