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2019

Genetics and Genomics

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Full-Text Articles in Life Sciences

Sensitive Detection Of Ebv Micrornas Across Cancer Spectrum Reveals Association With Decreased Survival In Adult Acute Myelocytic Leukemia, Mercedeh J. Movassagh, Cliff Oduor, Catherine Forconi, Ann M. Moormann, Jeffrey A. Bailey Dec 2019

Sensitive Detection Of Ebv Micrornas Across Cancer Spectrum Reveals Association With Decreased Survival In Adult Acute Myelocytic Leukemia, Mercedeh J. Movassagh, Cliff Oduor, Catherine Forconi, Ann M. Moormann, Jeffrey A. Bailey

Open Access Articles

Epstein Barr virus (EBV) is the etiologic agent involved in numerous human cancers. After infecting the host, EBV establishes a latent infection, with low levels of messenger RNA (mRNA) and protein expression, evolved to evade immune recognition. Conversely, EBV microRNAs (miRNA) are expressed ubiquitously and abundantly within infected cells. Their role in tumor biology and clinical outcomes across the spectrum of cancer is not fully explained. Here, we applied our bioinformatics pipeline for quantitative EBV miRNA detection to examine sequencing data of 8,955 individual tumor samples across 27 tumor types representing the breadth of cancer. We uncover an association ...


Comparing Sensitivity To Change Using The 6-Item Versus The 17-Item Hamilton Depression Rating Scale In The Guided Randomized Controlled Trial, Boadie W. Dunlop, Sagar V. Parikh, Anthony J. Rothschild, Michael E. Thase, Charles Debattista, Charles R. Conway, Brent P. Forester, Francis M. Mondimore, Richard C. Shelton, Matthew Macaluso, Jennifer Logan, Paul Traxler, James Li, Holly Johnson, John F. Greden Dec 2019

Comparing Sensitivity To Change Using The 6-Item Versus The 17-Item Hamilton Depression Rating Scale In The Guided Randomized Controlled Trial, Boadie W. Dunlop, Sagar V. Parikh, Anthony J. Rothschild, Michael E. Thase, Charles Debattista, Charles R. Conway, Brent P. Forester, Francis M. Mondimore, Richard C. Shelton, Matthew Macaluso, Jennifer Logan, Paul Traxler, James Li, Holly Johnson, John F. Greden

Open Access Articles

BACKGROUND: Previous research suggests that the 17-item Hamilton Depression Rating Scale (HAM-D17) is less sensitive in detecting differences between active treatment and placebo for major depressive disorder (MDD) than is the HAM-D6 scale, which focuses on six core depression symptoms. Whether HAM-D6 shows greater sensitivity when comparing two active MDD treatment arms is unknown.

METHODS: This post hoc analysis used data from the intent-to-treat (ITT) cohort (N = 1541) of the Genomics Used to Improve DEpression Decisions (GUIDED) trial, a rater- and patient-blinded randomized controlled trial. GUIDED compared combinatorial pharmacogenomics-guided care with treatment as usual (TAU) in patients with MDD. Percent ...


Intralingual And Intrapleural Aav Gene Therapy Prolongs Survival In A Sod1 Als Mouse Model, Allison M. Keeler, Marina Zieger, Carson Semple, Logan Pucci, Alessandra Veinbachs, Robert H. Brown Jr., Christian Mueller, Mai K. Elmallah Dec 2019

Intralingual And Intrapleural Aav Gene Therapy Prolongs Survival In A Sod1 Als Mouse Model, Allison M. Keeler, Marina Zieger, Carson Semple, Logan Pucci, Alessandra Veinbachs, Robert H. Brown Jr., Christian Mueller, Mai K. Elmallah

Pediatric Publications

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that results in death from respiratory failure. No cure exists for this devastating disease, but therapy that directly targets the respiratory system has the potential to prolong survival and improve quality of life in some cases of ALS. The objective of this study was to enhance breathing and prolong survival by suppressing superoxide dismutase 1 (SOD1) expression in respiratory motor neurons using adeno-associated virus (AAV) expressing an artificial microRNA targeting the SOD1 gene. AAV-miR(SOD1) was injected in the tongue and intrapleural space of SOD1(G93A) mice, and repetitive respiratory and ...


