Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes

Includes bibliographical references (pages 373-374).The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses.Published with support from the Colorado State University Libraries Open Access Research and Scholarship Fund

Simple guide to starting a research group

Conducting cutting-edge research and scholarship becomes more complicated with each passing year; forming a collaborative research group offers a way to navigate this increasing complexity. Yet many individuals whose work might benefit from the formation of a collaborative team may feel overwhelmed by the prospect of attempting to build and maintain a research group. We propose this simple guide for starting and maintaining such an enterprise

Conflicts and configurations in a liminal space: SoTL scholars’ identity development

Although academic identity has received attention in the literature, there have been few attempts to understand the influence on identity from engagement with the Scholarship of Teaching and Learning (SoTL). In this aper, we (a group of eight scholars from five different countries) describe how our interactions with SoTL have impacted the shaping of our academic identities. We have struggled to define the value, purpose, outcomes, and meanings of being a disciplined SoTL scholar, sometimes in addition to and sometimes in opposition to being a disciplinary scholar. Through analysis of our own 100-word reflective narratives, we identify common conflicts and configurations around our experiences of developing a SoTL identity. We describe how navigating among conflicting identities can lead us into a troublesome but deeply reflective liminal space, prompting profound realizations and the reconstruction of academic identity. Drawing on this notion of liminality helps us to understand our journeys as moving through a necessary and important transformational landscape, and allows us to suggest ways to support those engaging with SoTL to develop an integrative SoTL identity

Looking our limitations in the eye: A call for more thorough and honest reporting of study limitations

The replication crisis and subsequent credibility revolution in psychology have highlighted many suboptimal research practices such as p‐hacking, overgeneralizing, and a lack of transparency. These practices may have been employed reflexively but upon reflection, they are hard to defend. We suggest that current practices for reporting and discussing study limitations are another example of an area where there is much room for improvement. In this article, we call for more rigorous reporting of study limitations in social and personality psychology articles, and we offer advice for how to do this. We recommend that authors consider what the best argument is against their conclusions (which we call the “steel‐person principle”). We consider limitations as threats to construct, internal, external, and statistical conclusion validity (Shadish et al., 2002), and offer some examples for better practice reporting of common study limitations. Our advice has its own limitations — both our representation of current practices and our recommendations are largely based on our own metaresearch and opinions. Nevertheless, we hope that we can prompt researchers to write more deeply and clearly about the limitations of their research, and to hold each other to higher standards when reviewing each other's work

The role of positive selection in determining the molecular cause of species differences in disease

Related species, such as humans and chimpanzees, often experience the same disease with varying degrees of pathology, as seen in the cases of Alzheimer's disease, or differing symptomatology as in AIDS. Furthermore, certain diseases such as schizophrenia, epithelial cancers and autoimmune disorders are far more frequent in humans than in other species for reasons not associated with lifestyle. Genes that have undergone positive selection during species evolution are indicative of functional adaptations that drive species differences. Thus we investigate whether biomedical disease differences between species can be attributed to positively selected genes

Imprints, Vol. 3

Imprints, Vol. 3 Laura Lundgren, Stephen F Austin State UniversitySandra L. Standley, Stephen F Austin State UniversityMelissa Miller, Stephen F Austin State UniversityCurtis Simmons, Stephen F Austin State UniversityVaughn Hamilton, Stephen F Austin State UniversitySteve Geissen, Stephen F Austin State UniversityEdward Shelton, Stephen F Austin State UniversityJames L. Choron, Stephen F Austin State UniversityAnderson Kelley, Stephen F Austin State UniversityAndrew J. Urbanus, Stephen F Austin State UniversityGordon Garrett Conner, Stephen F Austin State UniversityJames Chionsini Jr., Stephen F Austin State UniversityPaul M. Thomason, Stephen F Austin State UniversityCarol McBrayerJessica Anton, Stephen F Austin State University Download Download Full Text (5.7 MB) Description Imprints is the official publication for Sigma Tau Delta, the honorary English fraternity. The editors welcome creative works submitted by contributors and also publish winners of the annual T. E. Ferguson Writing Contest. Especially welcom are poems, fiction pieces and essays of no more than 5,000 words in length. At this time, we would like to express our gratitude to David Whitescarver, Sigma Tau Delta faculty advisor, for his unrelenting optimism and valuable help in the preparation of this journal

Deliberation on Childhood Vaccination in Canada: Public Input on Ethical Trade-Offs in Vaccination Policy

Background: Policy decisions about childhood vaccination require consideration of multiple, sometimes conflicting, public health and ethical imperatives. Examples of these decisions are whether vaccination should be mandatory and, if so, whether to allow for non-medical exemptions. In this article we argue that these policy decisions go beyond typical public health mandates and therefore require democratic input. Methods: We report on the design, implementation, and results of a deliberative public forum convened over four days in Ontario, Canada, on the topic of childhood vaccination. Results: 25 participants completed all four days of deliberation and collectively developed 20 policy recommendations on issues relating to mandatory vaccinations and exemptions, communication about vaccines and vaccination, and AEFI (adverse events following immunization) compensation and reporting. Notable recommendations include unanimous support for mandatory childhood vaccination in Ontario, the need for broad educational communication about vaccination, and the development of a no-fault compensation scheme for AEFIs. There was persistent disagreement among deliberants about the form of exemptions from vaccination (conscience, religious beliefs) that should be permissible, as well as appropriate consequences if parents do not vaccinate their children. Conclusions: We conclude that conducting deliberative democratic processes on topics that are polarizing and controversial is viable and should be further developed and implemented to support democratically legitimate and trustworthy policy about childhood vaccination

Reply to: New Meta- and Mega-analyses of Magnetic Resonance Imaging Findings in Schizophrenia: Do They Really Increase Our Knowledge About the Nature of the Disease Process?

This work was supported by National Institute of Biomedical Imaging and Bioengineering Grant No. U54EB020403 (to the ENIGMA consortium)

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes