2009 Research Projects
Bean and Flowers
Spermicidal and microbicidal potentials
of fluorous surfactants
Barry Bean, Ph.D., Biological Sciences
Robert Flowers, Ph.D., Chemistry
Commonly used spermicides like nonoxynol-9 have some undesirable side effects and detrimental consequences for some infectious processes. As a result, improved and alternative spermicides are needed. We are synthesizing and testing novel chemical compounds; these may weaken sperm cells and microbes. The architecture of human sperm cells includes several distinctive membrane regions that undergo substantial changes during the life history of the sperm cell. Specific changes must take place within the compartments and membranous surfaces of sperm to make them able to fertilize an egg. Our preliminary survey has compared effects of
several novel compounds with those of nonoxynol-9, the most common commercial spermicide. Thus
far, we have identified several compounds that have clear spermicidal actions, but which seem relatively innocuous to HeLa cells (derived from human cervical cancer), yeast, or the common human fungal pathogen, Candida albicans. We propose to extend this survey significantly to include spermicidal potentials of additional compounds through a diversity oriented synthetic approach, and to expand pilot studies on their safety and microbiological effects. Outcomes may lead to new strategies for contraception, or improvements in prevention of disease and pregnancy.
Cheng and Gilchrist
Isolation and analysis of rare cells from biological
fluids using a reversible cell capture platform
Xuanhong Cheng, Ph.D., Bioengineering
James Gilchrist, Ph.D., Chemical Engineering
D'Andre LeVon Watson
As blood carries rich information about one’s health state, there has been a constant and strong research effort in developing novel technologies to isolate disease specific biomarkers and bioparticles from blood. A significant advance is in the recent demonstration of circulating cancer cell isolation from blood into a microdevice for early stage diagnosis and prognosis of cancer metastasis. However, these microdevices immobilize target cells, limiting conventional cell culture as well as downstream cellular, proteomic and genomic analyses. Thus, the goal of the current project is to develop microchips that allow reversible cell capture and release, and characterize the purity, yield and function of isolated cells.
Specifically, the microchip will contain a sacrificial magnetic bead monolayer deposited by a convective deposition process. Both mathematical modeling and experimentation will be carried out to investigate the magnetic bead deposition process and drag/liftoff of cell/microsphere aggregates. Following the monolayer creation, the magnetic bead-covered substrate will be incorporated into a microfluidic channel and functionalized with an antibody to recognize and immobilize target cells from a biological fluid. As this magnetic layer can be lifted from the substrate in the presence of a magnetic field, cells attached on top can be released to a suspended state with minimal damage. Released cells will be studied using conventional cell activity and function analysis to validate the performance of the microfluidic cell isolation platform. This project is expected to provide the participated students with a multi-disciplinary training in areas including hemodynamics, cell adhesion, flow cytometry, microfluidics, and microscopy.
Falk and Jain
Biocompatibility of nano-macro dual-porous
glass bone-replacement scaffolds
Matthias Falk, Ph.D., Biological Sciences
Himanshu Jain, Ph.D., Materials Science
One of the key challenges in today’s medicine is the treatment of organ failure or tissue loss. Advances in cell biology and material sciences have led to tissue engineering where healthy progenitor cells are delivered to the injured site on biocompatible scaffolds to regenerate lost or damaged tissue. This approach has delivered particularly successful results for bone replacement using bone-scaffolds made from CaO-P2O5-SiO2 based glass ceramics. Millions of patients have benefited from implants made from such bioactive glasses.
A macro porous structure of the glass scaffolds is necessary to obtain good implant incorporation through rapid vascularization and bone ingrowth, since such porosity promotes cell growth on the surface as well inside the scaffolds. For additional benefits, the scaffolds should consist of nanopores, which simulate the natural extracellular environment. We have recently developed two novel methods for fabricating such bioactive glasses based on: (a) conventional melt-quench method followed by selective heating and etching, and (b) a sol-gel procedure with polymerization induced phase separation.
In this BDSI Research Project we will fabricate such dual-porous glass bone-replacement scaffolds, and we will test their biocompatibility and bioactivity by monitoring the colonization and growth of bone and bone-precursor cells on the scaffolds. Nano-macro dual porosity glasses with different chemical composition, pore-characteristics, and bioactive coatings will be tested for cell attachment, migration, proliferation, and differentiation. Appropriate fluorescence-based cell detection methods have been established. Thus, this Summer Institute, in combination with our ongoing work supported by NSF and IMI-NFG will elucidate which scaffolds are the most promising ones. It will provide the basis for further testing of our glass scaffolds in vivo by our partners at Tissue Engineering Laboratory, Faculty of Dentistry, Alexandria University, Egypt.
