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zebrafish T cells

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https://www.readbyqxmd.com/read/28096348/transcriptomic-proteomic-and-metabolomic-landscape-of-positional-memory-in-the-caudal-fin-of-zebrafish
#1
Jeremy S Rabinowitz, Aaron M Robitaille, Yuliang Wang, Catherine A Ray, Ryan Thummel, Haiwei Gu, Danijel Djukovic, Daniel Raftery, Jason D Berndt, Randall T Moon
Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules, few of which have been identified. Here, we quantified the global abundance of transcripts, proteins, and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach, we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions, including development, bioelectric signaling, and amino acid and lipid metabolism...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28092684/biallelic-mutations-in-the-3-exonuclease-toe1-cause-pontocerebellar-hypoplasia-and-uncover-a-role-in-snrna-processing
#2
Rea M Lardelli, Ashleigh E Schaffer, Veerle R C Eggens, Maha S Zaki, Stephanie Grainger, Shashank Sathe, Eric L Van Nostrand, Zinayida Schlachetzki, Basak Rosti, Naiara Akizu, Eric Scott, Jennifer L Silhavy, Laura Dean Heckman, Rasim Ozgur Rosti, Esra Dikoglu, Anne Gregor, Alicia Guemez-Gamboa, Damir Musaev, Rohit Mande, Ari Widjaja, Tim L Shaw, Sebastian Markmiller, Isaac Marin-Valencia, Justin H Davies, Linda de Meirleir, Hulya Kayserili, Umut Altunoglu, Mary Louise Freckmann, Linda Warwick, David Chitayat, Susan Blaser, Ahmet Okay Çağlayan, Kaya Bilguvar, Huseyin Per, Christina Fagerberg, Henrik T Christesen, Maria Kibaek, Kimberly A Aldinger, David Manchester, Naomichi Matsumoto, Kazuhiro Muramatsu, Hirotomo Saitsu, Masaaki Shiina, Kazuhiro Ogata, Nicola Foulds, William B Dobyns, Neil C Chi, David Traver, Luigina Spaccini, Stefania Maria Bova, Stacey B Gabriel, Murat Gunel, Enza Maria Valente, Marie-Cecile Nassogne, Eric J Bennett, Gene W Yeo, Frank Baas, Jens Lykke-Andersen, Joseph G Gleeson
Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg(2+)-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) is a unique recessive syndrome characterized by neurodegeneration and ambiguous genitalia. We studied 12 human families with PCH7, uncovering biallelic, loss-of-function mutations in TOE1, which encodes an unconventional deadenylase...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28087841/single-cell-transcriptome-analysis-of-fish-immune-cells-provides-insight-into-the-evolution-of-vertebrate-immune-cell-types
#3
Santiago J Carmona, Sarah A Teichmann, Lauren Ferreira, Iain C Macaulay, Michael J T Stubbington, Ana Cvejic, David Gfeller
The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analysed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared to other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA-Sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a non-mammalian species...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28057273/eomesodermin-at-dawn-of-cell-fate-decisions-during-early-embryogenesis
#4
S Probst, S J Arnold
Proteins of the large family of T-box transcription factors are implicated in a broad spectrum of developmental processes. Loss-of-function mutations of T-box(Tbx) factors frequently cause severe embryonic phenotypes, often resulting from defects in cell fate specification and lineage differentiation. This review summarizes current knowledge on the functions of the T-box transcription factor Eomesodermin (Eomes) from postfertilization development until gastrulation stages of vertebrate embryos. Eomes exhibits evolutionary conserved functions in cell lineage specification and morphogenesis during gastrulation in all studied vertebrate model systems...
2017: Current Topics in Developmental Biology
https://www.readbyqxmd.com/read/28043811/honokiol-induces-proteasomal-degradation-of-aml1-eto-oncoprotein-via-increasing-ubiquitin-conjugase-ubch8-expression-in-leukemia
#5
Bin Zhou, Haiying Li, Chongyun Xing, Haige Ye, Jianhua Feng, Jianbo Wu, Zhongqiu Lu, Jing Fang, Shenmeng Gao
AML1-ETO is the most common oncoprotein leading to acute myeloid leukemia (AML), in which 5-year survival rate is only about 30%. However, currently there are no specific therapies for AML patients with AML1-ETO. Here, we report that AML1-ETO protein is rapidly degraded by Honokiol (HNK), a natural phenolic compound isolated from the plant Magnolia officinalis. HNK induced the degradation of AML1-ETO in a concentration- and time-dependent manner in leukemic cell lines and primary AML blasts with t(8;21) translocation...
