Victoria E. Prince - US grants

0091101
Prince

The Hox genes set up pattern along the anteroposterior axis of developing metazoan embryos. Hox cluster duplication events accompanied vertebrate origins and provided additional patterning information, likely allowing for more complex body plans to arise. Recent work from the P.I. and others has established that in the teleost lineage an additional genome duplication event has led to significant differences between the Hox organization and complement of tetrapods and teleosts. This study will focus on zebrafish hox genes in the anteriorly expressed paralogue group (PG) 1 as a paradigm to compare and contrast gene function and regulation in different vertebrate groups and hence to investigate Hox gene modification during evolution.

Preliminary studies have shown that the zebrafish PG1 hox genes are significantly different in terms of organization, expression, and potential function, from those of the tetrapod vertebrates such as mouse. Thus, zebrafish hoxa1a is expressed in a completely different manner to the orthologous mouse Hoxa-1 gene, having a novel anterior expression domain in the ventral midbrain. Furthermore, midbrain expression is shared by medaka, a distantly related teleost species. This study will take a broader comparative approach to determine when in vertebrate evolution this anterior expression arose. Conversely, the zebrafish hoxb1b gene has an expression pattern remarkably similar to that of the non-orthologous mouse Hoxa-1 gene. Preliminary experiments have established that mis-expression of PG1 genes causes a classic posteriorizing homeotic transformation of the hindbrain. Together these data suggest the hypothesis that zebrafish hoxb1b is functionally equivalent to mouse Hoxa-1; this hypothesis will be tested directly using a novel loss-of-function approach based on antisense morpholino RNAs. A similar approach will be used to test redundancy or synergy of function with the duplicate gene hoxb1a.

DESCRIPTION (provided by applicant): Our long-term objective is to use the advantages of the zebrafish model system to investigate how the vertebrate endoderm is regionalized such that endocrine and digestive organs, including the pancreas, are specified and develop in the correct location. The results of our studies may ultimately facilitate experiments to direct human stem cells to differentiate into specific pancreatic cell types in vitro. Such approaches offer promise for transplantation therapies for diabetes and pancreatic cancers. Our general strategy is to test the hypothesis that molecular mechanisms known to be important in regionalization of the neural ectoderm are also important for endoderm regionalization. In support of this hypothesis, we have established that the secreted signaling molecule retinoic acid (RA), which plays an important role in regionalization of both neural ectoderm and mesoderm, is critical to endoderm regionalization. Thus, RA is required for specification of the pancreas, and exogenous RA has the remarkable capacity to cause anterior endoderm to form large numbers of ectopic pancreatic cells. We propose specific aims to: (1) Determine whether RA is required for pancreas specification in tetrapod vertebrates; (2) Investigate the molecular and cellular mechanism of RA signal transduction during zebrafish pancreas specification; (3) Test the hypothesis that Hox and Parahox genes regionalize the endoderm; and (4) Investigate the roles of Wnt and FGF signaling molecules in regionalization of the endoderm. RA signals may be received in the endoderm where they act cell-autonomously to specify pancreas, or alternatively may be received in adjacent tissues, which then send secondary signals to the endoderm. We will use a cell transplantation approach to distinguish between these hypotheses. Hox genes, and related Parahox genes, encode evolutionarily conserved transcription factors. The vertebrate Hox genes regionalize ectoderm and mesoderm and are frequently RA targets. We are in the unique position of having cDNAs to all the zebrafish Hox genes, this will allow us to use gain and loss-of-function approaches (Mrna mis-expression and morpholino knockdown) to determine whether Hox genes also act to regionalize the endoderm. Finally, we will use a combination of knockdown, dominant-negative, and mis-expression approaches to investigate whether other secreted signaling molecules implicated in posteriorizing the neural ectoderm, FGFs and Wnts, are also involved in endoderm regionalization.

