An effector Peptide family required for Drosophila toll-mediated immunity.

In Drosophila melanogaster, recognition of an invading pathogen activates the Toll or Imd signaling pathway, triggering robust upregulation of innate immune effectors. Although the mechanisms of pathogen recognition and signaling are now well understood, the functions of the immune-induced transcriptome and proteome remain much less well characterized. Through bioinformatic analysis of effector gene sequences, we have defined a family of twelve genes - the Bomanins (Boms) - that are specifically induced by Toll and that encode small, secreted peptides of unknown biochemical activity. Using targeted genome engineering, we have deleted ten of the twelve Bom genes. Remarkably, inactivating these ten genes decreases survival upon microbial infection to the same extent, and with the same specificity, as does eliminating Toll pathway function. Toll signaling, however, appears unaffected. Assaying bacterial load post-infection in wild-type and mutant flies, we provide evidence that the Boms are required for resistance to, rather than tolerance of, infection. In addition, by generating and assaying a deletion of a smaller subset of the Bom genes, we find that there is overlap in Bom activity toward particular pathogens. Together, these studies deepen our understanding of Toll-mediated immunity and provide a new in vivo model for exploration of the innate immune effector repertoire.

14-3-3 mediates histone cross-talk during transcription elongation in Drosophila.

Post-translational modifications of histone proteins modulate the binding of transcription regulators to chromatin. Studies in Drosophila have shown that the phosphorylation of histone H3 at Ser10 (H3S10ph) by JIL-1 is required specifically during early transcription elongation. 14-3-3 proteins bind H3 only when phosphorylated, providing mechanistic insights into the role of H3S10ph in transcription. Findings presented here show that 14-3-3 functions downstream of H3S10ph during transcription elongation. 14-3-3 proteins localize to active genes in a JIL-1-dependent manner. In the absence of 14-3-3, levels of actively elongating RNA polymerase II are severely diminished. 14-3-3 proteins interact with Elongator protein 3 (Elp3), an acetyltransferase that functions during transcription elongation. JIL-1 and 14-3-3 are required for Elp3 binding to chromatin, and in the absence of either protein, levels of H3K9 acetylation are significantly reduced. These results suggest that 14-3-3 proteins mediate cross-talk between histone phosphorylation and acetylation at a critical step in transcription elongation.

Using the Intended-Enacted-Experienced Curriculum Model to Map the Vision and Change Core Competencies in Undergraduate Biology Programs and Courses.

One critical step in the challenging process of curricular reform is determining how closely a curriculum aligns with national recommendations. Here, we examine the alignment of teaching, assessment, and student experience in undergraduate biology courses with the Vision and Change core competency recommendations. We applied the intended-enacted-experienced curriculum model to obtain a more complete, multiperspective view of the curriculum. First, we developed and piloted the BioSkills Curriculum Survey with more than 100 biology instructors across five institutions. Using multilevel logistic regression modeling of the survey data, we found that instructors were equally likely to report teaching all competencies; however, they reported assessing some competencies more than others. After adding course characteristics to our model, we found that the likelihood of teaching certain competencies depended on course type. Next, we analyzed class materials and student perceptions of instruction in 10 biology courses in one department. Within this smaller sample, we found that instructors messaged a narrower range of competency learning outcomes on their syllabi than they reported teaching on the survey. Finally, modeling revealed that inclusion of an outcome on assessments, but not syllabi, increased the likelihood that students and their instructor agreed whether it was taught.

BioSkills Guide: Development and National Validation of a Tool for Interpreting the Vision and Change Core Competencies.

To excel in modern science, technology, engineering, and mathematics careers, biology majors need a range of transferable skills, yet competency development is often a relatively underdeveloped facet of the undergraduate curriculum. We have elaborated the Vision and Change core competency framework into a resource called the BioSkills Guide, a set of measurable learning outcomes that can be more readily implemented by faculty. Following an iterative review process including more than 200 educators, we gathered evidence of the BioSkills Guide's content validity using a national survey of more than 400 educators. Rates of respondent support were high (74.3-99.6%) across the 77 outcomes in the final draft. Our national sample during the development and validation phases included college biology educators representing more than 250 institutions, including 73 community colleges, and a range of course levels and biology subdisciplines. Comparison of the BioSkills Guide with other science competency frameworks reveals significant overlap but some gaps and ambiguities. These differences may reflect areas where understandings of competencies are still evolving in the undergraduate biology community, warranting future research. We envision the BioSkills Guide supporting a variety of applications in undergraduate biology, including backward design of individual lessons and courses, competency assessment development, and curriculum mapping and planning.

Combinatorial effects of transposable elements on gene expression and phenotypic robustness in Drosophila melanogaster development.

Embryonic patterning displays remarkable consistency from individual to individual despite frequent environmental perturbations and diverse genetic contexts. Stochastic influences on the cellular environment may cause transcription rates to fluctuate, but these fluctuations rarely lead to developmental defects or disease. Here we characterize a set of recessive alleles of the Toll pathway component tube that destabilize embryonic dorsoventral patterning in Drosophila melanogaster. Females bearing these tube alleles generate embryos of an unusually wide range of dorsalized phenotypes, with the distributions across this range being unique for each allele. We determine that the mutant lines have in common a retrotransposon insertion upstream of the tube transcription start site. Genetic and molecular approaches demonstrate that this insertion dramatically reduces maternal expression of tube, thereby uncovering the inherent variability in gene expression. We further find that additional transposable element insertions near the tube gene synergistically enhance the phenotype caused by the sensitizing upstream insertion. These studies document how phenotypic variability can arise from normally occurring fluctuations around reduced mean expression and illustrate the contribution of transposons, individually and combinatorially, to such a state.