Snowpack Properties Vary In Response To Burn Severity Gradients In Montane Forests, Jordan Maxwell, Samuel B. St. Clair Dec 2019

Snowpack Properties Vary In Response To Burn Severity Gradients In Montane Forests, Jordan Maxwell, Samuel B. St. Clair

Aspen Bibliography

Wildfires are altering ecosystems globally as they change in frequency, size, and severity. As wildfires change vegetation structure, they also alter moisture inputs and energy fluxes which influence snowpack and hydrology. In unburned forests, snow has been shown to accumulate more in small clearings or in stands with low to moderate forest densities. Here we investigate whether peak snowpack varies with burn severity or percent overstory tree mortality post-fire in a mid-latitude, subalpine forest. We found that peak snowpack across the burn severity gradients increased 15% in snow-water equivalence (SWE) and 17% in depth for every 20% increase in overstory ...


Chloroviruses, James L. Van Etten, Irina V. Agarkova, David D. Dunigan Dec 2019

Chloroviruses, James L. Van Etten, Irina V. Agarkova, David D. Dunigan

Virology Papers

Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 ...


Peroxiredoxin 6 And Inflammation In Alzheimer's Disease, Jared Ferrell-Penniman Dec 2019

Peroxiredoxin 6 And Inflammation In Alzheimer's Disease, Jared Ferrell-Penniman

Biological Sciences Theses and Dissertations

Alzheimer’s disease (AD) is known for its debilitating symptoms and poor prognosis. However, despite intense research into neurodegenerative diseases, there are few therapies targeted at the underlying mechanisms of the disease. Oxidative stress (OS) and inflammation are cellular phenomena thought to be key to the progression of the disease. Critically, peroxiredoxin 6 (Prx6), an antioxidant protein with multiple functions, has been identified from mammalian studies as a potential regulator of both OS and inflammation that may have a specific effect on AD. This project seeks to elucidate the role of Prx6 in AD as well as the underlying mechanisms ...


Genetic Analysis Of A Novel Ftsk Homolog, Hfka, In Streptomyces Coelicolor Development-Associated Chromosome Segregation, Sumedha Sethi Dec 2019

Genetic Analysis Of A Novel Ftsk Homolog, Hfka, In Streptomyces Coelicolor Development-Associated Chromosome Segregation, Sumedha Sethi

Electronic Theses and Dissertations

A quintessential phenomenon occurring during prokaryotic development is accurate segregation of the replicated genomes into the daughter cells. Key energy-dependent processes like chromosome condensation and subcellular partitioning of the genomes are driven by conserved proteins like SMC, ParB, FtsK. During its complex developmental cycle, Streptomyces coelicolor segregates its genomes into chains of unicellular spores when its multigenomic syncytial aerial hyphae undergo division.

A novel ftsK-like gene, hfkA (Homolog of FtsK protein A), was examined for function and localization during development-associated chromosome segregation. Individual deletions did not affect segregation, but a ΔhfkA ΔftsK mutant exhibited 8% anucleate spores ...


Identification Of The Hyaluronic Acid Pathway As A Therapeutic Target For Facioscapulohumeral Muscular Dystrophy, Alec M. Desimone, John D. Leszyk, Kathryn Wagner, Charles P. Emerson, Jr. Dec 2019

Identification Of The Hyaluronic Acid Pathway As A Therapeutic Target For Facioscapulohumeral Muscular Dystrophy, Alec M. Desimone, John D. Leszyk, Kathryn Wagner, Charles P. Emerson, Jr.

