Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns.

The nucleus is highly compartmentalized through the formation of distinct classes of membraneless domains. However, the composition and function of many of these structures are not well understood. Using APEX2-mediated proximity labeling and RNA sequencing, we surveyed human transcripts associated with nuclear speckles, several additional domains, and the lamina. Remarkably, speckles and lamina are associated with distinct classes of retained introns enriched in genes that function in RNA processing, translation, and the cell cycle, among other processes. In contrast to the lamina-proximal introns, retained introns associated with speckles are relatively short, GC-rich, and enriched for functional sites of RNA-binding proteins that are concentrated in these domains. They are also highly differentially regulated across diverse cellular contexts, including the cell cycle. Thus, our study provides a resource of nuclear domain-associated transcripts and further reveals speckles and lamina as hubs of distinct populations of retained introns linked to gene regulation and cell cycle progression.

An ant-plant mutualism through the lens of cGMP-dependent kinase genes.

In plant-animal mutualisms, how an animal forages often determines how much benefit its plant partner receives. In many animals, foraging behaviour changes in response to foraging gene expression or activation of the cGMP-dependent protein kinase (PKG) that foraging encodes. Here, we show that this highly conserved molecular mechanism affects the outcome of a plant-animal mutualism. We studied the two PKG genes of Allomerus octoarticulatus, an Amazonian ant that defends the ant-plant Cordia nodosa against herbivores. Some ant colonies are better 'bodyguards' than others. Working in the field in Peru, we found that colonies fed with a PKG activator recruited more workers to attack herbivores than control colonies. This resulted in less herbivore damage. PKG gene expression in ant workers correlated with whether an ant colony discovered an herbivore and how much damage herbivores inflicted on leaves in a complex way; natural variation in expression levels of the two genes had significant interaction effects on ant behaviour and herbivory. Our results suggest a molecular basis for ant protection of plants in this mutualism.

Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development.

Variation in the size and number of axial segments underlies much of the diversity in animal body plans. Here we investigate the evolutionary, genetic and developmental mechanisms driving tail-length differences between forest and prairie ecotypes of deer mice (Peromyscus maniculatus). We first show that long-tailed forest mice perform better in an arboreal locomotion assay, consistent with tails being important for balance during climbing. We then identify six genomic regions that contribute to differences in tail length, three of which associate with caudal vertebra length and the other three with vertebra number. For all six loci, the forest allele increases tail length, indicative of the cumulative effect of natural selection. Two of the genomic regions associated with variation in vertebra number contain Hox gene clusters. Of those, we find an allele-specific decrease in Hoxd13 expression in the embryonic tail bud of long-tailed forest mice, consistent with its role in axial elongation. Additionally, we find that forest embryos have more presomitic mesoderm than prairie embryos and that this correlates with an increase in the number of neuromesodermal progenitors, which are modulated by Hox13 paralogues. Together, these results suggest a role for Hoxd13 in the development of natural variation in adaptive morphology on a microevolutionary timescale.

A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes.

How locally adapted ecotypes are established and maintained within a species is a long-standing question in evolutionary biology. Using forest and prairie ecotypes of deer mice (Peromyscus maniculatus), we characterized the genetic basis of variation in two defining traits-tail length and coat color-and discovered a 41-megabase chromosomal inversion linked to both. The inversion frequency is 90% in the dark, long-tailed forest ecotype; decreases across a habitat transition; and is absent from the light, short-tailed prairie ecotype. We implicate divergent selection in maintaining the inversion at frequencies observed in the wild, despite high levels of gene flow, and explore fitness benefits that arise from suppressed recombination within the inversion. We uncover a key role for a large, previously uncharacterized inversion in the evolution and maintenance of classic mammalian ecotypes.

Leveraging Artificial Intelligence to Improve Chronic Disease Care: Methods and Application to Pharmacotherapy Decision Support for Type-2 Diabetes Mellitus.

