3790 research outputs found
Sort by
Sequencing and characterization of the Del/Tekay chromovirus family in Marshallia obovata (Asteraceae)
Get PDFLow coverage DNA sequencing data coupled with improved assembly methods are providing new insight into the repetitive fraction of the genomes of non-model organisms. In this study we explore the potential of these new approaches to characterize the Del/Tekay elements (chromodomain-containing Ty3/Gypsy retrotransposons) of the North American wildflower species Marshallia obovata. The Marshallia Del/Tekay chromoviruses are 8.3 Kbp in length with direct repeats of 1675 bp and 14 conserved domains across a 4506 bp gag-pol region. Read depth comparisons suggest that Del/Tekay elements are not highly abundant in M. obovata with approximately 144 unique copies per haploid genome of 6.5 Gbp (<0.02 %). Sequence variation was observed at less than 1 % of nucleotide positions overall with 60 % of variants occurring outside of any coding region. These results illustrate the utility of low coverage sequencing data for fine scale analyses of transposable elements present at low to moderate copy numbers within the genomes of non-model organisms. The Del/Tekay element sequences described here are the first for the plant family Asteraceae and are the first transposable elements of any kind described for the genus Marshallia. These initial results provide for future work on the evolutionary dynamics of Del/Tekay elements more broadly in the genus Marshallia and Asteraceae.PublishedYe
Simulated data and code for analysis of herpetofauna response to forest management in the Missouri Ozarks
Get PDFWe present predictor variables and R and Stan code for simulating and analyzing counts of Missouri Ozark herpetofauna in response to three forest management strategies. Our code performs four primary purposes: import predictor variables from spreadsheets; simulate synthetic response variables based on imported predictor variables and user-supplied values for data-generating parameters; format synthetic data for export to Stan; and analyze synthetic data.PublishedYe
Do Collaborative Multi-Institution Projects Drive End-User Traffic to Digital Collections?
No full textMany libraries participate in collaborative multi-institution digital collection projects because they promise to make it easier for end-users to find our materials. Creation and maintenance of these projects involves significant worker-hours, and participation often requires changes to collection metadata and software. But do these projects drive enough additional traffic to justify the extra work? This poster examines sources of end-user traffic for five digital collections during the 2015/16 academic year. Traffic to these collections from five collaborative projects is compared to traffic from other sources, such as university Web sites, Web search engines, and Google Scholar.Presente
Facilitating Interdisciplinary Competence: Collaboration Between Undergraduate Baccalaureate Nursing Students and Graduate Students Specializing in Communication Disorders
Get PDFThe fast-paced nature of the healthcare setting, coupled with the number of allied professionals involved, demands accurate and concise written communication. It is imperative that written communication between nursing and allied professionals be clear to ensure that the highest quality of care is provided and that patient safety is maintained. The authors feel the considerations documented by nursing students after reading an interdisciplinary evaluation report have the potential to improve the level of care provided to a patient and the patient’s experience of the care, as well as the student’s knowledge regarding allied healthcare. Students noted that reading the report had the potential to adjust their expectations of the patient’s communication abilities, cognition, or behavior and increase their awareness of the need to modify their own communication skills. If a nursing student understands the possibility of challenges in communicating with patients with communication disorders, this may carryover to future interactions, resulting in better patient care. Understanding patient concerns is critical for nurses, and this data indicates that reading a speech evaluation report provides the nurse with pertinent information.
