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Thyme Lab Publications

All Thyme Lab Publications on PubMed

Total: displaying 10 out of 28 results
  • Impairments of cerebellar structure and function in a zebrafish KO of neuropsychiatric risk gene znf536

    Thursday, February 08, 2024
    Author(s): Tae-Yoon Kim,Arkaprava Roychaudhury,Hyun-Taek Kim,Tae-Ik Choi,Seung Tae Baek,Summer B Thyme,Cheol-Hee Kim
    Source: Translational psychiatry
    Genetic variants in ZNF536 contribute to the risk for neuropsychiatric disorders such as schizophrenia, autism, and others. The role of this putative transcriptional repressor in brain development and function is, however, largely unknown. We generated znf536 knockout (KO) zebrafish and studied their behavior, brain anatomy, and brain function. Larval KO zebrafish showed a reduced ability to compete for food, resulting in decreased total body length and size. This phenotype can be rescued by...
  • Mitochondrial prodha regulates proliferation of radial glia-like cells in the zebrafish hindbrain

    Tuesday, December 19, 2023
    Author(s): Philip D Campbell,Isaiah Lee,Summer Thyme,Michael Granato
    Source: Molecular psychiatry
    No abstract
  • Mitochondrial proteins encoded by the 22q11.2 neurodevelopmental locus regulate neural stem and progenitor cell proliferation

    Wednesday, October 04, 2023
    Author(s): Philip D Campbell,Isaiah Lee,Summer Thyme,Michael Granato
    Source: Molecular psychiatry
    Microdeletion of a 3Mb region encompassing 45 protein-coding genes at chromosome 22q11.2 (22q11.2DS) predisposes individuals to multiple neurodevelopmental disorders and is one of the greatest genetic risk factors for schizophrenia. Defective mitochondrial function has been hypothesized to contribute to 22q11.2DS pathogenesis; however, which of the six mitochondrial genes contribute to neurodevelopmental phenotypes and their underlying mechanisms remain unresolved. To systematically test...
  • Behavioral analysis through the lifespan of disc1 mutant zebrafish identifies defects in sensorimotor transformation

    Friday, July 07, 2023
    Author(s): Brock R Pluimer,Devin L Harrison,Chanon Boonyavairoje,Eric P Prinssen,Mark Rogers-Evans,Randall T Peterson,Summer B Thyme,Anjali K Nath
    Source: iScience
    DISC1 is a genetic risk factor for multiple psychiatric disorders. Compared to the dozens of murine Disc1 models, there is a paucity of zebrafish disc1 models-an organism amenable to high-throughput experimentation. We conducted the longitudinal neurobehavioral analysis of disc1 mutant zebrafish across key stages of life. During early developmental stages, disc1 mutants exhibited abrogated behavioral responses to sensory stimuli across multiple testing platforms. Moreover, during exposure to an...
  • Multiple adaptations underly co-option of a CRISPR surveillance complex for RNA-guided DNA transposition

    Friday, June 02, 2023
    Author(s): Jung-Un Park,Michael T Petassi,Shan-Chi Hsieh,Eshan Mehrotra,Gabriel Schuler,Jagat Budhathoki,Vinh H Truong,Summer B Thyme,Ailong Ke,Elizabeth H Kellogg,Joseph E Peters
    Source: Molecular cell
    CRISPR-associated transposons (CASTs) are natural RNA-directed transposition systems. We demonstrate that transposon protein TniQ plays a central role in promoting R-loop formation by RNA-guided DNA-targeting modules. TniQ residues, proximal to CRISPR RNA (crRNA), are required for recognizing different crRNA categories, revealing an unappreciated role of TniQ to direct transposition into different classes of crRNA targets. To investigate adaptations allowing CAST elements to utilize attachment...
  • A single-cell transcriptome atlas of the maturing zebrafish telencephalon

    Tuesday, April 18, 2023
    Author(s): Shristi Pandey,Anna J Moyer,Summer B Thyme
    Source: Genome research
    The zebrafish telencephalon is composed of highly specialized subregions that regulate complex behaviors such as learning, memory, and social interactions. The transcriptional signatures of the neuronal cell types in the telencephalon and the timeline of their emergence from larva to adult remain largely undescribed. Using an integrated analysis of single-cell transcriptomes of approximately 64,000 cells obtained from 6-day-postfertilization (dpf), 15-dpf, and adult telencephalon, we delineated...
  • Mitochondrial genes in the 22q11.2 deleted region regulate neural stem and progenitor cell proliferation