OBJECTIVES: Artificial intelligence (AI), including predictive analytics, has great potential to improve the care of common chronic conditions with high morbidity and mortality. However, there are still many challenges to achieving this vision. The goal of this project was to develop and apply methods for enhancing chronic disease care using AI. METHODS: Using a dataset of 27,904 patients with diabetes, an analytical method was developed and validated for generating a treatment pathway graph which consists of models that predict the likelihood of alternate treatment strategies achieving care goals. An AI-driven clinical decision support system (CDSS) integrated with the electronic health record (EHR) was developed by encapsulating the prediction models in an OpenCDS Web service module and delivering the model outputs through a SMART on FHIR (Substitutable Medical Applications and Reusable Technologies on Fast Healthcare Interoperability Resources) web-based dashboard. This CDSS enables clinicians and patients to review relevant patient parameters, select treatment goals, and review alternate treatment strategies based on prediction results. RESULTS: The proposed analytical method outperformed previous machine-learning algorithms on prediction accuracy. The CDSS was successfully integrated with the Epic EHR at the University of Utah. CONCLUSION: A predictive analytics-based CDSS was developed and successfully integrated with the EHR through standards-based interoperability frameworks. The approach used could potentially be applied to many other chronic conditions to bring AI-driven CDSS to the point of care.

Establishing a multidisciplinary initiative for interoperable electronic health record innovations at an academic medical center.

OBJECTIVE: To establish an enterprise initiative for improving health and health care through interoperable electronic health record (EHR) innovations. MATERIALS AND METHODS: We developed a unifying mission and vision, established multidisciplinary governance, and formulated a strategic plan. Key elements of our strategy include establishing a world-class team; creating shared infrastructure to support individual innovations; developing and implementing innovations with high anticipated impact and a clear path to adoption; incorporating best practices such as the use of Fast Healthcare Interoperability Resources (FHIR) and related interoperability standards; and maximizing synergies across research and operations and with partner organizations. RESULTS: University of Utah Health launched the ReImagine EHR initiative in 2016. Supportive infrastructure developed by the initiative include various FHIR-related tooling and a systematic evaluation framework. More than 10 EHR-integrated digital innovations have been implemented to support preventive care, shared decision-making, chronic disease management, and acute clinical care. Initial evaluations of these innovations have demonstrated positive impact on user satisfaction, provider efficiency, and compliance with evidence-based guidelines. Return on investment has included improvements in care; over $35 million in external grant funding; commercial opportunities; and increased ability to adapt to a changing healthcare landscape. DISCUSSION: Key lessons learned include the value of investing in digital innovation initiatives leveraging FHIR; the importance of supportive infrastructure for accelerating innovation; and the critical role of user-centered design, implementation science, and evaluation. CONCLUSION: EHR-integrated digital innovation initiatives can be key assets for enhancing the EHR user experience, improving patient care, and reducing provider burnout.

The complete clinician model.

Historically, medical education has focused on acquiring knowledge of basic science and clinical medicine. Relationship management skills are an essential aspect of excellent clinicians that may have been overlooked in the educational curriculum and undervalued in practice. The complete clinician model is a theoretical model for clinician development that describes why knowledge acquisition and relationship management are both imperative skills to refine when progressing to be an excellent clinician. Four quadrants are described, with ideal progress going from the trainee quadrant to the golden quadrant, ultimately aiming for competence in both knowledge acquisition and relationship management. The pediatric resident milestones from the Accreditation Council for Graduate Medical Education were placed in the model to underscore the importance placed on both knowledge acquisition and relationship management skills. Relationship management training should be integrated into the medical curriculum. This model may be applicable to professional education in other health care disciplines.

The Tug1 lncRNA locus is essential for male fertility.

BACKGROUND: Several long noncoding RNAs (lncRNAs) have been shown to function as components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has greatly expanded, studying lncRNA function has been a challenge due to their diverse biological roles and because lncRNA loci can contain multiple molecular modes that may exert function. RESULTS: We previously generated and characterized a cohort of 20 lncRNA loci knockout mice. Here, we extend this initial study and provide a more detailed analysis of the highly conserved lncRNA locus, taurine-upregulated gene 1 (Tug1). We report that Tug1-knockout male mice are sterile with underlying defects including a low number of sperm and abnormal sperm morphology. Because lncRNA loci can contain multiple modes of action, we wanted to determine which, if any, potential elements contained in the Tug1 genomic region have any activity. Using engineered mouse models and cell-based assays, we provide evidence that the Tug1 locus harbors two distinct noncoding regulatory activities, as a cis-DNA repressor that regulates neighboring genes and as a lncRNA that can regulate genes by a trans-based function. We also show that Tug1 contains an evolutionary conserved open reading frame that when overexpressed produces a stable protein which impacts mitochondrial membrane potential, suggesting a potential third coding function. CONCLUSIONS: Our results reveal an essential role for the Tug1 locus in male fertility and uncover evidence for distinct molecular modes in the Tug1 locus, thus highlighting the complexity present at lncRNA loci.

