On-campus Research Opportunities (Undergraduate)

• Calit2 Summer Undergraduate Research Program
• Phil Bourne, School of Pharmacy
• Pieter Dorrestein, School of Pharmacy
• Sanjay Nigam, Pediatrics
• Pavel Pevzner, Computer Science and Engineering
• Milton Saier, Biological Sciences
• John Wooley, Pharmacology

Contact: http://ucsdstudents.calit2.net/contact.php
Last updated: 3/4/2009

Calit2 Summer Undergraduate Research Program

The UCSD Calit2 Summer Undergraduate Research Scholar Program provides college students with the opportunity to perform hands-on research under the guidance of a UCSD faculty advisor over a 10-week period. The student can either assist in an ongoing research project or propose a new project. Students choose and work with a faculty advisor to develop a research proposal as part of the application process. In keeping with Calit2's multidisciplinary thrust, students from all academic majors are encouraged to apply.

Students will attend weekly seminars to learn more about applying to and preparing for graduate school, funding opportunities for research, connecting with current UCSD graduate students, career opportunities in academia and industry, and making good scientific presentations. All participants will display the results of their research efforts at a poster session at the end of the program a Certificate of Merit will be awarded.

For more information, see the program website, this article, and the 2008 summer projects.

Application deadline for summer 2009 projects: Friday March 13, 2009 at noon.

Contact:
Last updated: 2/24/2009

Protein Data Bank (PDB) related Projects

1. Classification and Annotation of Membrane Proteins

The number of available 3D structures of membrane bound proteins is still a small but growing fraction of the PDB. This rotation project will compare current methodologies to identify membrane proteins and to classify them by topology. The objective is to develop an accurate method that uses either a combination of existing methods or a new method to classify membrane bound proteins given their 3D structures.

2. Mapping Protein Structures to Phylogenetic Trees

The goal of this rotation project is to develop a tool to easily navigate sequence and structure space of pharmaceutically relevant gene families, for example a dynamic displays of a phylogenetic tree that maps and compares available 3D structural information.

3. Classification and Annotation of Ligands in the PDB

Protein structures in the PDB are co-crystallized with many different ligands: inhibitors, agonists, antagonists, substrate analogs, precipitants, etc. This project will perform a systematic analysis of bound ligands and develop a classification scheme. The ligand properties will be correlated with binding site properties and linkages will be established with databases of experimental binding affinity data.

4. Graphical Display of Structure Quality

The PDB collects both structural models and the underlying experimental data. For x-ray structures structure factor files are available. These data can be used to calculate electron density maps and to develop measures of the goodness of fit on a per residue level (i.e. real-space correlation coefficients.). The goal of this project is to develop experimental confidence measures and map them graphically onto protein structures to highlight either well or purely defined regions of a structural model.

5. Visualization of Intermolecular Interactions

This project will develop innovative 3D visualization techniques for the display of protein-ligand and protein-protein interactions including hydrogen bonds, metal coordination, aromatic interactions, etc.

6. Exploring unusual protein structure relationships

With the increasing amount of protein structure information that is available in the PDB, more and more proteins showing unusual and surprising sequence and structural relationships can be discovered. In this rotation project we will explore such unusual relationships more closely: Depending on the background of the student we will either *) analyze existing methods for their applicability to detect unusual relationships or *) implement/improve algorithms for the detection of unusual relationships.

Contact:
Last updated: 3/4/2009

The Dorrestein laboratory is interested in the functional aspects and biosynthesis of post-translational modifications (PTMs). Of particular interest are orphan genes (genes currently assigned to have no known function) that are responsible for the generation of bioactive natural products (e.g. antibiotics, anti-cancer agents etc.) or PTMs. This research aims to understand the functions of such genes by the use of high-resolution mass spectrometry. To achieve this goal, the lab will have the most advanced mass spectrometer on the UCSD campus. Please see the Research page on the lab website for descriptions of current research projects.

Contact:
Last updated: 3/4/2009

Drug Response, Organ Development

Dr. Nigam's lab is interested in molecular and cellular mechanisms of branching morphogenesis as they relate to organ development (eg. kidney, lung).

They are also investigating the use of developmental approaches to 'tissue engineer' epithelial organs and molecular mechanisms of drug elimination by the kidney and the role of polymorphisms in determining human drug response.

Contact:
Last updated: 3/4/2009

See the Projects page on http://www.ubergrid.org for an extensive list of mass spec projects in the Pevzner lab and in collaborating labs. Project themes include mass spec, T-Rex Fossils, and Comparative Proteogenomics.

Contact:
Last updated: 3/4/2009

Protein Bioinformatics Projects Available:

1. Conduct bioinformatic analyses to characterize novel familes of transport proteins.
2. Identify distant relationships between protein families to determine superfamily associations.
3. Map protein evolutionary pathways by identifying internal repeats and establishing homology.

These projects will require familiarity with a variety of computer programs, several of which were developed in our lab. No prior experience is required, but a student must commit to at least 15 hrs of research effort per week. Literature research is also required so that the student gains a complete knowledge of the published literature concerning the project at hand. If a student has software development experience, we also have a need to develop new programs for protein family and genome analyses. Finally, our lab is concerned with genome analyses of transporters and have developed software for this purpose. If this is a primary interst of a student, such a project could be arranged.

Contact:
Last updated: 3/4/2009

My own research has focused on structure-function relationships in protein-nucleic acid complexes and the architecture of chromatin and ribonucleoproteins. Pharmacology should benefit strongly from new computational science thrusts on the campus and from the coordinated effort in structural genomics, a second phase of international genome projects aimed at using physical science tools to uncover the information content of newly discovered genetic information. We have bioinformatics projects for undergraduates, particularly from Bioengineering. [Website]