Accepted students are required to:

-Conduct your own small research project or work on part of an ongoing research project.
-Attend a weekly virtual meeting series arranged by CODCC staff that will include mentoring sessions and opportunities to troubleshoot issues or questions students may have.
-Complete all Compliance Training, Conflict of Interest Forms and/or any other training deemed necessary for your internship as soon as it is received.
-Report to work on time as designated by the mentor to work on assigned research project. Students are expected to work no more than 40 hours a week.
-Present a virtual poster at the end of the project about your experience. The date of the presentation will be determined by the NIH SenNet program.

Successful applicants will have:

-An interest in and passion for studying biological or computational sciences, or related STEM fields
-A demonstrated strong work ethic
-Some experience with lab work

Funding:

-Accepted students will receive a stipend, housing, travel, and technology assistance as needed.

Buck Institute

The Tissue Mapping Center at the Buck Institute aims to determine, molecularly and spatially, when and where senescent cells occur in humans and how their patterns of gene/protein expression and the Senescence-Associated Secretory Phenotypes (SASPs) vary with tissue physiology and age. The Buck TMC focuses on three human tissues: ovary, breast, and skeletal muscle.

We implemented a multi-omic approach for the analyses of these tissues, which includes cutting-edge spatial transcriptomic (CosMx, GeoMx) and proteomic techniques. The Schilling laboratory is focused on profiling the intracellular proteome and secretome (SASP) signatures associated with senescence in different tissues by leveraging cutting-edge quantitative proteomic workflows.

The candidate will learn about sample preparation for proteomic analysis, mass spectrometric data acquisitions using state-of-the-art mass spectrometers, and data processing to unbiasedly and comprehensively map the molecular profiles and dynamics of senescent cells in human tissues and explants. The candidate will predominantly work on our collaborative studies with the Koenigshoff and Phatnani Laboratory to understand how proteomes are remodeled during healthy aging, monitoring senescence, and disease conditions in lung and spinal cord, respectively.

The candidate should have a basic knowledge of biology and an understanding of basic laboratory techniques. We also encourage the candidate to provide some skill in computational coding using R and interest (or even knowledge) of working with big scientific data. The candidate will report to Prof. Birgit Schilling and work closely with Buck SenNet scientists Drs. Joanna Bons and Mark Watson. The candidate will be able to take part in all our Buck TMC SenNet meetings and collaborations.

Carnegie Mellon University

The Carnegie Mellon University research group aims to develop and implement the next generation of computational methods to perform learning, inference, and decision-making on biomedical and healthcare data for accelerating scientific knowledge discovery and generating confident and testable data-driven hypotheses.

The research group applies these methods to answer important scientific questions as well as emerging high-impact real-world problems. Examples include elucidating the molecular mechanisms underlying human genetic diseases as well as identifying the spatial organization of senescent cells, the identification of their neighboring cells and the identification of novel genes involved in cell-cell interactions that may be driving senescence.

The candidate will be introduced to computational and statistical approaches for analyzing and integrating single-cell and spatial transcriptomics data. The candidate will report to Dr. Jose Lugo-Martinez. 

Columbia University Irving Medical Center

The Suh Lab at Columbia University Irving Medical Center defines the molecular and cellular heterogeneity underlying senescent cell states in the brain as part of the Columbia University Senescence Tissue Mapping (CUSTMAP) Center. We are creating a multi-scale atlas of senescence in central nervous system, i.e. cortex, hippocampus, and spinal cord, across the adult human lifespan. In particular, the Suh lab will focus on validation of the CUSTMAP discoveries using human iPSC-derived primary cells including microglia, neurons, and astrocytes alone and in combination in co-culture models. For more detailed information about the research performed in the Suh Lab, please visit their website at https://www.yousinsuhlab.org/.

The student trainee in this position will receive experimental and computational training on a variety of techniques, including (but not limited to) molecular biology, microscopy, and cell culture.

The preferred candidate skills for this role include one or more years of hands-on experience in cell biology and molecular biology laboratory methods. The student will report directly to Dr. Yousin Suh.

Duke University (Roper Lab)

The Roper Lab at Duke University School of Medicine is affiliated with Duke Division of Gastroenterology, Department of Pharmacology and Cancer Biology, and Department of Cell Biology, and  is located on the first floor of GSRB-1 building. The GSRB-1 building hosts multidisciplinary laboratories and requisite support facilities spanning basic research and clinical departments focused on gastroenterology, and oncology.

