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System and Method for Designing Multi-Channel RF Pulses for MR Imaging A system and method for designing RF pulses for multi-channel and/or multi-dimensional spatially-selective applications using a linear approximation. Embodiments... Read More A system and method for designing RF pulses for multi-channel and/or multi-dimensional spatially-selective applications using a linear approximation. Embodiments of the system and method may use a generalized linear-class large tip angle approximation to design RF pulses for multi-channel and parallel transmission. Further, some of these approximations allow for the design of arbitrarily large flip angles, irregularly-shaped flip angle profiles, or arbitrary initial magnetization values. Embodiments of the system and method may also provide for the design of k-space trajectories which aid in maintaining assumptions of the various linear class approximations.
Creating Super-Resolution Images using Standard Photobleaching and Blinking Movies Current super-resolution microscopy techniques require special laser setups and fluorescent molecules (such as PALM and STORM) that allow the fluorophores to be... Read More Current super-resolution microscopy techniques require special laser setups and fluorescent molecules (such as PALM and STORM) that allow the fluorophores to be turned on and off so that only a small number of fluorophores are turned on at any time. With the Super Shrimp image analysis algorithm, super-resolution images can be created from images with high densities of fluorophores. The invention creates microscopy images that have 5 or more times better resolution than standard microscopy images while using the standard microscopic set up available in most laboratories. It allows use of any fluorescent molecule (including quantum dots) that blinks or photobleaches to pick fluorophores out of the fluorescent background, and it can work with thousands of fluorophores in an image. This image analysis algorithm can localize quantized drops in fluorescence even with a background to create super-resolution images from standard photobleaching movies. It does not require special photo-switchable fluorophores (PALM, STORM) or fluorophores with long-lived dark states (dSTORM). The data acquisition is accomplished in minutes instead of hours and it can use standard laboratory microscopic set up with any fluorescent molecule. The algorithm processes a movie in which fluorescent molecules or particles are photobleaching or blinking and looks for individual photobleaching events that can be located with high resolution (i.e. the position of the fluorescent molecules). A composite image with resolution much higher than the original movie can then be generated. Noise is reduced by rejecting fluorophores that are poorly fit by a Gaussian and frames are averaged. Benefits The image analysis algorithm to create super-resolution images using standard photobleaching and blinking movies provides the following benefits: Uses standard laboratory equipment. Enables sub-cellular structure examination Can be used with any fluorescent molecule that can be detected by a CCD camera. It can use high labeling densities Fast data acquisition
FRET Based High-Throughput Screening Advanced molecular imaging tools combined with investigative tools like biochemical and cell based assays have thepotential to unravel complex molecular processes... Read More Advanced molecular imaging tools combined with investigative tools like biochemical and cell based assays have thepotential to unravel complex molecular processes. These tools combined with high throughput screening can significantly impact diagnostics for cancer screening and accelerate drug discovery. These inventions are two new Fluorescence Resonance Energy Transfer (FRET) biosensor pairs, one composed of two new colors, mOrange2 and mCherry and the other composed of a modified high-sensitive ECFP/YPet pair that can significantly enhance the dynamic range of a variety of biosensors. The ECFP/YPet can detect signaling events with high spatio-temporal resolutions which makes it an ideal readout indicator for high throughput screening. FRET technology and genetically encoded FRET biosensors are very useful in detecting active molecular events inlive cells with high temporal and spatial resolutions. FRET occurs when two flurophores are in proximity with the emission spectrum of the donoroverlapping with the excitation spectrum of the acceptor. To date, the most popular FRET pair is cyan and yellow fluorescent proteins (CFP and YFP). The new FRET biosensor pairs mOrange2/mCherry are proteins with different colors and spectrally distinctive from the CFP/YFP pair. This invention opens up the possibility of lighting two diagnostic biomarkers in the same cell e.g., cancer cells, thus providing a double criterion high-fidelity assay to differentiate cancer vs. normal cells. To provide proof-of-concept that mOrange2 and mCherry are suitable as novel FRET biosensors, they were operably linked to the protein recognition sequence of MMP-MT1. MMP-MT1 is an enzyme belonging to the matrix metalloproteinase family that has known roles in cancer metastasis. The basis of this assay is that when MT1-MMP is inactive, the mCherry and mOrange2 and positioned in proximity and favor a strong FRET between the two moieties. Indeed, in-vitro assays established that the mOrange/mCherry pair can serve as a reliable and sensitive indicator of the status of MT1-MMP activation and can potentially be applied to other biomarker assays. The ECFP/YPet pair provides a high-sensitive biosensor for the visualization of molecular hierarchy at different subcellular locations inlive cells. In-vitro assays revealedthat the ECFP/YPet pair exhibits significantly enhanced dynamic range of the MT1-MMP biosensor compared to currently available CFP/YFP FRET pairs. When quantified, the ECFP/YPet pair showed a 570% change (% change in basal level upon stimulation of MT1-MMP) when compared to only 90-100% in existing FRET pairs. The ECFP/YPet pair has also been successfully applied to other classes of proteins, like kinases, that are important therapeutic targets in human cancer. These and other genetically engineered biosensors can serve as a research tool to monitor different signaling cascades in live mammalian cells with high sensitivity. The developed MT1-MMP biosensor and potentially other protein biosensors can provide a powerful tool for the spatiotemporal imaging of protein functions in cancer development e.g. detection of circulating tumor cells (CTCs). Furthermore, these biosensors can serve as an excellent high-throughput reporting system forthe detection of cancer and the development of inhibitors for cancer therapeutics. Benefits The novel mOrange2/mCherry pair presents a method to simultaneously visualize two active signaling events in the same cell when combined with existing FRET pairsThe ECFP/YPet pair can serve as a high-sensitive biosensor with significantly enhanced dynamic ranges compared to existing CFP/YFP FRET pairs. The ECFP/Ypet pair can be operably linked to any protein recognition sequence to detect activity of that protein in live cells. The pair also includes a positively charged tag which allows 100% efficiency ofdetection. This invention demonstrates an ECFP/Ypet pair operably linked to MT1-MMP, a tumor metastasis biomarker, to accurately detect circulating tumor cells in blood samples.