Open Access Articles

Facioscapulohumeral muscular dystrophy (FSHD) is linked to epigenetic derepression of the germline/embryonic transcription factor DUX4 in skeletal muscle. However, the etiology of muscle pathology is not fully understood, as DUX4 misexpression is not tightly correlated with disease severity. Using a DUX4-inducible cell model, we show that multiple DUX4-induced molecular pathologies that have been observed in patient-derived disease models are mediated by the signaling molecule hyaluronic acid (HA), which accumulates following DUX4 induction. These pathologies include formation of RNA granules, FUS aggregation, DNA damage, caspase activation, and cell death. We also observe previously unidentified pathologies including mislocalization of mitochondria and ...


A "Choose-Your-Own" Classroom-Based Activity That Promotes Scientific Inquiry About Rna Interference, Jeremy L. Hsu Dec 2019

A "Choose-Your-Own" Classroom-Based Activity That Promotes Scientific Inquiry About Rna Interference, Jeremy L. Hsu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

RNA interference (RNAi), the process that results in the degradation of a target gene’s mRNA, is a fundamental part of eukaryotic gene regulation and is also an important molecular technique that allows for experimental manipulation of gene expression without altering DNA sequences. Despite the importance of RNAi, there have been relatively few lecture-based activities designed to teach about the consequences of this process and counter common misconceptions. I present here an inquiry-based activity that is centered around a “choose your own experiment” design where students generate hypotheses and critically evaluate their ideas by choosing several simulated experiments. The activity ...


Comparative Pangenomics Of The Mammalian Gut Commensal Bifidobacterium Longum, Korin Albert, Asha Rani, David Sela Dec 2019

Comparative Pangenomics Of The Mammalian Gut Commensal Bifidobacterium Longum, Korin Albert, Asha Rani, David Sela

Open Access Articles

Bifidobacterium longum colonizes mammalian gastrointestinal tracts where it could metabolize host-indigestible oligosaccharides. Although B. longum strains are currently segregated into three subspecies that reflect common metabolic capacities and genetic similarity, heterogeneity within subspecies suggests that these taxonomic boundaries may not be completely resolved. To address this, the B. longum pangenome was analyzed from representative strains isolated from a diverse set of sources. As a result, the B. longum pangenome is open and contains almost 17,000 genes, with over 85% of genes found in < /=28 of 191 strains. B. longum genomes share a small core gene set of only ~500 genes, or ~3% of the total pangenome. Although the individual B. longum subspecies pangenomes share similar relative abundances of clusters of orthologous groups, strains show inter- and intrasubspecies differences with respect to carbohydrate utilization gene content and growth phenotypes.


Solenodon Genome Reveals Convergent Evolution Of Venom In Eulipotyphlan Mammals, Nicholas R. Casewell, Elinor K. Karlsson, Daniel Petras, Daren C. Card, Vivek Suranse, Alexis M. Mychajliw, David Richards, Ivan Koludarov, Laura-Oana Albulescu, Julien Slagboom, Benjamin-Florian Hempel, Neville M. Ngum, Rosalind J. Kennerley, Jorge L. Brocca, Gareth Whiteley Dec 2019

Solenodon Genome Reveals Convergent Evolution Of Venom In Eulipotyphlan Mammals, Nicholas R. Casewell, Elinor K. Karlsson, Daniel Petras, Daren C. Card, Vivek Suranse, Alexis M. Mychajliw, David Richards, Ivan Koludarov, Laura-Oana Albulescu, Julien Slagboom, Benjamin-Florian Hempel, Neville M. Ngum, Rosalind J. Kennerley, Jorge L. Brocca, Gareth Whiteley

Program in Bioinformatics and Integrative Biology Publications

Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan ...