    Monday, January 30, 2023
    Author(s): Philip D Campbell,Isaiah Lee,Summer Thyme,Michael Granato
    Source: bioRxiv : the preprint server for biology
    Microdeletion of a 3Mbp region encompassing 45 protein-coding genes at chromosome 22q11.2 (22q11.2DS) predisposes to multiple neurodevelopmental disorders and is one of the greatest genetic risk factors for schizophrenia. Defective mitochondrial function has been hypothesized to contribute to 22q11.2DS pathogenesis; however, which of the six mitochondrial genes contribute to neurodevelopmental phenotypes and their underlying mechanisms remain unresolved. To systematically test 22q11.2DS genes...
  • Mosaic and non-mosaic protocadherin 19 mutation leads to neuronal hyperexcitability in zebrafish

    Saturday, April 23, 2022
    Author(s): Barbara K Robens,Xinzhu Yang,Christopher M McGraw,Laura H Turner,Carsten Robens,Summer Thyme,Alexander Rotenberg,Annapurna Poduri
    Source: Neurobiology of disease
    Epilepsy is one of the most common neurological disorders. The X-linked gene PCDH19 is associated with sporadic and familial epilepsy in humans, typically with early-onset clustering seizures and intellectual disability in females but not in so-called 'carrier' males, suggesting that mosaic PCDH19 expression is required to produce epilepsy. To characterize the role of loss of PCDH19 function in epilepsy, we generated zebrafish with truncating pcdh19 variants. Evaluating zebrafish larvae for...
  • ZebraShare: a new venue for rapid dissemination of zebrafish mutant data

    Thursday, May 06, 2021
    Author(s): April DeLaurier,Douglas G Howe,Leyla Ruzicka,Adam N Carte,Lacie Mishoe Hernandez,Kali J Wiggins,Mika M Gallati,Kayce Vanpelt,Frances Loyo Rosado,Katlin G Pugh,Chasey J Shabdue,Khadijah Jihad,Summer B Thyme,Jared C Talbot
    Source: PeerJ
    CONCLUSION: ZebraShare provides an opportunity for researchers to directly share information about mutant lines within ZFIN, which is widely used by the community as a central database of information about zebrafish lines. Submissions of alleles with a phenotypic or unexpected phenotypes is encouraged to promote collaborations, disseminate lines, reduce redundancy of effort and to promote efficient use of time and resources. We anticipate that as submissions to ZebraShare increase, they will...
  • A Customizable Low-Cost System for Massively Parallel Zebrafish Behavioral Phenotyping

    Thursday, February 04, 2021
    Author(s): William Joo,Michael D Vivian,Brett J Graham,Edward R Soucy,Summer B Thyme
    Source: Frontiers in behavioral neuroscience
    High-throughput behavioral phenotyping is critical to genetic or chemical screening approaches. Zebrafish larvae are amenable to high-throughput behavioral screening because of their rapid development, small size, and conserved vertebrate brain architecture. Existing commercial behavioral phenotyping systems are expensive and not easily modified for new assays. Here, we describe a modular, highly adaptable, and low-cost system. Along with detailed assembly and operation instructions, we provide...
  • Macromolecular modeling and design in Rosetta: recent methods and frameworks

