An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair

AbstractThe Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies have suggested that, in addition to TPRT, L1 elements occasionally utilize an alternative endonuclease-independent pathway for genomic integration. To determine whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available primate genomes (human, chimpanzee and rhesus macaque) for endonuclease-independent recently integrated or lineage specific Alu insertions. We recovered twenty-three examples of such insertions and show that these insertions are recognizably different from classical TPRT-mediated Alu element integration. We suggest a role for this process in DNA double-strand break repair and present evidence to suggest its association with intra-chromosomal translocations, in-vitro RNA recombination (IVRR), and synthesis-dependent strand annealing (SDSA)

Modulating Glutathione Thiol Status Alters Pancreatic β-cell Morphogenesis in the Developing Zebrafish (Danio rerio) Embryo

Emerging evidence suggests that redox-active chemicals perturb pancreatic islet development. To better understand potential mechanisms for this, we used zebrafish (Danio rerio) embryos to investigate roles of glutathione (GSH; predominant cellular redox buffer) and the transcription factor Nrf2a (Nfe2l2a; zebrafish Nrf2 coortholog) in islet morphogenesis. We delineated critical windows of susceptibility to redox disruption of beta-cell morphogenesis, interrogating embryos at 24, 48 and 72 h post fertilization (hpf) and visualized Nrf2a expression in the pancreas using whole-mount immunohistochemistry at 96 hpf. Chemical GSH modulation at 48 hpf induced significant islet morphology changes at 96 hpf. Pro-oxidant exposures to tert-butylhydroperoxide (77.6 mu M; 10-min at 48 hpf) or tert-butylhydroquinone (1 mu M; 48-56 hpf) decreased beta-cell cluster area at 96 hpf. Conversely, exposures to antioxidant N-acetylcysteine (bolsters GSH pools; 100 mu M; 48-72 hpf) or sulforaphane (activates Nrf2a; 20 mu M; 48-72 hpf) significantly increased islet areas. Nrf2a was also stabilized in beta-cells: 10-min exposures to 77.6 mu M tert-butylhydroperoxide significantly increased Nrf2a protein compared to control islet cells that largely lack stabilized Nrf2a; 10-min exposures to higher (776 mu M) tert-butylhydroperoxide concentration stabilized Nrf2a throughout the pancreas. Using biotinylated-GSH to visualize in situ protein glutathionylation, islet cells displayed high protein glutathionylation, indicating oxidized GSH pools. The 10-min high (776 mu M) tert-butylhydroperoxide exposure (induced Nrf2a globally) decreased global protein glutathionylation at 96 hpf. Mutant fish expressing inactive Nrf2a were protected against tert-butylhydroperoxide-induced abnormal islet morphology. Our data indicate that disrupted redox homeostasis and Nrf2a stabilization during pancreatic beta-cell development impact morphogenesis, with implications for disease states at later life stages. Our work identifies a potential molecular target (Nrf2) that mediates abnormal beta-cell morphology in response to redox disruptions. Moreover, our findings imply that developmental exposure to exogenous stressors at distinct windows of susceptibility could diminish the reserve redox capacity of beta-cells, rendering them vulnerable to later-life stresses and disease

Clustering Attitudes and Behaviors of High/Low Involvement Grocery Shopper

The purpose of this exploratory and quantitative study was to examine the attitudes and behaviors of 14,807 grocery shop- pers. These respondents across the US were asked to answer attitudinal, behavioral, and demographic related questions. Shoppers were profiled by analyzing their responses to 16 relevant attitudinal and behavioral questions. A cluster analysis was performed followed by a discriminant analysis to deter- mine attitudinal and behavioral variables explaining cluster membership. A cross-tabulation analysis assessed demo- graphic variables that correlated with cluster membership. Two clusters were identified: high and low involvement grocery shoppers. In an event that has long been perceived as low involvement, a large percentage (53%) can be categorized as high involvement grocery shoppers. These shoppers tend to be younger. They were more likely to enjoy the hunt of finding products/deals, seek the advice of others and perceive that the products they buy reflect upon them. Grocery stores have a significant opportunity to target this high involvement shop- per. Grocery stores will need to create an integrative, engaging online and in-store experience to attract high involvement shoppers and ultimately increase store loyalty. The results of this research has significant communication, branding and digital marketing implications

