Intern - Salk Summer Undergraduate Research Fellowship (SURF)

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.

The program will run from 6/3/2024 – 8/9/2024

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

Eligibility Requirements:

Applicants must: 

• Be currently enrolled in an accredited undergraduate program
• Be entering their junior or senior year at the time of participating in the program.
  *If you are a graduate of a two- or four-year institution, please consider applying to one of our open positions.
• Have a minimum of 3.0 GPA
• Be able to commit to the program dates and requirements; this includes, but is not limited to, not enrolling in summer courses or participating in other internships while participating in the Salk SURF.
• Be eligible to work in the United States.

The expected pay for this position is $16.85 per hour. Salk Institute provides pay ranges representing its good faith estimate of what the institute reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location, and external market pay for comparable jobs.

Deadline for Applications is November 27, 2023. 

Applicants must submit the following documents with their application:

1. A resume or curriculum vitae (CV)
2. An unofficial transcript

*Professional and/or academic references will be required for candidates that are selected for the interview phase of the recruitment process.* 

Please contact jobs@salk.edu if you have any questions. 

Please review the project descriptions below.  Question #12 of the application will ask you to rank your top 3 project preferences (1 being the project that you most prefer).  

1. “Epigenomic mapping of the human brain” (Behrens Lab)

To be able to map any organ at a single cell level, one must pull apart each cell and analyze them individually. To do 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.

Skills & techniques you will learn through this project: Nuclei isolation, counting and assessing nuclei integrity, cryostat sectioning, processing of tissue for spatial transcriptomics

1.  “Non-invasive control of cells” (Chalasani Lab)  

We are developing a new technology. We use ultrasound to manipulate cellular function non-invasively. 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 these conserved behaviors. 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

Skills & techniques you will learn through this project: Ultrasound delivery, transgene expression in the brain and other cells, animal behavior, and physiological methods

1. “Single-cell epigenomic atlas of the human brain” (Ecker Lab) 

To map the brain at single-cell resolution, it is necessary to separate and delineate each cell for individual analysis. We have developed techniques that allow for the analysis of DNA methylation and spatial transcriptomics using a high throughput approach

Skills & techniques you will learn through this project: Nuclei isolation, magnetic bead DNA purification, PCR, cryostat sectioning, fluorescence staining for spatial transcriptomics

1. “The role of the tumor suppressor ARID1A in tumor immunity” (Hargreaves Lab) 

ARID1A is among the most frequently mutated tumor suppressors in human cancer (> 120,000 patients in the U.S. per year). However, there exists no FDA approved therapies to specifically target ARID1A mutant cancer cells. 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. Our findings offer important insights into how ARID1A loss impacts the tumor microenvironment with potential implications for therapeutic interventions such as checkpoint blockade therapy in ARID1A mutant cancers

Skills & techniques you will learn through this project: Western blot, RT-qPCR, protein/RNA purification, cell culture, data analysis

1. “Development of an Artificial Marmoset Embryo Model” (Lee Lab) 

Given the correct conditions, embryonic stem cells will spontaneously assemble themselves into structures that extremely closely resembles the embryos these cells originated from, bypassing the need for an egg and sperm entirely. These embryo-like structures, termed “blastoids,” closely resemble their real, blastocyst counterparts morphologically, transcriptionally, and even functionally; for instance, the most sophisticated mouse embryo models can develop heartbeat, fetal limbs, and the beginnings of a brain. So far, blastoid models exist for both mice and humans. However, mouse embryo models tell us little about human fertility and health, while human embryo models are subject to strict ethical limitations. To fill this gap, we have developed a blastoid model grown from the stem cells of the Common Marmoset. We are optimizing these blastoids and beginning to leverage them to investigate fundamental unanswered questions about primate early embryonic development

Skills & techniques you will learn through this project: Tissue culture, molecular cloning and genetic modification, immunofluorescence, confocal imaging and image analysis

1. “Quantifying animal behavior using deep learning” (Pereira Lab) 

Understanding how the brain gives rise to behavior is a core goal of neuroscience. 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

Skills & techniques you will learn through this project: Analyzing animal behavior datasets, using computer vision and deep learning tools, basic to advanced software engineering (based on intern’s goals)

1. “Understanding the neural circuits of social processing and emotional valence” (Tye Lab) 

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

Skills & techniques you will learn through this project: Mouse handling, behavioral experiments, histology, data analysis

1. “Understanding the role of periderm differentiation in root development” (Busch Lab) 

Plants are a major avenue to limiting global warming through carbon drawdown as these photosynthetic life forms have evolved to absorb CO2 from the atmosphere and fix this carbon in the form of biomaterials (e.g., leaves, stems, roots). 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. Within this project, we aim to decipher and understand the molecular mechanisms of periderm tissue formation and development. 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. Overall, this project will contribute to building stones to produce plants with higher suberin content and hence contribute to the decarbonization of our planet’s atmosphere

