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Description
Measurements of different molecular species from single cells have the potential to reveal cell-to-cell variations, which are precluded by population-based measurements. An increasing percentage of researches have been focused on proteins, for its central roles in biological processes. Immunofluorescence (IF) has been a well-established protein analysis platform. To gain comprehensive insights into cell biology and diagnostic pathology, a crucial direction would be to increase the multiplexity of current single cell protein analysis technologies.
An azide-based chemical cleavable linker has been introduced to design and synthesis novel fluorescent probes. These probes allow cyclic immunofluorescence staining which leads to the feasibility of highly multiplexed single cell in situ protein profiling. These highly multiplexed imaging-based platforms have the potential to quantify more than 100 protein targets in cultured cells and more than 50 protein targets in single cells in tissues.
This approach has been successfully applied in formalin-fixed paraffin-embedded (FFPE) brain tissues. Multiplexed protein expression level results reveal neuronal heterogeneity in the human hippocampus.
An azide-based chemical cleavable linker has been introduced to design and synthesis novel fluorescent probes. These probes allow cyclic immunofluorescence staining which leads to the feasibility of highly multiplexed single cell in situ protein profiling. These highly multiplexed imaging-based platforms have the potential to quantify more than 100 protein targets in cultured cells and more than 50 protein targets in single cells in tissues.
This approach has been successfully applied in formalin-fixed paraffin-embedded (FFPE) brain tissues. Multiplexed protein expression level results reveal neuronal heterogeneity in the human hippocampus.
ContributorsLiao, Renjie (Author) / Guo, Jia (Thesis advisor) / Borges, Chad (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2019
Description
Single-cell proteomics and transcriptomics analysis are crucial to gain insights of
healthy physiology and disease pathogenesis. The comprehensive profiling of biomolecules in individual cells of a heterogeneous system can provide deep insights into many important biological questions, such as the distinct cellular compositions or regulation of inter- and intracellular signaling pathways of healthy and diseased tissues. With multidimensional molecular imaging of many different biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal treatment.
As an urgent need to advance single-cell analysis, imaging-based technologies have been developed to detect and quantify multiple DNA, RNA and protein molecules in single cell in situ. Novel fluorescent probes have been designed and synthesized, which targets specifically either their nucleic acid counterpart or protein epitopes. These highly multiplexed imaging-based platforms have the potential to detect and quantify 100 different protein molecules and 1000 different nucleic acids in a single cell.
Using novel fluorescent probes, a large number of biomolecules have been detected and quantified in formalin-fixed paraffin-embedded (FFPE) brain tissue at single-cell resolution. By studying protein expression levels, neuronal heterogeneity has been revealed in distinct subregions of human hippocampus.
healthy physiology and disease pathogenesis. The comprehensive profiling of biomolecules in individual cells of a heterogeneous system can provide deep insights into many important biological questions, such as the distinct cellular compositions or regulation of inter- and intracellular signaling pathways of healthy and diseased tissues. With multidimensional molecular imaging of many different biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal treatment.
As an urgent need to advance single-cell analysis, imaging-based technologies have been developed to detect and quantify multiple DNA, RNA and protein molecules in single cell in situ. Novel fluorescent probes have been designed and synthesized, which targets specifically either their nucleic acid counterpart or protein epitopes. These highly multiplexed imaging-based platforms have the potential to detect and quantify 100 different protein molecules and 1000 different nucleic acids in a single cell.
Using novel fluorescent probes, a large number of biomolecules have been detected and quantified in formalin-fixed paraffin-embedded (FFPE) brain tissue at single-cell resolution. By studying protein expression levels, neuronal heterogeneity has been revealed in distinct subregions of human hippocampus.
ContributorsMondal, Manas (Author) / Guo, Jia (Thesis advisor) / Gould, Ian (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2018
Description
The understanding of normal human physiology and disease pathogenesis shows great promise for progress with increasing ability to profile genomic loci and transcripts in single cells in situ. Using biorthogonal cleavable fluorescent oligonucleotides, a highly multiplexed single-cell in situ RNA and DNA analysis is reported. In this report, azide-based cleavable linker connects oligonucleotides to fluorophores to show nucleic acids through in situ hybridization. Post-imaging, the fluorophores are effectively cleaved off in half an hour without loss of RNA or DNA integrity. Through multiple cycles of hybridization, imaging, and cleavage this approach proves to quantify thousands of different RNA species or genomic loci because of single-molecule sensitivity in single cells in situ. Different nucleic acids can be imaged by shown by multi-color staining in each hybridization cycle, and that multiple hybridization cycles can be run on the same specimen. It is shown that in situ analysis of DNA, RNA and protein can be accomplished using both cleavable fluorescent antibodies and oligonucleotides. The highly multiplexed imaging platforms will have the potential for wide applications in both systems biology and biomedical research. Thus, proving to be cost effective and time effective.
ContributorsSamuel, Adam David (Author) / Guo, Jia (Thesis director) / Liu, Wei (Committee member) / Wang, Xu (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Can a skill taught in a virtual environment be utilized in the physical world? This idea is explored by creating a Virtual Reality game for the HTC Vive to teach users how to play the drums. The game focuses on developing the user's muscle memory, improving the user's ability to play music as they hear it in their head, and refining the user's sense of rhythm. Several different features were included to achieve this such as a score, different levels, a demo feature, and a metronome. The game was tested for its ability to teach and for its overall enjoyability by using a small sample group. Most participants of the sample group noted that they felt as if their sense of rhythm and drumming skill level would improve by playing the game. Through the findings of this project, it can be concluded that while it should not be considered as a complete replacement for traditional instruction, a virtual environment can be successfully used as a learning aid and practicing tool.
