John McCutcheon, PhD - US grants

This IGERT award establishes the Montana Ecology of Infectious Disease (M-EID) program at the University of Montana. The program focus on ecology of infectious diseases addresses the need to train leaders in an emerging field of global and local importance with considerable scientific, societal, ethical and policy aspects. M-EID has three major components: 1) interdisciplinary, team-based training in mathematics, computation, and biology; 2) specific training in establishing collaboration, team-building, and effective communication among disciplines and to other societal sectors; 3) professional development and career enhancement. M-EID faculty are from mathematical, computational, ecosystem, and biological sciences. The main research focus areas encompass different temporal and spatial scales and different levels of biological organization, providing fertile ground for innovation in mathematics and computer science at the interface of biology. Through an interwoven curriculum and guided application and experimentation, M-EID trainees will develop expertise in a primary discipline that will be applied to an interdisciplinary research problem. Trainees will have explicit training in team building, communication across the sciences, and effective teaching. M-EID has relationships with individuals, institutions, and agencies in the U.S. and abroad providing Fellows with additional venues to develop academic excellence and career opportunities. M-EID focuses on recruitment of Native Americans and other underrepresented groups through ties with tribal colleges and undergraduate summer institutes serving minorities and women. This program will serve as a model for small- to mid-sized institutions in effective interdisciplinary graduate education emphasizing both academic excellence and effective collaborative and communication skills. IGERT is an NSF-wide program intended to meet the challenges of educating U.S. Ph.D. scientists and engineers with the interdisciplinary background, deep knowledge in a chosen discipline, and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to catalyze a cultural change in graduate education by establishing innovative new models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries.

At the University of Montana (UM), the Advancing Research through Network Improvements (ARNI) project provides dedicated high speed desktop and building level connections for several key sites housing active research requiring large bandwidth. This project removes an identified bottleneck and allows researchers to take advantage of the Northern Tier Network (NTN), a 10Gb network path spanning Seattle to Minneapolis. ARNI is a key component of a 10 year UM Information Technology Office (ITO) cyberinfrastructure improvement effort which developed a high-speed, high availability network path from the campus edge to the national information superhighway, and a resilient campus core network. ARNI greatly extends the ability of UM researchers to participate in their sphere of science, work in collaboration with other partners and disciplines at national and international levels, and extends the impact of these research efforts to students and to a broader research community. ITO, in collaboration with the Social Science Research Laboratory (SSRL) and researchers from the Division of Biological Sciences, Geography, and Geosciences, identified multiple scientific research projects that benefit directly from ARNI. These include projects that employ genomics methods in biological sciences, geodynamics research on earthquakes in East Africa and Central Asia, and a prototype system for predicting insect and climate-induced impacts on fire hazards in the western United States. A special aspect of this project is the direct association between IT professionals and the campus scientific research community which is providing sound IT solutions that are critical for future competitiveness in grant funding and academic contribution.

Insects are ideal model systems for studying associations between animals and microorganisms because of the diversity of interactions formed between them. These interactions, or symbioses, span a wide continuum of types, from those that are pathogenic and short-lived to those that are beneficial and stable over extremely long periods of time. Sap-feeding insects in particular have been shown to form intimate and stable symbioses with bacteria that live exclusively within insect cells. This strict intracellular lifestyle has profound effects on the symbiotic bacteria, effects that are dramatically manifest in their highly reduced genomes. This project will investigate a symbiosis involving a cicada that lives in the southwestern United States and its dual bacterial symbionts. One of these symbionts, named Hodgkinia, has a remarkably small genome encoding many fewer genes than was thought possible for an autonomous organism. The investigators will use both genetic and molecular techniques to uncover the mechanistic changes that have allowed Hodgkinia's extreme genome reduction. It is expected that adaptations in both the host insect and symbiont will be found that enable such dramatic gene loss. This work has broad-reaching consequences for the way we understand genome reduction in bacteria, the integration of organisms in the context of intimate symbioses, and the formation of cellular organelles such as mitochondria. The broader impacts of this project will involve the training of several undergraduate students, one graduate student, one postdoctoral fellow, and several K-12 teachers and students through collaboration with the Missoula County Public Schools and College of Education and Human Sciences at the University of Montana.

Endosymbiosis is a process whereby one cell takes up stable residence within another cell, occasionally allowing the new consortia to harness previously unexploited resources. For example, plants are able to use the Sun's energy because of an ancient endosymbiosis between a bacterium and a eukaryotic cell. Similarly, many sap-feeding insects-some of which are devastating crop pests-rely on bacterial endosymbionts to survive. Insect endosymbioses are useful models because they are of an intermediate age: old enough to show many parallels to mitochondria and chloroplasts, but recent enough to retain a clear bacterial character. Studying insect-bacterial symbioses thus provide insight into the forces and mechanisms involved in establishing and maintaining bacteria-host relationships. This proposal includes outreach through a children's science program to teach about bacterial symbioses.

Obligate insect endosymbionts have highly reduced genomes that have lost many genes compared to their free-living ancestors. Similar to organelles, some endosymbiont genomes contain fewer genes than thought necessary to support cellular life. This project will use the cicada endosymbiont Hodgkinia as a model to study how symbionts with reduced genomes function with so few genes. The PIs will investigate the structure and function of Hodgkinia-supporting insect tissues using a combination of cutting edge light and electron microscopy, with the aim of better understanding if and/or how insect hosts provide symbionts with essential cellular components. The awardee will answer these questions by labeling cicada proteins and RNAs to localize these gene products within symbiont-harboring tissues. The results of this study are important for understanding host-bacterial interactions, the evolution of organelles, and for improving microscopy methods on insect tissues.

All plant and animal cells contain mitochondria, the specialized structures that generate a cell's chemical energy. However, mitochondria are not just any cellular component; they are the result of an ancient bacterial infection. They essentially are bacteria that permanently live in our cells; they have become part of us. Until just a few years ago, it was thought that the mitochondrion (and its partner structure in plants, the chloroplast) was unique in biology. Recent work has shown that many mitochondrion-like relationships exist in biology. Insects in particular have repeatedly developed relationships with bacteria that have taken up permanent residence in their cells. These bacteria show many similarities to mitochondria, particularly in reference to genome structure. The goal of this project is to use recent discoveries about the bacteria that live inside cicadas as a window into the origin of mitochondria and chloroplasts and how they integrate with the cells in which they are found. . The work described in this project will use cutting-edge genomic experiments to accomplish these goals. This work is computationally intensive, and as such the educational component of this research will focus on teaching computer programming and its applications to Montana students at all levels. This work will have the important outcome of increasing the competitiveness of Montana students by giving them the computational tools they need to handle diverse, complex, and large sets of data.

Mitochondria originated only once in the history of life, a very long time ago, and the details of their evolution remain obscure. Research into the mitochondria of diverse plants, animals, and single-celled organisms has revealed striking diversity in mitochondrial genome structure and size. Insects acquired bacterial endosymbionts much more recently than the origin of mitochondria, and so many of the features associated with the origin and establishment of the mitochondria are seen in insect endosymbionts but are less evolved. Recent work has shown that, like mitochondria, some insect endosymbionts have undergone extensive genome fragmentation and expansion. This research will use genome sequencing, transcriptome sequencing, molecular evolution, and field biology to provide insight into why some endosymbiotic genomes stay stable, while others diversify. This project includes activities that will teach University of Montana undergraduates and graduate students the fundamentals of computer programming using genomic data. The proposal will bring together students of biology that lack any computational background with students from the graphical arts for whom data visualization techniques are routine into a single course. These students will work collaboratively with each other to create new ways of visualizing massive genome data.