George A. Brooks, Professor

Closed (1) Aging Research, Project 1: Center for Research and Education on Aging (CREA) Research Projects

Applications for Fall 2018 are now closed for this project.

Students may elect to participate in one of five CREA-related projects (1A-1E - please indicate on your application)

Project Summaries:
A. The creation of a Bioprinter, with the long term goal of printing human organs and limbs.
B. Construct a map of the components that drive the aging process.
C. Using Artificial Intelligence (AI) and a Natural Language Parser (NLP) to parse research papers that pertain to the biology of model organisms.
D. Creating biological simulations of pathways that play a role in the aging process.
E. The creation of visual interfaces that can describe large sets of biological data.
F. Virtual Reality head set to visualize large biological data sets.

Project Details:
A. The creation of a Bioprinter, that will be able to print tissues with a 3D printer that uses cells instead of ink. Develop Bioprinter and the histological protocols that are required in order to print tissue in 3D with the long term goal of printing human organs and limbs. We anticipate the time commitment for this research project to be 15 hours/week (2 credits).
B. Construct a map of the components that drive the aging process. The aging process is a complex set of changes that alter the way our systems work and interact with each other. The task is too construct a map that show the components of the systems and thier interactions as they change over time. We anticipate the time commitment for this research project to be 15 hours/week (2 credits).
C. Using Artificial Intelligence (AI) and a Natural Language Parser (NLP) to parse research papers that pertain to the biology of model organisms and deconstruct sentences in each research paper and derive the following details: The organism or organisms that were being described, the properties of the organism, i.e., (gender, age, spices etc.), determine in detail what is being described, determine the context in which the description is being made. Use a Living Systems Process Language (LSPL) to describe the process or processes that are being described in the research papers. Use the existing frame works such as the of anatomy and systems trees, cellular anatomy trees, KEGG pathways, physiological systems frame works, and other frame works that reside in the system, in order to add the new information to the existing model. We anticipate the time commitment for this research project to be 15 hours/week (2 credits).
D. Creating biological simulations of pathways that play a role in the aging process. Using a system that was developed at CREA, we create nodes that describe compounds such as insulin and how they interact with other compounds over time. Using a series of these interactions we can describe and simulate a pathway and how it functions over time. We anticipate the time commitment for this research project to be 15 hours/week (2 credits).
E. The creation of visual interfaces that can describe large sets of biological data. Create a visual interface that will allow a researcher to visualize and interact with the biological data that resides in a database which stores systems information that relates to the model organisms that we are attempting to describe with a Living Systems Process Language (LSPL) and various other methods. We anticipate the time commitment for this research project to be 15 hours/week (2 credits).
F. Virtual Reality head set to visualize large biological data sets.

Students will need to take instruction in EHS 101 on safe laboratory practices.

Day-to-day supervisor for this project: Steve Garan, Ph,D., Staff Researcher

Weekly Hours: to be negotiated

Related website: http://ib.berkeley.edu/faculty/brooksg.html
Related website: CREA.berkeley.edu

Closed (2) Exercise Metabolism, Project 2: Stable Isotopes in the Study of Metabolism

Closed. This professor is continuing with Spring 2018 apprentices on this project; no new apprentices needed for Fall 2018.

To follow the metabolism of specific compounds in the body, stable, non-radioactive tracers are given prior to and during the exercise period. Blood is sampled intermittently, and the metabolites are separated and the isotope ratios are determined. Depending on the metabolites involves, blood is treated in several ways, first to neutralize the acids, then a rough separation by column or thin layer chromatography, followed by derivitization to forms in which the ratios of isotopes can be detected by gas chromatography and mass spectrometry. These procedures require a solid understanding of chemistry. We anticipate the time commitment for this job to be 6 hours/week (2 credits).

URAP students applying for this project should have taken, or be currently enrolled in, Integrative Biology 123A or a comparable upper level course that focuses on human metabolism. In addition, some familiarity with basic lab procedures (such as pipetting, making solutions, etc.) is also required. If students handle human blood, they will be strongly advised to have, or get vaccinated against Hepatitis B. This is excellent training for a student interested career in biotechnology, ecology or petroleum chemistry.

Students will need to take instruction in EHS 101 on safe laboratory practices.

Day-to-day supervisor for this project: Michael A. Horning, Staff Researcher

Qualifications: IB 132 and IB 123A concurrent desired

Weekly Hours: to be negotiated

Related website: http://ib.berkeley.edu/faculty/brooksg.html

Closed (3) Exercise Metabolism, Project 3: Regulation of Muscle Cell Membrane Lactate Transporter Protein Expression

Closed. This professor is continuing with Spring 2018 apprentices on this project; no new apprentices needed for Fall 2018.

We are in the process of identifying the physiological signals responsible for lactate transporter expression. For this purpose when have developed a muscle cell culture system to study the influences of various putative factors in lactate transporter gene and protein expression. This project can cell culture, Western bottling (for protein detection), and RT-PCR for assessment of mRNA and pre-mRNA detection . We anticipate the time commitment for this job to be 6 hours/week (2 credits).

URAP students applying for this project should have taken, or be currently enrolled in, Integrative Biology 123A or a comparable upper level course that focuses on human metabolism. In addition, some familiarity with basic lab procedures (such as pipetting, making solutions, etc.) is also required. This is excellent training for a student interested in a career in biotechnology.

Students will need to take instruction in EHS 101 and safe laboratory practices and human laboratory animal care and handling.

Qualifications: IB 132 and IB 123A concurrent.

Weekly Hours: to be negotiated

Related website: http://ib.berkeley.edu/faculty/brooksg.html

Closed (4) Project 4: Metabolic Adaptions following Traumatic Brain Injury

Applications for Fall 2018 are now closed for this project.

The applicant will work with GSI/GSR Austin Peck on the discovery of metabolic signaling following Traumatic Brain Injury (TBI) to rats and mice. Responsibilities will run the full gambit from assisting in animal handling (including care and feeding), to data collection and analysis. Injured and uninjured control animals will be subjected to behavioral tests as well as numerous tests on living and postmortem animals. The techniques will include aspects of MRI on live animals and confocal microscopy on histological sections. As well, metabolic signaling pathways will be tracked via gene array analysis and Western blotting and Mass spectrometry. Microscopy and polarography studies will be used to determine the effects TBI on brain and muscle mitochondrial morphology and function.

Day-to-day supervisor for this project: Austin Peck, Ph.D. candidate

Qualifications: IB 132 and IB 123A concurrent. Students will need to take instruction in safe laboratory practices and humane laboratory animal care and handling.

Weekly Hours: to be negotiated

Related website: http://ib.berkeley.edu/faculty/brooksg.html
Related website: http://www.chori.org/Principal_Investigators/Kuypers_Frans_A/kuypers_overview.html