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Undergraduate Summer Research InternshipsThe Systems Biology community at Harvard invites interested undergraduates who will not have graduated by June 2009 to apply for research internships in the summer of 2009. Starting on Monday June 8 the internship will last for ten weeks (until Aug 14), or longer by mutual agreement. Interns will work on research projects in the labs of the Bauer Fellows and Systems Biology faculty whose work spans many fields of science, from biology (including genetics, cell biology, neuroscience, animal behavior and evolution) to applied mathematics and computation. The internship also includes field trips (for example to the Broad Institute and the Medical School), weekly seminars and lectures by distinguished faculty. In addition, we organize fun activities for the interns outside the lab. Each intern will have the opportunity to learn a range of cutting-edge genomics or bioinformatics techniques in the exciting, dynamic environment at the FAS Center for Systems Biology and the Department for Systems Biology at Harvard Medical School. The internships will be offered to Harvard students and students from other universities. We will help students, particularly non-Harvard students, to find housing near the Cambridge campus. Harvard students are encouraged to apply for PRISE and HCRP fellowships. The salary for a ten-week internship will be at least $4500 (depending on the cost of housing). Underrepresented minority students are particularly encouraged to apply. Unfortunately we cannot consider international students unless they are enrolled at US universities and have valid student or work visas. The projects of this year's internship are listed below.In addition to completing the online form, applicants will be asked to submit a resume, transcripts, two letters of recommendation, and a research statement. In your research statement please specify for which project(s) you are applying (you can apply for several projects) and why you are particularly interested in those projects. You are welcome to submit a personal statement, but this is optional. The deadline for applications is February 6 for Harvard students (to allow students to apply for PRISE fellowships) and February 13 for non-Harvard students. Intern Experiences in past years Internprojects in 2009 Project 1,
Kevin Foster Project 2, Kobi Benenson 3.Examining the genetic basis of migratory behavior in butterflies 4.Testing mechanisms of speciation in butterflies 5. Breaking through the mucus barrier
6. A yeast model for amyotrophic lateral sclerosis 7.The emergence of complexity during the origin of life Project 8-10, Suckjoon Jun
9. Finite lifespan of E.coli? 10. Manipulating chromosomes in a microfluidic device 11.Screening for natural microbial isolates that select against antibiotic resistance 12. Synthetic kinetochore in the budding yeast 13. Custom-built gene networks in human cells
15. Evolutionary Cell Biology: Theoretical Analysis of Evolutionary Forces Shaping Cytoskeletal Organization Project 16-17, Jeremy Gunawardena
17. Discovering steady state invariants in multisite phosphorylation systems. 18. Mathematical models in biology 19. Mathematical theory for stochastic processes in cells 20. Microfluidics based methods to count molecules in single cells 21. Mathematical modeling of shapes: Building a statistical dynamic model of cell shape and division using image analysis 22. Graph Theory: Atlas-based registration and matching of lineage trees
Project 1. Social evolution and cheating in
microbes
Applicants will benefit from knowledge of microbiology, microscopy and an interest in evolutionary questions.
Project 2. Biological Computers in Human Cells We use synthetic biology tools to build molecular computing systems and embed them in human cells. Our overarching goal is to reprogram cell behavior to achieve a desired outcome, for example make sure that dangerous cellular transformations are stopped before the cell gives rise to a malignant tumor.
Specifically, the summer projects will focus on the development of protein and RNA biosensors and their integration with the molecular computers. Techniques used in the lab include genetic engineering, human cell culture maintenance and manipulation, fluorescent microscopy and fluorescent-activated cell sorting (FACS), as well as substantial amount of biochemical assays such as gel electrophoresis, blots, RT-PCR, etc. Prior laboratory experience in at least some of these techniques is required, as well as familiarity with the fields of molecular computing and synthetic biology.
