The ProjectLab: AY2014-15 MQP Opportunities

What is the ProjectLab??

The Biology & Biotechnology ProjectLab provides MQP opportunities for students to work on projects directly affiliated with department faculty research in the in the department’s MQP lab on campus. This lab is located in Goddard Hall along with the rest of the teaching labs. This year 9 projects are available in the project lab that accommodate multiple student teams and approaches, and range from animal to plants in the areas of study. Each project is proposed and sponsored by a Biology & Biotechnology faculty member and designed so that the data from the project will contribute directly to that faculty member's current research. Daily work on the project will be overseen by the Project Lab Director (Mike Buckholt). Weekly meetings of the teams, the lab director, and the faculty sponsor will allow students to present their work to the group and to understand how their findings, along with those of other students working on the project, contribute to the overall research goals. Projects will run throughout the academic year and may start or continue into E term if student interest warrants. Not all students need to be registered for every term. Varying schedules of terms and credits can be accommodated.

Students interested in working in the ProjectLab should apply using the form at and return them to Mike Buckholt at or just send me the info if you have problems with the form.

The Projects

Sentinel species for water quality:

Crayfish can also be used as a model organism to examine local water quality. Nearly all of the chemicals we use, whether residential or industrial, eventually end in the watershed and in particular the sediment in the bottom of lakes and streams. Animals like crayfish that live in that environment can serve as excellent sentinel species to track accumulation of toxins. This project focuses on the distribution of polyaromatic hydrocarbons, in particular on benzo[a]pyrene (BaP). Previous projects have demonstrated a correlation between the level of BaP in crayfish tissue and river sediment where the crayfish were collected. Future work could follow one of two tracks: obtaining statistically significant correlations between sediment and crayfish levels of BaP, or investigations centered on the questions of how fast crayfish accumulate environmental BaP in their tissues and/or how fast accumulated BaP is metabolized and/or excreted.

Phytoestrogen project:

Phytoestrogens are plant compounds that can mimic the effects of human steroids. Since traditional hormone replacement therapies for post menopausal women have several associated health concerns, including a potential increase in the risk of breast cancer, phytoestrogens are often marketed as a safe and natural alternative to estrogen. However, these products vary considerably and are not well characterized or tested. Using a well characterized estrogen responsive breast epithelial cell line, we will test the effects of available phytoestrogen products on cell growth. We will also begin to characterize the products, separate the components and test them individually and in combinations using the cell model system. Preliminary studies suggest that some of these compounds may have anti-proliferative or pro-apoptotic effects, which may make them attractive from a therapeutic standpoint.

Techniques: Cell culture, Plate assays, Protein assays, Western Blotting, Protein gels, HPLC
Preferred team size 1-3 students

Project code: MB2-PE15

Investigating the function of plant nano-motors using RNAi-based knock-downs

Plant cells have the largest collection of intracellular motors from all eukaryotic cells. Some of these motors drive many important cellular functions, including mitosis, cytokinesis, intracellular transport, and secretion. Because of their large numbers, several of the motors are not well characterized and their functions are unknown. This MQP will focus on the characterization of some of these motors at the molecular level using RNA interference (RNAi). The initial phase of the research involves designing and building genetic constructs using advanced cloning techniques. Subsequent phases involve plant tissue culture, plant genetic modification, and fluorescence microscopy. After the completion of this project you will have developed extensive molecular and cellular biology skills. These skills will be beneficial for your future career and are not only limited to plant biology. Teams of 2-4 individuals are suggested, but single students are also encouraged to apply

Project Code MB2-PR15


Tissue culture, plant genetic modification, and fluorescence microscopy, RNAi.

Students: 2-4

Roundworm/nematode diversity in Central Massachusetts

Did you know that roundworms are one of the largest groups of animals inhabiting the planet? These organisms are present on land and water. There are both benign and pathogenic species found in many locales. Very little is known about the various species that inhabit the soil of New England and Massachusetts in particular. Knowing what species can be found here is the first step in understanding more about our soil ecology and the distribution of roundworms. The purpose of this MQP is to begin defining the species that can be found in our area. The initial phase of the project will involve collecting diverse soil samples from the surrounding area. The next phase of the project will include isolating and characterizing the nematodes present in the soil samples on both the macroscopic and molecular levels. These investigations will include characterization of brood size, morphometry and PCR techniques to complete the classification of nematodes. The data generated from the experiments will be then be overlaid on to the map of Central Massachusetts to show the species distribution. A secondary goal of this project is to develop a set of techniques that can eventually be used to turn this into a citizen science project in which K-12 students from all over could participate.