Huang and Vavylonis
Actin filament polymerization:
Modeling of elongation kinetics based on
analysis of TIRFM images
Xiaolei Huang, Ph.D., Computer Science & Engineering
Dimitrios Vavylonis, Ph.D., Physics
Actin proteins spontaneously assemble into long polymers to build networks and bundles of filaments that are used by cells to move and change shape. An experimental method to study the kinetics of single actin filament growth in vitro is total internal reflection microscopy (TIRFM). In TIRFM experiments, fluorescently-labeled actin filaments grow parallel to a glass slide by addition of monomers from a bulk solution. The kinetics of actin filament growth is captured in hundreds of microscopic images that record the nucleation and elongation of tens of individual actin filaments simultaneously.
Our team develops automated image analysis methods for measuring actin filament length versus time in TIRFM images of actin polymerization. In this way, we can systematically calculate the two basic parameters of actin polymerization kinetics: rate of filament elongation, and fluctuations in the average rate. The information is used to develop computational and mathematical models that describe the dependence of actin filament elongation rate and fluctuations on the concentration of actin and cofactors. In this way, we can study and understand the mechanisms that cells use to regulate the dynamics of the actin cytoskeleton.
Mullen and Lopresti
From Phenotype to Genotype:
Integrating bioinformatics, population genomics, and
quantitative genetics to identify the genes underlying adaptation
Sean Mullen, Ph.D., Biological Sciences
Daniel Lopresti Ph.D., Computer Sciences & Engineering
A major goal of modern research in evolutionary biology is to characterize, at a genetic level, the mechanisms of adaptive evolution. One issue of particular interest is whether changes in homologous genes underlie the independent evolution of similar adaptive phenotypes. Emerging research from Heliconius butterflies indicates that closely related species share a conserved genetic architecture for their mimetic wing color patterns. The project will generated a large number of orthologous SNP reference markers for use genotyping mapping families to localize the genomic regions underlying three of the most striking examples of wing pattern mimicry in butterflies.
The work will consist of two specific research objectives that are part of a broader effort to characterize the genes underlying mimicry in three divergent butterfly lineages. First, we will utilize next-generation sequencing technology (e.g. 454 pyrosequencing, SOLID) to generate high coverage transcriptome sequence data for Limenitis, Papilio and Heliconius. These data will then be trimmed, assembled, and annotated using a variety of bioinformatic tools and custom PERL scripts. Second, we will mine these data to identify a large number of orthologous SNPS across systems that will then be genotyped in each system and mapped to localize mimicry QTL. The combination of bioinformatics, population-level transcriptome data, and quantitative genetics will provide a robust comparative evolutionary framework for comparing the genetic architecture of mimicry in these three systems.
Undergraduates on this team will participate directly in the assembly and annotation of ESTs derived from the developing butterfly wing discs of several species. In addition, they will utilize both custom and pre-existing bioinformatic tools to mine these transcriptome data to identify single nucleotide polymorphisms for use in the construction of a SNP genotyping chip. 454 data for two species (Limenitis and Heliconius) already exist but undergraduates will also have the opportunity to help construct a normalized cDNA library for sequencing from a third species, Papilio polytes. Undergraduate participation will culminate in oral presentations of data analysis that will involve extended discussion of the different computational methodologies applied and the strengths and weakness of individual analytical approaches.
Tatic-Lucic, Perry, Voloshin and Neti
Multi-scale modeling of cellular mechanics
Svetlana Tatic-Lucic, Ph.D., Electrical & Computer Engineering
Susan Perry, Ph.D., Chemical Engineering
Arkady Voloshin, Ph.D., Mechanical Engineering & Mechanics
Sudhakar Neti, Ph.D., Mechanical Engineering & Mechanics
Hwa Bok Wee
There is increasing evidence which suggests that a link may exist between the intrinsic mechanical properties of cells and certain disease states. For instance, it is thought that the biomechanical properties of osteoblasts (bone –forming cells) change as a function of age, and this change could be a contributing factor to the pathogenesis of osteoporosis. Yet, elucidation of the relationship between the biomechanical properties of cells and disease states is still in its infancy, and the current methods of measuring the mechanical properties of cells (AFM, tensile testing) are not suitable for addressing many cells at one time. Therefore, a systematic platform for studying the mechanical compliance of various cell types, such as osteoblasts, fibroblasts, neurons and lung epithelial cells is of great interest for researchers investigating the pathophysiology of various diseases and the investigation of effective treatments.
The focus of our project, therefore, will be to build a BioMEMS (micro-electro-mechanical system) device that will have built in capabilities for cell positioning and for the reliable measurement of the mechanical compliance of biological cells to aid in this important area of research. Our interdisciplinary project is a collaborative effort between Svetlana Tatic-Lucic (Electrical and Computer Engineering and Bioengineering; BioMEMS device design and fabrication), Susan Perry (Bioengineering; cell culture), Arkady Voloshin (Mechanical Engineering, biomechanics) and Sudhakar Neti (Mechanical Engineering, dielectric positioning).