Salk SURF interns conduct hands-on research in a laboratory setting, interact extensively with research staff at a variety of levels and will participate during regular group discussions and lab meetings.  Interns are expected to participate in a variety of programmatic offerings through Salk’s Diversity, Equity & Inclusion (DEI) unit, some of which are directly related to research careers, and others that contribute to broad-based professional development. The summer culminates in a Capstone Presentation Symposium for a live and virtual audience comprised of family members, professors, mentors, advisors, and members of the general Salk community. The Symposium is an opportunity for interns to use skills they have learned about scientific communication to educate others about their summer research and its impact.

ESSENTIAL FUNCTIONS

• Read and discuss relevant research articles (learning how to do so if this is not an existing skill)
• Understand and abide by lab safety requirements
• Review and follow lab protocols
• Prepare and conduct experiment under the guidance of a research team
• Record and analyze data
• Maintain lab notebooks
• Participate in lab meetings, recommended research and other trainings
• Attend weekly enrichment sessions for summer interns
• Participate in professional development opportunities
• Prepare slides and a presentation about the summer research experience
• Deliver a formal presentation of summer research experience to a broad audience

SKILLS AND ABILITIES

• Strong attention to detail and effective notetaking skills
• Self-starter, organized, strong time management abilities
• Motivation and ability to investigate and troubleshoot problems that may arise in research
• Willingness to ask questions and be proactive in clarifying understanding
• Interest in data analysis and curiosity in approaches to it
• Excellent communication skills, both oral and written
• Strong interpersonal skills, including tact, diplomacy, and flexibility
• Respect and understanding for individuals from diverse backgrounds and cultures

Please review the project descriptions below and rank them in order of preferred interest (1 being the project you are most interested in) in application questions number 8. 

a. ARID1A is among the most frequently mutated tumor suppressors in human cancer, but no FDA-approved therapies exist to specifically target ARID1A mutant cancer cells. Interestingly, patients with ARID1A mutations respond better to immune checkpoint blockade in clinical trials. We find that ARID1A mutant cancers show signs of elevated immune responses in 4 out of the top 6 human cancer types harboring ARID1A mutations. To further investigate how ARID1A mutations effect the tumor-immune microenvironment, we derived an ARID1A deficient mouse melanoma cell line via CRISPR/Cas9 engineering for subcutaneous tumor injection experiments. Overall, mouse ARID1A mutant tumors grew slower and were more sensitive to immune checkpoint blockade. Continuing work will involve investigating how ARID1A mutation causes increased interferon gene expression and exploring which immune cells are important for the tumor immune response.

b. Human genomic DNA is packaged into chromatin, in which the basic repeating unit is the nucleosome, an assembly of ~147 DNA base pairs (bp) wound around a histone octamer core. The tight and compact structure of nucleosome makes access to genetic information is highly regulated. A group of proteins known as chromatin remodelers can access nucleosome DNA and expose the nucleosomal DNA, leading to gene expression activation. We are working with the chromatin remodeling Brg/Brahma Associated Factors (BAF) complex, a large multi-subunit assembly that is frequently mutated in human cancers. To better understand how the BAF complex alter nucleosomes, we aim to measure the dynamics of nucleosome engagement and DNA movement on an atomic scale. You will implement new methodologies for “stitching” nucleosomes to the DNA origami rotor, which contains a fluorescent marker at the end of one of the rotor “blades”. The findings in this research project will be important for future experiments in the lab aimed at imaging how the BAF complex engages and remodels the nucleosome.

c. Our genome exists in a chromatin-DNA complex within the nucleus of our cells. Chromatin consists of a repeating series of nucleosomes, each of which is encircled by 147bp DNA. In regulatory regions of the genome, however, the nucleosomes are displaced leaving an open chromatin region. The locations of open chromatin regulatory regions can be measured using a sequencing experiment called the Assay for Transposase Accessible Chromatin (ATAC-seq). The goal of this project will be to use software developed by our laboratory to identify regions of the genome that have allele-specific open chromatin. Allele-specific open chromatin occurs when the level of chromatin openness in one region of the genome differs between the two copies of a chromosome (maternal and paternal) within the cell. Sometimes allele-specific open chromatin occurs because of genetic differences between the two chromosomes. You will apply the software developed by our laboratory to estimate allele-specific open chromatin to a large ATAC-seq dataset from different cell types and human individuals. You will then use a machine learning approach to learn how differences in chromatin accessibility are encoded by the genome sequence.

d. Using a novel social exclusion paradigm and computer vision tools for behavioral motif discovery and quantification, we will capture the impact of social exclusion on subsequent responses to physical pain and identify neural correlates mediating this interaction.