Here is the example of one such nematode collected from California.

Project Code MB2-RW15


microscopy, morphometry, PCR, Bioinformatics
Students: 2-4.


Stressed out! Environmental toxins and the cellular stress response

The cellular stress response protects the cells of our bodies from harm during periods of acute stress such as abrupt temperature changes, energy depletion, and brief high-dose exposure to toxins. While we typically think of exposure to toxic or stressful conditions to be a bad thing, many studies have shown that low levels of chronic stress can actually be beneficial to cellular survival when cells are later exposed to an acute stress, a phenomenon known as adaptive stress response or hormesis. In this MQP, students will study the effects of a variety of environmental contaminants on the adaptive stress response and on cellular survival during acute stress. Common contaminants to be investigated include arsenic, bisphenol-A, and several pesticides.

Ecology and evolutionary biology

Ecology and evolutionary biology have strong applications in many areas, such as natural resource conservation, agriculture, and epidemiology. Projects in the discipline of applied ecology and evolutionary biology may be available in the following areas:

Insect-plant biology and integrated pest management.

While agricultural productivity has increased dramatically in the past 50 years, modern agricultural practices are generally costly in terms of their environmental impacts. The application of ecological theory has great potential for reducing negative impacts, and the practice of “integrated pest management” is one such application.

Biodiversity in North American crayfish.

Humans have many impacts on natural ecosystems, and these impacts generally contribute to decreasing biodiversity (the loss of species and populations). Our understanding this process is hampered by poor information on the distribution and patterns of biodiversity across taxonomic groups and geographic regions. North America is a center of biodiversity in freshwater crayfish, and this phylogenetically rich group of organisms can be used as an ideal model to understand evolutionary and biogeographic patterns of biodiversity in this region. Projects in this research focus will involve molecular phylogenetic and population genetic investigation, including both wet lab and bioinformatic components. Students will learn and/or practice skills in DNA manipulation, PCR, sequencing, and analysis of genetic data.

Project Code:MB2-CM15

Techniques: Field collection, DNA extraction and analysis, PCR, Sequencing, and analysis of molecular data, bioinfomatics



2014 Summer MQPs with Prof. Marja Bakermans


Housing developments and breeding bird community

This particular MQP examines the effects of low density housing developments on the distribution and breeding success of forest birds. Overall, across the northeast, forest birds have benefitted from forest maturation over the last several decades. Following large-scale abandonment of agriculture, forest cover in Massachusetts has rebounded from a low of about 30% during the late 1800s to over 60% today. This represents one of the great conservation success stories in North America. However, greater than 75% of forest land in Massachusetts is privately owned, and forest land in the state is now beginning to decline as thousands of acres of forest are cleared annually. Although single family homes account for only a portion of deforestation, the negative effects of these structures may extend far beyond their physical footprint. For example, due to an increase in available food associated with human habitation (e.g., garbage, bird feeding), nest predators (e.g., domestic cats, blue jays, squirrels) often have elevated abundances in suburban or exurban areas. This increase in nest predators may have profound effects reaching far into the forest interior and may be one reason that populations of many species of forest birds continue to decline in Massachusetts.

The goal of this project is to compare avian abundance, diversity, and nesting success at study sites in forests perforated by single-family homes compared to those in completely forested landscapes. At each site, we will conduct bird surveys and monitor nests to determine if they successfully fledge young. On a subset of nests we will use motion activated wildlife cameras to document nest predators. Lastly, students will quantify abiotic factors (e.g., local habitat characteristics) associated with each study site and nest location to evaluate its effect on nesting success. The results of this study will be used to improve our understanding of how single-family homes within a forested landscape alter the ecology of the forest ecosystem. If interested, students may have the opportunity to present their results at a local or regional conference. This project will be conducted in collaboration with the Massachusetts Division of Fisheries and Wildlife.
Techniques: field collection, behavioral observation, animal handling, camera trapping
Number of students: 2-4; E terms

Image: BioMap2 (Commonwealth of Massachusetts-DFG and The Nature Conservancy, 2010)