An age-of-allele test of neutrality for transposable element insertions

How natural selection acts to limit the proliferation of transposable elements (TEs) in genomes has been of interest to evolutionary biologists for many years. To describe TE dynamics in populations, many previous studies have used models of transposition-selection equilibrium that rely on the assumption of a constant rate of transposition. However, since TE invasions are known to happen in bursts through time, this assumption may not be reasonable in natural populations. Here we propose a test of neutrality for TE insertions that does not rely on the assumption of a constant transposition rate. We consider the case of TE insertions that have been ascertained from a single haploid reference genome sequence and have subsequently had their allele frequency estimated in a population sample. By conditioning on the age of an individual TE insertion (using information contained in the number of substitutions that have occurred within the TE sequence since insertion), we determine the probability distribution for the insertion allele frequency in a population sample under neutrality. Taking models of varying population size into account, we then evaluate predictions of our model against allele frequency data from 190 retrotransposon insertions sampled from North American and African populations of Drosophila melanogaster. Using this non-equilibrium model, we are able to explain about 80% of the variance in TE insertion allele frequencies based on age alone. Controlling both for nonequilibrium dynamics of transposition and host demography, we provide evidence for negative selection acting against most TEs as well as for positive selection acting on a small subset of TEs. Our work establishes a new framework for the analysis of the evolutionary forces governing large insertion mutations like TEs, gene duplications or other copy number variants.Comment: 40 pages, 6 figures, Supplemental Data available: [email protected]

Exposure to the Dental Environment and Prevalence of Respiratory Illness in Dental Student Populations

Objective: To determine if the prevalence of respiratory disease among dental students and dental residents varies with their exposure to the clinical dental environment. Methods: A detailed questionnaire was administered to 817 students at 3 dental schools. The questionnaire sought information concerning demographic characteristics, school year, exposure to the dental environment and dental procedures, and history of respiratory disease. The data obtained were subjected to bivariate and multiple logistic regression analysis. Results: Respondents reported experiencing the following respiratory conditions during the previous year: asthma (26 cases), bronchitis (11 cases), chronic lung disease (6 cases), pneumonia (5 cases) and streptococcal pharyngitis (50 cases). Bivariate statistical analyses indicated no significant associations between the prevalence of any of the respiratory conditions and year in dental school, except for asthma, for which there was a significantly higher prevalence at 1 school compared to the other 2 schools. When all cases of respiratory disease were combined as a composite variable and subjected to multivariate logistic regression analysis controlling for age, sex, race, dental school, smoking history and alcohol consumption, no statistically significant association was observed between respiratory condition and year in dental school or exposure to the dental environment as a dental patient. Conclusion: No association was found between the prevalence of respiratory disease and a student\u27s year in dental school or previous exposure to the dental environment as a patient. These results suggest that exposure to the dental environment does not increase the risk for respiratory infection in healthy dental health care workers

Physiological, behavioral and subjective sadness reactivity in frontotemporal dementia subtypes.

Frontotemporal dementia (FTD), a neurodegenerative disease broadly characterized by socioemotional impairments, includes three clinical subtypes: behavioral variant FTD (bvFTD), semantic variant primary progressive aphasia (svPPA) and non-fluent variant primary progressive aphasia (nfvPPA). Emerging evidence has shown emotional reactivity impairments in bvFTD and svPPA, whereas emotional reactivity in nfvPPA is far less studied. In 105 patients with FTD (49 bvFTD, 31 svPPA and 25 nfvPPA) and 27 healthy controls, we examined three aspects of emotional reactivity (physiology, facial behavior and subjective experience) in response to a sad film. In a subset of the sample, we also examined the neural correlates of diminished aspects of reactivity using voxel-based morphometry. Results indicated that all three subtypes of FTD showed diminished physiological responding in respiration rate and diastolic blood pressure; patients with bvFTD and svPPA also showed diminished subjective experience, and no subtypes showed diminished facial behavior. Moreover, there were differences among the clinical subtypes in brain regions where smaller volumes were associated with diminished sadness reactivity. These results show that emotion impairments extend to sadness reactivity in FTD and underscore the importance of considering different aspects of sadness reactivity in multiple clinical subtypes for characterizing emotional deficits and associated neurodegeneration in FTD

Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans

<p>Abstract</p> <p>Background</p> <p>Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species <it>Aggregatibacter actinomycetemcomitans </it>is a major etiologic agent of human periodontitis. Individual clonal types of <it>A. actinomycetemcomitans </it>may exhibit variable virulence and different patterns of disease association. This study examined the genome arrangement of <it>A. actinomycetemcomitans </it>using the genome sequences of serotypes a-c strains. The genome alignment and rearrangement were analyzed by the MAUVE and the GRIMM algorithms. The distribution patterns of genes along the leading/lagging strands were investigated. The occurrence and the location of repeat sequences relative to the genome rearrangement breakpoints were also determined.</p> <p>Results</p> <p>The genome arrangement of the serotype a strain D7S-1 is markedly different from the serotype b strain HK1651 or the serotype c strain D11S-1. Specific genome arrangements appear to be conserved among strains of the same serotypes. The reversal distance between D7S-1 and HK1651 by GRIMM analysis is also higher than the within-species comparisons of 7 randomly selected bacterial species. The locations of the orthologous genes are largely preserved between HK1651 and D11S-1 but not between D7S-1 and HK1651 (or D11S-1), irrespective of whether the genes are categorized as essential/nonessential or highly/nonhighly expressed. However, genome rearrangement did not disrupt the operons of the <it>A. actinomycetemcomitans </it>strains. A higher proportion of the genome in strain D7S-1 is occupied by repeat sequences than in strains HK1651 or D11S-1.</p> <p>Conclusion</p> <p>The results suggest a significant evolutionary divergence between serotype a strains and serotypes b/c strains of <it>A. actinomycetemcomitans</it>. The distinct patterns of genome arrangement may suggest phenotypic differences between serotype a and serotypes b/c strains.</p

