Much is known regarding the structure and logic of genetic regulatory networks. Less understood is the contextual organization of promoter signals used during transcription initiation, the most pivotal stage during gene expression. Here we show that promoter networks organize spontaneously at a dimension between the 1-dimension of the DNA and 3-dimension of the cell. Network methods were used to visualize the global structure of E. coli sigma (σ) recognition footprints using published promoter sequences (RegulonDB). Footprints were rendered as networks with weighted edges representing bp-sharing between promoters (nodes). Serial thresholding revealed phase transitions at positions predicted by percolation theory, and nuclei denoting short steps through promoter space with geometrically constrained linkages. The network nuclei are fractals, a power-law organization not yet described for promoters. Genome-wide promoter abundance also scaled as a power-law. We propose a general model for the development of a fractal nucleus in a transcriptional grammar.

Abstract:The language of gene expression displays topological symmetry. An important step during gene expression is the binding of transcriptional proteins to DNA promoters adjacent to a gene. Some proteins bind to many promoters in a genome, defining a regulon of genes wherein each promoter might vary in DNA sequence relative to the average consensus. Here we examine the linguistic organization of gene promoter networks, wherein each node in the network represents a promoter and links between nodes represent the extent of base pair-sharing. Prior work revealed a fractal nucleus in several σ-factor regulons from Escherichia coli. We extend these findings to show fractal nuclei in gene promoter networks from three bacterial species, E. coli, Bacillus subtilis, and Pseudomonas aeruginosa. We surveyed several non-σ transcription factors from these species and found that many contain a nucleus that is both visually and numerically fractal. Promoter footprint size scaled as a negative power-law with both information entropy and fractal dimension, while the latter two parameters scaled positively and linearly. The fractal dimension of the diffuse networks (d B = ~1.7) was close to that expected of a diffusion limited aggregation process, confirming prior predictions as to a possible mechanism for development of this structure.

The Preparing Future Faculty (PFF) initiative for graduate students was launched in the United States in 1993 as a partnership between the Council of Graduate Schools and the Association of American Colleges and Universities to prepare graduate students for faculty careers at different institutional types and to provide them with teaching‐related professional development. PFF programs have proliferated U.S. universities over the last two decades, but there has been limited research on the long‐term impact of these programs. This study at the University of Michigan examines the career paths and attitudes of graduate students who participated in an annual, intensive, five‐week PFF seminar between 2007 and 2013. The descriptive study explores the following research questions: (a) What are the career outcomes for PFF seminar participants compared with nonparticipants? (b) Does the exposure to a variety of institutional types in the PFF seminar lead to a greater appreciation of and openness to job opportunities at diverse institutions? and (c) Does the PFF seminar assist graduate students in their job searches and their chosen career paths? The results of this study contribute to our understanding of what universities can do to effectively prepare graduate students for their future careers.

Jennifer Wegner is an Assistant Director in Engineering Student Affairs at the University of Michigan, with responsibilities including student organization development, leading unit strategic objectives, and supporting university and college co-curricular initiatives. Her teaching and facilitation experiences include a mentorship/leadership course, LeaderShape R , first year seminars, and a university course on social psychology in residence settings. She is a member of the NASPA Center for Women National Board and co-founded the University of Michigan Women in Student Affairs chapter. Jennifer's research interests include the culture of busy, the intersection of women's higher education career ascension and professional development, and women's leadership development. She is currently a doctoral student at New England College and holds her M.Ed. in Higher Education Student Affairs from the University of Vermont and a B.A from Oakland University. Learning from Experiences: Examining Self-Reflections in Engineering Design Courses AbstractThis work assessed student reflective learning outcomes during a final Leadership/Mentorship course, after their participation in significant, experiential design projects in the University of Michigan's Multidisciplinary Design Program in the College of Engineering. Throughout the course, class discussions and assignments prompted students to reflect and examine their personal experiences in engineering design projects, their learning (both technical and professional), leadership, and team styles as well as understand group development and dynamics.A feature of the projects was the integration of students from diverse disciplines in engineering with other programs such as: Art, Architecture, Primary Sciences, Kinesiology, and Business. The diverse teams provided a rich environment but also created the complexity of multiple paradigms within the project teams. This course utilized the construct of Kolb's Experiential Learning Model 1 and Kavanagh's reflection exercises 2 to promote active reflection on students' team based engineering design project experiences. The in-class discussions and self-reflection based assignments not only helped students to more fully understand the technical aspects of engineering design, but also contributed to a greater understanding of working as a team and as competent, adaptive professionals.In a final reflection assignment, students described self-identified critical moments/milestones in their development (i.e., including design projects, classes, extracurricular activities, employment, etc.) and how the experience gained from those moments is important to their development as practicing professionals, effective mentors, and strong leaders. From these milestones, we identified common themes and experiences, including the impact on students' cognitive and professional identity development.Milestones were identified based on the forum for the experience such as classroom coursework, university-sponsored projects, extracurricular activities, stud...

Hybridization generates similarities among gene pools. This structure can be visualized and analyzed at the systems level using networks. Here we construct a network of the 315 woody plant species native or naturalized in the United States using data compiled by the Forest Service of the US Department of Agriculture (USFS). Each species is represented by a node in the network whose size is proportional to a recent census for live stems in the continental United States. Each of the 416 links between node pairs represents evidence for hybridization compiled from the USFS manual Silvics of North America. The total network resolved into 100 separate connected components or clusters (mean size, 3.15 species), with 44% of species linked to at least one other. Betula had the largest component (18 species) following by the separate Quercus clusters (17 red oaks and 16 white oaks); Q. velutina was the most genetically connected woody plant in the continental US. The number of species held together per component (i.e. size) scaled as a power-law albeit a slightly truncated one. The truncation suggests there are fewer than expected hybridizing species within the large woody genera of plants in the US.