We use butterflies as a model system to study the evolution and genetics of adaptation and speciation. We are looking for two motivated, energetic, and hard-working summer interns to work with us on exciting projects currently underway in the lab. Knowledge of basic genetics and previous lab experience would be helpful for these projects but they are not required. Project 3. Examining the genetic basis of migratory behavior in butterflies Recent research has identified genes that appear to play a role in flight performance and dispersal ability of butterflies. We are using a population genetics approach to examine whether these genes influence migratory behavior in butterfly species that migrate annually. The summer intern for this project will help clone portions of these genes and then screen DNA sequence variation in them, looking for associations between polymorphisms and migratory behavior. This project will entail various lab work including genomic DNA extraction, PCR amplification, DNA sequencing and genotyping. This project will also require butterfly collecting trips to locations around Boston. Project 4. Testing mechanisms of speciation in butterflies Hybrid speciation, or the process by which interbreeding between two species gives rise to a third lineage, is generally rare but it has occurred in multiple butterfly groups. We are examining the evolutionary history of the genome of a butterfly species which may have originated via hybridization. The summer intern for this project will isolate genes from throughout the genome, sequence these genes from the putative hybrid and parental species, and then use phylogenetic methods to trace the genome’s ancestry. This project will entail various lab work including genomic DNA extraction, PCR amplification, and DNA sequencing. Project 5. Breaking through the mucus barrier
Mucus is an important biogel that has critical roles in preserving our health. It lines many epithelial surfaces in our bodies and forms a barrier which shields us from infectious agents and toxins. Unfortunately, the mucus barrier is not perfect - certain viruses break through and cause damage ranging from a mild flu to serious cancer formation. The aim of this project is to understand how viruses break through the mucus barrier. We will use a combination of biochemistry and single particle tracking to address this question. This project will shed light on functional principles of biological barriers, but it is also potentially important for medicine, since it may lead to new approaches for preventing prevalent infectious diseases. The optimal candidate will benefit from a basic knowledge in biochemistry
and/or microscopy, or enthusiasm to learn. Project 6. A yeast model for amyotrophic lateral sclerosis We are interested in how protein misfolding disrupts proper cellular function. In humans, misfolding of the protein superoxide dismutase 1 (SOD1) is associated with the neurodegenerative disease amyotrophic lateral sclerosis (ALS); a mouse model of the disease also involves SOD1 misfolding. Although the disease is well-studied and has a complicated etiology, we believe that some of the basic cellular changes involved should appear in any eukaryotic cell. For example, protein misfolding exposes buried hydrophobic residues which stick to cell membranes and can open channels in them, disrupting ionic balances and causing cell death. Using the yeast S. cerevisiae, in which human SOD1 can be efficiently expressed, you will determine how wild-type SOD1 and various destabilized mutants associated with ALS interact with the cell membrane. You will use osmotic shock and staining techniques, coupled with direct visualization by microscopy as well as growth assays, to probe the relationship between the cellular burden of misfolded protein and membrane integrity. We study evolution at a molecular level using simple, stripped-down systems. Our goal is to understand how chemical changes in biomolecules translate into functional changes.
Project 9. Finite lifespan of E.coli?
