University of Arkansas

Ye, Kaiming

Dr. Kaiming Ye
Professor
Biomedical Engineering
Office: 3914 Engineering Research Center
Phone: 479-575-5315, 703-292-2161, 479-575-4489
E-mail: kye@uark.edu

Teaching and Research

- Molecular cell biology,
- Stem cell and regenerative medicine,
- Nanomedicine,
- Vaccine development,
- Biosensing and bioimaging and gene therapy,

Dr. Kaiming Ye, is a Professor, Department of Biomedical Engineering, College of Engineering, University of Arkansas. He also serves as a Program Director (a rotator), Biomedical Engineering Program at National Science Foundation. His research interest focuses on stem cell and regenerative medicine. He has published one book, one patent, and more than 65 papers in the field. He is best known for his creative works on developing 3D scaffolds for directing stem cell pancreatic differentiation, creating fluorescence nanosensors for both in vivo and in vitro continuous glucose monitoring, and formulating recombinant yeast influenza vaccines. His research has been continuously funded by NIH, NSF, JDRF, ABI and industries. He serves as executive/associate editor and editorial board member of 12 journals and has been invited to deliver keynote/plenary speeches at numerous international and national conferences. He has also served on numerous review panels and study sections for NIH and NSF. He is also a Program Evaluator of ABET accreditation for Biomedical Engineering Program.

Positions Available

• Stem cell, regenerative medicine, and biomaterials (postdoctoral and graduate assistantship)
• Influenza vaccine development (postdoctoral and graduate assistantship)

Courses taught

• BENG 3213: Biomedical Engineering: Methods and Applications
• BENG 5233: Tissue Engineering

The Stem cell and Tissue Engineering Lab focuses on organ and tissue regeneration, biomaterials, nanomedicine, nano-drug delivery, vaccine development, nanosensors, and single molecule imaging and detection. These works in essence address the fundamental biomedical engineering problems of developing new technologies for organ regenerative medicine and new intracellular indicators for studying stem cell differentiation and tissue regeneration/remodeling.
Research Interests

• Develop 3D tissue engineered scaffolds for directing lineage-specific differentiation of human embryonic and induced pluripotent stem (ES/iPS) cells into clinically-relevant cell lineages for cell replacement therapy
• Build biomimetic multicellular systems for organ development and regeneration
• Construct bioinspired materials for wound healing and bone and neuron regeneration
• Create fluorescent nanosensors for in vivo tracking stem cell proliferation and differentiation
• Advance nanoparticle-based controlled and targeted drug delivery for cancer treatment
• Develop implantable glucose sensors for continuous blood glucose monitoring in diabetic patients
• Engineer fluorescence nanaosensors for real-time measurement of glucose transport in insulin-resistance tissues and cells by visualizing glucose dynamics in these cells through fluorescence lifetime imaging microscopy (FLIM) measurement
• Formulate refrigeration-free influenza vaccines

Research Activities:

Differentiation of Human Pluripotent Stem Cells into Therapeutic Insulin-Producing Cells for Diabetes Cell Therapy. Islet transplantation brings a hope to diabetic patients who may one day be able to live normally without relying upon insulin-injection, frequent glucose monitoring and diet adjustment. However, the shortage of transplantable pancreatic islets has impaired the availability of this promising treatment for most patients. This lab focuses on the creation of a new renewable cell source for generating glucose-responsive, insulin-secreting pancreatic endocrine cells for use in cellular therapy of diabetes enabling the patients to restore their near-physiological secretion of insulin in response to the blood glucose levels. A three-dimensional stem cell differentiation system was developed and tested for directing human embryonic stem cell differentiation into clinically relevant pancreatic endocrine cells for diabetes treatment.

Immunohistochemical  staining of insulin-Producing islet-like cell clusters (IPCCs) formed in 3D mouse  ES cell pancreatic differentiation. (I) The IPCCs were examined after 25 days  of ES cell differentiation in either 3D or 2D environments. The cell nuclei  were counterstained with DAPI. Adult mouse islets severed as a positive  control. Images show a similar architecture pattern of cells between 3D induced  cell clusters (b, e, h, k), and adult islet cell clusters (a, d, g, j); that  is, the majority of 3D induced insulinþ cells are located at the center of the  clusters (b), while glucagonþ and somatostatinþ cells tend to be at their  periphery (h, k). In contrast, 2D induced cells exhibit a significantly  different pattern (c, f, i, l). (II) C-peptide staining of insulin-producing  cells through the ABC staining kit. More C-peptide–positive cells were observed  in 3D ES cell pancreatic differentiation (n) than in 2D differentiation (o).  (p) Serves as a negative control (PBS instead of C-peptide antibody was used  during the staining). (III) No cell clusters express undifferentiated mES cell  markers SSEA-1 or Oct-4 after 25 days of differentiation in  3D environments (r, t). (q, s) Undifferentiated mES cells, serving as a  positive control.

