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CRISPR AND Zebrafish

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https://www.readbyqxmd.com/read/29655639/glia-maturation-factor-beta-is-required-for-reactive-gliosis-after-traumatic-brain-injury-in-zebrafish
#1
Guo Yin, Mingjun Du, Rong Li, Ke Li, Xiaomin Huang, Dongbei Duan, Xiaolan Ai, Fang Yao, Lanlan Zhang, Ziyou Hu, Bingyi Wu
Gliosis is a hallmark of neural pathology that occurs after most forms of central nervous system (CNS) injuries including traumatic brain injury (TBI). Identification of genes that control gliosis may provide novel treatment targets for patients with diverse CNS injuries. Glia maturation factor beta (GMFB) is crucial in brain development and stress response. In the present study, GMFB was found to be widely expressed in adult zebrafish telencephalon. A gmfb mutant zebrafish was created using CRISPR/cas9. In the uninjured zebrafish telencephalon, glial fibrillary acidic protein (GFAP) fibers in gmfb mutants were disorganized and shorter than wild type zebrafish...
April 12, 2018: Experimental Neurology
https://www.readbyqxmd.com/read/29644996/simultaneous-lineage-tracing-and-cell-type-identification-using-crispr-cas9-induced-genetic-scars
#2
Bastiaan Spanjaard, Bo Hu, Nina Mitic, Pedro Olivares-Chauvet, Sharan Janjuha, Nikolay Ninov, Jan Philipp Junker
A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells...
April 9, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29621239/distinct-interactions-of-sox5-and-sox10-in-fate-specification-of-pigment-cells-in-medaka-and-zebrafish
#3
Yusuke Nagao, Hiroyuki Takada, Motohiro Miyadai, Tomoko Adachi, Ryoko Seki, Yasuhiro Kamei, Ikuyo Hara, Yoshihito Taniguchi, Kiyoshi Naruse, Masahiko Hibi, Robert N Kelsh, Hisashi Hashimoto
Mechanisms generating diverse cell types from multipotent progenitors are fundamental for normal development. Pigment cells are derived from multipotent neural crest cells and their diversity in teleosts provides an excellent model for studying mechanisms controlling fate specification of distinct cell types. Zebrafish have three types of pigment cells (melanocytes, iridophores and xanthophores) while medaka have four (three shared with zebrafish, plus leucophores), raising questions about how conserved mechanisms of fate specification of each pigment cell type are in these fish...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29619162/crispr-cas9-induced-shank3b-mutant-zebrafish-display-autism-like-behaviors
#4
Chun-Xue Liu, Chun-Yang Li, Chun-Chun Hu, Yi Wang, Jia Lin, Yong-Hui Jiang, Qiang Li, Xiu Xu
Background: Human genetic and genomic studies have supported a strong causal role of SHANK3 deficiency in autism spectrum disorder (ASD). However, the molecular mechanism underlying SHANK3 deficiency resulting in ASD is not fully understood. Recently, the zebrafish has become an attractive organism to model ASD because of its high efficiency of genetic manipulation and robust behavioral phenotypes. The orthologous gene to human SHANK3 is duplicated in the zebrafish genome and has two homologs, shank3a and shank3b ...
2018: Molecular Autism
https://www.readbyqxmd.com/read/29618800/a-rapid-crispr-cas-based-mutagenesis-assay-in-zebrafish-for-identification-of-genes-involved-in-thyroid-morphogenesis-and-function
#5
A Trubiroha, P Gillotay, N Giusti, D Gacquer, F Libert, A Lefort, B Haerlingen, X De Deken, R Opitz, S Costagliola
The foregut endoderm gives rise to several organs including liver, pancreas, lung and thyroid with important roles in human physiology. Understanding which genes and signalling pathways regulate their development is crucial for understanding developmental disorders as well as diseases in adulthood. We exploited unique advantages of the zebrafish model to develop a rapid and scalable CRISPR/Cas-based mutagenesis strategy aiming at the identification of genes involved in morphogenesis and function of the thyroid...
April 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29610331/evolutionary-emergence-of-the-rac3b-rfng-sgca-regulatory-cluster-refined-mechanisms-for-hindbrain-boundaries-formation
#6
Joaquín Letelier, Javier Terriente, Ivan Belzunce, Adria Voltes, Cristian Alberto Undurraga, Rocio Polvillo, Lucie Devos, Juan J Tena, Ignacio Maeso, Sylvie Retaux, José Luis Gomez-Skarmeta, Juan R Martínez-Morales, Cristina Pujades
Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b / rfng / sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis -regulatory interactions...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29608178/simultaneous-single-cell-profiling-of-lineages-and-cell-types-in-the-vertebrate-brain
#7
Bushra Raj, Daniel E Wagner, Aaron McKenna, Shristi Pandey, Allon M Klein, Jay Shendure, James A Gagnon, Alexander F Schier
The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR-Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development...
