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Impact of Metabolic Stress on Bacterial Surface Chemistry (Walker).
Walker’s research focuses on understanding the factors controlling bacterial adhesion and transport in subsurface and marine environments. Emphasis is on the kinetics of bacterial cell adhesion and transport and the influence of environmental and metabolic stress on the adhesive nature of bacterial cells. MY BEST @ UCR students will investigate the impact of metabolic stress on bacterial surface chemistry and the influence on the subsequent adhesive nature of the cell. A model bacterial species will be cultured under well-controlled and varied growth conditions, and at each metabolic state the cell surface chemistry with be analyzed for surface charge density, zeta potential, hydrophobicity, as well as for extracellular polymer content and composition. Under these growth conditions the cells will also be used in radial stagnation point flow (RSPF) experiments to quantify the kinetics of bacterial adhesion. The RSPF system consists of a specially designed flow cell simulating porous media and groundwater environments.
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Microfluidic Devices for Bacterial Sensing (Vullev).
For rational design and development of microfluidic biosensors, we need to gain a mechanistic understanding of the interaction of selected photomarkers with bacterial spores and vegetative bacteria. For this purpose, we conduct a series of spectroscopic and imaging studies of microfluidic devices loaded with samples of chromophores and strains of interest. During the first two weeks, students will be trained in the microfabrication, spectroscopic (i.e., UV/visible absorption, steady-state and time-resolved emission) and optical imaging (i.e., bright-field, phase-contrast and fluorescence microscopy) techniques. During the following week, the students will prepare prototypes of microfluidic devices according to procedures developed in our laboratory (Vullev et al., 2006), which potentially can be used as sensors, and test their dynamic performance: e.g., sample injection and mixing. Non-virulent strains of bacteria (i.e., strains that comply with biosafety level one) will be assigned to each student for investigating the interaction of the bacteria with a series of photomarkers. Based on their research, the MY BEST @ UCR students will be asked to make recommendations for possible ways for improvements in the sensing methods, specifically, in the choice of photomarkers and in the design of the microfluidic devices.
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Understanding Redox Species in the Mitochondria: Mathematical Insight (Rodgers).
A number of kinetic reactions take place inside and near the mitochondrion during respirations. Targeted gene therapy is now being suggested to modify these reactions in tumors as a possible treatment to cancer (Oberley et al., 2000). A number of animal models have been used to infer the efficacy of such treatment, but difficulty remains in interpreting these results. Recently we demonstrated that mathematical modeling and simulation are powerful tools in understanding these systems (Buettner et al., 2006) and simulation is quickly being recognized as critical for the next level of technological advancements (NSF, 2006). MY BEST @ UCR students will work with an interdisciplinary team to model a number of reactions or transport processes related to the mitochondria. They will have an opportunity to take ownership of their specific problem. MY BEST @ UCR students will learn to use mathematical modeling and simulation tools such as COMSOL®, FLUENT®, Mathematica®, Matlab® and TableCurve® to quickly formulate a model of a particular problem, prepare it for computation and then, most importantly, analyze the results and professionally present their findings.
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In Search of the Mechanisms of Sumoylation: Developing Novel Analytical Tools (Liao).
The study of JAK-STAT pathways led to the first isolation of the SUMO E3 ligase family (PIAS) in mammalian cells, which have strict substrate specificity in vivo. Although, to date, significant numbers of proteins involved in important physiological process have been identified as SUMO targets, the detailed mechanisms of sumoylation, including the substrate recognition/specificity, the regulation of sumoylation/desumoylation cycle, and the fate of sumyolated proteins are just emerging. Three families of SUMO ligases (E3s) have been discovered recently. These include the PIAS (Protein Inhibitor of Activated Stat) family proteins, nuclear pore protein RanBP2/Nup358, and polycomb group protein Pc2. The PIAS family of proteins was originally discovered as inhibitors of STAT transcription factor (Liao et al., 1998, 2000), and they negatively regulate STAT transcriptional activities. The recent successful development of the incorporation of unnatural amino acids in a site-specific manner and the completion of the human genome sequence enable us now to analyze the sumoylation process in the human genome in the context of signal transduction and genome integrity. MY BEST @ UCR students will work with the Liao laboratory to develop tools for sumoylation research, using bioengineering, chemical, and bio/chemoinformatics approaches.
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Cell Membrane Electromechanics (Anvari).
MY BEST @ UCR students will learn how to use optical tweezers for measurements of the electromechanical properties of the cochlear outer hair cells (OHCs) plasma membrane. Effectively, the OHC is a biological nano-electromechanical system. The OHCs are specialized sensory cells with force generating capabilities giving rise to the exquisite sensitivity and frequency resolving ability in normal hearing. Using optical tweezers, MY BEST @ UCR students will form plasma membrane tethers from the OHC lateral wall, and investigate the time-resolved membrane tethering force using optical detection techniques under applied electric field, and in presence of specific amphipathic agents. Inasmuch as the OHCs are implicated in some forms of sensory-neural and age related hearing loss, knowledge of how the cell normally functions may lead to treatment of some types of hearing loss.
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Emulating the Natural Mechanism for Efficient Cellulose Hydrolysis: Engineering a Mini-Cellulosome on a Yeast Cell Surface (Chen).
