Aaron Fields, Professor

Closed (1) Cartilage permeability and disc degeneration

Applications for fall 2021 are now closed for this project.

The Orthopaedic Biomechanics and Biotransport Laboratory at UCSF conducts research related to structure-function relationships in musculoskeletal tissues, with a particular focus on the mechanisms of nutrient transport in bone and cartilage and harnessing nutrient transport for tissue repair and regeneration. The lab combines engineering and biology approaches for (1) understanding the effects of aging and disease on structure-transport relationships and (2) developing translatable diagnostic and therapeutic strategies. An overall theme of this work is the use of advanced experimental and computational tools to measure how tissue constituents at the nano- and microscales impact whole-organ behavior. We maintain active collaborations with orthopaedic surgeons, radiologists and industry partners.

Low back pain is the leading cause of disability and is closely linked to disc degeneration. Intradiscal biologic therapy is a promising strategy for managing disc degeneration. However, an unresolved issue is whether a degenerated disc has adequate nutrient supply to support the higher metabolic demands required by these therapies. The overall premise of this project is that low cartilage endplate (CEP) permeability limits disc nutrient supply and cell function, and that we can identify patients with adequate nutrient supply who might benefit from intradiscal therapy through non-invasive assessment of CEP permeability. To do this, we’re combining newly developed MRI techniques with advanced quantitative analysis to assess how CEP permeability relates to the extent of disc degeneration.

This is a great opportunity for a computer science/engineering/biology students to learn and apply cutting-edge research tools at the intersection of engineering, biology and medicine.

Specific tasks for the URAP student will include developing computer algorithms and codes to process data from MR images, analyzing the results, and preparing figures for publication. All training will be provided.

Day-to-day supervisor for this project: Noah Bonnheim, Post-Doc

Qualifications: The student must be highly motivated and extremely detail-oriented. Background in computer science or engineering, good problem-solving skills, and excellent communication skills are essential. Experience with programming (e.g. C/C++, Python, Matlab, IDL, etc.) is required. This project is ideal for second-, third-, or fourth-year students. A summer internship in the lab and/or continuation the following year is possible. Work schedule can be tailored to accommodate the student’s course schedule.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: UCSF Parnassus Campus
513 Parnassus Avenue
San Francisco, CA 94143
Related website: http://fieldslab.ucsf.edu

Closed (2) Microdamage repair in bone

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

The Orthopaedic Biomechanics and Biotransport Laboratory at UCSF conducts research related to structure-function relationships in musculoskeletal tissues, with a particular focus on the mechanisms of nutrient transport in bone and cartilage and harnessing nutrient transport for tissue repair and regeneration. The lab combines engineering and biology approaches for (1) understanding the effects of aging and disease on structure-transport relationships and (2) developing translatable diagnostic and therapeutic strategies. An overall theme of this work is the use of advanced experimental and computational tools to measure how tissue constituents at the nano- and microscales impact whole-organ behavior. We maintain active collaborations with orthopaedic surgeons, radiologists and industry partners.

For this project, we aim to discover how osteocytes — the most numerous cells in our skeleton — repair bone microdamage, and how improper repair of bone microdamage affects its biomechanical behavior. Measurements of bone microdamage and biomechanical behavior will be made in healthy (cadaveric) bone samples and in bone samples from patients with hip osteonecrosis, which is a progressive disease that causes severe pain and ultimately, hip joint collapse.

This is a great opportunity for engineering/biology students to learn and apply cutting-edge research tools at the intersection of engineering, biology and medicine.

The student will be trained and help with various aspects of the project depending on background and interest, including biomechanical testing, microdamage quantification, image processing, and statistical data analysis. All training will be provided.

Day-to-day supervisor for this project: Jae-Young "Jerry" Jung

Qualifications: The student must be highly motivated and extremely detail-oriented. Good problem-solving skills and excellent communication skills are essential. Experience with programming (e.g. C/C++, Matlab, IDL, etc.) is helpful but not required. Preferred: Background in engineering or biology and prior experience with experimental testing and data acquisition. This project is ideal for second- or third-year students. A summer internship in the lab and/or continuation the following year is possible. The lab is located at the UCSF Parnassus campus. The campus is BART/Muni accessible. Work schedule can be tailored to accommodate the student’s course schedule and the commute from Berkeley.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: UCSF Parnassus Campus
513 Parnassus Avenue
San Francisco, CA 94143
Related website: http://fieldslab.ucsf.edu