ContributorsDinapoli, Allison (Co-author) / Tuznik, Richard (Co-author) / Kobayashi, Yoshihiro (Thesis director) / Nelson, Brian (Committee member) / Computer Science and Engineering Program (Contributor) / School of International Letters and Cultures (Contributor) / Computing and Informatics Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Last Hymn was created by the team of Tyler Pinho, Jefferson Le, and Curtis Spence with the desire to create an eccentric Role Playing Game focused on the exploration of a strange, dying world. Battles in the game are based off of rhythm games like Dance Dance Revolution using a procedural generation algorithm that makes every encounter unique. This is then complemented with the path system where each enemy has unique rhythm patterns to give them different types of combat opportunities. In Last Hymn, the player arrives on a train at the World's End Train Station where they are greeted by a mysterious figure and guided to the Forest where they witness the end of the world and find themselves back at the train station before they left for the Forest. With only a limited amount of time per cycle of the world, the player must constantly weigh the opportunity cost of each decision, and only with careful thought, conviction, and tenacity will the player find a conclusion from the never ending cycle of rebirth. Blending both Shinto architecture and modern elements, Last Hymn used a "fantasy-chic" aesthetic in order to provide memorable locations and dissonant imagery. As the player explores they will struggle against puzzles and dynamic, rhythm based combat while trying to unravel the mystery of the world's looping time. Last Hymn was designed to develop innovative and dynamic new solutions for combat, exploration, and mapping. From this project all three team members were able to grow their software development and game design skills, achieving goals like improved level design, improved asset pipelines while simultaneously aiming to craft an experience that will be unforgettable for players everywhere.
ContributorsPinho, Tyler (Co-author) / Le, Jefferson (Co-author) / Spence, Curtis (Co-author) / Nelson, Brian (Thesis director) / Walker, Erin (Committee member) / Kobayashi, Yoshihiro (Committee member) / Computer Science and Engineering Program (Contributor) / Computing and Informatics Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The ability to profile proteins allows us to gain a deeper understanding of organization, regulation, and function of different biological systems. Many technologies are currently being used in order to accurately perform the protein profiling. Some of these technologies include mass spectrometry, microarray based analysis, and fluorescence microscopy. Deeper analysis of these technologies have demonstrated limitations which have taken away from either the efficiency or the accuracy of the results. The objective of this project was to develop a technology in which highly multiplexed single cell in situ protein analysis can be completed in a comprehensive manner without the loss of the protein targets. This was accomplished in the span of 3 steps which is referred to as the immunofluorescence cycle. Antibodies with attached fluorophores with the help of novel azide-based cleavable linker are used to detect protein targets. Fluorescence imaging and data storage procedures are done on the targets and then the fluorophores are cleaved from the antibodies without the loss of the protein targets. Continuous cycles of the immunofluorescence procedure can help create a comprehensive and quantitative profile of the protein. The development of such a technique will not only help us understand biological systems such as solid tumor, brain tissues, and developing embryos. But it will also play a role in real-world applications such as signaling network analysis, molecular diagnosis and cellular targeted therapies.
ContributorsGupta, Aakriti (Author) / Guo, Jia (Thesis director) / Liang, Jianming (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
One obstacle which children with autism spectrum disorders (ASDs) face when learning in a public-school environment is the lack of feeling included when learning. In this study, the term inclusion refers to time that children with ASDs spend in general education settings, interacting and/or engaging with neurotypical students and teachers. Inclusion can help students with ASDs improve their social skills, as well as academic achievement, mental health, and future success (Camargo et al., 2014). Since children with ASDs often have difficulties with social interaction skills, this can prevent their successful inclusion in general education placements. Music is a type of behaviorally-based intervention, which has proven to be effective in helping students develop the skills necessary to be successfully included, and because it is a type of activity which can serve as a bit of a distraction from the social aspect of the interaction, it can help children practice social skills and interact in a comfortable way. This study examines how music is used in public school settings to help foster the skills necessary for autistic children to be involved in standard school curriculums in order to allow them to receive the full benefits from learning in a general education setting. This study was conducted by reviewing past literature on the benefits of inclusion in special education, the benefits of music for children with ASDs, and the difference in efficacy of music interventions when conducted in an inclusive setting. Interviews with special education teachers, music educators, and music therapists were also conducted to address examples of the impact of music in this research area. The study found that music is beneficial in allowing more students to be included in standard school curriculums, and data showed the trend that inclusion positively affected their social and academic development.
ContributorsVerma, Alisha (Author) / Kappes, Janelle (Thesis director) / Ruiz, Eugenia Hernandez (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
This project seeks to motivate runners by creating an application that selectively plays music based on smartwatch metrics. This is done by analyzing metrics collected through a person’s smartwatch such as heart rate or running power and then selecting the music that best fits their workout’s intensity. This way, as the workout becomes harder for the user, increasingly motivating music is played.
ContributorsDoyle, Niklas (Author) / Osburn, Steven (Thesis director) / Miller, Phillip (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor) / School of Music, Dance and Theatre (Contributor)
Created2023-05
Description
This project seeks to motivate runners by creating an application that selectively plays music based on smartwatch metrics. This is done by analyzing metrics collected through a person’s smartwatch such as heart rate or running power and then selecting the music that best fits their workout’s intensity. This way, as the workout becomes harder for the user, increasingly motivating music is played.
ContributorsDoyle, Niklas (Author) / Osburn, Steven (Thesis director) / Miller, Phillip (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor) / School of Music, Dance and Theatre (Contributor)
Created2023-05
ContributorsDoyle, Niklas (Author) / Osburn, Steven (Thesis director) / Miller, Phillip (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor) / School of Music, Dance and Theatre (Contributor)
Created2023-05