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Undergraduate Program: Research Opportunities: REU Program

Collaborative Projects

Students applying to our REU program will no doubt have divergent interests and backgrounds. Therefore, we have identified exciting collaborative project areas that fall under the umbrella heading of recognition system research and will be available for two students each. This project list is subject to change.

  1. Resource Allocation and Reproduction in Colias Butterflies
    (S. Lewis)
    Most butterflies feed only as caterpillars, and during metamorphosis they must confront the herbivores' dilemma: how should they best allocate limited nitrogen to maximize their growth, survival, and reproduction? Evolutionary theory predicts that organisms will prioritize specific traits that are most directly related to fitness. This REU project will experimentally manipulate the dietary nitrogen of Colias butterflies and measure changes in resource allocation. Nitrogen allocation to different tissues will be measured for both sexes, and adult mating behavior and reproductive success will be monitored in large outdoor flight enclosures. This project combines lab and field studies that will enhance our understanding of sexual selection and the evolution of sexual size dimorphism.
  2. How does a caterpillar "feel"? Sensory signaling in softbodied locomotion.
    (Barry Trimmer)
    In contrast to animals with stiff skeletons, soft-bodied animals have no easily defined joints. They can move in any plane by crumpling, rotating and bending. These movements are partly coordinated by central pattern generators but must also use information about body position (proprioception) and interactions with the environment (exteroception). It is not known how such sensory signaling is collected and incorporated into the control body of soft-bodied locomotion. This project will build on previous results from kinematic studies of the tobacco hornworm, Manduca sexta, to identify how they use sensory information during movement. The results of these studies are expected to contribute to our understanding of animal movements and to the construction of soft climbing and burrowing robots under development in the Tufts Neuromechanics and Biomimetic Devices Laboratory. This project is interdisciplinary with biologist and engineers working alongside one-another. Students will learn to be comfortable using both sophisticated equipment and custom-made devices built from plastic, glue and duct tape!
  3. Transcription and trinucleotide repeat instability in budding yeast
    (C. Freudenreich and M. Koch)
    Maintaining genome stability is critical for every cell. Several fatal genetic diseases originate from an expansion in a trinucleotide repeat (TNR), such as the CAG repeat. TNRs can assume unusual structures, and are therefore difficult to replicate and repair. This can lead to repeat instability (expansions and/or contractions). The Freudenreich lab explores instability of CAG repeats in a budding yeast model system, using an expanded CAG repeat from a human patient contained on a yeast artificial chromosome. Results show that transcription through the repeats can also cause CAG instability, and this REU project will investigate how that occurs. Students involved in this research project will use genetic and molecular techniques to address this research question.
  4. Recognition and repair of DNA double-strand breaks in Drosophila
    (M. McVey and V. Khodaverdian)
    Repair of DNA lesions is critical to genome stability and cell survival. One of the most serious types of DNA damage is the DNA double-strand break. Several different pathways of break repair have been described that promote accurate rejoining of breaks and therefore prevent genomic instability. When these preferred repair pathways are compromised, the use of inaccurate repair mechanisms can lead to cellular dysfunction, cancer, and premature aging. This REU project will investigate the effects of mutation of various DNA repair genes on genome stability and overall fitness in the model metazoan Drosophila anogaster. Undergraduates working on this project will apply both genetic and molecular techniques to gain insight into inaccurate repair mechanisms.
  5. The world of the wool-carder bee
    (P. Starks & K. Graham)
    The wool-carder bee, Anthidium manicatum, has a polygynous mating system featuring territorial defense by males. These males spend most of their time hovering over floral territories, waiting for females to visit in search of flowers, and violently confronting potential usurpers; beyond this, however, little is known about the behavior of this invasive bee species. This project will explore a variety of topics related to the behavioral ecology of A. manicatum, from male mating strategies to kin recognition. As such, students will have the opportunity to make significant contributions to our understanding of a largely unknown insect species. This REU project features a strong hands-on component, as students will assist with field work and observational studies. The project may also include day trips around New England to gather samples from a variety of populations (access to a car is preferable but not required). Students will work with animal behaviorists to master basic techniques/theories of behavioral research with expansions into conservation and invasion ecology.