Closed (3) Cartilage End Plate Permeability and Biomechanics

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

The Orthopaedic Biomechanics and Biotransport Laboratory at UCSF conducts research related to structure-function relationships in musculoskeletal tissues, with a particular focus on the mechanisms of nutrient transport in bone and cartilage and harnessing nutrient transport for tissue repair and regeneration. The lab combines engineering and biology approaches for (1) devise tools and delivery techniques for evaluating the translational potential of spinal therapies; and (2) characterize cartilage endplate composition using contrast-enhanced micro-CT and other biochemistry assays. An overall theme of this work is to address the enzymatic treatment parameters on CEP matrix composition/porosity, permeability, and biomechanical strength. We maintain active collaborations with orthopaedic surgeons, radiologists and industry partners.
Low back pain is the leading cause of disability and is closely linked to disc degeneration. Low cartilage endplate (CEP) permeability limits disc nutrient supply and cell function. Intradiscal biologic therapy is a promising strategy for managing disc degeneration. However, biologic therapies increase disc cellularity and stimulate matrix production, which places greater demands on the limited nutrient supply inside the avascular disc. The premise of this project is that low cartilage endplate (CEP) permeability limits disc nutrient supply and cell function, and that we can increase nutrient supply and thereby improve the efficacy of biologic therapies by enhancing CEP permeability. In this study we aim to measure the effects of enhancing CEP porosity on solute transport into intervertebral discs and to evaluate how far this treatment can affect its strength.
This is a great opportunity for engineering/biology students to learn and apply cutting-edge research tools at the intersection of engineering, biology and medicine.

Specific tasks for the URAP student will include biomechanical testing of the intact intervertebral disc, creep analysis, contrast-enhanced micro-CT image analysis, porosity measurements, biochemistry assays, analyzing the results, and preparing figures for publication. All training will be provided., Staff Researcher

Qualifications: Qualifications: The student must be highly motivated and extremely detail-oriented. Background in science/engineering, good problem-solving skills, and excellent communication skills are essential. Experience with Matlab is required. Experience with digital image processing is a bonus. This project is ideal for third-year students. A summer internship in the lab and/or continuation the following year is possible. The lab is located at the UCSF Parnassus campus. The campus is BART/Muni accessible. Work schedule can be tailored to accommodate the student’s course schedule and the commute from Berkeley.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: UCSF Parnassus Campus
513 Parnassus Avenue
San Francisco, CA 94143
Related website: http://fieldslab.ucsf.edu

Closed (4) Multiscale/multimodal imaging of human cartilage endplate

Applications for fall 2021 are now closed for this project.

The Orthopaedic Biomechanics and Biotransport Laboratory at UCSF conducts research related to structure-function relationships in musculoskeletal tissues, with a particular focus on the mechanisms of nutrient transport in bone and cartilage and harnessing nutrient transport for tissue repair and regeneration. The lab combines engineering and biology approaches for (1) understanding the effects of aging and disease on structure-transport relationships and (2) developing translatable diagnostic and therapeutic strategies. An overall theme of this work is the use of advanced experimental and computational tools to measure how tissue constituents at the nano- and microscales impact whole-organ behavior. We maintain active collaborations with orthopaedic surgeons, radiologists and industry partners.

Low back pain is the leading cause of disability and is closely linked to disc degeneration. Intradiscal biologic therapy is a promising strategy for managing disc degeneration. However, an unresolved issue is whether a degenerated disc has adequate nutrient supply to support the higher metabolic demands required by these therapies. The overall premise of this project is that low cartilage endplate (CEP) permeability limits disc nutrient supply and cell function, but we still do not know the details of the CEP tissue structure and its role on nutrient transport. Thus, our current focus is to identify the best way to image the CEP tissue using both non-invasive and invasive imaging techniques.

This is a great opportunity for engineering/biology students to learn and apply cutting-edge research tools at the intersection of engineering, biology and medicine.


Specific tasks for the URAP student will include evaluating and comparing multiscale/multimodal imaging and processing tools, developing machine learning-based 3D image segmentation & reconstruction algorithms and codes, and statistical analysis on image-based quantification data. The student will also have an opportunity to learn how a cadaveric tissue harvested and characterized in the lab. Scanning electron micrographs, transmission electron micrographs, and micro-computed tomograms will be used for the multiscale imaging and different imaging modalities from light, electron, and X-ray sources will be compared and selected for the multimodal imaging specifically for the CEP tissue.

Day-to-day supervisor for this project: Jae-Young "Jerry" Jung, Ph.D., , Post-Doc

Qualifications: Qualifications: The student must be highly motivated and detail-oriented. Background in science/engineering, good problem-solving skills, and excellent communication skills are essential. Experience with at least one of the programming languages (e.g. C/C++, Matlab, Python, R, etc.) is required. Proffered: Background in engineering or biology and prior experience with machine learning will be a plus. This project is ideal for second- or third-year students. A summer internship in the lab and/or continuation the following year is possible. The lab is located at the UCSF Parnassus campus. The campus is BART/Muni accessible. Work schedule can be tailored to accommodate the student’s course schedule and the commute from Berkeley.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: UCSF Parnassus Campus
513 Parnassus Avenue
San Francisco, CA 94143

Related website: http://fieldslab.ucsf.edu