Riboswitch Distribution in the Human Gut Microbiome Reveals Common Metabolite Pathways

Riboswitches are widely distributed, conserved RNAs which regulate metabolite levels in bacterial cells through direct, noncovalent binding of their cognate metabolite. Various riboswitch families are highly enriched in gut bacteria, suggestive of a symbiotic relationship between the host and bacteria. Previous studies of the distribution of riboswitches have examined bacterial taxa broadly. Thus, the distribution of riboswitches associated with bacteria inhabiting the intestines of healthy individuals is not well understood. To address these questions, we survey the gut microbiome for riboswitches by including an international database of prokaryotic genomes from the gut samples. Using Infernal, a program that uses RNA-specific sequence and structural features, we survey this data set using existing riboswitch models. We identify 22 classes of riboswitches with vitamin cofactors making up the majority of riboswitch-associated pathways. Our finding is reproducible in other representative databases from the oral as well as the marine microbiomes, underscoring the importance of thiamine pyrophosphate, cobalamin, and flavin mononucleotide in gene regulation. Interestingly, riboswitches do not vary significantly across microbiome representatives from around the world despite major taxonomic differences; this suggests an underlying conservation. Further studies elucidating the role of bacterial riboswitches in the host metabolome are needed to illuminate the consequences of our finding.

The transcription factor EBF1 non-cell-autonomously regulates cardiac growth and differentiation

Reciprocal interactions between non-myocytes and cardiomyocytes regulate cardiac growth and differentiation. Here, we report that the transcription factor Ebf1 is highly expressed in non-myocytes and potently regulates heart development. Ebf1-deficient hearts display myocardial hypercellularity and reduced cardiomyocyte size, ventricular conduction system hypoplasia, and conduction system disease. Growth abnormalities in Ebf1 knockout hearts are observed as early as embryonic day 13.5. Transcriptional profiling of Ebf1-deficient embryonic cardiac non-myocytes demonstrates dysregulation of Polycomb repressive complex 2 targets, and ATAC-Seq reveals altered chromatin accessibility near many of these same genes. Gene set enrichment analysis of differentially expressed genes in cardiomyocytes isolated from E13.5 hearts of wild-type and mutant mice reveals significant enrichment of MYC targets and, consistent with this finding, we observe increased abundance of MYC in mutant hearts. EBF1-deficient non-myocytes, but not wild-type non-myocytes, are sufficient to induce excessive accumulation of MYC in co-cultured wild-type cardiomyocytes. Finally, we demonstrate that BMP signaling induces Ebf1 expression in embryonic heart cultures and controls a gene program enriched in EBF1 targets. These data reveal a previously unreported non-cell-autonomous pathway controlling cardiac growth and differentiation.

Mapping hospital data to characterize residents' educational experiences

BACKGROUND

Experiential learning through patient care is fundamental to graduate medical education. Despite this, the actual content to which trainees are exposed in clinical practice is difficult to quantify and is poorly characterized. There remains an unmet need to define precisely how residents' patient care activities inform their educational experience.  METHODS: Using a recently-described crosswalk tool, we mapped principal ICD-10 discharge diagnosis codes to American Board of Internal Medicine (ABIM) content at four training hospitals of a single Internal Medicine (IM) Residency Program over one academic year to characterize and compare residents' clinical educational experiences. Frequencies of broad content categories and more specific condition categories were compared across sites to profile residents' aggregate inpatient clinical experiences and drive curricular change.

RESULTS

There were 18,604 discharges from inpatient resident teams during the study period. The crosswalk captured > 95% of discharges at each site. Infectious Disease (ranging 17.4 to 39.5% of total discharges) and Cardiovascular Disease (15.8 to 38.2%) represented the most common content categories at each site. Several content areas (Allergy/Immunology, Dermatology, Obstetrics/Gynecology, Ophthalmology, Otolaryngology/Dental Medicine) were notably underrepresented (≤ 1% at each site). There were significant differences in the frequencies of conditions within most content categories, suggesting that residents experience distinct site-specific clinical content during their inpatient training.

CONCLUSIONS

There were substantial differences in the clinical content experienced by our residents across hospital sites, prompting several important programmatic and curricular changes to enrich our residents' hospital-based educational experiences.

Building Virtual Health Training Tools for Residents: A Design Thinking Approach

The COVID-19 pandemic drove a rapid transition to virtual care experiences for graduate medical trainees. Core training competencies have expanded to incorporate virtual contexts, however there is limited knowledge of the optimal design of virtual care training tools for learners. In this study, we describe the application of a Design Thinking approach to the identification and co-design of novel training tools to support residents and precepting attending physicians in virtual ambulatory care practice. We applied the model of “Empathize, Define, Ideate, Prototype, and Test” via a mixed methods approach to (1) explore the needs, preferences, and concerns of Internal Medicine residents and outpatient precepting attendings regarding virtual ambulatory care training environments, and (2) evaluate, prototype, and test potential training tools. Eleven residents and eight attending physicians participated. Identified learner needs and problem areas included: improving virtual visit technical skills; acquiring virtual communication skills; adapting to the loss of shared in-person learning space and optimizing virtual learning environments; remediating non-virtual procedural competencies; and educating on new documentation requirements. Key solution areas included: virtual precepting support tools; digital information and education dissemination tools; and strategies for management of technical issues. Several prototypes were proposed, with a single tool (a virtual preceptor tip sheet) deployed in clinical practice. Residents found the workshop program improved their understanding of Design Thinking and its relevance to healthcare. Ultimately, Design Thinking can be deployed to engage medical trainees and precepting attendings in the effective development of novel educational tools for the virtual care learning environment.