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Mutations at the Darkener of apricot Locus Modulate Transcript
Mutations at the Darkener of apricot Locus Modulate Transcript

... 1993; ZACHAR, CHoU and BINGHAM1987). In general, the products of second-site modifier loci play a role in the expression of the mutation-causing transposable element, and in modifying its activity, result in an alteration of the mutant phenotype. We are seeking to understand the functions these modi ...
PDF manual - QIAGEN Bioinformatics
PDF manual - QIAGEN Bioinformatics

... all entries in sequence lists where one or more of the reads is 56bp or longer. The mapping parameters are: • Maximum number of mismatches. This parameter is available if you have selected at least one sequence list containing only short reads (shorter than 56 nucleotides, except in the case of colo ...
Conservation and diversification of gene function during mouthpart
Conservation and diversification of gene function during mouthpart

... have been investigated in great detail during Drosophila leg development. Here, hth, dac, and Dll are expressed in antagonistic domains, which help establish the proximal– distal axis of the adult leg (reviewed in Kojima 2004). Specifically, the combinatorial interaction between hth and its cofactor ...
Genomic Sequence Data - G3: Genes | Genomes | Genetics
Genomic Sequence Data - G3: Genes | Genomes | Genetics

... the sequencing of novel viral genomes from metagenomic datasets and the targeted assembly of genes-of-interest from whole-genome datasets. The motivation for PRICE was to facilitate the assembly of individual genomes of interest using complex, shotgun, metagenomic datasets, derived from virtually a ...
Horizontal transfer generates genetic variation in an asexual
Horizontal transfer generates genetic variation in an asexual

... other strains, we examined the read mappings for the other strains at the two positions of VdLs17 supercontig 1.9. Only the sequence type TA (17; T and A were linked by 17 reads) was found in strain St.100, formed by the REF allele T (27) and a type 1 SNP G/A (0/22) at the positions, and only the se ...
Supporting Information Parfenov et al. 10.1073/pnas.1416074111
Supporting Information Parfenov et al. 10.1073/pnas.1416074111

... mean-centered the RPKM values and divided by their SD for each exon. The lengths of the composite exons were transformed using the square root of the length. DNA Methylation and mRNA Expression Analysis. The Infinium HM450k array was used for TCGA Head and Neck samples (13). This platform includes p ...
Molecular Evolution of Overlapping Genes
Molecular Evolution of Overlapping Genes

... Overlapping genes are defined as a pair of protein-coding genes whose coding regions overlap on either the same strand or on the opposite strand. The sequence interdependence between two overlapping coding regions adds complexity to almost all molecular evolution analyses. Here, I use a comparative- ...
as a PDF - CiteSeerX
as a PDF - CiteSeerX

... B-DNA versus non-B-DNA (51), and organization, can affect homologous recombination and is also likely to affect recombination between diverged DNAs. For example, altered semiconservative replication in yeast DNA polymerase mutants can increase homologous recombination severalfold in a variety of sys ...
Modeling Trabecular Microstructure Evolution via Genetic Algorithm by Samuel W. L. Shames
Modeling Trabecular Microstructure Evolution via Genetic Algorithm by Samuel W. L. Shames

... the same set of points under the same stress state at three stages of evolution. The figure shows how drastically the microstructure of the system can change in only a small number of generations and how the general tendency is for the number of struts with a large strain energy—bright red struts—to ...
Hox Genes: Let`s Work Together
Hox Genes: Let`s Work Together

... but not Abd-B. So, mir-iab-8 miRNA might indirectly help Abd-B function in Antp, Ubx and abd-A free background in PS 13 and 14. Knock-out of miRNAiab-4 and miRNA-iab-8 miRNAs leads to higher expression of anterior Hox genes in the domain of posterior Hox genes (Bender, 2008). This suggests that thes ...
Costimulatory receptors in jawed vertebrates: Conserved
Costimulatory receptors in jawed vertebrates: Conserved

... (Tetraodon nigroviridis) and zebrafish (Danio rerio). In zebrafish, it was not possible to find sequences corresponding to exons 3 and 4 (encoding transmembrane and intracytoplasmic region) from the available genome assembly. The Ensembl zebrafish genome assembly (v36) had two copies of CD28 exons 1 and ...
The relationship between higher‑order chromatin structure and
The relationship between higher‑order chromatin structure and