Project 12. Synthetic kinetochore in the budding yeast Our lab is interested in the mechanism and control of mitosis in the budding yeast, Saccharomyces cerevisiae. One of the main events in mitosis involves the equal segregation of genetic material into two daughter cells, and the kinetochore, a multiprotein complex situated on the centromeres of chromosomes, is central to this process. The kinetochore provides the surface for microtubule attachment to chromosomes. It is also important for harnessing the force from microtubule depolymerization to drive the separation of sister chromatids. In addition, the kinetochore is an integral part of the spindle checkpoint, which prevent anaphase onset in the absence of correct microtubule attachments and ensure that the chromosomes are accurately segregated. Given the essential functions of the kinetochore in mitosis, it will be important to understand how it is assembled and regulated during the cell cycle. To develop a simple system to study the kinetochore, we have constructed a synthetic kinetochore in budding yeast by tethering a single kinetochore protein, Ask1p, to non-centromeric DNA. Ask1p can presumably recruit other kinetochore proteins and allow microtubule attachments, as we have shown that the synthetic kinetochore can perform many of the natural kinetochore functions. With the synthetic kinetochore, we can control when, where and how many kinetochores are assembled. Using video microscopy and other molecular techniques, we will tackle questions such as how the number of active kinetochore affects mitotic spindle structure, how the kinetochore is modified during cell cycle, as well as how the kinetochore is linked to the spindle checkpoint. The answers can further our understanding of the natural kinetochore and its multiple roles in mitosis. Project 13. Custom-built gene networks in human cells Decades of biology research have revealed the functions of proteins and DNA that regulate the expression of genes. Promoters, DNA binding motifs, activators, repressors, etc. work in concert to determine when and how genes are expressed. Gene regulators can regulate themselves and each other in networks that are reminiscent of an electronic circuit board. What happens when we extract parts (DNA and proteins) from nature to assemble a custom-made gene circuit? Can such a circuit predictably function in human cells? Our lab uses synthetic biology to assemble DNA sequences into artificial gene networks, we introduce these into human cells (in culture), then observe how the network is expressed via fluorescent proteins produced as output by the circuit. We use computer modeling to predict gene circuit behavior and to guide rational design of gene circuits. The project presents opportunities to investigate artificial gene circuit behavior in human cells, model circuit behavior using MATLAB, and explore how chromatin (the protein-DNA complex) can be used in an artificial circuit. You will gain experience with human/ mammalian cell culture, gene expression assays (Western and Northern blot), computer modeling, cytometry (microscopy and FACS), and standard molecular cloning techniques. Previous experience with standard molecular cloning techniques will be beneficial, but is not required. Project 14. Evolutionary Cell Biology: Comparative Analysis of Spindle Structure in Early Drosophila DevelopmentA wide variety of subcellular assemblies exist in a non-equilibrium steady state with a constant flux of molecules and energy continuously modifying and maintaining their architecture. A prime example of this is the spindle: a remarkable, self-organizing structure that segregates chromosomes during cell division. While approaches from genetics, cell biology, and biophysics are giving increase insight into mechanistic aspects of the behaviors of large-scale, subcellular ensembles such as the spindle, there is still very little understanding of the evolutionary forces ultimately responsible for shaping these structures. In this project we will attempt to gain insight into the evolutionary forces that determine the structure of the spindle by examining spindles formed during the early development of Drosophila. We will use immunofluorescence to compare spindles from Drosophila of closely related species and we will study the heritability of different aspects of spindle structure within a species. As the genomes of 12 Drosophila have been sequenced, we may also use approaches from bioniformatics to investigate the evolution of the molecules that make up the spindle (if this coincides with the interests of the intern). Project 15. Evolutionary Cell Biology: Theoretical Analysis of Evolutionary Forces Shaping Cytoskeletal OrganizationA wide variety of subcellular assemblies exist in a non-equilibrium steady state with a constant flux of molecules and energy continuously modifying and maintaining their architecture. A prime example of this is the spindle: a remarkable, self-organizing structure that segregates chromosomes during cell division. While approaches from genetics, cell biology, and biophysics are giving increase insight into mechanistic aspects of the behaviors of large-scale, subcellular ensembles such as the spindle, there is still very little understanding of the evolutionary forces ultimately responsible for shaping these structures. In this project we will attempt to gain insight into the evolutionary forces that determine the structure of the spindle by combining a comparative analysis of results available in the literature with phenomenological and population genetic theories. Such an analysis should help to determine how selection, neutral drift, and biophysical constraints conspire to produce subcellular organization. This work will require assembling a database of the architecture of spindles from different organisms, extracting quantitative information from this data, and using computer simulations to test different models of the evolution of the spindle. In addition, we may use approaches from bioniformatics