Ionic Helical Polypeptides - Non-Viral Gene Delivery with Improved Transfection Efficiency Tremendous potential exists for helical polypeptides that are water soluble (ionic) and remain stable at physiological conditions,... Read More Tremendous potential exists for helical polypeptides that are water soluble (ionic) and remain stable at physiological conditions, variable environmental conditions including pH fluctuations, temperature changes, and in the presence of denaturing agents for gene delivery and cell-membrane penetration over commercially available products. Libraries of helical polypeptides are screened for desired traits, i.e. efficient gene transfection compared to standard transfection reagents.
Bioresorbable Silicon Electronics for Neural Sensing Dr. John Rogers from the University of Illinois at Urbana-Champaign has developed bioresorbable silicon electronics that can be used for real-time sensing of neural... Read More Dr. John Rogers from the University of Illinois at Urbana-Champaign has developed bioresorbable silicon electronics that can be used for real-time sensing of neural electrical activity. This invention could prevent follow-up neural surgeries, and has potentials for long-term monitoring of patients. 2015-158 Photo for Web.png
Quantum Dots with Thin Coatings that Allow for Efficient Bioconjugation Dr. Andrew Smith from the University of Illinois has developed new quantum dots with a multidentate polymer coating that minimizes size while maintaining stability and... Read More Dr. Andrew Smith from the University of Illinois has developed new quantum dots with a multidentate polymer coating that minimizes size while maintaining stability and improving efficiency of conjugation. Quantum dots are promising agents for cellular and molecular imaging, but their bulky organic coatings have limited their use in cells. Dr. Smith's quantum dots are small, stable, and can be conjugated to targeting molecules and purified easily.
Algorithm Modified Deoxynybomycin for the Treatment of Gram-Negative Bacteria Dr. Hergenrother from the University of IL has developed a novel antibiotic that is effective against certain antibiotic-resistant gram-negative bacteria. His powerful... Read More Dr. Hergenrother from the University of IL has developed a novel antibiotic that is effective against certain antibiotic-resistant gram-negative bacteria. His powerful predictive algorithm determines accumulation of molecules in Gram-negative bacteria and enables conversion of known Gram-positive only antibiotics into novel compounds with Gram-negative potency.
Process for Making Modular Bioactuators Dr. Rashid Bashir has developed a process for manufacturing modular bioactuators. The process utilizes stereolithographic 3D printing to create injection... Read More Dr. Rashid Bashir has developed a process for manufacturing modular bioactuators. The process utilizes stereolithographic 3D printing to create injection molds for cell/hydrogel cultures and for skeletal scaffolds for the actuators. The resulting ring-like actuators can then be manually placed on the scaffold. This introduces a modular design that is customizable and transferable. These actuators are also triggered optogenetically and exhibit directional motion and 2D steering.
Method for Short Run-Time Spatial Gene Analysis Dr. Rashid Bashir has developed a novel method for spatial gene analysis that removes the need for purification and homogenizing steps typical in RNA amplification... Read More Dr. Rashid Bashir has developed a novel method for spatial gene analysis that removes the need for purification and homogenizing steps typical in RNA amplification techniques. This method combines microfabrication and bioengineering in a unique manner that allows for spatial gene analysis in 2 hours or less. The method uses a chip patterned with thousands of picoliter microwells with sharp edges that pixelate the tissue without cross contamination. This preserves spatial data and allows amplification in each microwell.
PathTracker Drs. Cunningham and Bashir have developed a novel point of care diagnostic device capable of detecting pathogen infection from a single drop of blood. A blood sample is... Read More Drs. Cunningham and Bashir have developed a novel point of care diagnostic device capable of detecting pathogen infection from a single drop of blood. A blood sample is channeled through a microfluidics device allowing amplification of viral DNA/RNA of interest, which is then detected using a uses smartphone. Infection information is then uploaded allowing tracking of infections geographically. Immediate uses for the technology are for diagnosis of viral infection in human patients (Zika, dengue, and Chikungunya) and diagnosis of respiratory infection in equine populations (Equine herpesvirus, Equine influenza, Strangles, Equine adenovirus type 1, and Equine arteritis virus). Further uses include water testing, food safety, and pharmaceutical quality control.

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