Identification of critical factors for forming collaborative relationships between physicians and pharmacists.

PURPOSE: The purpose of this study was to identify and describe strategies that have successfully achieved collaboration among physicians and pharmacists providing comprehensive medication management (CMM) to support development of CMM services. METHODS: A 2-phase, mixed-methods approach was employed to identify successful strategies for building pharmacist-physician relationships in primary care clinic settings. Phase I used a qualitative approach to identify strategies deemed successful in building relationships with physicians. An advisory group of pharmacists with experience building CMM practices assisted in the development of minimum criteria characterizing pharmacists as having strong collaborative relationships. Semi-structured interviews were conducted with 10 interviewees meeting established criteria. Researchers coded interview transcripts and identified the resulting strategies. Phase II employed a survey instrument to determine how frequently identified strategies are used and evaluate the relative level of perceived impact of each strategy, which was distributed to a national audience of pharmacists practicing in ambulatory care settings. Responses from pharmacists meeting prespecified criteria were included in the analysis. RESULTS: Thirty-three strategies were identified and grouped into 8 themes. In phase II, 104 survey respondents met defined criteria and were eligible to endorse use of identified strategies and rate their relative influence. CONCLUSIONS: Thirty-three strategies were identified and grouped into 8 themes to aid pharmacists practicing CMM in developing stronger collaborative relationships with physician colleagues. A national sampling found many of these strategies were employed by a majority of pharmacists, who had found them to be influential in creating collaborative relationships.

Social behaviour in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts.

Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviours and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviourally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms; most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between eusocial and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. The symbiosis between halictids and Sodalis therefore appears to be in its early stages.

Hard and soft selection on phenology through seasonal shifts in the general and social environments: A study on plant emergence time.

The timing of transition out of one life-history phase determines where in the seasonal succession of environments the next phase is spent. Shifts in the general environment (e.g., seasonal climate) affect the expected fitness for particular transition dates. Variation in transition date also leads to temporal variation in the social environment. For instance, early transition may confer a competitive advantage over later individuals. If so, the social environment will impose frequency- and density-dependent selection components. In effect, the general environment imposes hard selection, whereas the social environment imposes soft selection on phenology. We examined hard and soft selection on seedling emergence time in an experiment on Brassica rapa. In monoculture (uniform social environment), early emergence results in up to a 1.5-fold increase in seed production. In bicultures (heterogeneous social environment), early-emerging plants capitalized on their head start, suppressing their late neighbors and increasing their fitness advantage to as much as 38-fold, depending on density. We devised a novel adaptation of contextual analysis to partition total selection (i.e., cov(ω, z)) into the hard and soft components. Hard and soft components had similar strengths at low density, whereas soft selection was five times stronger than hard at high density.

Signals can trump rewards in attracting seed-dispersing ants.

Both rewards and signals are important in mutualisms. In myrmecochory, or seed dispersal by ants, the benefits to plants are relatively well studied, but less is known about why ants pick up and move seeds. We examined seed dispersal by the ant Aphaenogaster rudis of four co-occurring species of plants, and tested whether morphology, chemical signaling, or the nutritional quality of fatty seed appendages called elaiosomes influenced dispersal rates. In removal trials, ants quickly collected diaspores (seeds plus elaiosomes) of Asarum canadense, Trillium grandiflorum, and Sanguinaria canadensis, but largely neglected those of T. erectum. This discrepancy was not explained by differences in the bulk cost-benefit ratio, as assessed by the ratio of seed to elaiosome mass. We also provisioned colonies with diaspores from one of these four plant species or no diaspores as a control. Colonies performed best when fed S. canadensis diaspores, worst when fed T. grandiflorum, and intermediately when fed A. canadense, T. erectum, or no diaspores. Thus, the nutritional rewards in elaiosomes affected colony performance, but did not completely predict seed removal. Instead, high levels of oleic acid in T. grandiflorum elaiosomes may explain why ants disperse these diaspores even though they reduce ant colony performance. We show for the first time that different elaiosome-bearing plants provide rewards of different quality to ant colonies, but also that ants appear unable to accurately assess reward quality when encountering seeds. Instead, we suggest that signals can trump rewards as attractants of ants to seeds.