Estimating the retrotransposition rate of human Alu elements

Mobile elements such as Alu repeats have substantially altered the architecture of the human genome, and de novo mobile element insertions sometimes cause genetic disorders. Previous estimates for the retrotransposition rate (RR) of Alu elements in humans of one new insertion every ∼100-125 births were developed prior to the sequencing of the human and chimpanzee genomes. Here, we used two independent methods (based on the new genomic data and on disease-causing de novo Alu insertions) to generate refined Alu RR estimates in humans. Both methods consistently yielded RR on the order of one new Alu insertion every ∼20 births, despite the fact that the evolutionary-based method represents an average RR over the past ∼6 million years while the mutation-based method better reflects the current-day RR. These results suggest that Alu elements retrotranspose at a faster rate in humans than previously thought, and support the potential of Alu elements as mutagenic factors in the human genome. © 2006 Elsevier B.V. All rights reserved

A SINE-based dichotomous key for primate identification

For DNA samples or \u27divorced\u27 tissues, identifying the organism from which they were taken generally requires some type of analytical method. The ideal approach would be robust even in the hands of a novice, requiring minimal equipment, time, and effort. Genotyping SINEs (Short INterspersed Elements) is such an approach as it requires only PCR-related equipment, and the analysis consists solely of interpreting fragment sizes in agarose gels. Modern primate genomes are known to contain lineage-specific insertions of Alu elements (a primate-specific SINE); thus, to demonstrate the utility of this approach, we used members of the Alu family to identify DNA samples from evolutionarily divergent primate species. For each node of a combined phylogenetic tree (56 species; n = 8 [Hominids]; 11 [New World monkeys]; 21 [Old World monkeys]; 2 [Tarsiformes]; and, 14 [Strepsirrhines]), we tested loci (\u3e 400 in total) from prior phylogenetic studies as well as newly identified elements for their ability to amplify in all 56 species. Ultimately, 195 loci were selected for inclusion in this Alu-based key for primate identification. This dichotomous SINE-based key is best used through hierarchical amplification, with the starting point determined by the level of initial uncertainty regarding sample origin. With newly emerging genome databases, finding informative retrotransposon insertions is becoming much more rapid; thus, the general principle of using SINEs to identify organisms is broadly applicable. © 2006 Elsevier B.V. All rights reserved

Alu retrotransposition-mediated deletion

Alu repeats contribute to genomic instability in primates via insertional and recombinational mutagenesis. Here, we report an analysis of Alu element-induced genomic instability through a novel mechanism termed retrotransposition-mediated deletion, and assess its impact on the integrity of primate genomes. For human and chimpanzee genomes, we find evidence of 33 retrotransposition-mediated deletion events that have eliminated approximately 9000 nucleotides of genomic DNA. Our data suggest that, during the course of primate evolution, Alu retrotransposition may have contributed to over 3000 deletion events, eliminating approximately 900 kb of DNA in the process. Potential mechanisms for the creation of Alu retrotransposition-mediated deletions include L1 endonuclease-dependent retrotransposition, L1 endonuclease-independent retrotransposition, internal priming on DNA breaks, and promiscuous target primed reverse transcription. A comprehensive analysis of the collateral effects by Alu mobilization on all primate genomes will require sequenced genomes from representatives of the entire order. © 2005 Elsevier Ltd. All rights reserved

Alu retrotransposition-mediated deletion,”

Alu repeats contribute to genomic instability in primates via insertional and recombinational mutagenesis. Here, we report an analysis of Alu elementinduced genomic instability through a novel mechanism termed retrotransposition-mediated deletion, and assess its impact on the integrity of primate genomes. For human and chimpanzee genomes, we find evidence of 33 retrotransposition-mediated deletion events that have eliminated approximately 9000 nucleotides of genomic DNA. Our data suggest that, during the course of primate evolution, Alu retrotransposition may have contributed to over 3000 deletion events, eliminating approximately 900 kb of DNA in the process. Potential mechanisms for the creation of Alu retrotransposition-mediated deletions include L1 endonuclease-dependent retrotransposition, L1 endonuclease-independent retrotransposition, internal priming on DNA breaks, and promiscuous target primed reverse transcription. A comprehensive analysis of the collateral effects by Alu mobilization on all primate genomes will require sequenced genomes from representatives of the entire order

Longitudinal assessment of cognitive and psychosocial functioning after Hurricanes Katrina and Rita: Exploring disaster impact on middle-aged, older, and oldest-old adults

The authors examined the effects of Hurricanes Katrina and Rita on cognitive and psychosocial functioning in a lifespan sample of adults 6-14 months after the storms. Participants were recruited from the Louisiana Healthy Aging Study. Most were assessed during the immediate impact period and retested for this study. Analyses of pre- and post-disaster cognitive data confirmed that storm-related decrements in working memory for middle-aged and older adults observed in the immediate impact period had returned to pre-hurricane levels in the post-disaster recovery period. Middle-aged adults reported more storm-related stressors and greater levels of stress than the two older groups at both waves of testing. These results are consistent with a burden perspective on post-disaster psychological reactions. © 2012 Wiley Periodicals, Inc