Curing Hemophilia A By Nhej-Mediated Ectopic F8 Insertion In The Mouse, Jian-Ping Zhang, Xin-Xin Cheng, Mei Zhao, Guo-Hua Li, Jing Xu, Feng Zhang, Meng-Di Yin, Fei-Ying Meng, Xin-Yue Dai, Ya-Wen Fu, Zhi-Xue Yang, Cameron Arakaki, Ruijun Jeanna. Su, Wei Wen, Wen-Tian Wang, Wanqiu Chen, Hannah Choi, Charles Wang, Guangping Gao, Lei Zhang, Tao Cheng, Xiao-Bing Zhang Dec 2019

Curing Hemophilia A By Nhej-Mediated Ectopic F8 Insertion In The Mouse, Jian-Ping Zhang, Xin-Xin Cheng, Mei Zhao, Guo-Hua Li, Jing Xu, Feng Zhang, Meng-Di Yin, Fei-Ying Meng, Xin-Yue Dai, Ya-Wen Fu, Zhi-Xue Yang, Cameron Arakaki, Ruijun Jeanna. Su, Wei Wen, Wen-Tian Wang, Wanqiu Chen, Hannah Choi, Charles Wang, Guangping Gao, Lei Zhang, Tao Cheng, Xiao-Bing Zhang

Open Access Articles

BACKGROUND: Hemophilia A, a bleeding disorder resulting from F8 mutations, can only be cured by gene therapy. A promising strategy is CRISPR-Cas9-mediated precise insertion of F8 in hepatocytes at highly expressed gene loci, such as albumin (Alb). Unfortunately, the precise in vivo integration efficiency of a long insert is very low (~ 0.1%).

RESULTS: We report that the use of a double-cut donor leads to a 10- to 20-fold increase in liver editing efficiency, thereby completely reconstituting serum F8 activity in a mouse model of hemophilia A after hydrodynamic injection of Cas9-sgAlb and B domain-deleted (BDD) F8 donor plasmids. We ...


A Noncanonical Function Of The Telomerase Rna Component In Human Embryonic Stem Cells, Kirsten Ann Brenner Dec 2019

A Noncanonical Function Of The Telomerase Rna Component In Human Embryonic Stem Cells, Kirsten Ann Brenner

Arts & Sciences Electronic Theses and Dissertations

Telomeres are stretches of TTAGGG nucleotide repeats located at the ends of linear chromosomes that shorten with progressive cell division and prevent genomic instability at the cost of limiting a cell’s capacity to proliferate. This limitation can be overcome by telomerase, a ribonucleoprotein complex that elongates telomeres via reverse-transcription of the template telomerase RNA component (TERC). Recent studies have reported potential functions of TERC outside of its role in telomere maintenance. These noncanonical functions of TERC are however poorly defined, and the molecular mechanisms and biological relevance behind such functions remain elusive. Here, we generated conditional TERC knock-out human ...


Elucidating Enhancer Function In Epidermal Development And Filaggrin Loss-Of-Function Variants In African American Atopic Dermatitis, Mary Elizabeth Mathyer Dec 2019

Elucidating Enhancer Function In Epidermal Development And Filaggrin Loss-Of-Function Variants In African American Atopic Dermatitis, Mary Elizabeth Mathyer

Arts & Sciences Electronic Theses and Dissertations

The epidermis is the outermost tissue of the skin and provides the body’s first line of defense against external assaults. The epidermis is primarily composed of keratinocytes that terminally differentiate and rise apically toward the surface to form the semipermeable barrier of the skin. A hallmark of keratinocyte terminal differentiation is the expression of genes from the Epidermal Differentiation Complex (EDC) locus. Many of the EDC protein products contribute to the structural integrity of the skin barrier, evidenced by several gene knockouts such as loricrin, and even genetic variation within gene coding sequences, that modulate the integrity of the ...