to investigate the evolution of the molecules that make up the spindle. This project requires a highly motivated individual who is willing to work independently. A number of different directions are possible based on the interests of the intern. Some experience with programming is required. We study information processing in mammalian signalling pathways using a combination of experiment, computation and theory (http://vcp.med.harvard.edu/). Reversible phosphorylation on certain amino acid residues is one of the most widespread and significant mechanisms in signal transduction and some key regulatory proteins are phosphorylated on as many as 20-30 sites. A single molecule with n sites has an exponential number, 2n, of potential states, while a population of such molecules occupies a frequency distribution over these single molecule states. How do cells regulate and use this extraordinary combinatorial complexity? Project 16. Evolutionary conservation of phosphorylation sites and its relationship to function. Project 17. Discovering steady state invariants in multisite phosphorylation systems Project 18. Mathematical models in biology Project 19. Mathematical theory for stochastic processes in cells Project 20. Microfluidics based methods to count molecules in single cells The generation of noise by low copy molecules motivates our lab to develop assays to quantify low abundance proteins with single molecule resolution. Standard techniques for protein quantification, such as live-cell fluorescence microscopy and flow cytometry can provide relative measurements of abundant proteins in single cells. Quantitative western blotting can detect low abundance proteins, but requires large numbers of cells. Consequently, these methods are ill-suited to measuring the abundance of low copy proteins in single cells. In this project, you would work to develop a microfluidics-based assay for counting individual ?-galactosidase (?-gal) enzymes.Our proposed design is inspired by the work of Boris Rotman [1]. In the based assay, aqueous droplets are generated in a fluorous oil-surfactant mixture using flow-focusing on a microfluidic chip. Droplets of 50 um diameter (~66 pL) can be readily generated using this technique. The droplets will contain all components necessary for a ?-gal assay, including a substrate that becomes fluorescent when cleaved. When assaying a highly-diluted ?-gal solution, the assay readout will be digital—a droplet contains either 1 or 0 enzyme molecules. To determine the number of molecules in the solution, we will simply count the number of fluorescent droplets. The summer project will focus on establishing proof of principle, developing alternate reporters and adapting the assay to count plasmids with single-molecule resolution. The project will give you experience in microfluidic device development, fluorescence microscopy and standard molecular biology methods. [1] Rotman, B., Measurement of activity of single molecules of beta-D-galactosidase. Proc Natl Acad Sci U S A, 1961. 47: p. 1981-91. Project 21. Mathematical modeling of shapes: Building a statistical dynamic model of cell shape and division using image analysis In this project, the student will work on building a statistical model of the shape of the cell membrane and nucleus of cells 1) as a function of cell type, and 2) as a function of phase in the cell cycle. A dynamic model of cell division is required for solving more complex problems such as automatic cell type identification, cell tracking, and construction of cell lineage trees. The student will have multiple sets of 5D images (3D+time+multispectral) of zebrafish embryogenesis acquired using a multiphoton microscope to validate the model. The images capture the movement and division of cells during embryogenesis in zebrafish with the nucleus and membranes labeled in different colors. The cell cycle consists of 4 distinct phases, of which mitosis (M-phase) is critical for division. The M-phase by virtue of its small duration in the cell cycle is sparsely sampled in time. Moreover, a significant challenge lies in understanding the geometrical restructuring of the cell membrane and nucleus during the division process. Appropriate mathematical models need to be proposed or designed for representing these structures and then fit the data to select appropriate parameters. The student will receive adequate computational support, microscopy datasets and guidance in completing this project with a team of image analysis developers. The model will be used in other projects to solve segmentation and tracking problems. Project 22. Graph Theory: Atlas-based registration and matching of lineage trees In this project, we are interested in matching 4D (spatio-temporal) lineage trees generated by tracking cells during zebrafish embryogenesis. Lineage trees are essentially linear, attributed graph structures (binary trees) with many thousands of nodes corresponding to cell divisions. In the embryological context, these nodes have specific coordinates in space and time as well as attributes such as cell type and cell shape. The lineage trees are correlated in structure across different embryos in a complex and poorly understood way. There are likely correlations in the location of divisions, frequency of divisions, pattern of cell lineage, speed of cell migration to name a few. We are interested in using these correlations to help compare and “register” lineage trees extracted from different embryos. Therefore, we are interested in developing routines that match a pair of lineages and also build an atlas of their structure. There is a significant amount work in the graph theory literature on graph matching that the student can make use of. The student will receive adequate computational support, microscopy datasets and guidance in completing this project with a team of image analysis developers. This work will critically help us in understanding significant biological problems in embryogenesis.
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