Carnegie Mellon University

Summer Research Institute

The SRI research internship will include instruction and assessment of skills in data recording, analysis and interpretation as well as in the written and oral communication of scientific results.  All students will be trained in lab safety, maintenance of lab records and notebooks, preparation of research reports, use of the research literature, and oral and written presentation skills.  As part of the latter, every student will write two reports, present an oral research update to the rest of the group each week and give a final talk at the end of the summer. Throughout the summer, students will learn how to analyze, interpret and present experimental and computational data. Although different teams will use different specialized methods in their individual projects, all students will be exposed to the entire range of problems and approaches through weekly team project presentations. 

Learning Objectives

Students who successfully complete SRI will:

  • learn good practices for laboratory safety.
  • know how to search for information in the scientific literature and how to read a scientific paper.
  • know how to access and use essential public databases.
  • know how to access and use essential bioinformatics tools to analyze sequences and structures of nucleic acids and proteins.
  • understand good scientific practice for written and oral communication.
  • learn how to put together a clear and informative presentation and how to make effective use of audiovisual presentation tools.
  • be able to collaborate effectively in research teams.
  • be better prepared to engage in subsequent long-term individual research projects mentored by faculty in MCS or elsewhere.

Evaluation

Students choosing to register for 3 units of SURA will be evaluated based on the following criteria:

  • 25% - Weekly in-class presentations (100 points)
  • 25% - Boot Camp written report (100 points)
  • 25% - Final written report (100 points)
  • 25% - Class participation (100 points)

Schedule and Organization

All SRI fellows will meet in a joint class session once per week for instruction on common topics, to make presentations, and to receive assessment and feedback.

Each student will prepare two written reports, in the form of a scientific research papers with an abstract, background/introduction, materials and methods, results and discussion. The first will be on the common project carried out during Week 1 “Boot Camp” (see below). The second will be on the student’s team-specific project carried out during the rest of the summer.

Students will work in teams of two or three on research projects proposed by MCS faculty. These projects focus on biological problems but typically involve multi-disciplinary approaches including molecular biology, genetics, bioinformatics and computational biology, chemistry, biochemistry and structural biology, and cell and developmental biology. Regardless of project, all students will be trained in essential methods of molecular biology and biochemistry (see Weeks 1 & 2 below). Additional methods, such as fluorescence imaging, site-directed mutagenesis, DNA sequencing, protein structural analysis by NMR, physical chemistry of nucleic acid complexes, or use of specialized bioinformatics tools will be introduced in the specific team projects and may vary from year to year. Although not all students will use the more specialized methods, all will be exposed to them through weekly team project presentations. In addition, all students will be trained in lab safety, maintenance of lab records and notebooks, preparation of research reports, use of the research literature, and oral and written presentation skills. As part of the latter, every student will write two reports, present an oral research update to the rest of the class each week and give a final talk at the end of the summer. Throughout the summer, students will learn how to analyze, interpret and present experimental and computational data.

The summer will be divided into two sections:

Weeks 1 and 2: “Boot Camp”. During week 1 students will receive training in laboratory safety and in essential methods of molecular biology, biochemistry and bioinformatics, including purification and manipulation of DNA, molecular cloning and generation of expression constructs, bacterial transformation, electrophoretic analysis of DNA and proteins, and protein purification. Students will also receive instruction on maintenance of records and lab notebooks. This section will involve a common project so that all students share the same experience and learn the same set of basic skills. During week 2 students complete boot camp activities, including preparation of a written report, and they transition into their team projects.

Remainder of Summer: “Team Projects”.  Students will select among several project options according to their interests and work in teams of three on those specific projects. Once a week every team will give an oral presentation to the rest of the class and faculty describing the rationale, goals, approaches, current results and overall status of their project. In addition to general discussion, the students will receive faculty feedback not only on the science but also on communication skills. Students will present final oral and written reports at the end of the summer, and each team will present a poster on their research at the CNAST (Center for Nucleic Acid Science and Technology) Symposium.

Previous Years

Projects from previous years included:

  • Effect of aging on mRNA splicing in fruit flies
  • Sea urchin developmental genomics
  • Role of metal ions in protein-DNA interactions
  • Exploration of new anti-malarial drug targets
  • Intracellular signaling in the development of colon cancer
  • Internalization of opioid receptors
  • Characterization of fluorescent protein tags
  • Characterization of ribosomal assembly factors
  • Development of Crispr technology for genome editing in pathogenic fungi
  • Mutations in RNA editing enzymes