    Wednesday, June 03, 2020
    Author(s): Julia Koehler Leman,Brian D Weitzner,Steven M Lewis,Jared Adolf-Bryfogle,Nawsad Alam,Rebecca F Alford,Melanie Aprahamian,David Baker,Kyle A Barlow,Patrick Barth,Benjamin Basanta,Brian J Bender,Kristin Blacklock,Jaume Bonet,Scott E Boyken,Phil Bradley,Chris Bystroff,Patrick Conway,Seth Cooper,Bruno E Correia,Brian Coventry,Rhiju Das,René M De Jong,Frank DiMaio,Lorna Dsilva,Roland Dunbrack,Alexander S Ford,Brandon Frenz,Darwin Y Fu,Caleb Geniesse,Lukasz Goldschmidt,Ragul Gowthaman,Jeffrey J Gray,Dominik Gront,Sharon Guffy,Scott Horowitz,Po-Ssu Huang,Thomas Huber,Tim M Jacobs,Jeliazko R Jeliazkov,David K Johnson,Kalli Kappel,John Karanicolas,Hamed Khakzad,Karen R Khar,Sagar D Khare,Firas Khatib,Alisa Khramushin,Indigo C King,Robert Kleffner,Brian Koepnick,Tanja Kortemme,Georg Kuenze,Brian Kuhlman,Daisuke Kuroda,Jason W Labonte,Jason K Lai,Gideon Lapidoth,Andrew Leaver-Fay,Steffen Lindert,Thomas Linsky,Nir London,Joseph H Lubin,Sergey Lyskov,Jack Maguire,Lars Malmström,Enrique Marcos,Orly Marcu,Nicholas A Marze,Jens Meiler,Rocco Moretti,Vikram Khipple Mulligan,Santrupti Nerli,Christoffer Norn,Shane Ó'Conchúir,Noah Ollikainen,Sergey Ovchinnikov,Michael S Pacella,Xingjie Pan,Hahnbeom Park,Ryan E Pavlovicz,Manasi Pethe,Brian G Pierce,Kala Bharath Pilla,Barak Raveh,P Douglas Renfrew,Shourya S Roy Burman,Aliza Rubenstein,Marion F Sauer,Andreas Scheck,William Schief,Ora Schueler-Furman,Yuval Sedan,Alexander M Sevy,Nikolaos G Sgourakis,Lei Shi,Justin B Siegel,Daniel-Adriano Silva,Shannon Smith,Yifan Song,Amelie Stein,Maria Szegedy,Frank D Teets,Summer B Thyme,Ray Yu-Ruei Wang,Andrew Watkins,Lior Zimmerman,Richard Bonneau
    Source: Nature methods
    The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces...
  • Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions

    Tuesday, April 02, 2019
    Author(s): Summer B Thyme,Lindsey M Pieper,Eric H Li,Shristi Pandey,Yiqun Wang,Nathan S Morris,Carrie Sha,Joo Won Choi,Kristian J Herrera,Edward R Soucy,Steve Zimmerman,Owen Randlett,Joel Greenwood,Steven A McCarroll,Alexander F Schier
    Source: Cell
    Genomic studies have identified hundreds of candidate genes near loci associated with risk for schizophrenia. To define candidates and their functions, we mutated zebrafish orthologs of 132 human schizophrenia-associated genes. We created a phenotype atlas consisting of whole-brain activity maps, brain structural differences, and profiles of behavioral abnormalities. Phenotypes were diverse but specific, including altered forebrain development and decreased prepulse inhibition. Exploration of...
  • Kctd13 deletion reduces synaptic transmission via increased RhoA

    Thursday, November 02, 2017
    Author(s): Christine Ochoa Escamilla,Irina Filonova,Angela K Walker,Zhong X Xuan,Roopashri Holehonnur,Felipe Espinosa,Shunan Liu,Summer B Thyme,Isabel A López-García,Dorian B Mendoza,Noriyoshi Usui,Jacob Ellegood,Amelia J Eisch,Genevieve Konopka,Jason P Lerch,Alexander F Schier,Haley E Speed,Craig M Powell
    Source: Nature
    Copy-number variants of chromosome 16 region 16p11.2 are linked to neuropsychiatric disorders and are among the most prevalent in autism spectrum disorders. Of many 16p11.2 genes, Kctd13 has been implicated as a major driver of neurodevelopmental phenotypes. The function of KCTD13 in the mammalian brain, however, remains unknown. Here we delete the Kctd13 gene in mice and demonstrate reduced synaptic transmission. Reduced synaptic transmission correlates with increased levels of Ras homolog gene...
  • Internal guide RNA interactions interfere with Cas9-mediated cleavage

