#1 Arthoscopic Myometer (PI: Dr. Sam Ward, Radiology)

Muscle biopsies are an important source of research material for studying muscle pathology. The muscles of the rotator cuff are often injured, but poorly studied because the surgical approach to these muscles is frequently limited by extraordinarily small incisions and small instruments. The goal of this project is to design a self-contained instruement to biopsy these muscles through a 1/4 inch diamater portal.

#2 Stem Cell Differentiation Using Electromechanical Stimulation (PI: Dr. Adam Engler)

Maying intrinsic environmental cues are integrated together by stem cells in order for them to differentiate into a specific cell type. However, the coupling of electrical stimulation in stem cell differentiation is not known. Using our conventional hydrogel system, the team will design and micropattern an array of electrodes on a glass surface, which will be overlaid with our hydrogel. Stem cells cultured on top will then be monitored for a variety of differentiation measures.

#3 Personalized genome mapper (PI: Dr. Kun Zhang)

Rapid advances in DNA sequencing have made it possible to obtain individual human genome sequences at a reasonable price. However, analyzing hundreds of million DNA sequences generated for each individual requires an enormous of computational resources. In this project, we will develop and implement genome mapping algorithms using high-end video cards (Graphical Processing Units, GPUs), which potentially has advantages over standard CPUs in speed, cost and energy consumption.

In the project for 2008-2009, the team has built a linux workstation, and completed the proof-of-concept design (http://iacs5.ucsd.edu/~tpremchi/index.html). In 2009-2010, we will greatly expand the project by implementing a more advanced genome mapping algorithm in a more powerful GPU.

#4 A catheter design for intestinal lavage (PI: Dr. Geert Schmid-Schonbein)

Pancreatic digestive enzymes have recently been shown in our laboratory to cause autodigestion in physiological shock and multi-organ failure. Blockade of the digestive enzymes in the lumen of the intestine serves to minimize the autodigestion and the lethal progression of shock. There is a need to develop a new approach to block the digestive enzymes in trauma situation, at high risk for multiorgan failure.

This project is designed to develop a method to lavage the small intestine via a catheter. The small intestine is a collapsable tube so that specific fluid mechanical conditions need to be generated and bulk material be transported out of the lumen. The project will consist of an innovative approach to this problem. Students are expected to design and analyze a prototype and test it under preclinical conditions.

#5 Design and development of lactate sensors for marine mammal diving and equine exercise training (PI: Dr. Dale Baker)

Background:
Lactate plays an essential role as an indicator of diving and exercise intensity. There is much interest in an implantable lactate sensor that can be used in marine mammals (e.g. elephant seals) to determine their aerobic dive limit (ADL), it is defined as the dive duration beyond which blood lactate begins to accumulate. Horse trainers also rely on lactate levels to guide their exercise regime, and to avoid over-stressing the horses during training.

Problem definition:
Presently, there are no continuously implantable sensors to measurement blood lactate concentrations in marine mammals, horses or even humans.

#6 Cold Therapy Pad Analysis and Design (PI: Devin Lebrun, BREG)

Analysis and characterization of cold therapy effectiveness under real-life conditions including, but not limited to: pad thermodynamics, skin perfusion, and environmental effects. Create reproducible simulated-use test protocol which accurately represents real-life use conditions and performance. Suggest design changes to improve performance.

#7 A low-cost amplifier/conditioner for pressure gauges (PI: Dr. Jeff Omens)

Pressure waveforms are commonly measured clinically and experimentally. Many systems are commercially available for signal conditioning of pressure gauge signals using a fluid-filled system. Typical amplifiers and circuitry were discussed in BE186B.

Design group will research and design the electronic circuitry for the amplifier/conditioner. The circuit will then be prototyped on a bread board and tested for reliability, accuracy, signal/noise, etc. When the test circuit is complete, it will be reproduced on a circuit board and a final prototype amplifier box will be constructed and tested. All work will be done in the undergraduate design laboratory in PFBH.

#8 Leg Compression Device Design (PI: Dr. Alan Hargens, Orthopaedic Surgery)

Limb Compression Device that does not touch skin at the treatment site and can be sterilized internally. See image here.