December 30, 2016: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28035003/a-quininib-analogue-and-cysteinyl-leukotreine-receptor-antagonist-inhibits-vegf-independent-angiogenesis-and-exerts-an-additive-anti-angiogenic-response-with-bevacizumab
#6
Clare T Butler, Alison L Reynolds, Miriam Tosetto, Eugene T Dillon, Patrick Guiry, Gerard Cagney, Jacintha O'Sullivan, Breand Aacuten N Kennedy
Excess blood vessel growth contributes to the pathology of metastatic cancers and age-related retinopathies. Despite development of improved treatments, these conditions are associated with high economic costs and drug resistance. Bevacizumab (Avastin®), a monoclonal antibody against vascular endothelial growth factor (VEGF) is used clinically to treat certain types of metastatic cancers. Unfortunately, many patients do not respond or inevitably become resistant to bevacizumab, highlighting the need for more effective anti-angiogenic drugs with novel mechanisms of action...
December 29, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28028313/aberrant-activation-of-the-gimap-enhancer-by-oncogenic-transcription-factors-in-t-cell-acute-lymphoblastic-leukemia
#7
W-S Liau, S H Tan, P C T Ngoc, C Q Wang, V Tergaonkar, H Feng, Z Gong, M Osato, A T Look, T Sanda
The transcription factor TAL1/SCL is one of the most prevalent oncogenes in T-cell acute lymphoblastic leukemia (T-ALL), a malignant disorder resulting from leukemic transformation of thymus T-cell precursors. TAL1 is normally expressed in hematopoietic stem cells (HSCs) but is silenced in immature thymocytes. We hypothesize that TAL1 contributes to leukemogenesis by activating genes that are normally repressed in immature thymocytes. Herein, we identified a novel TAL1-regulated super-enhancer controlling the GIMAP locus, which resides within an insulated chromosomal locus in T-ALL cells...
December 28, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28004827/hs1bp3-negatively-regulates-autophagy-by-modulation-of-phosphatidic-acid-levels
#8
Petter Holland, Helene Knævelsrud, Kristiane Søreng, Benan J Mathai, Alf Håkon Lystad, Serhiy Pankiv, Gunnveig T Bjørndal, Sebastian W Schultz, Viola H Lobert, Robin B Chan, Bowen Zhou, Knut Liestøl, Sven R Carlsson, Thomas J Melia, Gilbert Di Paolo, Anne Simonsen
A fundamental question is how autophagosome formation is regulated. Here we show that the PX domain protein HS1BP3 is a negative regulator of autophagosome formation. HS1BP3 depletion increased the formation of LC3-positive autophagosomes and degradation of cargo both in human cell culture and in zebrafish. HS1BP3 is localized to ATG16L1- and ATG9-positive autophagosome precursors and we show that HS1BP3 binds phosphatidic acid (PA) through its PX domain. Furthermore, we find the total PA content of cells to be significantly upregulated in the absence of HS1BP3, as a result of increased activity of the PA-producing enzyme phospholipase D (PLD) and increased localization of PLD1 to ATG16L1-positive membranes...
December 22, 2016: Nature Communications
https://www.readbyqxmd.com/read/28003365/impairment-of-cargo-transportation-due-to-gbf1-mutation-disrupts-vascular-integrity-and-causes-hemorrhage-in-zebrafish-embryos
#9
Jing Chen, Xiaotong Wu, Likun Yao, Lu Yan, Lin Zhang, Juhui Qiu, Xingfeng Liu, Shunji Jia, Anming Meng
ADP-ribosylation factor (ARF) GTPases are activated by guanine nucleotide exchange factors including Golgi Brefeldin A-resistant factor 1 (Gbf1) and play important roles in regulating organelle structure and cargo-selective vesicle trafficking. However, the developmental role of Gbf1 in vertebrates remains elusive. In this study, we report the zebrafish mutant line tsu3994 that arises from ENU-mediated mutagenesis and is characterized by prominent intracerebral and trunk hemorrhage. The mutant embryos develop hemorrhage accompanied by fewer pigments and shorter caudal fin at day 2 of development...
December 21, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27994173/transgenic-overexpression-of-baff-regulates-the-expression-of-immune-related-genes-in-zebrafish-danio-rerio
#10
Li Zhang, Chao Liu, Xin Zhou, Ying Xie, Libo Su, Qi Geng, Binghui Liu, Shufeng Liu
The B-cell activating factor (BAFF) is a member of tumour necrosis factor (TNF) superfamily that specifically regulates B lymphocyte proliferation and survival. Excess BAFF leads to overproduction of antibodies for secretion, anti-dsDNA antibodies and a lupus-like syndrome in mice. To investigate whether transgenic overexpression of the zebrafish BAFF leads to immunoglobulin changes and/or early maturing of the immune system, a Tol2-GFP-2A-BAFF/His recombinant plasmid was constructed by inserting a 2A peptide between the green fluorescent protein (GFP) and BAFF sequences...
