Browsing by Subject "Recombination, Genetic"
Now showing items 1-13 of 13
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A functional analysis of the spacer of V(D)J recombination signal sequences.
(PLoS Biol, 2003-10)During lymphocyte development, V(D)J recombination assembles antigen receptor genes from component V, D, and J gene segments. These gene segments are flanked by a recombination signal sequence (RSS), which serves as the ... -
Ancestral population genomics: the coalescent hidden Markov model approach.
(Genetics, 2009-09)With incomplete lineage sorting (ILS), the genealogy of closely related species differs along their genomes. The amount of ILS depends on population parameters such as the ancestral effective population sizes and ... -
Complex evolutionary trajectories of sex chromosomes across bird taxa.
(Science, 2014-12-12)Sex-specific chromosomes, like the W of most female birds and the Y of male mammals, usually have lost most genes owing to a lack of recombination. We analyze newly available genomes of 17 bird species representing the avian ... -
Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains.
(PloS one, 2018-01)Functional mapping of the 5'LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by ... -
Dynamic evolution of base composition: causes and consequences in avian phylogenomics.
(Mol Biol Evol, 2011-08)Resolving the phylogenetic relationships among birds is a classical problem in systematics, and this is particularly so when it comes to understanding the relationships among Neoaves. Previous phylogenetic inference of birds ... -
Essential role of beta-adrenergic receptor kinase 1 in cardiac development and function.
(Proc Natl Acad Sci U S A, 1996-11-12)The beta-adrenergic receptor kinase 1 (beta ARK1) is a member of the G protein-coupled receptor kinase (GRK) family that mediates the agonist-dependent phosphorylation and desensitization of G protein-coupled receptors. ... -
Evidence that the human pathogenic fungus Cryptococcus neoformans var. grubii may have evolved in Africa.
(PLoS One, 2011-05-11)Most of the species of fungi that cause disease in mammals, including Cryptococcus neoformans var. grubii (serotype A), are exogenous and non-contagious. Cryptococcus neoformans var. grubii is associated worldwide with avian ... -
Identification and utilization of arbitrary correlations in models of recombination signal sequences.
(Genome Biol, 2002)BACKGROUND: A significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites, such as protein-binding sites in regulatory DNA. Current approaches sometimes ... -
Multiple, conserved cryptic recombination signals in VH gene segments: detection of cleavage products only in pro B cells.
(J Exp Med, 2007-12-24)Receptor editing is believed to play the major role in purging newly formed B cell compartments of autoreactivity by the induction of secondary V(D)J rearrangements. In the process of immunoglobulin heavy (H) chain editing, ... -
Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing.
(The New phytologist, 2017-01)Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate ... -
Polymorphisms of homologous recombination genes and clinical outcomes of non-small cell lung cancer patients treated with definitive radiotherapy.
(PloS one, 2011-01)The repair of DNA double-strand breaks (DSBs) is the major mechanism to maintain genomic stability in response to irradiation. We hypothesized that genetic polymorphisms in DSB repair genes may affect clinical outcomes among ... -
Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling.
(J Exp Med, 2003-01-20)The recombination signals (RS) that guide V(D)J recombination are phylogenetically conserved but retain a surprising degree of sequence variability, especially in the nonamer and spacer. To characterize RS variability, we ... -
Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.
(BMC Genomics, 2014-12-11)BACKGROUND: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded ...