    Saturday, June 11, 2016
    Author(s): Summer B Thyme,Laila Akhmetova,Tessa G Montague,Eivind Valen,Alexander F Schier
    Source: Nature communications
    The CRISPR/Cas system uses guide RNAs (gRNAs) to direct sequence-specific DNA cleavage. Not every gRNA elicits cleavage and the mechanisms that govern gRNA activity have not been resolved. Low activity could result from either failure to form a functional Cas9-gRNA complex or inability to recognize targets in vivo. Here we show that both phenomena influence Cas9 activity by comparing mutagenesis rates in zebrafish embryos with in vitro cleavage assays. In vivo, our results suggest that genomic...
  • Polq-Mediated End Joining Is Essential for Surviving DNA Double-Strand Breaks during Early Zebrafish Development

    Thursday, May 19, 2016
    Author(s): Summer B Thyme,Alexander F Schier
    Source: Cell reports
    No abstract
  • CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

    Wednesday, May 18, 2016
    Author(s): Kornel Labun,Tessa G Montague,James A Gagnon,Summer B Thyme,Eivind Valen
    Source: Nucleic acids research
    In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can...
  • Polq-Mediated End Joining Is Essential for Surviving DNA Double-Strand Breaks during Early Zebrafish Development

    Saturday, May 07, 2016
    Author(s): Summer B Thyme,Alexander F Schier
    Source: Cell reports
    Error-prone repair of DNA double-strand breaks (DSBs) has been postulated to occur through classical non-homologous end joining (NHEJ) in systems ranging from nematode somatic tissues to zebrafish embryos. Contrary to this model, we show that zebrafish embryos mutant for DNA polymerase theta (Polq), a critical component of alternative end joining (alt-EJ), cannot repair DSBs induced by CRISPR/Cas9 or ionizing radiation. In the absence of DSBs, polq mutants are phenotypically normal, but they do...
  • Computational Design of DNA-Binding Proteins

    Thursday, April 21, 2016
    Author(s): Summer Thyme,Yifan Song
    Source: Methods in molecular biology (Clifton, N.J.)
    Predicting the outcome of engineered and naturally occurring sequence perturbations to protein-DNA interfaces requires accurate computational modeling technologies. It has been well established that computational design to accommodate small numbers of DNA target site substitutions is possible. This chapter details the basic method of design used in the Rosetta macromolecular modeling program that has been successfully used to modulate the specificity of DNA-binding proteins. More recently,...
  • Massively parallel determination and modeling of endonuclease substrate specificity

    Thursday, November 13, 2014
    Author(s): Summer B Thyme,Yifan Song,T J Brunette,Mindy D Szeto,Lara Kusak,Philip Bradley,David Baker
    Source: Nucleic acids research
    We describe the identification and characterization of novel homing endonucleases using genome database mining to identify putative target sites, followed by high throughput activity screening in a bacterial selection system. We characterized the substrate specificity and kinetics of these endonucleases by monitoring DNA cleavage events with deep sequencing. The endonuclease specificities revealed by these experiments can be partially recapitulated using 3D structure-based computational models....
  • Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs

    Saturday, May 31, 2014
    Author(s): James A Gagnon,Eivind Valen,Summer B Thyme,Peng Huang,Laila Akhmetova,Andrea Pauli,Tessa G Montague,Steven Zimmerman,Constance Richter,Alexander F Schier
    Source: PloS one
    The CRISPR/Cas9 system has been implemented in a variety of model organisms to mediate site-directed mutagenesis. A wide range of mutation rates has been reported, but at a limited number of genomic target sites. To uncover the rules that govern effective Cas9-mediated mutagenesis in zebrafish, we targeted over a hundred genomic loci for mutagenesis using a streamlined and cloning-free method. We generated mutations in 85% of target genes with mutation rates varying across several orders of...
  • Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus

    Tuesday, April 01, 2014
    Author(s): Yupeng Wang,Iram F Khan,Sandrine Boissel,Jordan Jarjour,Joseph Pangallo,Summer Thyme,David Baker,Andrew M Scharenberg,David J Rawlings
    Source: Nucleic acids research
    LAGLIDADG homing endonucleases (LHEs) are compact endonucleases with 20-22 bp recognition sites, and thus are ideal scaffolds for engineering site-specific DNA cleavage enzymes for genome editing applications. Here, we describe a general approach to LHE engineering that combines rational design with directed evolution, using a yeast surface display high-throughput cleavage selection. This approach was employed to alter the binding and cleavage specificity of the I-Anil LHE to recognize a...
  • Redesigning the specificity of protein-DNA interactions with Rosetta