Fluorescence nanosensors for both in vivo and in vitro continuous glucose monitoring. These inventions represent our creative works in developing new and innovative glucose sensors for both in vivo and in vitro continuous glucose monitoring. Two types of glucose sensors have been developed in this lab: one for continuous monitoring of glucose in the blood and the other for continuous monitoring of glucose transport in living cells.

Diabetes mellitus is one of the major health care problems in the world. It is a well-established fact that more frequent blood glucose monitoring can prevent many long-term complications associated with diabetes. However, the nature of the finger-stick glucose testing restricts its utility for maintaining strict levels of the blood glucose concentration. This dilemma has resulted in a worldwide effort to develop new glucose sensors for fast, painless, and convenient glucose monitoring.

To respond to these challenges, we created a glucose indicator protein (GIP) by integrating an optical signal transduction function directly into a glucose binding protein (GBP). Our strategy is to incorporate fluorescence reporter groups into a GBP in such a manner that the spatial separation between the fluorescence moieties change upon glucose binding, generating a signal for optical detection. This new molecular design capitalized on the FRET method that has been widely used in bioassays. This new design is a paradigm shift in glucose sensor development that has long been focused on the use of GOX and off-time glucose monitoring. The realization of this new sensor mechanism enabled continuous glucose monitoring, and could eventually supplant traditional finger-sticking glucose measurement by implanting these sensors beneath the skin. The original GIP was developed based on a wild type GBP isolated from E. coli. It responds to glucose in a range on the order of 10 mM of glucose. To employ this GIP for monitoring blood glucose concentrations, its operational range needs to be elevated to an order of mM. After analyzing the X-ray structure of the GBP, we identified the mutation sites that could shift the glucose binding constant from mM to mM. Using site-directed mutagenesis, we successfully created a GBP mutant which glucose binding constant is about 7.86 mM. The sugar binding assay indicated that it is highly specific for glucose binding. A microsensor developed based on this GIP has an optional range from 0 to 32 mM of glucose and its response time to sudden glucose changes is within 100s, suitable for continuous glucose monitoring.

This sensor can provide real-time monitoring of blood glucose concentrations while helping patients avoid painful and inconvenient finger-sticking or skinpricking glucose monitoring. They can potentially be implanted beneath the skin for continuous glucose monitoring. The development and commercialization of these technologies will eventually get rid of finger-sticking glucose measurements, improving the life qualify of diabetic patients. 

Fluorescence microscopy measurement of single molecule in living cells. Using another GBP mutant which glucose constant is at about 131 mM, we developed a fluorescence nanosensor that allows for the visualization of intracellular glucose in living cells. The integration of a gene encoding this fluorescence nanosensor allows for biosynthesis of the sensor by cells for continuous reporting changes in intracellular glucose concentrations in response to changes in extracellular glucose concentrations. Both FRET and a frequency-domain (FD) FLIM measurement were developed for visualizing of glucose dynamics within living cells. With these measurements, we determined the glucose uptake and clearance rates in murine skeletal muscle cells. They are about 31 and 101s, respectively. We also discovered uniform distribution of glucose within cytoplasm with high glucose concentration in the region close to membrane and low glucose concentration in a region close to cell nucleus.  This sensor enables direct and real-time monitoring of glucose transport in insulin-sensitive cells by visualizing glucose dynamics in these cells through FRET-FLIM imaging microscopy measurement. It can be used for high-throughput screening of anti-diabetes drugs that target to glucose transporters in peripheral tissues that develop insulin-resistance. These sensors can also be employed for characterizing the underlying mechanisms responsible for the development of abnormal glucose transport in obese and diabetic patients. Data accumulated from these studies will provide insights into the pathogenesis of diabetes

A Nano-Drug Delivery Platform for Simultaneous Cancer Imaging and Drug Delivery. This project focuses on development of a novel nanoparticle bioconjugate for image-guided delivery of anti-cancer drugs into tumors such as prostate tumors.

Refrigeration-Free Vaccines. This project focuses on formulating refrigeration-free vaccines against infectious disease such as influenza virus infection. The vaccines are developed through a cell surface engineering technique developed in this laboratory.

Selected Publications

Book

• Ye, K. and Sha Jin (2011) “Human Embryonic and Induced Pluripotent Stem Cells”, Springer, Humana Press, New York, USA, ISBN 978-1-61779-266-3