DESCRIPTION (provided by applicant): The core mission of the pre-doctoral Developmental Biology Training Program (DBTP) is to produce highly qualified, independent research scientists who are trained to take a broad interdisciplinary approach to developmental biology problems. This mission is consistent with the philosophy of the Division of Biological Sciences (BSD) at the University of Chicago, which seeks to avoid artificial boundaries between disciplines and to encourage broad based interaction and collaboration. The interdisciplinary and collaborative nature of the DBTP is enhanced by the structure of the BSD: researchers in all of the clinical and basic science departments are housed in close proximity and united under one administrative and intellectual framework. The DBTP trainers are a vibrant group of thirty-two well-funded researchers, including both experienced senior faculty and talented junior faculty, who are based in nine different basic science and clinical departments. To produce researchers trained in a variety of areas relevant to human health and disease, the DBTP builds on long-standing University of Chicago strengths in developmental biology: of particular importance in this context is the research being conducted in the genetics of model organisms, in mouse molecular genetics, in evolutionary developmental biology, and in developmental neurobiology. Further, during this first funding period, strategic new hires have enabled the program to expand or develop research strengths in the following areas: the cellular basis of development, stem cell biology, and the use of computation/modeling/systems level approaches in developing systems. DBTP trainees are carefully selected from six interdisciplinary graduate training programs: training grant support begins as they enter their second year of graduate studies and generally extends for two years, subject to competitive renewal. We propose to continue to support four trainees each year, allowing us to be highly selective while maintaining a critical cohort of current and previous trainees. Trainees benefit from a strategically designed curriculum that includes three core and three supplemental formal courses in developmental biology, and from an extensive range of supplemental training-related activities. Among these activities are the DBTP sponsored developmental biology Seminar Series and journal/data presentation club, an annual retreat, biennial DBTP mini-retreats, and a biannual, student-run, one-day DBTP symposium. In summary, the DBTP integrates a wide range of varied training approaches to prepare exceptional future leaders in developmental biology research and education.

This NSF MRI Award funds the acquisition of a confocal microscope to expand the research capabilities of faculty at University of Chicago and at the Field Museum of Natural History for conducting research in the fields of organismal and evolutionary biology.Topics of study include examining the functions of ectopic neurons as models for exploring neural circuit evolution in zebrafish, germ band pattern development in flies, the response of plants to bacterial infection and the organization of song circuit neurons in birds. The microscope would provide essential imaging capabilities of cellular and sub cellular structures. The microscope benefits students by allowing them to gain experience in the application of research techniques in classes and independent projects. The results of the research and teaching efforts will be broadly disseminated through abstracts and peer reviewed publications, as well as by active participation of students and faculty at
professional meetings.

? DESCRIPTION (provided by applicant): The University of Chicago Biological Sciences Division (BSD) has a traditional culture of academic research with training and exposure focused predominantly on research career paths in the academy. Yet ten years post-graduation, less than one-quarter (~21%) of our trainees become faculty members in a research-intensive institution. When surveyed, 86% of our trainee respondents supported a more concerted effort to prepare them for jobs outside academia and over 90% of faculty respondents believed their mentees should be provided exposure to a range of career options that use their training. A few enterprising pre- and postdocs have begun to capitalize on expanding translational and education-training programming outside the BSD. Major collaborators in these programs include our Booth School of Business (regularly ranked #1 in the world), its Polsky Center for Entrepreneurship, and our Center for Technology Development & Ventures (UChicagoTech). The University's new Center for Teaching Excellence has also attracted growing participation. These efforts reflect a culture shifting significantly towards broader engagement with innovation and interdisciplinary collaboration, fueled by trainee demand and the reality of fewer faculty job opportunities. With solid support of the President, Provost, and Deans of the University, we propose a program, Chicago Options-In-Careers Empowerment (my- CHOICE), to systematically provide a BSD on-ramp to link to, legitimize, leverage, and help grow these pro- grams, expanding career exposure offerings to our pre- and postdoctoral trainees. We are partnering with UChicagoTech, Polsky and a vast network of internal and external individuals we call Mentors from career areas including biotech, entrepreneurship, medicine, science policy and law, science communication, teaching, and administration to develop and implement this program. We will greatly expand existing Postdoc and Bio- tech Association seminar series to provide broad career path EXPOSURE, create a range of mini-courses for more in-depth EDUCATION in career domains, and guide trainees to a growing set of opportunities for deeper EXPERIENCE in areas of focus. We will use existing infrastructure, and add no extension to training time. We will also hold a portion of the myCHOICE programming in a new facility, the Chicago Innovation Exchange, an accelerator/incubator/event space, to locate myCHOICE events alongside many exemplars of PhDs pursuing non-academic careers. We have developed an innovative evaluation plan to test the hypotheses that more extensive participation in myCHOICE predicts greater trainee career choice empowerment, satisfaction with chosen career, and improved correlation between the FASEB myIDPCareer Fit assessment and career selection. We seek also to quantify the change in academic cost (the salary/lifestyles trainees would sacrifice to be an academic) as they progress through myCHOICE. We will establish strong bidirectional dissemination mecha- nisms, within and outside the University, to share and learn from other BEST programs. Our proposal enjoys extremely strong institutional support and commitment to sustainability beyond the funding period.