This research project emphasizes the efficiency of hydrolysis and synergy among cellulases, rather than focusing on the amount of enzymes produced or used. To emulate the success of a natural mechanism for efficient cellulose hydrolysis, a mini-cellulosome will be assembled on a yeast cell surface, enabling the ethanol-producing strain to utilize cellulose and concomitantly ferment it to ethanol. More importantly, by organizing these cellulases in an ordered structure, the enhanced synergy will increase the efficiency in hydrolysis, and thereby enhance ethanol production.
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Individually-addressable Nanowire Sensors Arrays for Nucleic Acids and Proteins (Mulchandani).
MY BEST @ UCR students will learn how to apply the tools of nanotechnology and biotechnology for the creation of next generation nano-bioanalytical devices. These devices will be valuable analytical tools in homeland security, food safety, environmental monitoring and health care. Students will perform research on electrochemical synthesis/fabrication of oligonucleotidesfunctionalized 1-D nanowires using our recently reported one-step, in-situ and individually addressable conducting polymer nanowires arrays fabrication technique for label-free, rapid, sensitive and selective detection of complementary oligonucleotides. The students will also explore the synthesis/fabrication of molecularly imprinted one-dimensional conducting polymer nanowires using the techniques currently being developed in our laboratory for label-free detection of viruses through the label-free detection of coat proteins.
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Bio-Inspired Synthetic Processes (Kisailus).
One major area of research in the Kisailus group at UC Riverside involves studying the processes of biomineralization in order to understand the mechanisms controlling the synthesis and organization (through self-assembly) of the resulting structures. The ultimate goals of our research are to develop novel “bio-inspired” synthetic processes toward novel, technologically relevant materials. To achieve this, we investigate the interactions between the organic and inorganic phases present in these biominerals and understand how they control the nucleation and growth of the material. We then use biologically derived macromolecules (from the organism itself) or synthetic analogs of these molecules, based on lessons learned from analysis of the biological system, to direct the growth of crystalline and amorphous materials in a controlled manner. By modifying the size, shape, phase and orientation of these nanostructures, we can specifically control the resulting properties that are displayed.
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Patch-clamp Electrophysiology for Determining the Calcium Channel Activity in Whole Cells (Zanello).
As part of the overall goal of this NSF proposal for undergraduate education in biology, the Zanello laboratory will offer research opportunities in patch-clamp electrophysiology under the framework of a specific mini-project intended to be completed within a year. The selected students will learn to collect whole-cell current data from the activity of voltage-gated calcium channels expressed in a heterologous cell system such as the CHO cell line. Calcium currents will be recorded with a HEKA EPC-10 patch-clamp amplifier, and analyzed with the Bruxton software for electrophsyiology. Simultaneously with calcium channel activation, the student will record whole-cell capacitance as a measure of exocytosis. Calcium currents and exocytosis will be characterized pharmacologically with dihydropiridine (DHP) agonists and the steroid hormone vitamin D3. We will study the hypothesis that vitamin D3 has binding affinity on DHP-sensitive channels, and therefore constitutes a natural agonist for L-type calcium channels. The modulatory function of the steroid on ion channel activities will be modeled by means of simulation of channel conductance and open and closed states in the presence and absence of the ligand, and structural protein-ligand interaction.
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Biological applications of optical coherence tomography. (Park).
Despite incredible technological advances, histology remains the gold standard for the study of many biological structures. The inherently destructive nature of histological preparation (biopsy/removal, fixation, sectioning) can be limiting, e.g., in longitudinal studies of developing structures. Optical coherence tomography (OCT) has found increasing utility in biological and clinical situations by providing an “optical biopsy.” OCT is a non-contact minimally-invasive technique capable of rapidly acquiring 2D and 3D cross-sectional images similar in dimension and geometry to histological sections. This has proven useful in a wide range of fields, from clinical situations using 3D imaging of the retina for improving diagnosis of ocular diseases such as glaucoma and age-related macular degeneration and endoscopic cardiac imaging for detection of vulnerable plaques that cause heart attacks and strokes, to more basic scientific studies linking thermal injury to collagen denaturation. MY BEST @ UCR students will apply OCT to answer a biological question, and will be expected to customize and engineer the imaging system as needed. Although the primary focus of projects will be on acquisition and interpretation of images for biological research, students will be exposed to a wider range of physical science and engineering topics, including optics, computer programming (Visual C++), and data analysis (Matlab).
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Novel Microfabrication Process Technology Development for Biomedical Applications. (Rao).
Microelectromechanical Systems (MEMS) technology provides considerable promise for enhancing diagnostics and therapeutics, and enabling realization of powerful new tools for scientific discovery in biomedical applications. This promise largely arises from the opportunity MEMS technology provides for miniaturization, massive parallelization, and high-density multifunctional integration, which enables significant increases in performance and ease of use, as well as considerable reductions in size and cost. Within the Biomedical Microdevices Laboratory (BML) at UCR, we seek to develop novel microfabrication process technologies that serve as fundamental enablers for MEMS-based devices and instruments that address critical needs in public health and provide compelling new capabilities for facilitating scientific inquiry and advancing understanding in areas of medical relevance. Students participating in the MY BEST @ UCR program in the BML will be primarily involved in discovery-level research focused on novel microfabrication process technology development, but may also have opportunity to participate in other aspects of MEMS device development, including device design, analysis, and characterization. Examples of potential application contexts within which such efforts will be undertaken include: a) Next-generation stents for cardiovascular intervention; b) Microneedle devices for minimally-invasive drug delivery; c) Robust neuroprostheses for direct and selective interfacing with neural tissues; and d) Microfluidic devices for ultrahigh throughput cellular manipulation.
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