Research Projects by Subject

Note: Each research project will involve background reading for the interns provided by their mentors. Each research project will involve a final presentation by the interns.

Interns are expected to work collaboratively on the same project and/or data set. This may preclude rising seniors from submitting papers based on such projects to the Intel Science Talent Search competition.

Molecular, Cell & Developmental Biology

Code Research Project Descriptions
MCD-01 Title: Effects of Stromal Androgen Receptor on Prostate Cancer Initiation
Primary mentor: Corrigan Horton
Faculty advisor: Prof. Zhu Wang
Other mentors: Yueli Liu
Location: UCSC Main Campus
Number of interns: 2

Project description: The steroid hormone, androgen, plays critical roles in prostate development and cancer progression through its nuclear receptor, androgen receptor (AR). The normal prostate gland consists of a stromal layer that includes abundant smooth muscle cells, as well as an epithelial layer containing luminal and basal cells. AR is highly expressed in epithelial luminal cells and stromal smooth muscle cells. However, whether stromal AR plays a tumor-suppressing or tumor-promoting role remains controversial. This project aims to address this question by investigating the effects of AR gene loss specifically in the prostate stroma under various tumor-initiating conditions using mouse models in vivo.

Tasks: Depending on the SIP interns’ areas of interest, they may help in collecting mouse prostate samples, processing tissues for immunofluorescence staining, image acquisition, and most importantly, quantification and interpretation of staining results for various samples.    

URL: http://mcd.ucsc.edu/faculty/wang.html
Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON


Code Research Project Descriptions
MCD-02 Title: Investigating Cell Division in Fruit Flies
Primary mentor: Lotti Brose
Faculty advisor: Prof. Bill Sullivan
Location: UCSC Main Campus
Number of interns: 2

Project description: All cells must divide properly to ensure growth or reproduction of the organism. In multi-cellular organisms, failure to divide properly can lead to a host of issues, including cancer. Several processes must come together in a tightly-regulated manner to ensure proper cell division. The mentor is interested in the timing, regulation, and outcome of cell divisions in different stages of life of the fruit fly, Drosophila melanogaster. These organisms are small, reproduce rapidly, and are an excellent model for genetic manipulation and cell biology. The SIP interns and mentor will use genetics, molecular biology, and microscopy to study how machinery required for cell division affects the development of the fly.

Tasks: The SIP interns will be involved in characterizing cell division anomalies in flies expressing mutations in a protein that regulates cell division. Specifically, the interns will use light and fluorescent microscopy to determine the effects of these mutations on cell division in the adult fly and in the fly embryo. Further, the SIP interns will learn techniques in Drosophila genetics and molecular biology, as well as receive training in data analysis, reading scientific journal articles, and presenting their findings in a group setting.

URL: http://sullivan.mcdb.ucsc.edu
Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON OFF OFF

Special age requirement: The applicant must be 16 years old by June 12, 2017.

Code Research Project Descriptions
MCD-03 Title: Engineering of a RNA Binding Protein
Primary mentor: Dr. Tonio Schuetze
Faculty advisor: Prof. Melissa Jurica
Location: UCSC Main Campus
Number of interns: 2

Project description: RNA is a class of molecules that is widely used in cells. RNA can be bound by a class of proteins called RNA-binding proteins. The SIP interns will use basic cloning and protein purification technique to prepare a RNA binding protein for use in functional assays. The interns and mentor will need to genetically modify the protein to abolish the enzymatic activity. After purification, the interns and mentor will need to validate the RNA-binding function while enzymatic activity is abolished.              

Tasks: The SIP interns will gain insight into the work of a molecular biology lab. The interns will learn about macro-molecular biomolecules and their function. The SIP interns will experience how a lab is organized and learn many basic lab techniques like making buffer, cloning and E. coli expression systems which are widely used in biomedical environments. The SIP interns will need lab safety training.

URL: http://bio.research.ucsc.edu/people/jurica/home.htm
Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON REM REM ON ON ON ON ON

Special age requirement: The applicant must be 16 years old by June 12, 2017.

Code Research Project Descriptions
MCD-04 Title: Molecular Mechanisms Regulating Neural Stem Cell Differentiation
Primary mentor: Dr. Yue Zhang
Faculty advisor: Prof. Bin Chen
Location: UCSC Main Campus
Number of interns: 2

Project description: The human brain is the most complicated organ in our body. It contains billions of neurons and these neurons form trillions of connection with one another. All neurons in the brain are not identical. They can be divided into hundreds of different types based on their functions, axonal projections, morphology, and gene expression. In addition to neurons, the brain contains glial cells, which supports and maintains the proper functions of neurons. Glial cells in the brain can be classified into two major cell types: astrocytes and oligodendrocytes. During embryonic development, neural stem cells divide and produce diverse neuronal cell types, astrocytes and oligodendrocytes. It is not completely understood how the decision is made for the neural stem cells to generate these diverse cell types. The mentor's research group and other researchers have found that neural stem cells are multipotent during early brain development: each neural stem cell sequentially generates different types of neurons, astrocytes and oligodendrocytes. For example, in the developing cerebral cortex, neural stem cells first generate excitatory neurons, followed by the production of both glial cell types. This project aims to identify the genes that direct neural stem cells in the cerebral cortex to switch from generating neurons to producing glial cells.

Tasks: The SIP interns will participate in lab research studies. Under the guidance of their postdoctoral mentor, the SIP interns will assist in collecting brain samples from mice carrying mutations in candidate genes that may regulate neural stem cell lineage switch. The interns will learn to genotype the mice, make brain sections, and perform anatomical and molecular analysis of the brains. The SIP interns will learn techniques used in molecular biology and immunohistochemistry. The interns will also learn to use epifluorescence microscopes to compare normal brains to brains carrying mutated genes.

Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Lab work
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON

Special age requirement: The applicant must be 16 years old by June 12, 2017.

Code Research Project Descriptions
MCD-05 Title: Analysis of Transcription Factor Binding Sites at the Nkx3.1 Gene Locus
Primary mentor: Dr. Qing Xie
Faculty advisor: Prof. Zhu Wang
Location: UCSC Main Campus
Number of interns: 2

Project description: Nkx3.1 is a gene that is specifically expressed in the prostate. It is also a tumor-suppressor gene that is frequently down-regulated during cancer initiation. We have recently obtained preliminary data indicating that such down-regulation occurs at the transcriptional level. Therefore, identification of potential transcription factor bindings sites at the Nkx3.1 gene locus will provide clues to our understanding of its gene regulatory mechanism. The project seeks to identify potential transcription factor binding sites at the Nkx3.1 locus in both the human and mouse genomes. The goal is to provide candidates that can be experimentally tested in mouse prostate cancer models.

Tasks: The SIP interns are expected to use the UCSC genome browser and the TRANSFAC database to identify potential transcription factor binding sites at the Nkx3.1 gene locus in both the human and mouse genomes. A comparison of the results obtained in the two species will be evaluated. The interns will be expected to fomulate next-step testable hypotheses based on the in silico analyses and previous findings in the relevant literature.

URL: http://wanglab.ucsc.edu
Required skills for interns prior to acceptance: None
Skills intern(s) will acquire/hone: Computer programming; statistical data analysis
Program Week Number: 1 2 3 4 5 6 7 8 9 10
Mentor's availability: ON ON ON ON ON ON ON ON ON ON