BSCD Research Foundations in Genetics and Genomics Fellowship - 2020

Extended application deadline - all BSCD Fellowship application deadlines have been extended to April 17th. Please bear in mind that while BSCD Summer Fellowships are currently scheduled to proceed these opportunities may have to be modified or cancelled if the situation warrants. More information about the current status of on-campus research can be found on the University’s research continuity planning for COVID-19 site.  

Rapid advances in genome editing and high-throughput sequencing techniques continue to open new areas of discovery with applications to both basic research and human health. The Research Foundations in Genetics and Genomics Fellowship provides an opportunity for students to conduct research in any area of biology that involves genetic and genomic approaches and methodologies. Fellows will be matched with a host lab or can pre-arrange a host laboratory with a faculty member (PI). While projects focused on genetics, epigenetics and gene regulation will be encouraged, additional topics with links to genetics and development will be considered. In addition to conducting full-time research, Fellows will attend a weekly group workshop to learn about state-of-the-art techniques and present their research to each other. The goals are for students to engage in full-time primary research, gain exposure to the big questions in fields that utilize genetic and genomic approaches and learn to present and communicate their research.

The Fellowship awards a $5000 stipend for the summer research period, as well as $1500 for research expenses and supplies made available to the PI.

The primary responsibility of each Fellow is to conduct a research project under the supervision of a faculty PI. Fellows will perform research tasks on a full-time basis for the 10-week summer quarter. Students will work with an identified mentor within the host lab to design and outline a project and to carry out that project under the direct supervision of the identified mentor(s).  Mentors will also support the undergraduate research intern by providing relevant project literature and including the intern in laboratory activities such as group meetings and journal clubs. The specific tasks will be dependent on the lab and project, but are likely to involve animal, tissue or cell culture, molecular biology, next-generation sequence data analysis and genome browsing, and other experimental and computational techniques. Fellows will meet weekly with the Fellowship Directors, Heather Marlow (hmarlow@uchicago.edu) and David Pincus (pincus@uchicago.edu), to present cutting-edge methodologies as well as their projects and results to one another. At the end of the summer, Fellows will present their research in a mini-symposium.

The main requirement is interest in genetics and genomics and a desire to conduct full-time research. Some biological training is required, but a declared major in biology is not necessary.

Undergraduates who have completed at least one year in the college.

-      Statement explaining your interest in genetics and genomics and any past research experiences. If you have a pre-arranged PI, please outline the proposed project. Up to 1 page.

-      Resume or CV

-      Unofficial transcript

Please Note: If you are applying to multiple BSCD Fellowship Grants, please fill out the following BSCD Preference Form - https://careeradvancement.wufoo.com/forms/bscd-research-2020/

April 10, 2020

Projects:

Genetics of butterfly wing patterning and behavior

We study the genetic basis of wing pattern mimicry in butterflies as well as behavioral genetics related to mating behavior and migration. Over the summer we will be investigating how genetic variation and gene regulation contribute to color patterning in Heliconius and swallowtail butterflies. We will also be investigating the molecular genetic basis of mating behavior in Heliconius as well as migration behavior in the monarch butterfly. This research involves a combination of insect husbandry, behavioral assays, laboratory work to extract and process DNA and RNA, and bioinformatics analyses.

The Spitz lab studies the long-distance regulation of genes in vertebrate lineages and interplay between 3D organization and gene activity.

In vertebrates, genes can be regulated by control elements (enhancers) that lie hundreds of kilobases away. These control elements are important for determining how and when genes are active in an organism. Loss of or ectopic enhancer-promoter interactions contribute to a wide range of developmental defects and cancers, illustrating the importance of the associated mechanisms and notably of the 3D organization of the genome. In the proposed project, you will develop and test new molecular switches to regulate these interactions and the 3D folding of the genome.

We recently identified the conserved transcription factor CFI-1 (ortholog of mammalian Arid3a) as an important player in motor neuron diversity.

However, the downstream targets of this factor remain unknown.

Through single-cell RNA-sequencing, we recently identified dozens of putative transcriptional targets of this poorly characterized transcription factor.

The goal of the summer research internship will be to validate 5-10 of these targets by generating transgenic reporter animals and/or fluorescent RNA in situ hybridization.

Title: Determinants of 3D genome remodeling during the yeast heat shock response.

Description: The heat shock response (HSR) is a transcriptional program that cells in all kingdoms of life activate in response to elevated temperature and other environmental stresses. The HSR includes genes encoding chaperones that serve to counteract protein misfolding and aggregation. Recently, we have discovered that HSR target genes located on different chromosomes in yeast transiently coalesce into transcriptionally active foci in the yeast nucleus during heat shock. We have found that this intergenic clustering requires the transcription factor Hsf1, but we do not yet know which regions of Hsf1 are responsible. The summer student would learn to perform a chromosome conformation capture (3C) assay to monitor intergenic interactions and apply it to a panel of Hsf1 mutants to determine the regions required for this dynamic phenomenon.

The undergraduate intern would explore epigenetic change in early embryos of the common midge Chironomus that are implemented in response to the activity of its anterior determinant gene, panish (Klomp et al, 2015, Science 348, 1040-1042). The hypothesis to be tested in this project is that panish functions throughout the embryo, not just anterior, and affects default mutant developmental pathways of zygotic genes in the posterior embryo. The project requires, a combination of established RNAi and CRISPR experiments and genotyping of a specific site, the CRISPR target. 

Projects in the lab integrate information from single cell-RNA sequencing, chromatin-based assays and genetics to understand how transcription is precisely regulated in the context of development. The summer undergraduate intern would generate transgenic lines that will facilitate conditional knockdown of transcription factors required for cell fate specification in the sea anemone nervous system. This would involve microinjection, microscopy and training in standard molecular biology techniques. Additional opportunities to assist in performing scRNA-seq experiments and genomics assays would be provided based on student interest.

We are currently focusing on the evolution of transcription factor specificity for DNA response elements. For the summer project, the student will work with a graduate student or postdoc in the lab using high-throughput experimental techniques to characterize the huge number of possible mutational paths that could have caused ancestral proteins to evolve the ability to recognize new DNA binding sites.