Predictors of Students’ Achievement in a Blended Learning Course

Massive Open Online Courses (MOOCs) have been at the center of media attention and hyperbole since 2012. Physics I: Classical Mechanics was a physics course offered by an elite private university in the northeastern United States in the fall of 2014. This course was offered in a blended learning format using a MOOC platform. There were 476 students enrolled in the course, but only 266 of them completed the course. In order to better understand the behavior and academic performance of students in this course, several mathematical models were used to examine the relationship between their grades and their use of the course materials. More specifically, the focus of this paper is the relationship between students’ online problem checking behaviors for questions that required handwritten solutions and their academic performance in the course. All of the data comprising students’ behaviors on the MITx platform are available as a “click stream” log of every action taken by each individual. Several mathematical models were used to create features describing these behavior patterns, and all of these features together were used to build a regression tree, which predicted students’ academic achievement. The results from this model indicated that students who checked their answers more frequently generally received better grades on average. Moreover, students who had more interaction with course materials generally had higher average grades than those who interacted with the platform less. Results also indicated that the group of students whose last problem check was correct received better grades than the other group whose last problem check was not correct. The group of students who started to do the homework earlier in the week also received better grades. The results of this paper are going to help the instructor to build better course outlines and provide students more useful instructions to achieve better grades

Near-Infrared MOSFIRE Spectra of Dusty Star-Forming Galaxies at 0.2<z<4

We present near-infrared and optical spectroscopic observations of a sample of 450$\mu$m and 850$\mu$m-selected dusty star-forming galaxies (DSFGs) identified in a 400 arcmin$^2$ area in the COSMOS field. Thirty-one sources of the 102 targets were spectroscopically confirmed at $0.2<z<4$, identified primarily in the near-infrared with Keck MOSFIRE and some in the optical with Keck LRIS and DEIMOS. The low rate of confirmation is attributable both to high rest-frame optical obscuration in our targets and limited sensitivity to certain redshift ranges. The high-quality photometric redshifts available in the COSMOS field allow us to test the robustness of photometric redshifts for DSFGs. We find a subset (11/31$\approx35$%) of DSFGs with inaccurate ($\Delta z/(1+z)>0.2$) or non-existent photometric redshifts; these have very distinct spectral energy distributions from the remaining DSFGs, suggesting a decoupling of highly obscured and unobscured components. We present a composite rest-frame 4300--7300\AA\ spectrum for DSFGs, and find evidence of 200$\pm$30 km s$^{-1}$ gas outflows. Nebular line emission for a sub-sample of our detections indicate that hard ionizing radiation fields are ubiquitous in high-z DSFGs, even more so than typical mass or UV-selected high-z galaxies. We also confirm the extreme level of dust obscuration in DSFGs, measuring very high Balmer decrements, and very high ratios of IR to UV and IR to H$\alpha$ luminosities. This work demonstrates the need to broaden the use of wide bandwidth technology in the millimeter to the spectroscopic confirmations of large samples of high-z DSFGs, as the difficulty in confirming such sources at optical/near-infrared wavelengths is exceedingly challenging given their obscuration.Comment: 14 pages, 13 figures, ApJ accepted. Composite DSFG Halpha spectrum available at www.as.utexas.edu/~cmcasey/downloads.htm

A Gap Analysis of Biodiversity Research in Rocky Mountain National Park: A Pilot Study on Spiders

Research on biodiversity and the relationship between organisms is imperative to establish management practices for the conservation of protected areas. The E.O. Wilson Biodiversity Foundation (EOWBF) formed our team of four Duke University students as the first of many ATBI/BioBlitz SWAT teams to travel to protected areas and develop approaches to conduct biodiversity research that can inform their conservation. Our project consisted of two elements. First, our team assessed the current status of biodiversity research at Rocky Mountain National Park (RMNP) to determine major gaps in the understanding of biodiversity. We used available species lists from research conducted in the Park to ensure that the National Park species database, NPSpecies, contained the most up-to-date information. Our team then added 645 species of plants and fungi to the database through this process. One of the identified gaps was a lack of research on spiders in the park. The second element of our study was a pilot analysis of spider biodiversity, to identify as many species in the park as possible and to relate their occurrences to environmental variables. Over 300 spider specimens were collected, 157 of which were identified, representing 51 species. Specimens were collected from three non-wilderness sites in RMNP at three different times of day (morning, afternoon, and night), over a span of ten days (July 16 - 25, 2014). The three sites represent a range of elevations (2,398 - 2,923 meters) and habitats. Cost-effective methods were utilized and evaluated for future spider research. We propose a more thorough spider survey in RMNP that can better inform management of the Park by providing information about spider diversity, abundance, function, and how spiders can be used as ecological indicators