    Tuesday, February 11, 2014
    Author(s): Summer Thyme,David Baker
    Source: Methods in molecular biology (Clifton, N.J.)
    Building protein tools that can selectively bind or cleave specific DNA sequences requires efficient technologies for modifying protein-DNA interactions. Computational design is one method for accomplishing this goal. In this chapter, we present the current state of protein-DNA interface design with the Rosetta macromolecular modeling program. The LAGLIDADG endonuclease family of DNA-cleaving enzymes, under study as potential gene therapy reagents, has been the main testing ground for these in...
  • Reprogramming homing endonuclease specificity through computational design and directed evolution

    Tuesday, November 26, 2013
    Author(s): Summer B Thyme,Sandrine J S Boissel,S Arshiya Quadri,Tony Nolan,Dean A Baker,Rachel U Park,Lara Kusak,Justin Ashworth,David Baker
    Source: Nucleic acids research
    Homing endonucleases (HEs) can be used to induce targeted genome modification to reduce the fitness of pathogen vectors such as the malaria-transmitting Anopheles gambiae and to correct deleterious mutations in genetic diseases. We describe the creation of an extensive set of HE variants with novel DNA cleavage specificities using an integrated experimental and computational approach. Using computational modeling and an improved selection strategy, which optimizes specificity in addition to...
  • Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design

    Tuesday, March 20, 2012
    Author(s): Summer B Thyme,David Baker,Philip Bradley
    Source: Journal of molecular biology
    Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif...
  • Mining endonuclease cleavage determinants in genomic sequence data

    Saturday, July 23, 2011
    Author(s): Mindy D Szeto,Sandrine J S Boissel,David Baker,Summer B Thyme
    Source: The Journal of biological chemistry
    Homing endonucleases have great potential as tools for targeted gene therapy and gene correction, but identifying variants of these enzymes capable of cleaving specific DNA targets of interest is necessary before the widespread use of such technologies is possible. We identified homologues of the LAGLIDADG homing endonuclease I-AniI and their putative target insertion sites by BLAST searches followed by examination of the sequences of the flanking genomic regions. Amino acid substitutions in...
  • A synthetic homing endonuclease-based gene drive system in the human malaria mosquito

    Friday, April 22, 2011
    Author(s): Nikolai Windbichler,Miriam Menichelli,Philippos Aris Papathanos,Summer B Thyme,Hui Li,Umut Y Ulge,Blake T Hovde,David Baker,Raymond J Monnat,Austin Burt,Andrea Crisanti
    Source: Nature
    Genetic methods of manipulating or eradicating disease vector populations have long been discussed as an attractive alternative to existing control measures because of their potential advantages in terms of effectiveness and species specificity. The development of genetically engineered malaria-resistant mosquitoes has shown, as a proof of principle, the possibility of targeting the mosquito's ability to serve as a disease vector. The translation of these achievements into control measures...
  • Exploitation of binding energy for catalysis and design

    Friday, October 30, 2009
    Author(s): Summer B Thyme,Jordan Jarjour,Ryo Takeuchi,James J Havranek,Justin Ashworth,Andrew M Scharenberg,Barry L Stoddard,David Baker
    Source: Nature
    Enzymes use substrate-binding energy both to promote ground-state association and to stabilize the reaction transition state selectively. The monomeric homing endonuclease I-AniI cleaves with high sequence specificity in the centre of a 20-base-pair (bp) DNA target site, with the amino (N)-terminal domain of the enzyme making extensive binding interactions with the left (-) side of the target site and the similarly structured carboxy (C)-terminal domain interacting with the right (+) side. Here...
  • Mechanistic study of competitive sp(3)-sp(3) and sp(2)-sp(3) carbon-carbon reductive elimination from a platinum (IV) center and the isolation of a C-C agostic complex

    Tuesday, July 17, 2007
    Author(s): Brian L Madison,Summer B Thyme,Sarra Keene,B Scott Williams
    Source: Journal of the American Chemical Society
    No abstract