Skills & techniques you will learn through this project: Plant phenotyping, microscopy, DNA isolation, PCR and genotyping, data analysis

1. “Increasing carbon capture in plants – a single cell approach” (Busch Lab) 

As part of The Harnessing Plants Initiative, we are aiming to produce plants with root systems able to store increased amounts of carbon, for longer periods underground. One way to achieve this is to develop plants with bigger, deeper roots. Another approach is to develop plants that fill their roots with increased levels of the carbon-rich biopolymer, suberin. A key part of our research is to understand how the root cells that produce suberin are formed. To do this we have been using the cutting-edge technology, single cell sequencing. Using this method we can find out, at the gene expression level, what gives different cell types their identity. How is a suberin cell made? Which genes are required? We have already conducted the single cell sequencing on numerous species and have uncovered several genes that we want to understand more deeply. As our intern, you would have the opportunity to help us on this journey of discovery

Skills & techniques you will learn through this project: Plant phenotyping, microscopy, DNA isolation, PCR and genotyping, data analysis

1.  “Identifying genes to enhance soil carbon sequestration” (Busch Lab) 

Researchers are diligently trying to decrease the presence of carbon in the atmosphere due to the challenges posed by global warming and climate change. One way we’re looking into using is the special abilities of plants. We’re studying how suberin is related to the total amount of roots a plant has. Right now, we’re busy figuring out which genes are involved in making more suberin. Once we know that, we want to put those genes into crops, like the plants we grow for food, so they can store more carbon in their roots

Skills & techniques you will learn through this project: DNA/RNA isolation, PCR, gel electrophoresis, sequencing, cloning, gene editing/CRISPR, plant growth and phenotyping

1. “Exploring the Role of CA19-9-modified Fibulin 3 in Pancreatic Tumorigenesis” (Engle Lab)  

Pancreatic ductal adenocarcinoma (PDA) is a highly lethal malignancy with a five-year survival rate of less than 11%, making it one of the deadliest cancers. Despite extensive research on the correlation between epidermal growth factor receptor (EGFR) and various cancer-related pathways in pancreatic tumorigenesis, targeted therapies against EGFR have shown modest efficacy, with most patients quickly developing resistance. Understanding the molecular mechanisms underlying this resistance is crucial for developing new treatment strategies. Our research focuses on Fibulin 3 (FBLN3), a secreted glycoprotein that is modified by the glycan carbohydrate antigen 19-9 (CA19-9) and that stimulates EGFR signaling. In this study, we aim to determine the CA19-9 dependent and independent functions of FBLN3 in PDA using innovative CA19-9-expressing PDA mouse and organoid models. Our investigation holds the potential to uncover novel insights into the molecular pathways involved in pancreatic cancer progression and to identify FBLN3 as a potential therapeutic target for improved treatment of this devastating disease

Skills & techniques you will learn through this project: Western blot, virus transfection and transduction, qPCR, RNA isolation, mouse study, IHC

1. “Could computational ‘DNA-stitching’ eliminate the need for large sequence inputs in DNA-epigenetic machine learning models?” (McVicker Lab)

Genome-wide association studies have revealed thousands of variants associated with traits, however it is unclear which variants are causative. One promising approach is the use of deep learning models which predict epigenetic measurements from DNA sequence. Efforts to improve epigenetic prediction models have largely been focused on extending the ‘receptive field’, or the maximum sequence length the model can take as input. The current state-of-the-art model, Enformer, has input >200kbp, but benchmarking indicates that Enformer utilizes a very small fraction of the input sequence to predict gene expression. For this summer project, we propose to test if ‘DNA-stitching’ could overcome the limited receptive field of DNA to epigenetic models, leveraging the observation that most of the sequence context is uninformative. If Enformer can make similar epigenetic predictions using stitched DNA sequences, it could greatly enhance machine learning models by reducing the computational burden of training on long sequence inputs.

Skills & techniques you will learn through this project: Python string manipulation, sequencing, machine learning, scientific visualization, data analysis

The Salk Institute is an internationally renowned research institution that values diversity, equity, and inclusion. We seek bold and interactive leaders passionate about exploring new frontiers in science. Our collaborative community embraces diverse perspectives and unique life experiences, fostering innovation, and a sense of belonging. Together, we strive to improve the wellbeing of humanity through groundbreaking research.

Equal Opportunity Employer/Protected Veterans/Individuals with Disabilities

The contractor will not discharge or in any other manner discriminate against employees or applicants because they have inquired about, discussed, or disclosed their own pay or the pay of another employee or applicant. However, employees who have access to the compensation information of other employees or applicants as a part of their essential job functions cannot disclose the pay of other employees or applicants to individuals who do not otherwise have access to compensation information, unless the disclosure is (a) in response to a formal complaint or charge, (b) in furtherance of an investigation, proceeding, hearing, or action, including an investigation conducted by the employer, or (c) consistent with the contractor’s legal duty to furnish information. 41 CFR 60-1.35(c)