#9 Engineered Pancreatic Iset Device (PI: Dr. David Gough)

We will start with a review of all aspects of the problem, then narrow the focus to a smaller project that can be completed during the course. The specifics of the project will be identified in the first quarter, and will depend largely on student input and capabilities. The plan is to address a limited aspect of the technology but, of course, not develop the complete device. Experiments will be limited to benchtop studies, not animal studies.

#10 The Perfect Nap (PI: Dr. Jeff Omens)

The sleep cycle consists of five stages: 1, 2, 3, 4, and REM. A nap is most productive when you obtain REM sleep and awaken during a light stage of sleep. This kind of nap will leave you refreshed from the REM and less groggy by not waking up from deep sleep. An EEG can be used to monitor the subject’s stage of sleep, and computer software can be used to recognize the patterns and trigger an alarm at the appropriate time. The EEG would need to be safe and comfortable enough to wear during sleep, and the alarm would need to be adjustable so that a person can give a “wake-up” time range.

#11 Swine Flu: Bioengineering Approach to Prevention and Treatment (PI: Dr. Amy Sung)

Influenza viruses killed millions of people in past pandemics. They have hemagglutinin and neuraminidase on the surfaces, which undergo mutations and assortments, making vaccination and anti-vital medication difficult and costly. This project will use the principles of bioengineering to develop a universal design to prevent infections by influenza viruses of any strains or subtypes and enhance the removal of viruses from tissues in a timely fashion.

#12 Knee Measurement System (PI: Dylann Ceriani, BREG)

Analysis and characterization of leg contour data using the previous design prototype or a new design. Analysis of Breg’s current custom brace manufacturing process and how the new measurement system can be implemented in a cost effective manner, including procurement of digital data, automated digital measurement, and incorporation of contour measurements into the brace forming process.

#13 Design and Development of hydrogel based vascular grafts (PI: Dr. Shyni Varghese)

Most of the currently available synthetic vascular grafts are made from Dacron or Teflon. These materials are not only bio-inert but also exhibits mechanical and structural mismatch with the native vascular tissue. Note to mention the additional complications arise from their hydrophobic nature. On a structural perspective one can argue that vascular tissue is a reinforced hydrogel system with enhanced mechanical properties and directionality. This project explores the possibility of designing hydrogel systems with enhanced mechanical properties (e.g. toughness and elasticity) and evaluating the applicability of such custom designed hydrogels as vascular grafts. This project hinges on our lab’s ability to create hydrogels with enhanced elasticity while retaining their ability to imbibe large quantities of water (~95%).

#14 Low-Cost Respiratory Rate Monitor (PI: Dr. Carlos Vera)

During surgery it can be critically important to monitor the presence or absence of breathing, as well as during recovery. This device should produce an audio pulse (a “beep”) each time the patient breathes. If the impedance plethysmography approach is used, the electrodes should be permanent and reusable. Display of the respiratory rate is a secondary feature. Alarms for respiratory rate are a secondary feature. Device must be highly reliable.

Relevant additional specifications
Cost: <$20 in quantities of 1
Cost: <$5 in quantities of 500

#15 Designing and building synthetic gene networks (PI: Dr. Jeff Hasty)

From an engineering perspective, the connection between genes and proteins generates molecular network diagrams that resemble complex electrical circuits. Systematic understanding of such networks will require the development of a mathematical framework for describing circuitry. Recent experimental advances in both sequencing and genetic engineering have made this approach feasible through the design and implementation of synthetic gene networks amenable to mathematical modeling and quantitative analysis. As with the construction of electrical circuits, the gene circuit approach uses mathematical computational tools in the analysis of a proposed circuit diagram, while novel experimental techniques are used to construct the networks according to the model blueprint.

Engineering of synthetic gene networks will benefit a wide variety of existing fields and enable us to harness cells for applications that are not feasible today. Synthetic gene networks could, for example, enable the creation of programmed bacteria cells that could produce a desired protein at specific concentrations and durations, and allow engineers to “turn on” bacteria when they are needed. Applications include tissue engineering, molecular fabrication of biomaterials and nano-structures, synthesis of pharmaceutical products, and biosensing.