March 28, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29604249/requirement-of-zebrafish-pcdh10a-and-pcdh10b-in-melanocyte-precursor-migration
#8
Jason S Williams, Jessica Y Hsu, Christy Cortez Rossi, Kristin Bruk Artinger
Melanocytes derive from neural crest cells, which are a highly migratory population of cells that play an important role in pigmentation of the skin and epidermal appendages. In most vertebrates, melanocyte precursor cells migrate solely along the dorsolateral pathway to populate the skin. However, zebrafish melanocyte precursors also migrate along the ventromedial pathway, in route to the yolk, where they interact with other neural crest derivative populations. Here, we demonstrate the requirement for zebrafish paralogs pcdh10a and pcdh10b in zebrafish melanocyte precursor migration...
March 28, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29590639/neutrophil-specific-knockout-demonstrates-a-role-for-mitochondria-in-regulating-neutrophil-motility-in-zebrafish
#9
Wenqing Zhou, Lingyan Cao, Jacob Jeffries, Xiaoguang Zhu, Christopher J Staiger, Qing Deng
Neutrophils are fast-moving cells essential for host immune functions. Although they primarily rely on glycolysis for ATP, isolated primary human neutrophils depend on mitochondrial membrane potential for chemotaxis. However, it is not known whether mitochondria regulate neutrophil motility in vivo , and the underlying molecular mechanisms remain obscure. Here, we visualized mitochondria in an interconnected network that localizes to the front and rear of migrating neutrophils using a novel transgenic zebrafish line...
March 28, 2018: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/29590089/whole-organism-clone-tracing-using-single-cell-sequencing
#10
Anna Alemany, Maria Florescu, Chloé S Baron, Josi Peterson-Maduro, Alexander van Oudenaarden
Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination...
March 28, 2018: Nature
https://www.readbyqxmd.com/read/29556895/efficient-genome-editing-in-cultured-cells-and-embryos-of-debao-pig-and-swamp-buffalo-using-the-crispr-cas9-system
#11
Xiaoping Su, Kuiqing Cui, Shanshan Du, Hongli Li, Fenghua Lu, Deshun Shi, Qingyou Liu
Myostatin (MSTN), a protein encoded by growth differentiation factor 8 (GDF8), is primarily expressed in skeletal muscle and negatively regulates the development and regeneration of muscle. Accordingly, myostatin-deficient animals exhibit a double-muscling phenotype. The CRISPR/Cas9 system has proven to be an efficient genome-editing tool and has been applied to gene modification in cells from many model organisms such as Drosophila melanogaster, zebrafish, mouse, rat, sheep, and human. Here, we edited the GDF8 gene in fibroblasts and embryos of Debao pig and swamp buffalo using the CRISPR/Cas9 system...
March 19, 2018: In Vitro Cellular & Developmental Biology. Animal
https://www.readbyqxmd.com/read/29556077/a-conserved-shh-cis-regulatory-module-highlights-a-common-developmental-origin-of-unpaired-and-paired-fins
#12
Joaquín Letelier, Elisa de la Calle-Mustienes, Joyce Pieretti, Silvia Naranjo, Ignacio Maeso, Tetsuya Nakamura, Juan Pascual-Anaya, Neil H Shubin, Igor Schneider, Juan Ramón Martinez-Morales, José Luis Gómez-Skarmeta
Despite their evolutionary, developmental and functional importance, the origin of vertebrate paired appendages remains uncertain. In mice, a single enhancer termed ZRS is solely responsible for Shh expression in limbs. Here, zebrafish and mouse transgenic assays trace the functional equivalence of ZRS across the gnathostome phylogeny. CRISPR/Cas9-mediated deletion of the medaka (Oryzias latipes) ZRS and enhancer assays identify the existence of ZRS shadow enhancers in both teleost and human genomes. Deletion of both ZRS and shadow ZRS abolishes shh expression and completely truncates pectoral fin formation...
March 19, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29545372/tbx20-regulates-angiogenesis-through-the-prok2-prokr1-pathway
#13
Shu Meng, Qilin Gu, Xiaojie Yang, Jie Lv, Iris Owusu, Gianfranco Matrone, Kaifu Chen, John P Cooke, Longhou Fang
Background -Angiogenesis is integral for embryogenesis, and targeting angiogenesis improves the outcome of many pathological conditions in patients. TBX20 is a crucial transcription factor for embryonic development, and its deficiency is associated with congenital heart disease. However, the role of TBX20 in angiogenesis has not been described. Methods -Loss- and gain-of-function approaches were used to explore the role of TBX20 in angiogenesis both in vitro and in vivo Angiogenesis gene array was used to identify key downstream targets of TBX20...
March 15, 2018: Circulation
https://www.readbyqxmd.com/read/29544468/a-parental-requirement-for-dual-specificity-phosphatase-6-in-zebrafish
#14
Jennifer M Maurer, Charles G Sagerström
BACKGROUND: Signaling cascades, such as the extracellular signal-regulated kinase (ERK) pathway, play vital roles in early vertebrate development. Signals through these pathways are initiated by a growth factor or hormone, are transduced through a kinase cascade, and result in the expression of specific downstream genes that promote cellular proliferation, growth, or differentiation. Tight regulation of these signals is provided by positive or negative modulators at varying levels in the pathway, and is required for proper development and function...
