I. Experimental Biophysics
Biophysical Techniques as an alternative way for measuring efficacy of gene therapy for Hemoglobin Disorders
Sickle cell disease (SCD) and β-thalassemia is a devastating inherited disorder of hemoglobin that both shortens and reduces the quality of life. Beginning in early childhood, chronic vaso-occlusive events lead to a central nervous system vasculopathy causing impaired intellectual development and, in some patients, devastating strokes. Hydroxyurea therapy diminishes the frequency of crisis but curative therapies are desperately needed. Although bone marrow (BM) transplantation is an established curative therapy, it is limited by the availability of appropriate donors. It is gene therapy that holds the promise of easily availability curative therapy for patients with these hemoglobin disorders. Recently, a research team at Saint Jude Children's Research Hospital, has used g-globin lentiviral vector for HSC transduction and high level, therapeutic expression of HbF in the BERK SC mouse and β-thai mouse models. The therapeutic efficacy of this particular or other gene therapies in hemoglobin disorders is usually measured by the percentage of HbF expressed in the red blood cells (RBCs) and the resulting improvement of the disease phenotype and lifespan of the animals. However, it is also important and beneficial if any additional therapeutic efficacy measurements are conducted on the RBCs for better and effective development of gene therapy for these hemoglobin disorders.
We are interested in developing experimental biophysics techniques based on the application of laser tweezers to the study of the elasto-mechanical properties of the RBCs at the cellular and molecular level that can used as an alternative measurement of therapeutic efficacy of gene therapy against hemoglobin disorders. Normal RBCs can deliver oxygen to body tissues by squeezing through capillaries narrower than the formal diameter of a RBC. Flexibility of RBCs is drastically diminished by blood disorders such as SCD, and can lead to various vaso-oclusive events. This research project has been initiated recently and has been conducted in collaboration with a research team led by Dr. Derek Persons at Saint Jude Children's Research Hospital, who has used g-globin lentiviral vector for HSC transduction and high level, therapeutic expression of HbF in the BERK SC mouse and β-thai mouse models. Recently, for BERK SC mouse model we have successfully carried out a study in the efficacy of gene therapy based on the Response of the RBCs to shear deformation which submitted for publication to American Biophysical Journal
Role of Erythrocytes and Lymphocytes Mechanical and Morphological Properties in Stroke
Stroke is cardiovascular diseases affecting millions in America. Stroke is the third leading cause of death in the United States. In the U.S. about 700,000 strokes occur each year. Among these individuals over 160,000 die each year. The incidence of stroke increases with age, affects more men than women, and shows higher death rates among African Americans even at younger ages. The southeastern United States has the highest stroke mortality rates in the country and the contributing factors are not completely clear. Stroke can be caused, directly or indirectly, by abnormalities of the red (Erythrocytes) and the white (Lymphocytes) blood cells. During blood circulation, these blood cells undergo a reversible deformation to accommodate those blood vessels which are smaller in diameter than their sizes. When our blood cells fail to properly deform, they can block circulation and prevent blood from reaching different parts of our body, for example, in the case of stroke, from reaching to the brain. Therefore, it is vital to have a deeper understanding of the structural, mechanical and morphological properties of blood cells. In our biophysics research laboratory we have been engaged in developing a novel optical device called 'Ellipsometric-tweezers' which enables us to explore and better understand the structural, mechanical and morphological properties of human blood cells at the cellular and molecular level. Ellipsometric-tweezers is designed to integrate an ellipsometer with an optical and/or magnetic tweezers. It can potentially provide a better insight to how a living blood cell surface texture change when the cell undergoes a continuous linear or/and rotational deformations. Moreover, it can be used to study the dynamics of cell membrane receptors within a living cell, while the cell subject to different magnitudes of mechanical stress. Such studies are vital in order to fully understand these cells and also to provide new insights into stroke in relation to these cells.
Currently, our laboratory is equipped with eight watt 1064 nanometer infrared laser used to form dual-trap optical tweezers on piezo-driven nanostage attached to an inverted IX 51 Olympus microscope coupled to a digital imaging device interfaced with a PC. The dual-trap optical tweezers is fully operational and have been used to study the response of normal human RBCs to distributed, concentrated, or sheer stress of piconewtons order of magnitude under different physiological environment. Currently, we are conducting similar studies in sickle cell RBCs and also building the Ellipsometric-tweezers with a second more advanced IX 71 Olympus microscope.
