Genomics clarifies taxonomic boundaries in a difficult species complex.

Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted in a new approach to taxonomic identification that stands to greatly reduce much of this conflict. This approach is ideal for species complexes, where divergence times are recent (evolutionarily) and lineages less well defined. The California Roach/Hitch fish species complex is an excellent example, experiencing a convoluted geologic history, diverse habitats, conflicting species designations and potential admixture between species. Here we use this fish complex to illustrate how genomics can be used to better clarify and assign taxonomic categories. We performed restriction-site associated DNA (RAD) sequencing on 255 Roach and Hitch samples collected throughout California to discover and genotype thousands of single nucleotide polymorphism (SNPs). Data were then used in hierarchical principal component, admixture, and FST analyses to provide results that consistently resolved a number of ambiguities and provided novel insights across a range of taxonomic levels. At the highest level, our results show that the CA Roach/Hitch complex should be considered five species split into two genera (4 + 1) as opposed to two species from distinct genera (1 +1). Subsequent levels revealed multiple subspecies and distinct population segments within identified species. At the lowest level, our results indicate Roach from a large coastal river are not native but instead introduced from a nearby river. Overall, this study provides a clear demonstration of the power of genomic methods for informing taxonomy and serves as a model for future studies wishing to decipher difficult species questions. By allowing for systematic identification across multiple scales, taxonomic structure can then be tied to historical and contemporary ecological, geographic or anthropogenic factors

Food Education in schools: why do some headteachers make this a priority?

This thesis concerns the reasons why some primary school headteachers in England include Food Education so prominently in their school’s pedagogical curriculum. School leaders are seen as the ‘architects’ of transforming the food culture within a school setting. The current inclusion of Food Education in the English National Curriculum focuses on teaching children about how food choices can have a positive impact on their own physical health and well-being. My study investigates if there are other reasons why a set of recognised leaders in Food Education include this learning focus in their school’s curriculum despite the fact that this is not an area for which they are held accountable. This qualitative research study is based on semi-structured interviews with ten primary school headteachers in England. The responses from the face-to-face semi-structured interviews with the headteachers are submitted to Reflective Thematic Analysis which leads to two contributions to the literature, summarised below. The theoretical framework takes a social constructionist approach, focusing on the interpretation of the school leaders’ views, experiences and practices of including Food Education into their school’s curriculum. My findings reveal that the headteachers who do include Food Education in their school’s pedagogical curriculum do not use it solely to support the healthy eating agenda. By shaping the school ethos and culture through the communication of their personal and professional values and vision, they are also able to extend the wider benefits of Food Education to positively influence other aspects of the school and the wider community. Their use of the ‘pedagogical curriculum’ as a stimulus has enabled them to enact what I call ‘pedagogical commensality’ which supports school connectedness and has the potential to have wide ranging benefits to both the children's academic and health outcomes and the wider community. Recommendations relate to government policy on incorporating learning about food in its broader context into the English National Curriculum. By including the social, cultural, political, environmental, aesthetic and sustainable benefits of food, schools could provide learning opportunities that extend beyond the narrow bio-pedagogical focus that Food Education currently occupies and could support key areas such as community cohesion, personal values development and inclusion. This has implications for the professional development of school leaders and the inclusion of Food Education curriculum in Initial Teacher Training programmes. This thesis claims new knowledge in relation to how Food Education can be used as an embodiment of the headteacher’s values-based leadership approach; and how ‘pedagogical commensality’ can be used as a tool to support the personal and social development of the children and the school community

Beyond pre-loading: understanding the associations between pre-, side- and back-loading drinking behavior and risky drinking

This study examined the interaction between pre-, side- and back-loading drinking behaviors and their relationship to risky drinking, modeling to account for demographic characteristics. The study was based on an online non-probability panel survey of Victorian adults (18. +) who purchased packaged liquor for off premises consumption in the previous 12. months. Initially, 2545 participants entered the study, with 536 screened out, leaving a sample of 2008 respondents. While pre-loading was the most commonly reported loading behavior, back-loading and side-loading were reported almost as frequently. We found a clear association between loading and risky drinking behavior. Respondents who reported engaging in all loading behaviors were more likely to report regular very risky drinking. Age and sex were significant factors influencing the relationship between loading types and risky drinking behavior; income, marital status, and the interaction between sex and age were not significant factors. We show a broad range of loading behaviors associated with increased levels of risky drinking. Future research should seek to investigate these loading behaviors among a general population sample

Transforming spaces: Fostering student-centered learning through the intentional design of formal and informal learning spaces