  6. Changing patterns of aggression over the colony cycle of the European paper wasp
    (P. Starks & J. Pilowsky)
    Paper wasps are able to distinguish nestmates from non-nestmates by sight and scent, and typically respond with more aggression toward non-nestmates. However, no recognition system is perfect, and animals can gain a fitness advantage by adjusting their aggressive responses to social recognition cues based on the costs of making a mistake. We predict that because the costs of accidentally letting in an intruder to the nest change over the course of the paper wasps' colony cycle, the intensity of their aggressive behavior will change as well. This project involves capturing paper wasps from the wild and quantifying their aggression toward nestmates and non-nestmates in captive behavioral studies. Students will learn how to survey and capture wasps in the field, to safely handle the animals, and to plan and conduct ethological studies.
  7. Geophagia in honey bees?
    (P. Starks & R. Bonoan)
    While honey bees are important pollinators, there is currently little known concerning mineral preferences and requirements. Minerals known to be physiologically important in other insects (such as sodium and calcium) are found in a honey bee’s diet in both nectar and pollen sources. However, honey bees reared during a pollen shortage obtain similar quantities of most minerals when compared with those reared in more favorable conditions. This implies that honey bees acquire micronutrients from sources other than pollen and nectar. Historically, the ingestion of soil—geophagia—is known to function as a mineral supplement in various mammalian herbivores. Is it possible that honey bees also partake in this activity? This field project will investigate whether or not honey bees prefer water sources based on mineral content, therefore utilizing water (or soil) as a source for micronutrients. The preparation of mineral solutions will require some lab work however, the majority of the project will be done via observational studies in the field. Aside from acquiring field skills, students will aid in experimental design and management of honey bee colonies. Data collected will lend insight to honey bee health and nutrition as well as the evolution of diet and foraging preferences.
  8. Nutritional ecology of a native insect adapting to exotic invasive plant
    (F. Chew)
    The native mustard white butterfly is adapting to garlic mustard, an exotic, invasive plant that is very attractive to egg-laying female butterflies, but which kills many caterpillars. This "evolutionary trap" is mediated by the attraction of egg-laying female butterflies to plant chemicals, but the unsuitability of the plant for many of the caterpillars. More recently, there is evidence that the mustard white is evolving an escape from this "evolutionary trap." We have found that caterpillars show widely variable growth responses to garlic mustard ranging from early death (from starvation due to a feeding deterrent?) to slow growth (6 weeks versus the more usual 2.5 weeks) to rapid, robust growth. This project will collect data on nutritional assimilation indices to examine differences between families of the mustard white that appear to be completely adapted to the new plant, and others whose performance is less stellar. Some field work in Boston and western MA, some weekend work.
  9. Host shifts and evolutionary adaptations in a native insect adapting to exotic invasive plant
    (F. Chew)
    Introduced plants related to the normal host plants of native insects provide opportunities for host shift and evolutionary adaptation. This project will involve work with the native butterfly Pieris napi oleracea and some of several exotic invasive plants now being used as hosts by this butterfly. Conservation biologists are concerned that its native host plant is disappearing, but the butterfly appears to be making a transition to several novel introduced hosts. We will observe butterfly egg-laying behavior, assess the suitability of the plants for caterpillar offspring, and examine to what degree differing traits contribute to a plant that butterflies respond positively to, and find suitable. This project will involve some fieldwork in western Massachusetts, has opportunity for a student that may be able to start as early as May 15 (with a compensatory slow period from third week in July to end of the REU program in August), and will require some several hours of work each weekend through mid-July.