Genomic Contributors To Individual Differences In Reward-Related Neural Activity, Lindsay Jane Michalski Dec 2019

Genomic Contributors To Individual Differences In Reward-Related Neural Activity, Lindsay Jane Michalski

Arts & Sciences Electronic Theses and Dissertations

Aberrant reward-related behavior, including impulsive and risk-taking behaviors, is a common feature of externalizing psychopathology (e.g., attention deficit hyperactivity disorder, antisocial personality disorder, and substance-use disorders). Through imaging studies, these behaviors have been linked to dysregulated reactivity within a diffuse reward-related corticostriatal neural network, including the striatum, frontal regions (namely orbital, ventromedial, and dorsolateral cortices), the insula, and the hippocampus. Because variability in risk-taking behavior and related psychopathology is moderately-to-largely heritable (i.e., with estimates ranging from 40 – 80%), a genetically-informed approach is well-positioned to provide valuable insight into the etiology of reward-related neural and behavioral phenotypes that characterize ...


Long-Term Therapeutic Efficacy Of Intravenous Aav-Mediated Hamartin Replacement In Mouse Model Of Tuberous Sclerosis Type 1, Shilpa Prabhakar, Pike See Cheah, Xuan Zhang, Max Zinter, Maria Gianatasio, Eloise Hudry, Roderick T. Bronson, David J. Kwiatkowski, Anat Stemmer-Rachamimov, Casey A. Maguire, Miguel Sena-Esteves, Bakhos A. Tannous, Xandra O. Breakefield Dec 2019

Long-Term Therapeutic Efficacy Of Intravenous Aav-Mediated Hamartin Replacement In Mouse Model Of Tuberous Sclerosis Type 1, Shilpa Prabhakar, Pike See Cheah, Xuan Zhang, Max Zinter, Maria Gianatasio, Eloise Hudry, Roderick T. Bronson, David J. Kwiatkowski, Anat Stemmer-Rachamimov, Casey A. Maguire, Miguel Sena-Esteves, Bakhos A. Tannous, Xandra O. Breakefield

Open Access Articles

Tuberous sclerosis complex (TSC) is a tumor suppressor syndrome caused by mutations in TSC1 or TSC2, encoding hamartin and tuberin, respectively. These proteins act as a complex that inhibits mammalian target of rapamycin (mTOR)-mediated cell growth and proliferation. Loss of either protein leads to overgrowth in many organs, including subependymal nodules, subependymal giant cell astrocytomas, and cortical tubers in the human brain. Neurological manifestations in TSC include intellectual disability, autism, hydrocephalus, and epilepsy. In a stochastic mouse model of TSC1 brain lesions, complete loss of Tsc1 is achieved in homozygous Tsc1-floxed mice in a subpopulation of neural cells in ...


Selection Of An Efficient Aav Vector For Robust Cns Transgene Expression, Killian S. Hanlon, Miguel Sena-Esteves, Eloise Hudry, Casey A. Maguire Dec 2019

Selection Of An Efficient Aav Vector For Robust Cns Transgene Expression, Killian S. Hanlon, Miguel Sena-Esteves, Eloise Hudry, Casey A. Maguire

Open Access Articles

Adeno-associated virus (AAV) capsid libraries have generated improved transgene delivery vectors. We designed an AAV library construct, iTransduce, that combines a peptide library on the AAV9 capsid with a Cre cassette to enable sensitive detection of transgene expression. After only two selection rounds of the library delivered intravenously in transgenic mice carrying a Cre-inducible fluorescent protein, we flow sorted fluorescent cells from brain, and DNA sequencing revealed two dominant capsids. One of the capsids, termed AAV-F, mediated transgene expression in the brain cortex more than 65-fold (astrocytes) and 171-fold (neurons) higher than the parental AAV9. High transduction efficiency was sex-independent ...


