The ProjectLab: 2015-16 MQP Opportunities

What is 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 (GH 006) along with the rest of the teaching labs. This year 7 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 http://www.wpi.edu/Images/CMS/Bio/new-projectlab-application.pdf and return them to Mike Buckholt at mbuckhol@wpi.edu or just send me the info if you have problems with the form.

 

The Projects

 

The Phytoestrogen and Artemisinin Projects:

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.

Artemisinin is a plant derived compound that has been used as a treatment for malaria thre is also evidence that it can affect the growth of cancer cells. This aspect of the project will explore the proliferative or antiproliferative effects of artemisinin on cancer cells lines to evaluate its usefulness as a natural anticancer compound. This is a new project for the project lab and will allow for a lot student input and direction.

Techniques: Cell culture, Plate assays, Protein assays, Western Blotting, Protein gels, HPLC

Preferred team size 1-3 students

Project codes: MB2-PE16 or MB2-AR16

 

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.

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

Students: 2-4

Project Code: MB2-CM16

 

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

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

Students: 2-4

Project Code MB2-PR16

 

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.

The picture is an example of one such nematode collected from California.

Techniques: microscopy, morphometry, PCR, Bioinformatics

Project Code MB2-RW16

 

Synthetic Biology

Are you interested in genetic engineering? Would you like to try and solve a global problem using biology as a tool? This MQP opportunity will give students experience in the emerging field of Synthetic Biology, defined loosely as 1) the design and construction of new biological parts, devices and systems; and 2) the re-design of existing natural biological systems for useful purposes. Specific topics for these projects will be student-defined and will begin with the framing of a problem. Students will then use the scientific literature to design solutions to that problem, which they will then build and test in the lab. The model organism we will use for this project is the bacteria E. coli. You will be amazed what these little bacteria can do! Interested students are encouraged to visit igem.org/About to learn more about synthetic biology and view sample projects.

Techniques: cloning, transformation, bacterial culture, PCR, sequencing, microscopy, plate reader assays

Preferred team size: 2-3 students

Project Code: MB2-SB16

 

2015 Summer MQPs with Prof. Marja Bakermans

Connecting migratory bird populations with feather isotope analysis
This particular MQP uses molecular methods to examine the migration ecology of migratory songbirds. For songbirds, migration is the least understood portion of their life-cycle as these species move over vast distances and are too small for advanced telemetry devices like satellite tags. As a result, researchers are now using molecular methods to answer questions about bird migration. A full understanding of migration ecology is critical for bird conservation because greater than 80% of annual mortality has been found to occur during migration.

For this project, students will prepare feather samples for a Hydrogen stable isotope analysis. Isotopes differ in their number of neutrons, giving them a different atomic mass. Hydrogen occurs as Hydrogen-1 and Hydrogen-2 or Deuterium. The ratios of the Hydrogen isotopes vary across the globe, and due to patterns in precipitation, Deuterium becomes less common as you move away from the poles. This isotopic “signature” moves up through the food chain because an organism’s H isotope reflects what it ingests. This isotopic signature is incorporated into a bird’s feathers when they replace their plumage (molt) after breeding but before they initiate fall migration. Once a feather is fully grown the tissue becomes inert, and its composition is retained indefinitely.

Feather samples have already been collected for six species of migratory birds (Magnolia Warbler, Yellow-rumped Warbler, American Redstart, Lincoln’s Sparrow, White-throated Sparrow, and Dark-eyed Junco). All samples were collected at the Powdermill Avian Research Center in southwest Pennsylvania during fall migration in 2010. For each species, feather samples were collected on a variety of age (hatching-year, after-hatching year) and, when possible, sex (male, female) classes were identified. Results from the isotope analysis will be used to examine migration patterns for each species and whether separate age and sex categories show different patterns. This project offers students the opportunity to use state-of-the-art technology to learn about animal migration.

Techniques: cleaning and preparing samples, analysis of isotope data

Number of students: 2-3; A-C terms

 

Image source: http://www.animalmigration.org/stable_isotopes/index.htm

 

Conservation science for American Kestrels

American Kestrel, Falco sparverius, the smallest and most colorful falcon in North America has been experiencing precipitous population declines throughout New England (-5.2%/year, Sauer et al. 2014) due to loss of breeding habitat and declines in food supply. This species is a secondary cavity nester that uses cavities excavated by other species or human-built nest boxes. Recently, Massachusetts Division of Fisheries and Wildlife and its partners have installed >40 nest boxes in Massachusetts and are monitoring nesting activities. This project will collaborate with Massachusetts Division of Fisheries and Wildlife and examine 1) differences between occupied and unoccupied nest boxes and 2) nest provisioning and reproductive success rates at occupied boxes. Students will locate nesting pairs of American Kestrels and monitor nests throughout the summer (i.e., mid-May through early-July). Data collection will include date of laying, clutch size, interactions with other species (e.g., invasive species, European Starling, Sturnus vulgaris), nest predation rates, provisioning rate, and type of food prey brought to nests. Once nestlings are large enough (i.e., 18 – 22 days old) students will help with data collection of banding efforts by Andrew Vitz, Mass Wildlife State Ornithologist.

Techniques: field collection, behavioral observation, animal handling

Number of students: 2-3; E terms