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Articles 1 - 12 of 12
Full-Text Articles in Biotechnology
Transcriptomic Profiling Of Engineered Human Gene Integration In The Mouse Genome Following In Vitro Gene Editing, Ethan Potts, Made Harumi Padmaswari, Christopher Nelson
Transcriptomic Profiling Of Engineered Human Gene Integration In The Mouse Genome Following In Vitro Gene Editing, Ethan Potts, Made Harumi Padmaswari, Christopher Nelson
Biomedical Engineering Undergraduate Honors Theses
Gene replacement is a promising method of therapy for genetic diseases. However, safety and efficacy are areas that need more research. This experiment aims to use RNA sequencing and bioinformatic techniques to provide answers to these questions and provide direction to future studies to develop a gene replacement therapeutic. C2C12 mouse myoblast cells were transfected with a vector containing a CRISPR-Cas9 system and the Human Factor IX (hF9) gene in order to hijack target genes and integrate the hF9 gene. The two target genes, myoglobin (Mb) and creatine kinase (Ckm), were chosen for their high rate of expression and low …
Hira Gene Mutation In Arabidopsis Via Crispr, Kelly Chen, Claire Shippy, Tara Phelps-Durr
Hira Gene Mutation In Arabidopsis Via Crispr, Kelly Chen, Claire Shippy, Tara Phelps-Durr
SACAD: Scholarly Activities
The purpose of this study is to mutate the Histone Repressor A (HIRA) gene in a mustard plant (Arabidopsis) using CRISPR technology. HIRA is a chromatin-remodeling protein that is required for proper development in both plants and animals. Creating new changes (mutations) in HIRA will help us better understand the mechanism of how HIRA regulates transcription, which is important for understanding developmental disorders in animals, as well as how improper development leads to a reduction in crop yields in plants
The Impact Of Mutations In The Arabidopsis Apetela (Ap3) Gene, Hazel R. Frans, Tara Phelps-Durr
The Impact Of Mutations In The Arabidopsis Apetela (Ap3) Gene, Hazel R. Frans, Tara Phelps-Durr
SACAD: Scholarly Activities
The purpose of this research is to understand the molecular functioning of the Arabidopsis thaliana Apetela (Ap3) gene. We created mutations in two sites of the gene, AP3-3 and AP3-5. These are predicted to change AP3 protein structure, which may result in a mutated flower. Analyzing the effects of new mutations allows an understanding of protein formation both in plants and humans.
Comprehensive Long- And Short- Read Sequencing Approaches To Screen The Mutational Landscape After Therapeutic Crispr-Editing For Duchenne Muscular Dystrophy, Mary Jia, Made Harumi Padmaswari, Landon Burcham, Shilpi Agrawal, Alexis Ivy, Abbey Bryan, Christopher E. Nelson
Comprehensive Long- And Short- Read Sequencing Approaches To Screen The Mutational Landscape After Therapeutic Crispr-Editing For Duchenne Muscular Dystrophy, Mary Jia, Made Harumi Padmaswari, Landon Burcham, Shilpi Agrawal, Alexis Ivy, Abbey Bryan, Christopher E. Nelson
Biomedical Engineering Undergraduate Honors Theses
Duchenne muscular dystrophy (DMD) is an X-linked muscle wasting disease caused by mutations in the Dmd gene resulting in non-functional dystrophin. Adeno-associated virus (AAV)-mediated delivery of classical CRISPR systems resulting in double-stranded breaks (DSBs) has yielded promise as a curative DMD therapeutic. However, the consequences of AAV-CRISPR require more thorough characterization. PCR-enriched short-read amplicon sequencing at cut sites is the most common method of sequencing CRISPR editing, but PCR bias results in unreliable quantification of on-target edits. We analyze orthogonal long- and short-read sequencing approaches to screen the outcomes of CRISPR technologies at the DNA and RNA-level for DMD. We …
Encoding Permanent Records Of Transcription In The Genome, Francesco Ettore Emiliani
Encoding Permanent Records Of Transcription In The Genome, Francesco Ettore Emiliani
Dartmouth College Ph.D Dissertations
Current approaches to study cellular transcriptional states offer only a single frame in the life of a cell, often in a destructive fashion. This means that our state snapshot neither has the context of the past, nor the ability to be traced into the future. To overcome this, we present a technology that can permanently encode gene expression for later recovery. Our technology uses transcriptional responses to guide CRISPR/AsCas12a to ‘write’ information into the cell’s own genome, creating a permanent and heritable record of this response. By placing a set of AsCas12a guides under the control of a Wnt-responsive TCF/LEF …
Crispr/Cas9-Induced Fad2 And Rod1 Mutations Stacked With Fae1 Confer High Oleic Acid Seed Oil In Pennycress (Thlaspi Arvense L.), Brice A. Jarvis, Trevor B. Romsdahl, Michaela G. Mcginn, Tara J. Nazarenus, Edgar B. Cahoon, Kent D. Chapman, John C. Sedbrook
Crispr/Cas9-Induced Fad2 And Rod1 Mutations Stacked With Fae1 Confer High Oleic Acid Seed Oil In Pennycress (Thlaspi Arvense L.), Brice A. Jarvis, Trevor B. Romsdahl, Michaela G. Mcginn, Tara J. Nazarenus, Edgar B. Cahoon, Kent D. Chapman, John C. Sedbrook
Department of Biochemistry: Faculty Publications