December 2016: Journal of Genetics
https://www.readbyqxmd.com/read/27993727/quantum-dot-interactions-and-flow-effects-in-angiogenic-zebrafish-danio-rerio-vessels-and-human-endothelial-cells
#11
Xiao-Yu Jiang, Christopher D Sarsons, M Juliana Gomez-Garcia, David T Cramb, Kristina D Rinker, Sarah J Childs
Nanoparticle (NP) interactions with biological tissues are affected by the size, shape and surface chemistry of the NPs. Here we use in vivo (zebrafish) and in vitro (HUVEC) models to investigate association of quantum dots (QDs) with endothelial cells and the effect of fluid flow. After injection into the developing zebrafish, circulating QDs associate with endothelium and penetrate surrounding tissue parenchyma over time. Amino-functionalized QDs cluster, interact with cells, and clear more rapidly than carboxy-functionalized QDs in vivo, highlighting charge influences...
December 18, 2016: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/27965016/cross-reactivity-of-monoclonal-antibodies-against-cd4-1-and-cd8%C3%AE-of-ginbuna-crucian-carp-with-lymphocytes-of-zebrafish-and-other-cyprinid-species
#12
Ryuichiro Miyazawa, Yuta Matsuura, Yasuhiro Shibasaki, Shintaro Imamura, Teruyuki Nakanishi
We have monoclonal antibodies (mAbs) against CD4-1 (6D1) and CD8α (2C3) in ginbuna crucian carp Carassius auratus langsdorfii. In our previous studies we showed that 2C3 mAb positive cells are the primary cell type showing specific cytotoxicity against allogeneic targets, suggesting that CD8α(+) lymphocytes in ginbuna are equivalent to cytotoxic T lymphocytes (CTLs) in mammals. We further demonstrated the helper T cell function of 6D1 mAb positive cells by studying mixed leukocyte culture (MLC) and hapten/carrier effects...
December 11, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27959755/multisystem-anomalies-in-severe-combined-immunodeficiency-with-mutant-bcl11b
#13
Divya Punwani, Yong Zhang, Jason Yu, Morton J Cowan, Sadhna Rana, Antonia Kwan, Aashish N Adhikari, Carlos O Lizama, Bryce A Mendelsohn, Shawn P Fahl, Ajithavalli Chellappan, Rajgopal Srinivasan, Steven E Brenner, David L Wiest, Jennifer M Puck
Background Severe combined immunodeficiency (SCID) is characterized by arrested T-lymphocyte production and by B-lymphocyte dysfunction, which result in life-threatening infections. Early diagnosis of SCID through population-based screening of newborns can aid clinical management and help improve outcomes; it also permits the identification of previously unknown factors that are essential for lymphocyte development in humans. Methods SCID was detected in a newborn before the onset of infections by means of screening of T-cell-receptor excision circles, a biomarker for thymic output...
1, 2016: New England Journal of Medicine
https://www.readbyqxmd.com/read/27940156/tbx20-drives-cardiac-progenitor-formation-and-cardiomyocyte-proliferation-in-zebrafish
#14
Fei Lu, Adam Langenbacher, Jau-Nian Chen
Tbx20 is a T-box transcription factor that plays essential roles in the development and maintenance of the heart. Although it is expressed by cardiac progenitors in all species examined, an involvement of Tbx20 in cardiac progenitor formation in vertebrates has not been previously described. Here we report the identification of a zebrafish tbx20 mutation that results in an inactive, truncated protein lacking any functional domains. The cardiac progenitor population is strongly diminished in this mutant, leading to the formation of a small, stretched-out heart...
January 15, 2017: Developmental Biology
https://www.readbyqxmd.com/read/27917506/comparative-in-vitro-toxicity-assessment-of-perfluorinated-carboxylic-acids
#15
Cecon T Mahapatra, Nur P Damayanti, Samuel C Guffey, Jennifer S Serafin, Joseph Irudayaraj, Maria S Sepúlveda
Perfluoroalkyl and polyfluoroalkyl substances (PFASs) are synthetic fluorinated compounds that are highly bioaccumulative and persistent organic pollutants. Perfluorooctanoic acid (PFOA), an eight-carbon chain perfluorinated carboxylic acid, was used heavily for the production of fluoropolymers, but concerns have led to its replacement by shorter carbon chain homologues such as perfluorohexanoic acid (PFHxA) and perfluorobutanoic acid (PFBA). However, limited toxicity data exist for these substitutes. We evaluated the toxicity of PFOA, PFHxA and PFBA on a zebrafish liver cell line and investigated the effects of exposure on cell metabolism...
