Extending Microbes to Molecules or Phage Hunters
Antibiotic resistance is a growing problem. Recently there have been too few new drugs or ways of combating infection entering the drug pipeline. This project will allow students to choose from a range of options to search for solutions to this problem. Because WPI is part of national effort to find antibiotic producing organisms from environmental samples (BB 2905/290X Microbes to Molecules) students can opt to test putative antibiotic producing samples already isolated and work on purifying and characterizing the antibiotic compounds they produce to determine if they are new and novel. Students could also opt to start from scratch in the isolation process or even explore what types of environmental samples yield the best results. As part of the effort there is also a need to determine the best long term storage method to maintain the viability isolated microbial samples so that we can create a national repository. Students may also choose to explore the option of isolating bacteriophage that might have therapeutic benefits. The direction of these projects can be very student driven and they may be of interest to students that have taken Microbes to molecules or Phage Hunters but taking the course is not a requirement.
Techniques: Will vary depending on the particular project but may include aseptic technique, inhibition assays, TLC, extractions, gel electrophoresis, bioinformatics, phage and bacterial isolation, restriction digestion, PCR, DNA sequencing and HPLC
Preferred team size: 2-4 students
Project code: MB2-MM17
New drugs for an old disease: screening for natural compounds to target tuberculosis
The goal of this project is to screen natural products produced by soil microbes to find new compounds with activity against mycobacteria, the bacteria that cause tuberculosis. Students will screen microbes banked from “Microbes to Molecules” projects to identify those capable of inhibiting the growth of Mycobacterium smegmatis, a model organism with similarity to Mycobacterium tuberculosis. They will then characterize the effects of the microbes on M. smegmatis and determine the nature of the molecules responsible. Important questions that must be answered are:
Does the microbial product kill M. smegmatis or merely inhibit its growth? Can resistant M. smegmatis mutants be selected for, and if so, which genes are mutated? What is the genus and species of the microbe producing the compound? Does sterilized culture medium from the microbe retain anti-mycobacterial activity? Is the anti-mycobacterial activity conferred by a protein, peptide, or small molecule?
Techniques: Will vary depending on the particular project but may include aseptic technique, inhibition assays, TLC, extractions, gel electrophoresis, bioinformatics, phage and bacterial isolation, restriction digestion, PCR, DNA sequencing, yeast two hybrid screens and HPLC
Preferred team size: 2-4 students
Project code: MB2-MS17
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 there 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
Preferred team size: 2-4 students
Project Code: MB2-CM16
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.
Techniques: microscopy, morphometry, PCR, Bioinformatics
Project Code: MB2-RW16
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. Additionally, students will investigate the levels of contaminants in local water and soil samples and correlate these exposure levels to cellular stress responses in the lab. The specific stress conditions or toxins investigated can be adapted to fit students’ interests. Students will learn cell culture, fluorescence microscopy, digital image analysis, PCR, Western blotting, and DNA cloning and expression.
Techniques: cell culture, fluorescence microscopy, digital image analysis, PCR, Western blotting, and DNA cloning and expression.
Preferred team size: 2-6 students (two teams possible)
Project Code: MB2-AS
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