Project Roster 2007

Sessions 1 & 2: June 26 - July 26

Exploring “Invisible” Patterns in Nature: How Is That Possible?

Advisors: Jasquelin Pena, Civil and Environmental Engineering -&- Kate Smallenburg, Molecular and Cell Biology

Students will learn how scientists look for patterns in nature that cannot be seen with the naked eye. A scanning electron microscope will help us do this.

Discovering and Navigating GIS and GPS

Advisor: Esther Zeledon, Environmental Science, Policy and Management

Ever wonder how the GPS in your car works and how satellite images, roadmaps and other data are put into this device? In this session, you will learn how a GPS works, get an opportunity to input your own data into a GPS and input your data into a GIS database (which holds GPS data).

Session 1: June 26–July 10

Discovering Splice Site Sequences: An Introduction to Molecular Biology

Advisors: Yuri Bendaña (Session 1 Project Leader) Bio-Engineering -&- Angela Brooks (Session 2 Project Leader) Molecular and Cell Biology

Objective: Students will learn about basic molecular biology in the context of bioinformatics. They will learn the basics of using the UCSC Genome Browser as a tool to visualize biological sequence data. They will apply their knowledge of basic molecular biology and use the UCSC Genome Browser to “discover” how intron-exon boundaries are defined in the cell.

Outcome:

• Gain knowledge of basic molecular biology
  • Central dogma
  • Alternative Splicing
• Learn about the field of computational biology and genomics
  • Sequence Alignments (not in detail, just introducing the concept)
• Learn how to navigate the UCSC Genome Browser, a tool used by many computational biologists
• Develop individual thinking skills as well as working with a group on a research project
• Have fun and learn that you can do biological research based on data easily accessible on the Internet
• Connect their project to cases of aberrant splicing that causes disease: ex.

Exploring Biochemical Reactions: What Do They Reveal?

Advisor: Bryan L. Jackson, Department of Chemistry

In this project, students will learn about biochemical reactions and their use in understanding biology. The students will research the use of fluorophores on proteins for imaging of live cells on the internet. In the lab, the students will react a fluorophore to a protein and determine the optimum pH for this reaction.

Searching for Alternative Energies: Is Solar Energy the Answer?

Advisor: Kenneth Miguel Armijo, Reynaldo Gueria, Deparmtent of Mechanical Engineering

The students will research alternative energies, as well as current energies and then figure out the differences between them. At the end of the program, I will then provide more information and have them research fuel cells and solar energy systems as they relate to the research that we are doing.

Digital Arithmetic Adder Circuits: What Are the Design Tradeoffs?

Advisor: Douglas Densmore, Department of Electrical Engineering and Computer Science

What are the tradeoffs that need to be made in digital arithmetic adder circuits? How can one go about designing for these tradeoffs?

Field Trip (possibility): Visit Intel or Xilinx in the south bay (both semiconductor companies) for a tour of the clean room (the place where they make microchips).

Notes: The first session is going to work for me better than the second. I have no special needs for this project.

What Is Thermal Conductivity? Why Do We Care?

Advisors: Kyle Sundqvist, Bruno Serfass, Department of Physics

What is thermal conductivity, and what’s it good for? How do we measure it? The scope of this project is to explore thermal conductivity and its origin in materials.

Session 2: July 12–July 26

Python Madness: Discovering Conserved Exonic Regulatory Sequences

Advisor: Angela Brooks, Molecular and Cell Biology

Students will try to identify regions of DNA that have conserved exonic regulatory sequences. These sequences might help to regulate alternative splicing. Students will get an overview of the Python programming language as a tool to identify the regions of DNA.

Testing for E. coli in Strawberry Creek: What Will We Discover?

Advisors: Gregory Ruiz, Civil and Environmental Engineering -&- Dave Dauphine

After conducting much research, the students will test Strawberry Creek water for E. coli. The major sources of pollution for the creek are dog defecation and surface runoff so this is a contaminant they will be likely to find in at least some of their samples. As far as heavy metals go, I have found data about chromate, lead, mercury, and cadmium being present but not arsenic.

There is a really easy way to test for E. coli called Coliscan Easygel. Coliscan Easygel tests are available through the Micrology Laboratories’ website at a cost of $19.95 per kit. Each kit contains the materials to run ten tests. With two kits, each student can be responsible for several tests.

It takes 24 hours for results to develop if the samples are incubated at 35 degrees Celsius and longer if the samples are left at room temperature. Note that it is possible to make your own incubator out of cardboard boxes and a low watt light bulb. We could either let the samples develop in my apartment, or David could leave them to develop in his lab space.

I have found multiple reports about high school students using Coliscan Easygel, so I am sure these students can work with them as well.

Field Trip: We would visit a sampling site off of the main campus. Possible sites are near the Botanical Gardens or Strawberry Creek Park. We would probably be using public transportation.

Exploring Microbial Diversity in Your Fridge! What Will We Discover?

Advisors: Karelyn Cruz, Plant and Microbial Biology -&- Daniela Goltsman, Department of Environmental Science, Policy and Management

Using items typically found in everyone’s refrigerator, students will learn about microbial diversity by isolating and visualizing bacteria present in our everyday life. The class will use our group’s lab facilities in Hilgard 113.

This lab experience will be focus in culturing, visualizing and identifying bacterial classes in your refrigerator. Students will learn basic culturing techniques and the use of fluorescence microscopy by using the Fluorescence in situ hybridization (FISH) technique. Before starting with the lab techniques we will review some basic principles in microbiology, cell structure and microbial diversity.

Cryogenics: What’s So Cool About Them?

Advisor: Erin Quealy, Department of Physics

We will investigate the process of cooling materials and the use of cryogenics in detector systems. In the process we will learn about temperature, liquid nitrogen and helium, storage containers for cold material, and application of cooling systems to science. A telescope camera being built in my lab will serve as an example system, and students will have hands on work with cryogens.