e. To be able to map any organ at a single cell level, one must be able to pull apart each cell and analyze them individually. To be able to approach the task of mapping one trillion cells, we have developed techniques that allows us to analyze cells in a high throughput system. For this we separate the cellular nuclei and sort them in 384-well plates such that each single nuclei is analyzed using multiomic approaches and robotics. To then be able to map them back to the brain, we use spatial transcriptomics that allows detection of up to 1000 transcripts in a single slice of brain. You will learn how to produce nuclei, count them and assess their integrity. As well, you will learn how to do cryostat sectioning and processing for spatial transcriptomics.

f. Duchenne muscular dystrophy is a devastating genetic disease caused by mutations in the dystrophin gene. Patients with this disease develop paralysis early in life and ultimately succumb to cardiac failure. Genetic therapy is an emerging field which aims to cure genetic diseases by mechanistically targeting pathology at the level of DNA. Currently, Adeno-associated viruses are used as the gold standard gene delivery vector but have limited cargo capacity, preventing the delivery of efficacious gene replacements or gene editing systems. The Pfaff lab has developed a novel RNA technology that overcomes this issue. We have leveraged this technology to develop candidate therapies including CRISPR-Cas9 base editing systems and gene replacement systems. These systems have been validated in vitro and by direct intramuscular injection in model mice. This summer research opportunity involves characterizing these therapies when delivered intravenously in model mice. Characterizations will involve animal model techniques such as dissections and behavioral testing. We will quantify changes in DNA, RNA, and proteins using molecular biology techniques and microscopy. An ideal candidate will be one who is enthusiastic about biomedical science, molecular biology, and open to working with mouse models.

g. We are interested in understanding how the nervous system detects external threats and generates fear-like, and anxiety-like behavior. We are using nematodes to model this conserved behavior. Specifically, we find that C. elegans alters its behavior in response to predator. Using a combination of behavioral analysis, genetic methods, imaging tools and pharmacology, we aim to reveal the underlying genes, neurons and circuits.

h. Understanding how the brain gives rise to behavior is a core goal of neuroscience. In order to make sense of neural activity, it is essential that we have precise and quantitative descriptions of what animals are doing when they are performing complex behaviors. This is complicated by the fact that natural, freely-moving animal behavior is difficult to describe and automatically quantify. To address this, we have developed a deep learning-based software tool called SLEAP to allow non-technical users to leverage artificial intelligence to track the precise movements of any type or number of animals. Owing to its ease-of-use, SLEAP is in use in hundreds of labs in dozens of countries all around the world to study everything from single cells to insects, rodents, fish and even plants! This project will deal with improving SLEAP through the development of new algorithms, or by using it to tackle novel biological problems to explore its applicability in a new scientific area. The specific goals of the project will be developed jointly with the applicant and may involve training in software engineering, computer science, or behavioral & computational neuroscience depending on the applicant’s area of interest. Experience with Python is recommended but not required, and we will provide extensive training in computer programming to meet the expectations of the project.

i. Age-related hearing loss and cognitive decline are two major public health issues that are potentially related: Having age-related hearing loss is correlated with a 300% increased risk for dementia. We hypothesize that this is due to concomitant loss of synapses in both the brain and cochlea during the aging process. To test this hypothesis, we are developing workflows to image cochlear and cortical synapses from the same animals. This project may involve any combination of: Preparing tissues for high resolution fluorescence microscopy of synapses (wet lab), performing high resolution microscopy (combination of wet and dry lab), or analyzing the images acquired using high resolution microscopy (dry lab).

j. Global warming is an existential thread for humans. To limit global warming to 1.5ºC or 2ºC over the next century, carbon drawdown at a large scale will be necessary. Engineering plants that transfer more of this fixed carbon into the soil and in ways that the carbon doesn’t decompose quickly, promises to facilitate carbon removal from the atmosphere at a large scale. One way to contribute to this is to develop plants that increase the amounts of long-lived carbon-polymers in the root. One highly suitable carbon-polymer for this is suberin, which is produced in specific tissues of the root, such as root periderm or root exodermis. We want to increase the abundance of these tissues. This project aims to decipher and understand the molecular mechanisms of periderm tissue formation and development. Periderm tissue is present in most eudicots’ plants and is composed of three different cell types – phellogen, phelloderm and phellem. Understanding how periderm differentiation is regulated during root development will provide key insights into how to produce more suberin for long-term carbon sequestration in the soil. For this, we combine genetic and genomic approaches to elucidate the transcriptional networks that coordinate differentiation within the periderm and its role in suberin production. The project will include the application of several experimental methods, such as plant phenotyping, microscopy, DNA isolation, PCR and genotyping, as well as data analysis.