Pennycress (Thlaspi arvense L.) is being domesticated as an oilseed cash cover crop to be grown in the off-season throughout temperate regions of the world. With its diploid genome and ease of directed mutagenesis using molecular approaches, pennycress seed oil composition can be rapidly tailored for a plethora of food, feed, oleochemical and fuel uses. Here, we utilized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology to produce knockout mutations in the FATTY ACID DESATURASE2 (FAD2) and REDUCED OLEATE DESATURATION1 (ROD1) genes to increase oleic acid content. High oleic acid (18:1) oil is valued for its oxidative stability that is …
Multiplexed Crispr Libraries For Cancer Functional Genomics, Jintan Liu
Multiplexed Crispr Libraries For Cancer Functional Genomics, Jintan Liu
Dissertations and Theses (Open Access)
High-throughput forward genetic screenings are invaluable tools to systematically explore genetic interactions and to link gene disruption with disease contexts. The adaptation of CRISPR/Cas9 has improved the sensitivity and specificity of functional screenings. Despite this advance, there remains a long-standing need to improve functional screenings with smaller and more versatile pooled libraries. Capitalizing on the inherent multiplexing capability of a class 2 CRISPR enzyme AsCpf1, we developed a multiplexed, high throughput screening strategy that has avoided the usual trade-off between library size and library penetration, allowing library minimization without sacrificing gene targeting efficiency. We optimized the AsCpf1 protein for functional …
An Analysis Of Crispr-Cas Gene Editing In Agriculture, Ashley Laliberte
An Analysis Of Crispr-Cas Gene Editing In Agriculture, Ashley Laliberte
Honors Scholar Theses
The CRISPR-Cas system is a promising form of gene editing, especially for the agriculture industry. The ability to make single-nucleotide edits within a gene of interest, without the need to introduce foreign DNA, is a powerful tool for designing healthier and more efficient crops and food animals. This system provides opportunity for increased nutritional value, decreased food waste, and more economically and environmentally sustainable food production. Though this biotechnology is facing mechanistic limitations due to off-target effects and inefficient homology-directed repair, vast improvements have already been made to improve its efficacy. The CRISPR-Cas system is already the most advanced form …
Looking For Maize Genes Involved In Cold Response: Producing Knockouts For Arabidopsis Homologs Of Maize Candidate Genes Using A Crispr/Cas9 Approach, Katie Hillmann
Departmental Honors Projects
Most of today’s maize is cultivated outside its original climate zone, where yields are constrained by the changes in climate. Maize is especially vulnerable to high temperatures and drought stress, both of which negatively affect corn yields. An important strategy to combat this is early sowing, which avoids the effects of summer droughts and high temperatures in many places around the globe. However, maize is a cold sensitive species (Sanghera et al., 2011), making improvement to cold stress crucial for its adaption. The relatively new system CRISPR (Clustered regularly-interspaced short palindromic repeats)/Cas9 offers the potential to study cold-stress related …
Targeted Epigenetic Editing Using Optogenetic Tools, Joshua Hahn, Chongli Yuan
Targeted Epigenetic Editing Using Optogenetic Tools, Joshua Hahn, Chongli Yuan
The Summer Undergraduate Research Fellowship (SURF) Symposium
Epigenetics markers, such as DNA methylation and histone post-translational modifications, are modifications to the structure of DNA that impact gene expression without altering the genetic code. Among them, DNA methylation plays a critical role in various biological processes including the differentiation of stem cells, regulation of gene expression, and adaptation to environmental signals. The ability to modify DNA methylation at particular genes in various cell types is thus desirable for engineering specific cell phenotypes. Although technologies exist that can alter DNA methylation at target genes, these techniques lack spatial and temporal resolution and are not able to selectively edit individual …
Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots
Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots
STAR Program Research Presentations
The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few …
Hiv Vaccines: Progress, Limitations And A Crispr/Cas9 Vaccine, Omar A. Garcia Martinez
Hiv Vaccines: Progress, Limitations And A Crispr/Cas9 Vaccine, Omar A. Garcia Martinez
Biology: Student Scholarship & Creative Works
ABSTRACT: The HIV-1 pandemic continues to thrive due to ineffective HIV-1 vaccines. Historically, the world’s most infectious diseases, such as polio and smallpox, have been eradicated or have come close to eradication due to the advent of effective vaccines. Highly active antiretroviral therapy is able to delay the onset of AIDS but can neither rid the body of HIV-1 proviral DNA nor prevent further transmission. A prophylactic vaccine that prevents the various mechanisms HIV-1 has to evade and attack our immune system is needed to end the HIV-1 pandemic. Recent advances in engineered nuclease systems, like the CRISPR/Cas9 system, have …