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Unravelling the spatial and biomechanical dynamic of fracture healing in mice
Fracture healing is a complex process that involves inflammation, angiogenesis, and bone remodeling. The remodelling process helps maintain bone density, repair micro-damage that occurs due to everyday activities, and adapt bones to the specific needs of an individual's body. Mechanical loading is a crucial factor in the regulation of fracture healing. The forces and strains experienced by the bone during everyday activities influence the cellular responses, callus formation, bone deposition, remodelling, and, ultimately, the successful recovery of the fractured bone. The mechanisms underlying spatial cell reorganization during loading, which contributes to fracture healing, remain unclear. The project aims to investigate and explore the fracture healing process of mice using spatial transcriptome changes in response to mechanical loading. By shedding light on this aspect, the project aims to contribute to the broader understanding of fracture healing and potentially pave the way for more effective treatment strategies in the future.
Keywords: Spatial transcriptomics, Dimensionality reduction, Spatial expression pattern, Spatial interaction, Cell Segmentation and Visualization, Fracture healing, Bone
**Who We are:**
Laboratory for Bone Biomechanics (Müller Group) works on musculoskeletal systems. The group develops a quantitative model of bone at the cellular, molecular, tissue, and organ levels. We seek a highly motivated Bachelor's or master’s student dedicated to creating a multimodal transcriptome analysis framework to deepen bone fracture healing. This project offers an opportunity to gain valuable work experience within a highly interdisciplinary and international team.
**Project Description**
Fracture healing is a complex process that involves a series of biological events, including inflammation, angiogenesis, and bone remodelling. This remodelling process helps maintain bone density, repair micro-damage that occurs due to everyday activities, and adapt bones to the specific needs of an individual's body. In essence, bone remodelling during fracture repair is a sophisticated and dynamic orchestration of cellular activities that reabsorb excess bone and revitalize the bone tissue to its former strength and functionality, ultimately facilitating a seamless and enduring restoration of the injured bone. The healing process is physiologically complex, involving both biological and mechanical aspects. Mechanical loading is a crucial factor in the regulation of fracture healing. The forces and strains experienced by the bone during everyday activities influence the cellular responses, callus formation, bone deposition, remodelling, and, ultimately, the successful recovery of the fractured bone. Effective control of mechanical loading is pivotal in treating and recovering fractures, ensuring the best possible healing and functional results.
However, the mechanisms underlying spatial cell reorganization during loading, which contributes to fracture healing, remain unclear. Therefore, the project aims to investigate and explore the fracture healing process of mice using spatial transcriptome changes in response to mechanical loading. By shedding light on this aspect, we aim to contribute to the broader understanding of fracture healing and potentially pave the way for more effective treatment strategies in the future.
**Who We are:** Laboratory for Bone Biomechanics (Müller Group) works on musculoskeletal systems. The group develops a quantitative model of bone at the cellular, molecular, tissue, and organ levels. We seek a highly motivated Bachelor's or master’s student dedicated to creating a multimodal transcriptome analysis framework to deepen bone fracture healing. This project offers an opportunity to gain valuable work experience within a highly interdisciplinary and international team.
**Project Description**
Fracture healing is a complex process that involves a series of biological events, including inflammation, angiogenesis, and bone remodelling. This remodelling process helps maintain bone density, repair micro-damage that occurs due to everyday activities, and adapt bones to the specific needs of an individual's body. In essence, bone remodelling during fracture repair is a sophisticated and dynamic orchestration of cellular activities that reabsorb excess bone and revitalize the bone tissue to its former strength and functionality, ultimately facilitating a seamless and enduring restoration of the injured bone. The healing process is physiologically complex, involving both biological and mechanical aspects. Mechanical loading is a crucial factor in the regulation of fracture healing. The forces and strains experienced by the bone during everyday activities influence the cellular responses, callus formation, bone deposition, remodelling, and, ultimately, the successful recovery of the fractured bone. Effective control of mechanical loading is pivotal in treating and recovering fractures, ensuring the best possible healing and functional results. However, the mechanisms underlying spatial cell reorganization during loading, which contributes to fracture healing, remain unclear. Therefore, the project aims to investigate and explore the fracture healing process of mice using spatial transcriptome changes in response to mechanical loading. By shedding light on this aspect, we aim to contribute to the broader understanding of fracture healing and potentially pave the way for more effective treatment strategies in the future.
Developing a Robust R/Python Framework for Seamless Integration of Multimodal Data, Subcellular Spatial Transcriptomics, Cell Segmentation, and Advanced Analysis Leveraging the Power of High-Performance Cluster Computing with a Focus on the 10X Visium Sequencing Platform.
**Requirements:**
• B.Sc or M.Sc. in Bioinformatics, Data science, computational biology, Physics, Mathematics or a related field.
• Proficiency in R/Bioconductor, Python, or a similar programming language
• Familiarity with tools for the analysis of single-cell or spatial transcriptomics methods (Seurat, Scanpy), Image analysis (Napari, QuPath, ImageJ), Bash scripting, Python packaging, Parallel computing
Developing a Robust R/Python Framework for Seamless Integration of Multimodal Data, Subcellular Spatial Transcriptomics, Cell Segmentation, and Advanced Analysis Leveraging the Power of High-Performance Cluster Computing with a Focus on the 10X Visium Sequencing Platform.
**Requirements:**
• B.Sc or M.Sc. in Bioinformatics, Data science, computational biology, Physics, Mathematics or a related field.
• Proficiency in R/Bioconductor, Python, or a similar programming language
• Familiarity with tools for the analysis of single-cell or spatial transcriptomics methods (Seurat, Scanpy), Image analysis (Napari, QuPath, ImageJ), Bash scripting, Python packaging, Parallel computing
Please get in touch with me to get more detailed information about the project by email or reach out in person at Gloriastrasse 37/39, 8092 Zürich, Switzerland.
Email: amit.singh@hest.ethz.ch
LinkedIn: https://www.linkedin.com/in/amit-singh-63373417
Please get in touch with me to get more detailed information about the project by email or reach out in person at Gloriastrasse 37/39, 8092 Zürich, Switzerland.
Each year the IDEA League offers the students of its partner universities over 180 monthly grants for a short-term research exchange. In general, these grants are awarded based on academic merit. For more information visit http://idealeague.org/student-grant/
ETH for Development (ETH4D) aims to develop innovations that are directly relevant to improving the livelihoods of people in low-resource settings and to educate future leaders in sustainable development.