Synthesis And Preclinical Validation Of Novel P2y1 Receptor Ligands As A Potent Anti-Prostate Cancer Agent., Hien Thi Thu Le, Tatu Rimpilainen, Saravanan Konda Mani, Akshaya Murugesan, Olli Yli-Harja, Nuno R Candeias, Meenakshisundaram Kandhavelu Dec 2019

Synthesis And Preclinical Validation Of Novel P2y1 Receptor Ligands As A Potent Anti-Prostate Cancer Agent., Hien Thi Thu Le, Tatu Rimpilainen, Saravanan Konda Mani, Akshaya Murugesan, Olli Yli-Harja, Nuno R Candeias, Meenakshisundaram Kandhavelu

Articles, Abstracts, and Reports

Purinergic receptor is a potential drug target for neuropathic pain, Alzheimer disease, and prostate cancer. Focusing on the structure-based ligand discovery, docking analysis on the crystal structure of P2Y


Interfacing Electronic And Genetic Circuits, Robbyn K. Anand, Kira L. Rahn Dec 2019

Interfacing Electronic And Genetic Circuits, Robbyn K. Anand, Kira L. Rahn

Chemistry Publications

Synthetic genetic circuits leverage the information processing capability of biological machinery to tackle complex sensing tasks, yet they lack many of the advantages inherent to electrical computation. Now, an interface has been designed that provides an electrical output for synthetic genetic circuits.


The Pseudomonas Aeruginosa Accessory Genome Elements Influence Virulence Towards Caenorhabditis Elegans, Alejandro Vasquez-Rifo, Isana Veksler-Lublinsky, Zhenyu Cheng, Frederick M. Ausubel, Victor R. Ambros Dec 2019

The Pseudomonas Aeruginosa Accessory Genome Elements Influence Virulence Towards Caenorhabditis Elegans, Alejandro Vasquez-Rifo, Isana Veksler-Lublinsky, Zhenyu Cheng, Frederick M. Ausubel, Victor R. Ambros

Open Access Articles

BACKGROUND: Multicellular animals and bacteria frequently engage in predator-prey and host-pathogen interactions, such as the well-studied relationship between Pseudomonas aeruginosa and the nematode Caenorhabditis elegans. This study investigates the genomic and genetic basis of bacterial-driven variability in P. aeruginosa virulence towards C. elegans to provide evolutionary insights into host-pathogen relationships.

RESULTS: Natural isolates of P. aeruginosa that exhibit diverse genomes display a broad range of virulence towards C. elegans. Using gene association and genetic analysis, we identify accessory genome elements that correlate with virulence, including both known and novel virulence determinants. Among the novel genes, we find a viral-like mobile ...


Conservation Insights For Endemic Alpine Plants (Nabalus Spp.) Facing Global Environmental Change, Kristen Haynes Dec 2019

Conservation Insights For Endemic Alpine Plants (Nabalus Spp.) Facing Global Environmental Change, Kristen Haynes

Dissertations and Theses

Amid the current global biodiversity crisis spurred by anthropogenic environmental changes, determining conservation priorities and the extinction vulnerability of rare taxa are tasks of critical importance. Organisms can avoid environmental change-induced extinction through three possible response modes: evolutionary adaptation, migration (range shift), and tolerance through phenotypic plasticity. In this dissertation, I leveraged transplant experiments and population genomics to assess the ability of rare alpine rattlesnake-roots (Nabalus spp.) to adapt, migrate, and/or tolerate environmental change. I also employed these same techniques to define conservation units and priorities within two endemic alpine taxa (Nabalus boottii and Nabalus trifoliolatus var. nanus) and ...


Future Climate Change Will Have A Positive Effect On Populus Davidiana In China, Jie Li, Guan Liu, Qi Lu, Yanru Zhang, Guoqing Li, Sheng Du Dec 2019

Future Climate Change Will Have A Positive Effect On Populus Davidiana In China, Jie Li, Guan Liu, Qi Lu, Yanru Zhang, Guoqing Li, Sheng Du

Aspen Bibliography

Since climate change significantly affects global biodiversity, a reasonable assessment of the vulnerability of species in response to climate change is crucial for conservation. Most existing methods estimate the impact of climate change on the vulnerability of species by projecting the change of a species’ distribution range. This single-component evaluation ignores the impact of other components on vulnerability. In this study, Populus davidiana (David’s aspen), a tree species widely used in afforestation projects, was selected as the research subject under four future climate change scenarios (representative concentration pathway (RCP)2.6, RCP4.5, RCP6.0, and RCP8.5). Exposure ...