#16 Designing and constructing microfluidic devices (PI: Dr. Jeff Hasty)

Many high-throughput research methods face limitations due to the lack of whole cell experimentation. This leads to potential false positives from molecules that may not truly interact in vivo because of reduced spaial proximity, organelle comparmentalization, or regulation via other pathways. In contrast, microfluidics intoruces the ability to study cells effectively with high-resolution and localized applicatin of experimental conditions in physiologically relevant environments. Additionally, the ability to massively array devices on a chip at the micron level opens the door for high-throuput, high fidelity experimentation to aid in accurate and precise experimentation and assay development.

Microfluidics technology has the potential to transform and revolutionize scientific research because of their capability to manipulate experimental samples at the nanolitervolumes and provide the opportunity to study cells effectively with high-resolution and localized application. Devices benefit from their small scale, low cost production, reduction in waste yield, increased speed of experimental techniques, and overall allowed integration of functionally diverse systems on a single device.

#17 MRI-compatible optical imager for space- and time-resolved measurements of neuronal activity using fluorescent indicators with concurrent acquisition of fMRI data (PI: Dr. Anna Devor, Neurosciences and Radiology)

The MR-compatible optical imager will use optical fibers to bring illumination light into the bore of the MRI scanner and a high-density coherent fiber bundle to transmit the optical signal to a detector, a CCD camera. We will optimize the instrument to work with the 7T horizontal-bore scanner at The Center for fMRI. The distal side of the imager will be integrated into MR-compatible animal holder and will consist of a mirror, optical fiber bundle and a positioning mechanism. The positioning mechanism will secure the mirror-coupled end of the bundle ~1/2 inch above the animal head. This distance is enough to accommodate a radiofrequency (RF) MRI coil and an optical well around the cortical window. The MR-compatible dielectric mirror will image a cortical exposure onto the coherent fiber bundle that will transmit the image to the CCD camera ~30 ft away from the 7T scanner.

The other end of the bundle will be equipped with a lens that will allow focusing and zoom and will be coupled to the CCD detector. The signal from the high-density coherent bundle will be imaged onto the detector using the focusing lens. A non-coherent fiber bundle attached to a light source will be used for illumination. Illumination light from will be passed through an excitation filter. The detected signal will be filtered by a filter cube consisted of a dichroic mirror and an emission filter. The filter cube will be positioned between the high-density fiber bundle and the CCD camera and will ensure transmission of only the emitted fluorescence to the detector. This configuration will allow acquiring fluorescent images of neuronal activity with high temporal and spatial resolution simultaneously with BOLD fMRI for direct correlation of neuronal and hemodynamic activity.

#18 Swine Flu: Bioengineering Approach to Diagnosis (PI: Dr. Amy Sung)

Influenza viruses killed millions of people in past pandemics. The influenza A genome contains eight pieces of RNA, which undergo mutations and assortment, making specific DNA and immunological diagnosis time-consuming and costly. There are also other infections (e.g., common cold) causing flu-like illness (ILI) symptoms. An initial diagnosis that can be done quickly and economically before sending samples to CDC or other laboratories would be desirable. This project will use the principles of bioengineering to develop a universal design to detect influenza viruses which can be used by patients at home or professionals in the office.

#19 Design of ECG Measurement and Holding Device for Cardiac MRI (Dr. Karen Christman)

Small animal cardiac MRI is a valuable technique to measure cardiac function post disease, treatment, or gene knockout. ECG Gated MRI allows for tracking the images through the cardiac cycle.

Challenges:

• Movement of electrodes inside and outside the magnet causing interference with ECG signal
• Time consuming positioning of the animal

The Design Project:

• Design easy to use rodent cradle with built-in insulated electrodes for ECG measurement

#20 Refining Characterization of Nanoparticles used with in vitro Diagnostic Assays (PI: Paul Schlunt, Beckman Coulter)

Project will involve refining specifications for nanoparticles used in established in vitro diagnostic products. The use of commerically available nanoparticels is rapidly expanding, but true characterization of those particles for their many uses is not properly understood. In vitro diagnotics require very specific performance criterion, and the demands for precision are increasing. Production of coated particles is based upon proprietary avidin-biotin technology. Most desirable outcome would be a model for created coated particles with effectively the same performance from different raw material lots. Information would allow specifications more beneficial to both vendor and customer.