A sample project in biochemistry for undergraduate students:
Cloning and Sequencing Lactate Dehydrogenase (LDH) gene
LDH is an abundant enzyme involved in anaerobic fermentation in animals and plants. Students will amplify this conserved gene from a novel genome (ginger, for example) whose LDH gene sequence is not known to date. Students will extract genomic DNA from the chosen plant and amplify the LDH gene using PCR and nested PCR. Students have to design and test the primers for PCR on the known LDH gene sequences. If successful, the PCR products will be purified, cloned into a plasmid vector and the ligated vector will be transformed into the appropriate bacteria host. Further steps include amplifying, purifying and sequencing the plasmid DNA. Extensive bioinformatics analysis will be followed to analyze the new LDH gene sequences.
The new data generated can be deposited in GenBank and the project is suitable for undergraduate research and presentation.
A sample project for graduate students: Early Chemistry on Earth
How could amino acids be polymerized in a non-living system? Catalysis by clay is known. Rock surfaces may also provide catalytic surfaces. The results of the Miller-Urey experiments show a good mix of amino acids which yield amphiphilic, short peptides such as VVVVVE. Many hydrophobic amino acids were produced as well as lesser amounts of Asp (D) and Glu (E). Such peptides would form micelles, vesicles, etc as shown by Zheng et al. at MIT. The goal of this project is to devise hypotheses which can be tested by not so complicated experiments. We can try one or both of the followings: 1. polymerizing esters of amino acids. 2. self-organizing of peptides of random sequences.
My research interests focus on the synthesis and reactivity of borylated organic substrates. Applications include the synthesis of novel ligands for metal organic framework materials of exceptional surface area and the synthesis of novel analogues of Tamoxifen (commercially marketed as Nolvadex™ or Soltamox™), one of the most pervasive anti-estrogenic breast cancer treatments currently approved by the FDA. Both projects involve transition metal catalyzed organometallic synthesis incorporating inert atmosphere techniques. Reactivity studies involving palladium catalyzed Suzuki coupling reactions to assemble the molecules with specific design features are a key component of both projects.
Additional projects include: (i) the catalyzed oligomerization/polymerization of dimethylsulfoxide (DMSO); (ii) the synthesis of biaryl derivatives for antibacterial activity; (iii) science education related to cyclodiborazane compounds.
Students involved in this research will be trained on the use of modern instrumentation in order to characterize intermediates and products including FTNMR and FTIR spectroscopy and GCMS analysis. In addition, student researchers will gain significant training in the use of inert atmosphere techniques involving dual manifold Schlenk lines or an inert atmosphere drybox.
Development of student scientists will be the primary focus of my research program. Students in my lab will be presented with the opportunity to develop synthesis techniques and skills in the pursuit of small biologically active natural and unnatural products that may allow for future cooperation with other scientists to test their biological activities, or in the development of novel and useful synthesis methodologies. Students will serve a vital role in the experimental investigation. I will work closely with the students, giving them increased freedom to make decisions, and encourage them to individually solve daily synthetic challenges as they develop into competent investigators. Students who study in my lab will be well suited to serve as laboratory scientists in the chemical industry, government labs, or be prepared well to begin a graduate career in a top-tier research institution. Specific interests include compounds that belong to polyphenolic and alkaloid families, as well as other secondary metabolites. Development of new and useful chemical transformations is another interest of mine. These include the use of microwave-enhanced chemistry to develop organic reactions in aqueous media. While performing research with me, students will get exposed to air-free glassware, chromatography, distillation, and other organic techniques. They will analyze products with NMR (H1, C13, and 2D), GC-MS, and IR.
My research efforts are focused on two primary areas of focus: utilizing new technology /new teaching methods in the classroom and developing unique inquiry-based laboratories/demonstrations.
For the introduction of new technology into the classroom, students will be involved actively with developing novel classroom uses for technologies such as handheld tablets, smart boards, classroom clickers, and "App" development. A typical student project might involve a student developing an "App" which can be utilized in the classroom, or a unit where clicker technology can be utilized and assessed. In addition to technologic based educational studies, I am interested in utilizing novel teaching method(s) in the classroom, and assessing their usefulness in enhancing student learning (examples include meta/cognitive study skills)
Another avenue of research a student might focus on will be assisting in the ongoing efforts to author and develop novel, inquiry-based labs that can be utilized in a Chemistry Curriculum (with a particular focus in General Chemistry II, and the Chemistry for Non-Science Majors Laboratory Course at the College level). A typical project might involve a student developing a new chemistry laboratory or chemical demonstration.
(PHYSICAL / COMPUTATIONAL CHEMISTRY)
My research interests involve the development of computational methods, in particular, the construction of consistent basis sets for extrapolation to the complete basis set limit. Reliable benchmarks for the development of wavefunction methods are lacking, owing to the prohibitively expensive computational resources required for such high-level theories. As such, extrapolations using a consistently constructed family of basis sets can be utilized to obtain these benchmarks in a more cost-effective manner.
As computational chemistry is inherently multidisciplinary, there are plenty of opportunities for utilizing calculations in the elucidation of molecular structures, stabilities, and mechanisms. An example of a project in this direction would be the use of DFT (density functional theory) techniques to investigate organic light emitting diode (OLED) type complexes, and how varying the functional groups on the ligands affect properties such as fluorescence, structure or reactivity. There are plenty of opportunities to provide computational support to ongoing experimental research in the department, for example, involving the quantum mechanical investigation of the structural and proton NMR properties of various cyclodiborazane derivatives synthesized in the Lesley laboratory.
(GENERAL / ANALYTICAL / INSTRUMENTAL CHEMISTRY)
I am interested in researching the interface of biology and environmental chemistry to determine human health implications. One of these research projects seeks to improve the measurement of arsenic in water and soil samples using commercially available field kit technology, employing digital image analysis to improve the accuracy of the devices. Another research project uses mass spectrometry methods to examine endocrine disrupting molecules in fish tissue to explore the connection between environmental contaminants and their impact on biological systems. These projects are intended to engage students in the areas of fundamental research, critical thinking, writing skills, speaking and preparation for employment.
(GENERAL / MEDICINAL CHEMISTRY / CHEMICAL GENOMICS)
My research interests are focused on medicinal chemistry. In particular, I am interested in the design and synthesis of novel, biologically-active molecules with the potential to address unmet medical needs. These molecules can serve as a starting point for drug discovery and as valuable research tools to investigate complex biological systems. In this context, students in my lab have the opportunity to develop skills in synthetic organic chemistry, ligand design, and the interpretation of biological screening data. We use a variety of techniques such as molecular modeling, traditional and parallel organic synthesis, flash chromatography, HPLC, NMR, and MS. Therapeutic areas of interest include cancer, inflammation, and neuroscience.
(GENERAL / BIOPHYSICAL CHEMISTRY / BIOCHEMISTRY)
My research group focuses on finding new antimicrobial therapies. Antibiotic resistance is a global public health concern. One of our primary research projects pertains to understanding and disrupting how bacteria communicate via quorum sensing. We rationally design small molecules to selectively bind and interfere with bacterial communication to inhibit bacterial infection and biofilm formation as an alternative to antibiotics. The other project we are focused on is finding new therapies for Lyme Disease. It has become the most common insect-borne disease and impacts upwards of 300,000 people in the United States. Our research group is interested discovering and isolating compounds from natural plant extracts that exhibit promising activity against Lyme infection and determining how these small molecules interact with bacterium responsible for Lyme. Students in my research group will learn standard organic synthesis techniques, including rotary evaporation, flash chromatography, TLC, HPLC, NMR, and MS.