  10. Latent effects of nutrition on sexual selection in cabbage butterflies
    (F.Chew & S. Lewis)
    Latent effects are experiences that occur early in an individual's life that may later affect fitness outcomes. As herbivores, cabbage butterflies assimilate as caterpillars all the nitrogen they will use as adults. For females this includes the provision of protein for egg yolks; for males this includes not only a protein-rich spermatophore given as a "nuptial gift" by the male to the female at mating, but also nitrogen for white wing pigments that are believed to contribute to a male's sexual attractiveness. This project will examine effects of limited larval nitrogen on mating behavior and follow-up on earlier experiments showing that males reared on nitrogen-deficient diets have nitrogen-poor spermatophores compared to males reared with normal levels of nitrogen in the diet. some field work in Boston and western MA, some weekend work.
  11. Stress responses in wild birds
    (L.M. Romero)
    We know that stress can have a multitude of bad effects, but we also know that in certain circumstances stress is beneficial, especially in relation to wild, free-living animals. This research will aim to increase our understanding of how the endocrine and physiological mechanisms underlying stress help wild animals survive stressful stimuli such as predators, storms, or anthropogenic changes. In order to explore this further, students will work with an endocrinologist, a physiologist, and an ecologist to design experiments to assess how wild birds respond to various stressful stimuli. Undergraduates will take an integrative approach to stress, focusing on neuroscience, endocrinology, and ecology. Focus will be on hypothesis testing, experimental design, and laboratory techniques (including standard endocrinological techniques including taking blood samples, hormone and receptor assays, and statistical analyses).
  12. Genetics of Ecological Speciation
    (E. Dopman & C. Wadsworth)
    According to the biological species concept, species arise from the evolution of barriers to gene exchange between diverging lineages. Ecological barriers, the result of ecologically-based natural selection, consist of habitat and temporal differences that limit gene exchange. The nature of ecological barriers, their genetic basis, and their impact on patterns of reproductive isolation and gene flow are largely unknown. This project will build on previous results from genetic studies of the European corn borer, Ostrinia nubilalis, to identify the molecular basis of temporal isolation. Because ecological barriers are regarded by some as among the most important forms of reproductive isolation in plants and animals, the results of these studies are expected to contribute to our fundamental understanding of the origin and maintenance of Earth's biodiversity. Students involved in these studies will work with a geneticist and will use modern physiological, computational, or molecular biology methods.
  13. Effects of exotic insects on a native tree
    (C. Orians & R. Schaeffer)
    The invasive hemlock woolly adelgid is causing widespread and rapid decline of eastern hemlock in North America. Despite fears that this insect would eliminate hemlocks from southern New England, mortality in this area is occurring much more slowly than predicted. It has been hypothesized that the interaction with another exotic insect, the elongate hemlock scale, could be the cause for this reduced mortality. Understanding how the interaction of invasive species changes eastern hemlock's physiology during the course of infestation is crucial in assessing the impact of these destructive pests and to establish appropriate management. More specifically, this project focuses on studying nutritional, defense-related, and biomechanical plant changes that may ultimately explain mortality or lack thereof in response to these harmful pests.
  14. Studying large-scale expansions of trinucleotide repeats in a yeast experimental system
    (Sergei Mirkin and Jane Kim)
    Simple sequence repeats in genomic DNA occur in coding and non-coding regions of genes throughout the human genome. Whereas short repeats (or longer repeats with interruptions) are stably inherited and have no pathological effects, expanded repeats have been shown to cause over 30 hereditary disorders in humans. Repeat expansions in human pedigrees are large-scaled; that is, the number of repeats could increase from several dozen to several thousand in just a few generations. Our lab has developed two experimental systems in budding yeast to investigate the mechanism of large-scale repeat expansions. The difference between the two systems is whether the repeats are located in a transcribed or non-transcribed region. This REU project will investigate the mechanism of expansion of various trinucleotide repeats using these two systems. Undergraduates working on this project will employ genetic and molecular approaches to understand the genes controlling large-scale expansions as well as potential differences in the profile of instability of various trinucleotide repeats.