March 15, 2018: BMC Developmental Biology
https://www.readbyqxmd.com/read/29543903/an-automated-system-for-rapid-cellular-extraction-from-live-zebrafish-embryos-and-larvae-development-and-application-to-genotyping
#15
Christopher J Lambert, Briana C Freshner, Arlen Chung, Tamara J Stevenson, D Miranda Bowles, Raheel Samuel, Bruce K Gale, Joshua L Bonkowsky
Zebrafish are a valuable model organism in biomedical research. Their rapid development, ability to model human diseases, utility for testing genetic variants identified from next-generation sequencing, amenity to CRISPR mutagenesis, and potential for therapeutic compound screening, has led to their wide-spread adoption in diverse fields of study. However, their power for large-scale screens is limited by the absence of automated genotyping tools for live animals. This constrains potential drug screen options, limits analysis of embryonic and larval phenotypes, and requires raising additional animals to adulthood to ensure obtaining an animal of the desired genotype...
2018: PloS One
https://www.readbyqxmd.com/read/29534099/genetic-analysis-of-zebrafish-homologs-of-human-foxq1-foxq1a-and-foxq1b-in-innate-immune-cell-development-and-bacterial-host-response
#16
Alison M Earley, Cameron T Dixon, Celia E Shiau
FOXQ1 is a member of the forkhead-box transcription factor family that has important functions in development, cancer, aging, and many cellular processes. The role of FOXQ1 in cancer biology has raised intense interest, yet much remains poorly understood. We investigated the possible function of the two zebrafish orthologs (foxq1a and foxq1b) of human FOXQ1 in innate immune cell development and function. We employed CRISPR-Cas9 targeted mutagenesis to create null mutations of foxq1a and foxq1b in zebrafish...
2018: PloS One
https://www.readbyqxmd.com/read/29503817/cystathionine-%C3%AE-synthase-is-necessary-for-axis-development-in-vivo
#17
Shubhangi Prabhudesai, Chris Koceja, Anindya Dey, Shahram Eisa-Beygi, Noah R Leigh, Resham Bhattacharya, Priyabrata Mukherjee, Ramani Ramchandran
The cystathionine ß-synthase (CBS) is a critical enzyme in the transsulfuration pathway and is responsible for the synthesis of cystathionine from serine and homocysteine. Cystathionine is a precursor to amino acid cysteine. CBS is also responsible for generation of hydrogen sulfide (H2 S) from cysteine. Mutation in CBS enzyme causes homocysteine levels to rise, and gives rise to a condition called hyperhomocysteinuria. To date, numerous mouse knockout models for CBS enzyme has been generated, which show panoply of defects, reflecting the importance of this enzyme in development...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29500194/an-efficient-platform-for-generating-somatic-point-mutations-with-germline-transmission-in-the-zebrafish-by-crispr-cas9-mediated-gene-editing
#18
Yibo Zhang, Zhiwei Zhang, Wei Ge
Homology-directed recombination (HDR)-mediated genome editing is a powerful approach for both basic functional study and disease modeling. Although some studies have reported HDR-mediated precise editing in non-rodent models, the efficiency of establishing pure mutant animal lines that carry specific amino acid substitutions remains low. Furthermore, because the efficiency of nonhomologous end joining (NHEJ)-induced insertion and deletion (indel) mutations is normally much higher than that of HDR-induced point mutations, it is often difficult to identify the latter in the background of indel mutations...
March 2, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29494622/ahr2-required-for-normal-behavioral-responses-and-proper-development-of-the-skeletal-and-reproductive-systems-in-zebrafish
#19
Gloria R Garcia, Sean M Bugel, Lisa Truong, Sean Spagnoli, Robert L Tanguay
The aryl hydrocarbon receptor (AHR) is a conserved ligand-activated transcription factor required for proper vertebrate development and homeostasis. The inappropriate activation of AHR by ubiquitous pollutants can lead to adverse effects on wildlife and human health. The zebrafish is a powerful model system that provides a vertebrate data stream that anchors hypothesis at the genetic and cellular levels to observations at the morphological and behavioral level, in a high-throughput format. In order to investigate the endogenous functions of AHR, we generated an AHR2 (homolog of human AHR)-null zebrafish line (ahr2osu1) using the clustered, regulatory interspaced, short palindromic repeats (CRISPR)-Cas9 precision genome editing method...
2018: PloS One
https://www.readbyqxmd.com/read/29471431/making-waves-new-developments-in-toxicology-with-the-zebrafish
#20
Katharine A Horzmann, Jennifer L Freeman
The laboratory zebrafish (Danio rerio) is now an accepted model in toxicologic research. The zebrafish model fills a niche between in vitro models and mammalian biomedical models. The developmental characteristics of the small fish are strategically being used by scientists to study topics ranging from high-throughput toxicity screens to toxicity in multi- and transgenerational studies. High-throughput technology has increased the utility of zebrafish embryonic toxicity assays in screening of chemicals and drugs for toxicity or effect...
February 19, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
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