... The slowed sedimentation of what we have termed ‘open’ chromatin fibres may be due to the presence of multiple discontinuities in the 30 nm fibre structure (Figure 1). These might be attributable to DHSs (DNase I‑hypersensitive sites). For example, the slowed sedimentation of a 6 kb fragment of the ...
Number 48, 2001 35
Number 48, 2001 35

... which suggests RIP as the cause for barrenness in crosses involving segmental aneuploids is referred to as the ‘RIP hypothesis’. Consistent with this hypothesis, cytological studies indicated that sexual development in these crosses is arrested at about the same stage, when RIP is known to occur or ...
Interrogating the Function of Metazoan Histones using
Interrogating the Function of Metazoan Histones using

... for the maintenance of Polycomb target gene repression, demonstrating that histone residues can perform an essential function in gene regulation. These results underscore the essential roles played by these two histone residues in gene expression and animal development. Finally, in contrast to curre ...
Complete genome sequence of the thermophilic Thermus sp
Complete genome sequence of the thermophilic Thermus sp

... followed by CCB_US3_UF1 (13 genes), T. thermophilus HB27 (18 genes), and HB8 (18 genes). Interestingly, no prophage-related genes are found in these four genomes, implying the occurrence of clustered regularly interspaced short palindromic repeats (CRISPRs). CRISPR is characterized as a type of anti ...
Tandem duplications and the limits of natural
Tandem duplications and the limits of natural

... neutral markers (Nielsen et al. 2005). We compare the SFS for duplications with the SFS for SNPs from 8-30 bp of short introns used as a putatively neutral proxy to determine whether duplicates are subject to selection (Figure S1). The SFS for duplications is significantly different from that of int ...
Pax8, a murine paired box gene expressed in the developing
Pax8, a murine paired box gene expressed in the developing

... of these mechanisms is hampered mainly due to the lack of mutants in which the genes involved in the developmental control are affected. However, a number of developmental mutants have been identified in Drosophila (Lewis, 1978; Niisslein-Volhard and Wieschaus, 1980), facilitating the isolation of t ...
Identification of editing positions in the ndhB transcript from maize
Identification of editing positions in the ndhB transcript from maize

... of the used sequencing primers). The positions of the six editing sites within the sequence of the ndhB coding strand and with respect to the encoded amino acids are indicated in Figure 2. Five of the affected ndhB triplets are edited at the second codon position as was observed for all chloroplast ...
Molecular and genetic characterization of genes involved in maize
Molecular and genetic characterization of genes involved in maize

... properties that help prevent desiccation of the plant (Hadley, 1989). In addition, cuticular waxes have a reflective property that provides protection from UV radiation (Reicosky and Hanover, 1987). Cuticular waxes have also been shown to have important roles in protection from frost induced injury ...
IMPROVE SMALL RNA-MEDIATED GENE SILENCING
IMPROVE SMALL RNA-MEDIATED GENE SILENCING

... We now have a much greater understanding of the gene silencing pathways in plants and their crucial roles in a variety of biological regulation processes, such as development, plant defense against invading viral nucleic acids, and epigenetic modifications. siRNA directed target repression can occur ...
jsm2003 - University of Wisconsin–Madison
jsm2003 - University of Wisconsin–Madison

... additive effects may be most important (Wright/Fisher debate) statistical goal: maximize number of correctly identified QTL ...
DNA
DNA

... More Terminology • The genome is an organism’s complete set of DNA • a bacteria contains about 600,000 DNA base pairs • human and mouse genomes have some 3 billion ...
Discovering the Distribution of Palindromic Sequences in the
Discovering the Distribution of Palindromic Sequences in the

... and quaternary structures of RNA are important to its function and expression; if an RNA molecule was mutated by a deletion or other mutation (particularly large mutations), RNA expression will be compromised as it may be too susceptible to enzymes or it may be unable to unwind during expression. Sm ...
Slides: background and project plan
Slides: background and project plan

... Genome sequences • Many genomes have been sequences, including those of viruses, microbes, plants and animals. • Human: – 23 pairs of chromosomes – 3+ Gbps (bps = base pairs) , only ~3% are genes – ~25,000 genes ...
A Fitness-Independent Evolvability Measure for Evolutionary
A Fitness-Independent Evolvability Measure for Evolutionary

... GRN dynamics. In this evolutionary algorithm, a population of µ individuals creates an offspring population of λ individuals by changing the parents with Gaussian mutations. In addition to the mutation operator, other biologically plausible genetic operators, including gene duplication, deletion and ...
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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.
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