The Alu Ya-lineage is a group of related, short interspersed elements (SINEs) found in primates. This lineage includes subfamilies Ya1-Ya5, Ya5a2 and others. Some of these subfamilies are still actively mobilizing in the human genome. We have analyzed 2482 elements that reside in the human genome draft sequence and focused our analyses on the 2318 human autosomal Ya Alu elements. A total of 1470 autosomal loci were subjected to polymerase chain reaction (PCR)-based assays that allow analysis of individual Ya-lineage Alu elements. About 22% (313/1452) of the Ya-lineage Alu elements were polymorphic for the insertion presence on human autosomes. Less than 0.01% (5/1452) of the Ya-lineage loci analyzed displayed insertions in orthologous loci in non-human primate genomes. DNA sequence analysis of the orthologous inserts showed that the orthologous loci contained older pre-existing Y, Sc or Sq Alu subfamily elements that were the result of parallel forward insertions or involved in gene conversion events in the human lineage. This study is the largest analysis of a group of "young", evolutionarily related human subfamilies. The size, evolutionary age and variable allele insertion frequencies of several of these subfamilies makes members of the Ya-lineage useful tools for human population studies and primate phylogenetics.
Phosphatidylinositol (PI) and its phosphorylated derivatives known as phosphoinositides (PIPs), are essential regulators of cell signaling and membrane trafficking, cytoskeletal dynamics, and nuclear functions. Disruption of PI metabolism is associated with disorders such as immune dysfunction, cardiovascular disease, and cancer; therefore, there is currently great interest in studying PIPs and their metabolic enzymes. Here, we describe a method for the separation of fluorescent PI and its seven fluorescent phosphorylated derivatives by CE-LIF. The CE method utilizes a Tris buffer and sodium deoxycholate in the presence of 30% 1-propanol and 5% of a dynamic coating reagent, EOTrol low reverse (EOTrol LR). It is simple, fast, highly sensitive, and it offers LODs in the order of 1.5 amol. The effect of cations such as lithium, sodium, potassium, cesium, barium, manganese, zinc, magnesium, calcium, spermine, and gentamicin were evaluated. Calcium and magnesium provided the best selectivity and resolution for the separation of the analytes while magnesium offered the best data reproducibility. The developed CE method would be useful in the studies of enzymatic activity in the PI and PIPs metabolic pathways using CE-based in vitro and CE cell-based assays, and/or for drug screening.
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