The Roper Lab occupies approximately 2,000 square feet of space, plus adjacent shared equipment rooms, a light microscopy room, two offices, shared computer space, and two cold rooms. The lab is focused on studying mechanisms of intestinal stem cell function in the context of injury, aging, and cancer.  (Further details about the lab’s work can be found on the lab website: http://www.roperlab.org).

The candidate will join an ongoing project funded by an NIH U54 grant seeking to understand the effects of aging on senescence across human tissues, with a focus on the colon. The candidate will focus on studying the effects of senolytic agents on colon organoid lines derived from healthy subjects enrolled in the U54 study. The goal of this research will be to reverse aging-related senescence using novel senolytic agents. The candidate will report directly to Dr. Roper.

Duke University (Xie Lab)

The Xie Lab at Duke University is part of the Department of Biostatistics & Bioinformatics and Division of Integrative Genomics.

The Xie Lab has developed a tool to study cell functional states and enhancing cell-cell interaction measurements. The CUSP student can apply this tool to our collected data from both normal/healthy lung and colon to study the differences between senescent and non-senescent cells, and also the interactions between senescent and immune cells. We expect the CUSP student to have experience to code in Python.

The candidate will report directly to Dr Xie and more information on the lab can be found here: https://jichunxie.github.io/index.html).

Mayo Clinic (Baker Lab)

The Baker laboratory at Mayo Clinic in Rochester Minnesota focuses on a variety of techniques to characterize the accumulation of senescent cells in aged and diseased tissue in mice. Our main models involved neurodegenerative disease and age-associated tumorigenesis, where we can both promote and prevent the senescent cell state using novel animal models.

The candidate will work with other Baker lab team members to specifically work on establishing the location and identity of senescent cells from the aging and diseased mouse spinal cord. Techniques that will be learned include animal handling, behavioral testing, histology, RNA isolation, gene expression profiling, and in situ senescent cell characterization.

Candidates will have an opportunity to participate in SenNet meetings and other scholarly activities for visiting students at Mayo Clinic.

Mayo Clinic (Schafer Lab)

The Schafer laboratory at Mayo Clinic in Rochester Minnesota focuses on using spatial mapping to characterize aged and senescent cell fates in the mouse and human brain. The candidate will work with Schafer lab team members to learn and utilize spatial mapping analysis platforms and will report directly to the PI and another team member who will directly supervise their project.

Candidates should have basic neuroscience knowledge and experience with at least one of the following: mouse neuroanatomy, immunohistochemical or immunofluorescent mouse brain imaging and microscopy, or computational analysis of single cell or spatial data using R or python. The candidate will have the opportunity to participate in ongoing SenNet meetings and other learning activities at Mayo Clinic.

Ohio State University

The Davis Heart Research Lung Institute at Ohio State University focuses on the preparation, in vitro culture, and analyses of the novel technique of precision cut lung slices. Studies characterize markers of senescence using different stimuli and time points in the distinct lung cell types.

The candidate will receive training in the laboratory of Dr. Mauricio Rojas and Ana L. Mora and will work directly under the supervision of postdoctoral fellows Drs. Lorena Rosas and Natalia Vanegas. The candidate will also be integrated into our weekly SenNet meetings.

University of California San Diego

The University of California San Diego research site processes mouse tissues and performs targeted assays for presence and absence of senescent cells, e.g., immunofluorescence, immunohistochemistry, qPCR, RNA-scope.

The candidate will assist and/or shadow as appropriate during the application of the major data generation platforms, single cell sequencing, MERFISH and CODEX. In addition, the student will participate in in vivo validation approaches, e.g. in vivo CRISPR/Cas9 genome editing to knock out genes of interest implicated in cell senescence.

University of Michigan

The University of Michigan research site, located in Ann Arbor, MI, focuses on technology development and applications related to Seq-Scope, which can produce high-resolution spatial transcriptomics datasets.

For further specific information about research performed at this site, please visit their website (https://lee.lab.medicine.umich.edu/).