InpublishedYe
Hall effect control of magnetotail dawn-dusk asymmetry: A three-dimensional global hybrid simulation
Get PDFMagnetotail reconnection and related phenomena (e.g., flux ropes, dipolarizing flux bundles, flow bursts, and particle injections) occur more frequently on the duskside than on the dawnside. Because this asymmetry can directly result in dawn-dusk asymmetric space weather effects, uncovering its physical origin is important for better understanding, modeling, and prediction of the space weather phenomena. However, the cause of this pervasive asymmetry is unclear. Using three-dimensional global hybrid simulations, we demonstrate that the Hall physics in the magnetotail current sheet is responsible for the asymmetry. The current sheet thins progressively under enhanced global convection; when its thickness reaches ion kinetic scales, some ions are decoupled from the magnetized electrons (the Hall effect). The resultant Hall electric field E-z is directed toward the neutral plane. The Hall effect is stronger (grows faster) on the duskside; i.e., more ions become unmagnetized there and do not comove with the magnetized dawnward E-z x B-x drifting electrons, thus creating a larger additional cross-tail current intensity j(y) (in addition to the diamagnetic current) on the duskside, compared to the dawnside. The stronger Hall effect strength on the duskside is controlled by the higher ion temperature, thinner current sheet, and smaller normal magnetic field B-z there. These asymmetric current sheet properties are in turn controlled by two competing processes that correspond to the Hall effect: (1) the dawnward E x B drift of the magnetic flux and magnetized ions and electrons and (2) the transient motion of the unmagnetized ions which do not execute E x B drift.PublishedYe
Classification of a Hypervirulent Aeromonas hydrophila Pathotype Responsible for Epidemic Outbreaks in Warm-Water Fishes
Get PDFLineages of hypervirulent Aeromonas hydrophila (vAh) are the cause of persistent outbreaks of motile Aeromonas septicemia in warm-water fishes worldwide. Over the last decade, this virulent lineage of A. hydrophila has resulted in annual losses of millions of tons of farmed carp and catfish in the People's Republic of China and the United States (US). Multiple lines of evidence indicate US catfish and Asian carp isolates of A. hydrophila affiliated with sequence type 251 (ST251) share a recent common ancestor. To address the genomic context for the putative intercontinental transfer and subsequent geographic spread of this pathogen, we conducted a core genome phylogenetic analysis on 61 Aeromonas spp. genomes, of which 40 were affiliated with A. hydrophila, with 26 identified as epidemic strains. Phylogenetic analyses indicate all ST251 strains form a coherent lineage affiliated with A. hydrophila. Within this lineage, conserved genetic loci unique to A. hydrophila were identified, with some genes present in consistently higher copy numbers than in non-epidemic A. hydrophila isolates. In addition, results from analyses of representative ST251 isolates support the conclusion that multiple lineages are present within US vAh isolated from Mississippi, whereas vAh isolated from Alabama appear clonal. This is the first report of genomic heterogeneity within US vAh isolates, with some Mississippi isolates showing closer affiliation with the Asian grass carp isolate ZC1 than other vAh isolated in the US. To evaluate the biological significance of the identified heterogeneity, comparative disease challenges were conducted with representatives of different vAh genotypes. These studies revealed that isolate ZC1 yielded significantly lower mortality in channel catfish, relative to Alabama and Mississippi vAh isolates. Like other Asian vAh isolates, the ZC1 lineage contains all core genes for a complete type VI secretion system (T6SS). In contrast, more virulent US isolates retain only remnants of the T6SS (clpB, hcp, vgrG, and vasH) which may have functional implications. Collectively, these results characterize a hypervirulent A. hydrophila pathotype that affects farmed fish on multiple continents.PublishedYe
Reconfiguring Auburn University's Main Library for Engaged Active Student Learning
Get PDFIn the face of changes in teaching and learning, academic libraries are responding with changes of their own. New pedagogies are creating opportunities for libraries to connect directly to the curriculum and support students who are being asked to work in new ways. It is one thing to recognize that change is needed, however, and another to design changes that will effectively support emerging ways of teaching and learning, especially when it is still early days in the change process. Such was the case at Auburn University, where a project to construct a new classroom building specifically for Engaged Active Student Learning (EASL) classes provided the library with an opportunity to renovate its main floor. The new Mell Classroom Building will incorporate in its entry atrium the library façade, and the library’s third and fourth floors will connect to hallways in the new structure. Library leaders seized the opportunity to provide space specifically to support the out-of-class-time academic activities of students in EASL classes.Publishedn
Is natural defense capacity correlated with allocation of dry mass to the stem in loblolly pine?
Get PDFIn addition to selecting loblolly pine (Pinus taeda L.) genotypes for superior growth, the concept of customized genetic selection may apply where tree vigor is threatened by insects and disease. A study conducted with seedlings from 15 loblolly pine genotypes found significant correlation between phenolic production and foliage mass when dry mass allocation to the stem was relatively low. Validation of this relationship in trees was attempted among four genetic sources of juvenile loblolly pine. Tree biomass allocation information was collected from six individuals per genotype at age 5 years in 2009. Five years later in January 2015, foliage and branch tip tissues were assessed for total phenolic concentrations. While tree biomass allocation differed significantly, total phenolic concentrations were similar among the four loblolly pine genotypes. Observations during this study suggest that our effort to validate this relationship in trees should be repeated during the growing season when carbon demands are at their highest and in stand conditions that exclude the possibility of light limitations to carbon fixation.Ye