Book Chapters

• S. Jin, J.C. Leach, and K. Ye (2009) “Chapter 43: Nanoparticle-based Gene Therapy” in Methods in Molecular Biology book series ”Microfluids, Nanotechnologies, and Physical Chemistry Science in Separation, Detection, and Analysis of Biomolecules”, 544: 547-557, ed. Lee, W. James, Humana Press, USA
• S. Jin and K. Ye (2009) “Chapter 3: siRNA to Antiviral Treatment” in Book “Small Interfering RNA Research”, 65-84, ed. K. Yamada and S. Hayashi, Nova Science Publishers, Inc., USA
• Veetil, J., Jin, S. and Ye, K. (2010) “Chapter 5: FRET-Based Nanosesnors for Intracellular Glucose Monitoring” in “Nanosensors: Theory and Applications in Industry, Healthcare and Defense”, 169-181, ed. T.C. Lim, CRC Press, Florida, USA
• Veetil, JV, Ravindranathan, S., Jin, S., and Ye, K. (2012) Microfluidic glucose sensors” in “Microfluidic Applications for Human Health”, ed. Demirci, U., Langer, B., Khademhosseini, A., World Scientific Publishing, Hackensack, NJ, in press
• In the book “Frontiers of Combinatorial Bioengineering” edited by M. Ueda., (2004) CMC Publishers. Tokyo, Japan
• Ye, K.       Chapter 2: E. coli protein display and its application for directed-evolution of proteins
• Ye, K.       Chapter 5: Construction of a combinatorial library
• Ye, K.       Chapter 7: Retroviral peptide display libraries
• Ye, K.       Chapter 11: RNA interference and siRNA libraries

Patent
Ye, K. and Jin, S. (2010) “pH Insensitive Glucose Indicator Proteins”, US 12/902725
Selected Peer-Reviewed Publications

• Jin, S., Yao, H., Krisanarungson, P., Haukas, K., and Ye, K. (2012) Porous Membrane Substrates Offer Better Niches to Enhance the Wnt Signaling and Promote Human Embryonic Stem Cell Growth and Differentiation, Tissue Engineering Part A (in press)
• Zhu, Y., Dong, Z., Weijinya, UC, Jin, S., and Ye, K. (2011) Determination of mechanical properties of soft tissue scaffolds by atomic force microscopy indentation. J. Biomechanics, 44, 2356-2361
• Jin, S. Ellis, E., Veetil, JV, Yao, H., Ye, K. (2011) Visualization of HIV Protease Inhibition Using a Novel FRET Molecular Probe, Biotechnol. Prog. 4, 1107-1114
• Jin, S., Veetil, J., Garrett, R., Ye, K. (2011) Construction of a panel of glucose indicator proteins for continuous glucose monitoring. Biosensors and Bioelectronics. 26, 3427-3431.
• Veetil, V.J., Jin, S. and Ye, K. (2010) A Glucose Sensor Protein for Continuous Glucose Monitoring. Biosensors and Bioelectronics, 26, 1650-1655
• Geels, M. and Ye, K., (2010) Development in high-yield system expressed vaccines. Recent patents on Biotechnology, 4, 189-197
• Pan, Z., Cunningham, D.S., Zhu, T., Ye, K., Koepsel, R.R., Domach, M.M., Ataai, M.M. (2010) Enhanced recombinant protein production in pyruvate kinase mutant of Bacillus subtillis. Appl. Microbiol. Biotechnol. 85, 1769-1778
• Geels, M. and Ye, K., (2010) Development in high-yield system expressed vaccines. Recent patents on Biotechnology, 4, 189-197
• Wang, X and K. Ye (2009) Three-dimensional differentiation of embryonic stem cells into islet-like insulin-producing clusters. Tissue Engineering Part A, 15, 1941-1952
• Veetil, J., and Ye, K. (2009) Tailored carbon nanotubes for tissue engineering applications. Biotechnol. Prog. 25, 709-721
• Garett, J.R., Wu, X., Sha, J. and Ye, K. (2008) pH-insensitive Glucose Indicators, Biotechnol. Prog. 24, 1085-1089
• J. Xie, K.R., Aatre, V.K., Varadan, J.V. Veetil, and K. Ye (2008) Synthesis of aligned carbon nanotubes by microwave chemical vapor deposition and investigation of their covalent bonding with antibodies for bio-applications. International Journal of Nanoparticles, 1, 119-135.
• Veetil, J.V. and Ye, K. (2007) Development of immunosensors using carbon nanotubes, Biotechnol. Prog. 23:517-531.
• Jin, S. and Ye, K. (2007) Nanoparticle-mediated Drug Delivery and Gene Therapy, Biotechnol. Prog. 23, 32-41.
• Ye, K. and Ueda, M. (2006) Combinatorial Bioengineering: Editorial. Biotechnol. Prog. 22, 923-923.
• Ye, K. and Jin, S. (2006) Potent and specific inhibition of retrovirus production by co-expression of multiple siRNAs directed against different regions of viral genomes. Biotechnol. Prog. 22, 45-52.
• Ye, K., Jin, S., Mohammad, M.A., and Schultz, J. S. (2004) Tagging retroviruses with a metal binding peptide and one-step purification with immobilized metal affinity chromatography. J. Virol. 78:9820-9827
• Ye, K.  Jin, S., and Schultz, J.S. (2004) Genetic engineering of a fluorescent cell marker for labeling CD34+ hematopoietic stem cells. Biotechnol. Prog. 20:561-565.
• Ye, K. and Schultz, S. J. (2003). Genetic Engineering of an allosterically based glucose indicator protein for continuous glucose monitoring by fluorescent resonance energy transfer. Analytic Chemistry, 75: 3451-3459.