The candidate will report to the PI, Dr. Jun Hee Lee, along with the lab supervisor (grad student or postdoc) who will be assigned to the student. A background in molecular biology and biochemistry is preferred, but not required.

University of Minnesota (2 positions)

The University of Minnesota Tissue Mapping Center (MN TMC) is focused on mapping senescent cells within human adipose and liver tissues. The candidate will be involved in spatial and single cell techniques to characterize senescence and learn aging biology research techniques in Dr. Laura Niedernhofer’s lab at the University of Minnesota.

The Midwest Murine Tissue Mapping Center (MM TMC) is focused on mapping senescent cells within mouse adipose, brain, liver, muscle and lung tissues. Adipose, liver, and brain tissue research is conducted at the University of Minnesota, muscle research is conducted at Mayo Clinic, Rochester, and lung research is conducted at Northwestern University. The candidate will be involved in spatial and single cell techniques to characterize senescence and learn aging biology research techniques.

University of Pittsburgh

The Koenigshoff lab at the University of Pittsburgh is focused on deciphering mechanisms involved in lung aging and regeneration, with the aim of identifying novel therapeutic targets relevant for age-related chronic lung diseases, such as idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD).

The Koenigshoff lab is composed of a multi-disciplinary group of people from different backgrounds and cultures with the guiding principle that diverse viewpoints and perspectives will lead to more creative and innovative, and thus better, science.

The candidate will be introduced to human tissue-derived models of lung aging and analyze senescence associated proteins. Major methodologies include cell and tissue culture as well as molecular biological analysis techniques. The candidate will work together with two TriState SenNet Postdoctoral Fellows in the laboratory and be integrated into our weekly SenNet meetings.

University of Rochester Medical Center

The research group at the University of Rochester Medical Center is dedicated to developing a single-cell atlas of cellular senescence that is developmentally programmed in human pediatric to adult lungs, utilizing both experimental methods and data analysis.

The selected candidate will receive comprehensive training within the laboratories of Dr. Irfan Rahman and Dr. Dongmei Li, gaining exposure to state-of-the-art techniques and methodologies relevant to single-cell analysis and cellular senescence research. They will work closely under the guidance of experienced postdoctoral fellows and Ph.D. students, ensuring a robust and supportive learning environment. The candidate will be involved in collaborative projects, contributing to experimental design, data collection, and analysis, which will help develop both technical skills and critical thinking.

Washington University

The Washington University Senescence Tissue Mapping Center (WU-SN-TMC) is examining the dynamics and heterogeneity of senescence across bone marrow and liver tissues. As part of this effort, we are also examining abdominal fat.

The intern would learn how to collect and process human tissues to examine the differences between visceral and subcutaneous fat specimens for downstream spatial analyses.

The intern would work under the supervision of Dr. Ryan Field, the Chief of Surgical Oncology and the Director of the Washington University Solid Tumor Tissue Bank and Registry. Dr. Fields is an MPI for the WU-SN-TMC and his research largely focuses on (1) mechanisms of cancer metastases and (2) novel in vitro and small animal models of cancer.

Yale University

Yale University has two Tissue Mapping Centers (TMCs), both working on mapping senescent cells in primary and secondary lymphoid organs to improve our understanding of cellular senescence in development, aging and disease (https://medicine.yale.edu/pathology/research/sennet/).

The Human TMC, led by Drs. Rong Fan and Stephanie Halene, focuses on characterizing primary lymph tissues from younger and older human subjects. The Murine TMC, under the direction of Drs. Vishwa Deep Dixit and Ruth Montgomery, focuses on murine models to characterize senescent cells in spleen, lymph node, and thymus. Both programs utilize high-throughput, high-resolution single cell and spatial omics technologies to characterize senescent cell heterogeneity.

The CUSP student will be co-advised by two laboratories within the Yale TMCs, and co-trained on relevant benchwork, as well as on computational analysis. The student will participate in laboratory meetings and in the monthly joint meeting of both TMCs. The student will characterize senescent cell markers in lymphoid organs from younger and older humans or mice using a variety of techniques such as immunohistochemistry, DBiT-seq, and spatial omics (PhenoCycler), and learn how to computationally analyze the data from these assays. The candidate should have a basic knowledge of molecular biology and immunology.

Ten simple rules for students navigating summer research experiences for undergraduates (REU) programs: from application to program completion.