The Ethical Implications Of Bioengineering Advancements, Mainstream Media Coverage Of Those Developments, And The Future Of Motherhood, Aliff Abad, Katherine Gregory Dec 2019

The Ethical Implications Of Bioengineering Advancements, Mainstream Media Coverage Of Those Developments, And The Future Of Motherhood, Aliff Abad, Katherine Gregory

Publications and Research

How do the media interpret reproductive interventions that involve genetic testing? When a scientist performed the first known genetic editing on twins, Lulu and Nana, he ignored ethical considerations of CRISPR use. This project provides a content analysis based on a review of popular science and newspaper articles. Our interpretation of these articles suggest that there is a lack of critical understanding of this unethical procedure and a similar attitude towards future genetic developments. While the public is curious about the repercussions of genetic editing, not enough focus is applied to the ethics of conducting such a procedure.


A Minimal Crispr-Cas3 System For Genome Engineering, Bálint Csörgő, Lina M. León, Ilea J. Chau-Ly, Alejandro Vasquez-Rifo, Joel D. Berry, Caroline Mahendra, Emily D. Crawford, Jennifer D. Lewis, Joseph Bondy-Denomy Dec 2019

A Minimal Crispr-Cas3 System For Genome Engineering, Bálint Csörgő, Lina M. León, Ilea J. Chau-Ly, Alejandro Vasquez-Rifo, Joel D. Berry, Caroline Mahendra, Emily D. Crawford, Jennifer D. Lewis, Joseph Bondy-Denomy

University of Massachusetts Medical School Faculty Publications

CRISPR-Cas technologies have provided programmable gene editing tools that have revolutionized research. The leading CRISPR-Cas9 and Cas12a enzymes are ideal for programmed genetic manipulation, however, they are limited for genome-scale interventions. Here, we utilized a Cas3-based system featuring a processive nuclease, expressed endogenously or heterologously, for genome engineering purposes. Using an optimized and minimal CRISPR-Cas3 system (Type I-C) programmed with a single crRNA, large deletions ranging from 7 - 424 kb were generated in Pseudomonas aeruginosa with high efficiency and speed. By comparison, Cas9 yielded small deletions and point mutations. Cas3-generated deletion boundaries were variable in the absence of a homology-directed ...


Gmr41f05, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh Dec 2019

Gmr41f05, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50133

  • ID - GMR41F05
  • Location - 2R: 18139042, 18142672
  • Base pairs - 3630


Gmr40c09, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh Dec 2019

Gmr40c09, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

  • ID - GMR40C09
  • Location - 2R: 18132203, 18134987
  • Base pairs - 2784


Gmr41h07, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh Dec 2019

Gmr41h07, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 46241

  • ID - GMR41H07
  • Location - 2R: 18150920, 18154671
  • Base pairs - 3751


Gmr39h01, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh Dec 2019

Gmr39h01, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50066

  • ID - GMR39H01
  • Location - 2R: 18153797, 18156108
  • Base pairs - 2311


Gmr36a10, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh Dec 2019

Gmr36a10, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 49373

  • ID - GMR36A10
  • Location - 2R: 18116788, 18120701
  • Base pairs - 3913


Gmr42h01, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh Dec 2019

Gmr42h01, Anuradha Chimata Venkatakrishnan, Oorvashi Roy Pula, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 48150

  • ID - GMR42H01
  • Location - 2R: 18158419, 18162751
  • Base pairs - 4332