II. Synthetic Photonic Band-gaps
Synthetic Photonic Crystals
?Colloidal particles, such as silica, are particles having size ranging between several nanometers and several millimeters and can be suspended in a liquid. Because of their tunability, in size, shape, as well as in chemical composition, and their ability to self-assemble they find applications in the development of advanced materials like photonic crystals. Typically, colloids self-assemble into face centered cubic (FCC) or body centered cubic (BCC) structures which determines their optical and electrical properties. Recently, we have demonstrated that by changing the chemical composition of the liquid in which the colloids are suspended in and using optical tweezers, it is possible to assemble the colloids in a new stable structure [ Journal of Modern Optics, 54, P 1529-1536]. Currently, we are involved in developing new stable synthetic structures, specifically simple cubic and diamond structures, by trapping and manipulating different sizes of silica beads using optical tweezers in saline water solution.
III. Theoretical Quantum Optics and Quantum Information
Entangled Photons and Quantum Teleportation
In quantum teleportation process information can be transmitted from one place to another using the principle of quantum mechanics. For a faithful transmission of information fully entangled particles is necessary. Quantum distillation is a protocol which is useful to produce fully entangled state from partly entangled states. In quantum distillation by operating locally on a large number of identical partly entangled pairs, one can concentrate their entanglement into a smaller number of maximally entangled pairs. Polarization entangled photons produced by spontaneous parametric conversion (SPDC) can be used in quantum distillation. These photons are also spectrally entangled that depends on the spectral composition of the pump photons and the nature of optical isotropy of the crystal used in SPDC. Recently we have reported that factors affect the degree of polarization entanglement of the photons [ Optics Research Letter, Volume 2009, Article ID 387580]. Therefore, it is important to study such effects in quantum teleportation and quantum distillation protocols. Currently, we are studying, theoretically, the effect of spectral entanglement in quantum teleportation protocol using the polarization states of two pairs of photons produced by two independent SPDC process. We are also interested in exploring various quantum optical schemes that optimize the entanglement and squeezing of the twin photons produced by SPDC.
IV. Computational Biophysics
Simulations and free energy calculations on membrane binding of lipidated peptides
Interactions between membrane proteins and lipids are essential to a huge variety of cellular processes, including transport, signaling and membrane biogenesis. However, little is understood of the role of protein'lipid interactions in these processes. This is because lipids and proteins can influence each other in so many different ways. Lipids may affect the structure of membrane proteins by influencing their backbone conformation, the tilt and rotation angles of their transmembrane segments, or the orientation of their sidechains. Posttranslational lipid-modified proteins are commonly involved in regulation of the signal transmission processes across membranes. Typical among fatty-acid-modified proteins is the Ras proteins. Ras proteins mediate signaling pathways that control cell proliferation, development, and apoptosis. Malfunction in the regulatory action of ras proteins leads to uncontrolled cell growth, or cancer, manifested by the fact that about one-third of all human cancers carry a mutated form of ras proteins. Therefore, much effort has been made toward understanding the thermodynamics and kinetics of membrane targeting by ras proteins and peptides derived from them. These studies are particularly crucial for the design of selective inhibitors against a variety of diseases, including anticancer agents that specifically target N-, K-, or H-ras.
Several studies on the structures and dynamics of membrane bound ras proteins based on modeling and molecular dynamics (MD) simulations have been carried out. In these studies the relationships among membrane-insertion depth, backbone localization, and membrane perturbation and structural arguments in support of the proposed participation of ras in the organization of membrane nanoclusters have been extensively discussed. Our current research project focuses on potential of mean force (PMF) calculations to determine the membrane affinity of the K-ras anchor, which is an 11-residue peptide extracted from the full-length K-ras protein and representing the membrane interacting polycationic and farnesylated C-terminus. The membrane will be modeled by a lipid bilayer composed of palmitoyloleoylphosphocholine (POPC) lipids containing 23% palmitoyloleoylphosphoglycerol (POPG). Test calculations with a small system suggests that a bilayer of 256 lipids in a water box with an estimated total system size of 100,000 atoms will be sufficient. A complete, well-equilibrated PMF calculation for the insertion (and the reverse process of extraction) of the peptide into (and from) the bilayer will take up to a microsecond on aggregate (20 windows, each run for 50ns). We will use the Adaptive Biasing Force (ABF) method which relies on a series of fully atomistic MD simulations to sample configurational space. The simulations will be done with the NAMD program and the CHARMM force field.
I am very new to this area of research. In fact it is initiated very recently under the guidance of our collaborator at Dr. Alemayehu Gorfe at the University of Texas Medical School at Houston and therefore it is in a very infant stage.