December 5, 2016: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/27907103/tbx20-is-an-essential-regulator-of-embryonic-heart-growth-in-zebrafish
#16
Steffen Just, Linda Raphel, Ina M Berger, Anja Bühler, Mirjam Keßler, Wolfgang Rottbauer
The molecular mechanisms that regulate cardiomyocyte proliferation during embryonic heart growth are not completely deciphered yet. In a forward genetic N-ethyl-N-nitrosourea (ENU) mutagenesis screen, we identified the recessive embryonic-lethal zebrafish mutant line weiches herz (whz). Homozygous mutant whz embryos display impaired heart growth due to diminished embryonic cardiomyocyte proliferation resulting in cardiac hypoplasia and weak cardiac contraction. By positional cloning, we found in whz mutant zebrafish a missense mutation within the T-box 20 (Tbx20) transcription factor gene leading to destabilization of Tbx20 protein...
2016: PloS One
https://www.readbyqxmd.com/read/27902705/neuronal-ndrg4-is-essential-for-nodes-of-ranvier-organization-in-zebrafish
#17
Laura Fontenas, Flavia De Santis, Vincenzo Di Donato, Cindy Degerny, Béatrice Chambraud, Filippo Del Bene, Marcel Tawk
Axon ensheathment by specialized glial cells is an important process for fast propagation of action potentials. The rapid electrical conduction along myelinated axons is mainly due to its saltatory nature characterized by the accumulation of ion channels at the nodes of Ranvier. However, how these ion channels are transported and anchored along axons is not fully understood. We have identified N-myc downstream-regulated gene 4, ndrg4, as a novel factor that regulates sodium channel clustering in zebrafish. Analysis of chimeric larvae indicates that ndrg4 functions autonomously within neurons for sodium channel clustering at the nodes...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27880902/forward-genetic-screens-in-zebrafish-identify-pre-mrna-processing-pathways-regulating-early-t-cell-development
#18
Norimasa Iwanami, Katarzyna Sikora, Andreas S Richter, Maren Mönnich, Lucia Guerri, Cristian Soza-Ried, Divine-Fondzenyuy Lawir, Fernando Mateos, Isabell Hess, Connor P O'Meara, Michael Schorpp, Thomas Boehm
Lymphocytes represent basic components of vertebrate adaptive immune systems, suggesting the utility of non-mammalian models to define the molecular basis of their development and differentiation. Our forward genetic screens in zebrafish for recessive mutations affecting early T cell development revealed several major genetic pathways. The identification of lineage-specific transcription factors and specific components of cytokine signaling and DNA replication and/or repair pathways known from studies of immunocompromised mammals provided an evolutionary cross-validation of the screen design...
November 22, 2016: Cell Reports
https://www.readbyqxmd.com/read/27876801/ppfia1-drives-active-%C3%AE-5%C3%AE-1-integrin-recycling-and-controls-fibronectin-fibrillogenesis-and-vascular-morphogenesis
#19
Giulia Mana, Fabiana Clapero, Emiliano Panieri, Valentina Panero, Ralph T Böttcher, Hui-Yuan Tseng, Federico Saltarin, Elena Astanina, Katarzyna I Wolanska, Mark R Morgan, Martin J Humphries, Massimo M Santoro, Guido Serini, Donatella Valdembri
Basolateral polymerization of cellular fibronectin (FN) into a meshwork drives endothelial cell (EC) polarity and vascular remodelling. However, mechanisms coordinating α5β1 integrin-mediated extracellular FN endocytosis and exocytosis of newly synthesized FN remain elusive. Here we show that, on Rab21-elicited internalization, FN-bound/active α5β1 is recycled to the EC surface. We identify a pathway, comprising the regulators of post-Golgi carrier formation PI4KB and AP-1A, the small GTPase Rab11B, the surface tyrosine phosphatase receptor PTPRF and its adaptor PPFIA1, which we propose acts as a funnel combining FN secretion and recycling of active α5β1 integrin from the trans-Golgi network (TGN) to the EC surface, thus allowing FN fibrillogenesis...
November 23, 2016: Nature Communications
https://www.readbyqxmd.com/read/27866707/a-functional-variant-associated-with-atrial-fibrillation-regulates-pitx2c-expression-through-tfap2a
#20
Jiangchuan Ye, Nathan R Tucker, Lu-Chen Weng, Sebastian Clauss, Steven A Lubitz, Patrick T Ellinor
The most significantly associated genetic locus for atrial fibrillation (AF) is in chromosomal region 4q25, where four independent association signals have been identified. Although model-system studies suggest that altered PITX2c expression might underlie the association, the link between specific variants and the direction of effect on gene expression remains unknown for all four signals. In the present study, we analyzed the AF-associated region most proximal to PITX2 at 4q25. First, we identified candidate regulatory variants that might confer AF risk through a combination of mammalian conservation, DNase hypersensitivity, and histone modification from ENCODE and the Roadmap Epigenomics Project, as well as through in vivo analysis of enhancer activity in embryonic zebrafish...
December 1, 2016: American Journal of Human Genetics
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