Beyond deficit-based models of learners' cognition: Interpreting engineering students' difficulties with sense-making in terms of fine-grained epistemological and conceptual dynamics

Researchers have argued against deficit-based explanations of students' troubles with mathematical sense-making, pointing instead to factors such as epistemology: students' beliefs about knowledge and learning can hinder them from activating and integrating productive knowledge they have. In this case study of an engineering major solving problems (about content from his introductory physics course) during a clinical interview, we show that "Jim" has all the mathematical and conceptual knowledge he would need to solve a hydrostatic pressure problem that we posed to him. But he reaches and sticks with an incorrect answer that violates common sense. We argue that his lack of mathematical sense-making-specifically, translating and reconciling between mathematical and everyday/common-sense reasoning-stems in part from his epistemological views, i.e., his views about the nature of knowledge and learning. He regards mathematical equations as much more trustworthy than everyday reasoning, and he does not view mathematical equations as expressing meaning that tractably connects to common sense. For these reasons, he does not view reconciling between common sense and mathematical formalism as either necessary or plausible to accomplish. We, however, avoid a potential "deficit trap"-substituting an epistemological deficit for a concepts/skills deficit-by incorporating multiple, context-dependent epistemological stances into Jim's cognitive dynamics. We argue that Jim's epistemological stance contains productive seeds that instructors could build upon to support Jim's mathematical sense-making: He does see common-sense as connected to formalism (though not always tractably so) and in some circumstances this connection is both salient and valued.Comment: Submitted to the Journal of Engineering Educatio

Black Stork Down: Military Discourses in Bird Conservation in Malta

Tensions between Maltese hunters and bird conservation NGOs have intensified over the past decade. Conservation NGOs have become frustrated with the Maltese State for conceding to the hunter lobby and negotiating derogations from the European Union’s Bird Directive. Some NGOs have recently started to organize complex field-operations where volunteers are trained to patrol the landscape, operate drones and other surveillance technologies, detect illegalities, and lead police teams to arrest poachers. We describe the sophisticated military metaphors which conservation NGOs have developed to describe, guide and legitimize their efforts to the Maltese public and their fee-paying members. We also discuss why such groups might be inclined to adopt these metaphors. Finally, we suggest that anthropological studies of discourse could help understand delicate contexts such as this where conservation NGOs, hunting associations and the State have ended in political deadlock

An alu-based phylogeny of gibbons (hylobatidae)

Gibbons (Hylobatidae) are small, arboreal apes indigenous to Southeast Asia that diverged from other apes ∼15-18 Ma. Extant lineages radiated rapidly 6-10 Ma and are organized into four genera (Hylobates, Hoolock, Symphalangus, and Nomascus) consisting of 12-19 species. The use of short interspersed elements (SINEs) as phylogenetic markers has seen recent popularity due to several desirable characteristics: the ancestral state of a locus is known to be the absence of an element, rare potentially homoplasious events are relatively easy to resolve, and samples can be quickly and inexpensively genotyped. During radiation of primates, one particular family of SINEs, the Alu family, has proliferated in primate genomes. Nomascus leucogenys (northern white-cheeked gibbon) sequences were analyzed for repetitive content with RepeatMasker using a custom library. The sequences containing Alu elements identified as members of a gibbon-specific subfamily were then compared with orthologous positions in other primate genomes. A primate phylogenetic panel consisting of 18 primate species, including 13 gibbon species representing all four extant genera, was assayed for all loci, and a total of 125 gibbon-specific Alu insertions were identified. The resulting amplification patterns were used to generate a phylogenetic tree. We demonstrate significant support for Symphalangus as the most basal lineage within the family. Our findings also place Nomascus as a derived lineage, sister to Hoolock, with the Nomascus-Hoolock clade sister to Hylobates. Further, our analysis groups N. leucogenys and Nomascus siki as sister taxa to the exclusion of the other Nomascus species assayed. This study represents the first use of SINEs to determine the genus level phylogenetic relationships within the family Hylobatidae. These relationships have been resolved with robust support at most internal nodes, demonstrating the utility of SINE-based phylogenetic analysis. We postulate that hybridization and rapid radiation may have contributed to the complex and contradictory findings of the previous studies. Our findings will aid in the conservation of these threatened primates and inform future studies of the biogeographical history and distribution of modern gibbon species. © 2012 The Author