  15. Engineering phospho-recognition domains
    (Stephen Fuchs and Adam Lothrop)
    The C-terminal domain (CTD) of RNA polymerase II is extensively post-translationally modified during transcription, forming a "CTD code" that orchestrates the binding of a multitude of transcription-associated factors to the CTD. Antibody-based detection of these modifications is widely used, but results are extremely variable. A potentially powerful and innovative solution is to engineer protein scaffolds to recognize specific patterns of CTD post-translational modifications with high affinity and specificity. Novel domains will be engineered using a variety of molecular biology approaches including random and site-directed mutagenesis and yeast display. Peptides that mimic the CTD with different modifications will be used in iterative selection to evolve proteins with novel binding characteristics. The overall goal is to develop a highly specific class of reagents capable of recognizing distinct RNA polymerase II CTD structures, which could potentially serve as both diagnostic and therapeutic tools.
  16. Biomechanics of swimming in turbulent flows
    (E. Tytell)
    My laboratory studies the fluid dynamics, muscle mechanics, and neural control of swimming in fishes. Each of these aspects of swimming are linked to each other, and our work is aimed at understanding how the linkages allow fish to swim stably and effectively through a complex and unpredictable environment. This project will build on some of our previous work to examine the energetics, mechanics, and neural control patterns for fish as they interact with vortices in the water around them. This is a highly interdisciplinary project in which the student will work with members of the laboratory to develop a device to generate vortices in a controlled manner, then quantify the flow patterns using flow visualization techniques. Then, the bulk of the study will be spent filming fish swimming in various types of vortex flows and measuring muscle activity. Mechanical engineering experience is helpful but not required, and students should have some experience or interests in animal physiology.
  17. Neuromuscular control of acceleration in fishes
    (E. Tytell)
    My laboratory studies the fluid dynamics, muscle mechanics, and neural control of swimming in fishes. Each of these aspects of swimming is linked to each other, and our work is aimed at understanding how the linkages allow fish to swim stably and effectively through a complex and unpredictable environment. This project will examine how fishes accelerate in a straight line, examining muscle activity, body motion, and fluid motion. Students involved in the project will learn techniques for measuring muscle activity, for quantifying body motion, and for measuring fluid motion. Based on the results, they will be able to estimate how the fish produces and controls forces for acceleration, something that is currently not known.
  18. Movement, demography, and ecology of checkerspot butterflies
    (E. Crone and L. Brown)
    Predicting how landscape composition affects wildlife populations requires linking responses at individual, population, and landscape levels. We study across these levels to understand the influence of a declining native host plant and an abundant nonnative host plant on movement and demography of the Baltimore checkerspot butterfly (BCB). BCB adults lay eggs on both the native and nonnative host plants, but survival of the different life stages from egg to caterpillar to butterfly can vary depending on the host plant used. Further, the ability of BCBs to exploit populations of both host plants across changing landscapes depends on the propensity with which they will cross hard (e.g., forest) or soft boundaries (e.g., open fields or country roads), as well as how far into these matrix (nonhabitat) vegetation types individuals are willing to travel before turning back. This project explores several aspects of decisions made by individual BCBs and their consequences for populations dynamics. We will collect local scale movement data on BCBs, and student projects may specifically focus on decisions made by butterflies at the border between habitat and nonhabitat vegetation. Students may also choose to study the implications of host plant choice on larval success and adult behavior. Specifically, does the host plant on which individuals are reared influence rates of larval parasitism? And, does the origin of an adult influence future host plant choice for laying eggs? Students working on this project will learn about butterfly biology, develop critical skills in experimental design, and learn methods for collection and analysis of movement, behavior, and mark-recapture data.
  19. Mechanisms and consequences of bacterial-fungal interactions in cheese rind model communities
    (Benjamin Wolfe)
    Species interactions between bacteria and fungi are are widespread in nature, but we have a limited understanding of how these two microbial groups recognize and respond to one another at a molecular level. My lab is using model microbial communities from cheese and other fermented foods to understand the mechanistic basis of bacterial-fungal interacts and the consequences of these interactions for community assembly. This REU project will use in vitro reconstructions of cheese communities and RNA-seq (transcriptomics) to identify a list of candidate genes and pathways associated with cheese rind bacterial-fungal interactions. We'll also develop transposon mutagenesis libraries for a subset of bacterial species to experimentally dissect the genetic basis for these widespread and economically important microbial interactions.

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