Transforming the academic experience and success of students by building Active Learning Classrooms (ALCs) is increasing, but ALCs are still fewer than traditional classroom spaces. These new learning spaces create an inherent tension between increasing student enrollments and active learning environments. Accommodating increased class sizes does not have to exclude fostering an active learning space. We have an opportunity every time a classroom is renovated or a new building is built to intentionally acknowledge and engage this tension to positively influence student learning and success. As we renovate and construct new learning spaces on our campuses, it is not only important to understand how the “built pedagogy” (Monahan 2000, 2002) and “architecture as pedagogy” (Orr 1993, 1997) of our spaces can help or hinder more active learning pedagogies, but also how to support effective teaching in these spaces (Levesque-Bristol, 2019). While many institutions are prioritizing active learning as old classrooms get renovated, few are doing so at the broad campus-wide scope necessary to affect larger-scale culture change (Park & Choi, 2014). Two such institutions that are developing and supporting large-scale active learning spaces are the Technological University Dublin (TU Dublin) and Purdue University (Indiana, USA). TU Dublin and Purdue are conducting collaborative research focusing on how each institution’s new, large-scale construction of formal and informal learning spaces is impacting teaching and learning

Towards Space-like Photometric Precision from the Ground with Beam-Shaping Diffusers

We demonstrate a path to hitherto unachievable differential photometric precisions from the ground, both in the optical and near-infrared (NIR), using custom-fabricated beam-shaping diffusers produced using specialized nanofabrication techniques. Such diffusers mold the focal plane image of a star into a broad and stable top-hat shape, minimizing photometric errors due to non-uniform pixel response, atmospheric seeing effects, imperfect guiding, and telescope-induced variable aberrations seen in defocusing. This PSF reshaping significantly increases the achievable dynamic range of our observations, increasing our observing efficiency and thus better averages over scintillation. Diffusers work in both collimated and converging beams. We present diffuser-assisted optical observations demonstrating $62^{+26}_{-16}$ppm precision in 30 minute bins on a nearby bright star 16-Cygni A (V=5.95) using the ARC 3.5m telescope---within a factor of $\sim$2 of Kepler's photometric precision on the same star. We also show a transit of WASP-85-Ab (V=11.2) and TRES-3b (V=12.4), where the residuals bin down to $180^{+66}_{-41}$ppm in 30 minute bins for WASP-85-Ab---a factor of $\sim$4 of the precision achieved by the K2 mission on this target---and to 101ppm for TRES-3b. In the NIR, where diffusers may provide even more significant improvements over the current state of the art, our preliminary tests have demonstrated $137^{+64}_{-36}$ppm precision for a $K_S =10.8$ star on the 200" Hale Telescope. These photometric precisions match or surpass the expected photometric precisions of TESS for the same magnitude range. This technology is inexpensive, scalable, easily adaptable, and can have an important and immediate impact on the observations of transits and secondary eclipses of exoplanets.Comment: Accepted for publication in ApJ. 30 pages, 20 figure

Characterization of the Atmosphere of the Hot Jupiter HAT-P-32Ab and the M-dwarf Companion HAT-P-32B

Copyright © 2015 IOP PublishingWe report secondary eclipse photometry of the hot Jupiter HAT-P-32Ab, taken with Hale/Wide-field Infra-Red Camera (WIRC) in H and KS bands and with Spitzer/IRAC at 3.6 and 4.5 μm. We carried out adaptive optics imaging of the planet host star HAT-P-32A and its companion HAT-P-32B in the near-IR and the visible. We clearly resolve the two stars from each other and find a separation of 2.''923 ± 0.''004 and a position angle 110fdg64 ± 0fdg12. We measure the flux ratios of the binary in g'r'i'z' and H and KS bands, and determine T eff= 3565 ± 82 K for the companion star, corresponding to an M1.5 dwarf. We use PHOENIX stellar atmosphere models to correct the dilution of the secondary eclipse depths of the hot Jupiter due to the presence of the M1.5 companion. We also improve the secondary eclipse photometry by accounting for the non-classical, flux-dependent nonlinearity of the WIRC IR detector in the H band. We measure planet-to-star flux ratios of 0.090% ± 0.033%, 0.178% ± 0.057%, 0.364% ± 0.016%, and 0.438% ± 0.020% in the H, KS , 3.6 and 4.5 μm bands, respectively. We compare these with planetary atmospheric models, and find they prefer an atmosphere with a temperature inversion and inefficient heat redistribution. However, we also find that the data are equally well described by a blackbody model for the planet with T p = 2042 ± 50 K. Finally, we measure a secondary eclipse timing offset of 0.3 ± 1.3 minutes from the predicted mid-eclipse time, which constrains e = 0.0072 +0.0700}_-0.0064 when combined with radialNASACenter for Exoplanets and Habitable Worlds at the Pennsylvania State UniversityPennsylvania State UniversityEberly College of SciencePennsylvania Space Grant ConsortiumNational Science Foundation - Graduate Research Fellowship ProgramNatural Science and Engineering Research Council of CanadaJPL/SpitzerCalifornia Institute of Technology - NASA Sagan FellowshipAlfred P. Sloan FoundationCalifornia Institute of TechnologyInter-University Centre for Astronomy and AstrophysicsNational Science FoundationMt. Cuba Astronomical FoundationSamuel Oschi