Nerves, the major communication pathways of our brain and spinal cord, are made of many individual communication fibers called axons. Each axon carries information from one single nerve cell (neuron). As an embryo develops, these fibers have to connect up correctly in order to make working neural circuits. Before these connections can form, the neurons have to move from the place they are born to the location where they will perform their role. Previously, the Principal Investigators have studied this process in the facial nerve, which controls facial expressions, and found that a single "pioneer" neuron guides the movement of the remaining neurons to their final destinations. Where do pioneer neurons come from, how do they know where to go, and how do other neurons know how to follow them? This project will address these questions in developing zebrafish embryos (animals with facial nerves similar to humans). Zebrafish embryos are transparent, and the experiments use specially-engineered zebrafish whose facial neurons are fluorescently labeled to make their cell migration visible. Experiments will also examine the roles of particular molecules found on the cell surface that are important for cell migration (cell adhesion molecules). A new kind of 3-dimensional imaging (light sheet microscopy) will be used to measure cell movements, and new software will be developed to visualize and analyze cell movement data. Once developed and tested at the University of Chicago and the Marine Biological Laboratory, these software tools will be made freely available. The project will additionally provide training opportunities for high school, undergraduate and graduate students; introduce elementary and middle school students to research; and engage the public via interactive displays at the Museum of Science and Industry (MSI).

Subsets of neurons migrate tangentially within the neuroepithelial plane, often over significant distances. To better understand mechanisms underlying tangential migration that are important for neural circuit formation, this project focuses on facial branchiomotor neurons (FBMNs), which undergo a tangential migration that is conserved in vertebrates ranging from fishes to mammals. The study will utilize zebrafish embryos as they are accessible, transparent, and a powerful genetic model. Migrating FBMNs will be imaged in transparent zebrafish embryos with genetically marked cells, and tracked using light sheet microscopy. The Principal Investigator recently described the pioneer neuron as the first FBMN to migrate on each side of the hindbrain, and demonstrated the critical role of this neuron. Aim 1 will study the newly recognized pioneer neuron by establishing its cellular origins and tracking its subsequent trajectory through development. FBMN tangential migration also relies on interactions with two different pre-laid axon tracts and both interactions depend on adhesion molecule N-Cadherin. Aim 2 will investigate the role of N-Cadherin in mediating interactions between FBMNs and axon tracts, and whether it functions autonomously within neurons during migration. Additional adhesion molecules important for FBMN migration will be identified using RNAseq. An integral part of this project will be the development of new, broadly-applicable computational tools to analyze imaging data.

Current research in biology is producing increasingly large and complex sets of data. These data could represent, for example: DNA sequences, images of the brain, or number of species in an ecosystem. In each case, unlocking the information within these big data sets requires sophisticated mathematical and computational approaches. The standard curriculum for graduate students in biological sciences was designed well before this data deluge. As a consequence, today's graduate students are not being adequately trained for their future careers. At the same time, there are growing concerns that scientists are sometimes unable to reproduce published findings. This inability often results from poor data analysis strategies. The future success of the US biological research mission hinges on training students to use data analysis approaches that are both rigorous and reproducible. This National Science Foundation Research Traineeship (NRT) award in the Innovations in Graduate Education (IGE) Track to the University of Chicago seeks to meet this need by developing a new and effective approach to the training of early stage graduate students in the quantitative analysis of biological data.

The overarching goal of this program is to teach students to critically evaluate quantitative analysis methods in the scientific literature, and to acquire good programming habits that support reproducibility and rigor in their own research. An interdisciplinary team of quantitative biologists will direct and lead the program, exposing students to the faculty that can advise them in future work. The training program begins with an intensive residential week-long boot camp that brings together students across diverse sub-fields of biology to promote teamwork and prepare them for interdisciplinary research. The boot camp includes introductory tutorials in computer programming, statistics, and modeling in modern biology, as well as more advanced tutorials in statistical approaches to large data sets and practical lessons in organizing and sharing code and data. The boot camp is capped off with a series of workshops in which students apply what they have learned to real biological data spanning a wide range of fields. A subsequent on-campus course builds on and reviews these concepts, and integrates training in rigor and reproducibility with concepts of responsible research. We hypothesize that this program will produce trainees who are well-prepared for the future scientific workforce. We will evaluate the impact of this intervention through quizzes, surveys, and targeted interviews. All teaching materials and data sets used in the workshops will be shared online so that any university can implement a similar training module on their own campus.

The NSF Research Traineeship (NRT) Program is designed to encourage the development and implementation of bold, new, potentially transformative models for STEM graduate education training. The Innovations in Graduate Education Track is dedicated solely to piloting, testing, and evaluating novel, innovative, and potentially transformative approaches to graduate education.