Infrared laser ablation sample transfer of tissue DNA for genomic analysis

© 2017, Springer-Verlag Berlin Heidelberg. Infrared (IR) laser ablation was used to remove material from tissue sections mounted on microscope slides, with subsequent capture in a solvent-containing microcentrifuge tube. Experiments conducted with a 3200-bp double-stranded plasmid DNA template demonstrated IR-laser ablation transfer of intact DNA. The transfer efficiency and the molecular integrity of the captured DNA were evaluated using Sanger sequencing, gel electrophoresis, and fluorimetric analysis. The plasmid DNA was reproducibly transferred with an efficiency of 59 ± 3% at laser fluences of between 10 and 20 kJ/m2 at a wavelength of 3 μm. IR laser ablation sample transfer was then used to ablate and capture DNA from 50-μm-thick rat brain and kidney tissue sections. DNA was extracted from the captured material using five commercial DNA extraction kits that employed significantly divergent methodologies, with all kits recovering sufficient DNA for successful amplification by polymerase chain reaction (PCR). Four sets of primers were employed, targeting one region of the CYP 11b2 gene (376 bp) and three different regions of the Snn1g gene (298, 168, and 281 bp). The PCR results were not consistently reliable when using unpurified ablation samples; however, after extraction, all samples produced PCR products of the expected size. This work expands the sampling capabilities of IR laser ablation, demonstrating that DNA can be isolated from tissue samples for genomic assays. Due to the small size of the ablation regions (1 mm2), this technique will be useful for sampling discrete cell populations from tissue sections. [Figure not available: see fulltext.]

RNA sampling from tissue sections using infrared laser ablation

© 2019 Elsevier B.V. RNA was obtained from discrete locations of frozen rat brain tissue sections through infrared (IR) laser ablation using a 3-μm wavelength in transmission geometry. The ablated plume was captured in a microcentrifuge tube containing RNAse-free buffer and processed using a commercial RNA purification kit. RNA transfer efficiency and integrity were evaluated based on automated electrophoresis in microfluidic chips. Reproducible IR-laser ablation of intact RNA was demonstrated with purified RNA at laser fluences of 3–5 kJ/m 2 (72 ± 12% transfer efficiency) and with tissue sections at a laser fluence of 13 kJ/m 2 (79 ± 14% transfer efficiency); laser energies were attenuated ∼20% by the soda-lime glass slides used to support the samples. RNA integrity from tissue ablation was \u3e90% of its original RIN value (∼7) and the purified RNA was sufficiently intact for conversion to cDNA and subsequent qPCR assay

Functional analyses of tiptop and antennapedia in the embryonic development of Oncopeltus fasciatus suggests an evolutionary pathway from ground state to insect legs

In insects, selector genes are thought to modify the development of a default, or \u27ground state\u27, appendage into a tagma-specific appendage such as a mouthpart, antenna or leg. In the best described example, Drosophila melanogaster, the primary determination of leg identity is thought to result from regulatory interactions between the Hox genes and the antennal-specifying gene homothorax. Based on RNA-interference, a functional analysis of the selector gene tiptop and the Hox gene Antennapedia in Oncopeltus fasciatus embryogenesis is presented. It is shown that, in O. fasciatus, tiptop is required for the segmentation of distal leg segments and is required to specify the identity of the leg. The distal portions of legs with reduced tiptop develop like antennae. Thus, tiptop can act as a regulatory switch that chooses between antennal and leg identity. By contrast, Antennapedia does not act as a switch between leg and antennal identity. This observation suggests a significant difference in the mechanism of leg specification between O. fasciatus and D. melanogaster. These observations also suggest a significant plasticity in the mechanism of leg specification during insect evolution that is greater than would have been expected based on strictly morphological or molecular comparisons. Finally, it is proposed that a tiptop-like activity is a likely component of an ancestral leg specification mechanism. Incorporating a tiptop-like activity into a model of the leg-specification mechanism explains several mutant phenotypes, previously described in D. melanogaster, and suggests a mechanism for the evolution of legs from a ground state

DNA methylation variation of human-specific Alu repeats

<p>DNA methylation is the major repression mechanism for human retrotransposons, such as the Alu family. Here, we have determined the methylation levels associated with 5238 loci belonging to 2 Alu subfamilies, AluYa5 and AluYb8, using high-throughput targeted repeat element bisulfite sequencing (HT-TREBS). The results indicate that ∼90% of loci are repressed by high methylation levels. Of the remaining loci, many of the hypomethylated elements are found near gene promoters and show high levels of DNA methylation variation. We have characterized this variation in the context of tumorigenesis and interindividual differences. Comparison of a primary breast tumor and its matched normal tissue revealed early DNA methylation changes in ∼1% of AluYb8 elements in response to tumorigenesis. Simultaneously, AluYa5/Yb8 elements proximal to promoters also showed differences in methylation of up to one order of magnitude, even between normal individuals. Overall, the current study demonstrates that early loss of methylation occurs during tumorigenesis in a subset of young Alu elements, suggesting their potential clinical relevance. However, approaches such as deep-bisulfite-sequencing of individual loci using HT-TREBS are required to distinguish clinically relevant loci from the background observed for AluYa5/Yb8 elements in general with regard to high levels of interindividual variation in DNA methylation.</p