Characterization of the atmosphere of the hot Jupiter HAT-P-32Ab and the M-dwarf companion HAT-P-32B

We report secondary eclipse photometry of the hot Jupiter HAT-P-32Ab, taken with Hale/WIRC in H and Ks bands and with Spitzer/IRAC at 3.6 and 4.5 micron. We carried out adaptive optics imaging of the planet host star HAT-P-32A and its companion HAT-P-32B in the near-IR and the visible. We clearly resolve the two stars from each other and find a separation of 2.923" +/- 0. 004" and a position angle 110.64 deg +/- 0.12 deg. We measure the flux ratios of the binary in g' r' i' z' and H & Ks bands, and determine Teff = 3565 +/- 82 K for the companion star, corresponding to an M1.5 dwarf. We use PHOENIX stellar atmosphere models to correct the dilution of the secondary eclipse depths of the hot Jupiter due to the presence of the M1.5 companion. We also improve the secondary eclipse photometry by accounting for the non-classical, flux-dependent nonlinearity of the WIRC IR detector in the H band. We measure planet-to-star flux ratios of 0.090 +/- 0.033%, 0.178 +/- 0.057%, 0.364 +/- 0.016%, and 0.438 +/- 0.020% in the H, Ks, 3.6 and 4.5 micron bands, respectively. We compare these with planetary atmospheric models, and find they prefer an atmosphere with a temperature inversion and inefficient heat redistribution. However, we also find that the data are equally well-described by a blackbody model for the planet with Tp = 2042 +/- 50 K. Finally, we measure a secondary eclipse timing offset of 0.3 +/- 1.3 min from the predicted mid-eclipse time, which constrains e = 0.0072 +0.0700/-0.0064 when combined with RV data and is more consistent with a circular orbit.Comment: 16 pages, 12 figures. Accepted for publication in Ap

Prion Protein Polymorphisms Affect Chronic Wasting Disease Progression

Analysis of the PRNP gene in cervids naturally infected with chronic wasting disease (CWD) suggested that PRNP polymorphisms affect the susceptibility of deer to infection. To test this effect, we orally inoculated 12 white-tailed deer with CWD agent. Three different PRNP alleles, wild-type (wt; glutamine at amino acid 95 and glycine at 96), Q95H (glutamine to histidine at amino acid position 95) and G96S (glycine to serine at position 96) were represented in the study cohort with 5 wt/wt, 3 wt/G96S, and 1 each wt/Q95H and Q95H/G96S. Two animals were lost to follow-up due to intercurrent disease. The inoculum was prepared from Wisconsin hunter-harvested homozygous wt/wt animals. All infected deer presented with clinical signs of CWD; the orally infected wt/wt had an average survival period of 693 days post inoculation (dpi) and G96S/wt deer had an average survival period of 956 dpi. The Q95H/wt and Q95H/G96S deer succumbed to CWD at 1,508 and 1,596 dpi respectively. These data show that polymorphisms in the PRNP gene affect CWD incubation period. Deer heterozygous for the PRNP alleles had extended incubation periods with the Q95H allele having the greatest effect

Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation

Next-generation sequencing is becoming increasingly common in clinical laboratories worldwide and is revolutionizing clinical molecular testing. However, the large amounts of raw data produced by next-generation sequencing assays and the need for complex bioinformatics analyses present unique challenges. Proficiency testing in clinical laboratories has traditionally been designed to evaluate assays in their entirety; however, it can be alternatively applied to separate assay components. We developed and implemented a multi-institutional proficiency testing approach to directly assess custom bioinformatics and variant interpretation processes. Six clinical laboratories, all of which use the same commercial library preparation kit for next-generation sequencing analysis of tumor specimens, each submitted raw data (FASTQ files) from four samples. These 24 file sets were then deidentified and redistributed to five of the institutions for analysis and interpretation according to their clinically validated approach. Among the laboratories, there was a high rate of concordance in the calling of single-nucleotide variants, in particular those we considered clinically significant (100% concordance). However, there was significant discordance in the calling of clinically significant insertions/deletions, with only two of seven being called by all participating laboratories. Missed calls were addressed by each laboratory to improve their bioinformatics processes. Thus, through our alternative proficiency testing approach, we identified the bioinformatic detection of insertions/deletions as an area of particular concern for clinical laboratories performing next-generation sequencing testing